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Richardson, David C.

Overview:

Protein structure, folding, and design; 3D computer graphics; x-ray crystallography.

Positions:

Professor of Biochemistry

Biochemistry
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 1968

Ph.D. — Massachusetts Institute of Technology

Grants:

MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
September 01, 2015
End Date
August 31, 2019

Occurrence and Functional Roles of High Energy Base Pairs in DNA

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Collaborator
Start Date
September 15, 2015
End Date
July 31, 2019

PHENIX: New methods for automation in macromolecular crystallography

Administered By
Biochemistry
AwardedBy
Ernest Orlando Lawrence Berkeley National Laboratory
Role
Co-Principal Investigator
Start Date
August 31, 2006
End Date
July 31, 2017

Bioinformatics and Computational Biology Training Program

Administered By
Basic Science Departments
AwardedBy
National Institutes of Health
Role
Mentor
Start Date
July 01, 2005
End Date
June 30, 2016

Automated detection of protein crystals in high-throughput crystallography experiments

Administered By
Duke Human Vaccine Institute
AwardedBy
North Carolina Biotechnology Center
Role
Major User
Start Date
April 01, 2014
End Date
April 30, 2015

New Kind of Quality Management for X-ray & NMR Models

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
May 01, 2005
End Date
March 31, 2015

"Low-Resolution Interiors & Interfaces Can Achieve High-Resolution Accuracy"

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
August 01, 2009
End Date
July 31, 2014

Automated NMR Assignment and Protein Structure Determination

Administered By
Computer Science
AwardedBy
National Institutes of Health
Role
Collaborator
Start Date
September 16, 2006
End Date
November 30, 2012

Inverse Kinematics, Sterics & Data - To Fit RNA Backbone

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
June 01, 2005
End Date
May 31, 2010

Predoctoral Fellowship Awards for Students with Disabilities (F31)

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
May 01, 2006
End Date
December 31, 2009

Molecular mechanisms of nitrosative stress resistance

Administered By
Medicine, Pulmonary, Allergy, and Critical Care Medicine
AwardedBy
National Institutes of Health
Role
Collaborator
Start Date
August 01, 1999
End Date
July 31, 2005

Analysis and Design of Protein Structures

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 01, 1984
End Date
August 31, 2004

All-Atom Contact Analysis in Improving Structure Quality

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
July 01, 2001
End Date
June 30, 2004

Molecular Biophysics Training Program

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 01, 1994
End Date
June 30, 1999

Molecular Biophysics Training Program

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 01, 1994
End Date
June 30, 1999

Molecular Biophysics Training Program

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 01, 1994
End Date
June 30, 1999

Study Of Crystallization & Solution Properties Of Redesign

Administered By
Biochemistry
AwardedBy
National Aeronautics and Space Administration
Role
Principal Investigator
Start Date
July 01, 1993
End Date
December 31, 1998

Analysis & Design Of Protein Structures

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 01, 1984
End Date
December 31, 1998

Cancer Center Core Support Grant

Administered By
Medicine, Medical Oncology
AwardedBy
National Institutes of Health
Role
Co-Principal Investigator
Start Date
September 01, 1976
End Date
December 31, 1998

Comprehensive Cancer Center Core Support Grant

Administered By
Medicine, Medical Oncology
AwardedBy
National Institutes of Health
Role
Co-Principal Investigator
Start Date
September 01, 1976
End Date
December 31, 1998

Comprehensive Cancer Center Core Support Grant

Administered By
Medicine, Medical Oncology
AwardedBy
National Institutes of Health
Role
Co-Principal Investigator
Start Date
September 01, 1976
End Date
December 31, 1998

Study Of Crystallization And Solution Properties Of Redesi

Administered By
Biochemistry
AwardedBy
National Aeronautics and Space Administration
Role
Principal Investigator
Start Date
July 01, 1993
End Date
June 30, 1996

Macromolecular Crystallography And Protein Chemistry

Administered By
Biochemistry
AwardedBy
National Aeronautics and Space Administration
Role
Principal Investigator
Start Date
September 01, 1990
End Date
August 31, 1991

Crystallographic Analysis Of Protein Structures

Administered By
Biochemistry
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 01, 1987
End Date
June 01, 1989
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Awards:

Distinguished Speaker, NC section of ACS. American Chemical Society.

Type
State
Awarded By
American Chemical Society
Date
January 01, 2012

Gordon Hammes Teaching & Mentoring Award. Duke University.

Type
University
Awarded By
Duke University
Date
January 01, 2009

Amgen Award for Innovation in Protein Science. Protein Society.

Type
National
Awarded By
Protein Society
Date
January 01, 1995

Special Achievement Award, BioTechnology Winter Symposium. BioTechnology.

Type
National
Awarded By
BioTechnology
Date
January 01, 1995

Science Digest 100 Best Innovations of 1985. Science Digest.

Type
National
Awarded By
Science Digest
Date
January 01, 1985

Publications:

Molprobity's ultimate rotamer-library distributions for model validation.

Here we describe the updated MolProbity rotamer-library distributions derived from an order-of-magnitude larger and more stringently quality-filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side-chains with satisfactory justification for their given conformation, we added residue-specific filters for electron-density value and model-to-density fit. The combined new protocol retains a million residues of data, while cleaning up false-positive noise in the multi- χ datapoint distributions. It enables unambiguous characterization of conformational clusters nearly 1000-fold less frequent than the most common ones. We describe examples of local interactions that favor these rare conformations, including the role of authentic covalent bond-angle deviations in enabling presumably strained side-chain conformations. Further, along with favored and outlier, an allowed category (0.3-2.0% occurrence in reference data) has been added, analogous to Ramachandran validation categories. The new rotamer distributions are used for current rotamer validation in MolProbity and PHENIX, and for rotamer choice in PHENIX model-building and refinement. The multi-dimensional χ distributions and Top8000 reference dataset are freely available on GitHub. These rotamers are termed "ultimate" because data sampling and quality are now fully adequate for this task, and also because we believe the future of conformational validation should integrate side-chain with backbone criteria. Proteins 2016; 84:1177-1189. © 2016 Wiley Periodicals, Inc.

Authors
Hintze, BJ; Lewis, SM; Richardson, JS; Richardson, DC
MLA Citation
Hintze, BJ, Lewis, SM, Richardson, JS, and Richardson, DC. "Molprobity's ultimate rotamer-library distributions for model validation." Proteins 84.9 (September 2016): 1177-1189.
PMID
27018641
Source
epmc
Published In
Proteins: Structure, Function and Bioinformatics
Volume
84
Issue
9
Publish Date
2016
Start Page
1177
End Page
1189
DOI
10.1002/prot.25039

Cover Image, Volume 84, Issue 9

Authors
Hintze, BJ; Lewis, SM; Richardson, JS; Richardson, DC
MLA Citation
Hintze, BJ, Lewis, SM, Richardson, JS, and Richardson, DC. "Cover Image, Volume 84, Issue 9." Proteins: Structure, Function, and Bioinformatics 84.9 (September 2016): C1-C1.
Source
crossref
Published In
Proteins: Structure, Function and Bioinformatics
Volume
84
Issue
9
Publish Date
2016
Start Page
C1
End Page
C1
DOI
10.1002/prot.25109

Computational Methods for RNA Structure Validation and Improvement.

With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. To make clean biological interpretations from three-dimensional structures, it is imperative to have high-quality, accurate RNA crystal structures available, and the community has thoroughly embraced that goal. However, due to the many degrees of freedom inherent in RNA structure (especially for the backbone), it is a significant challenge to succeed in building accurate experimental models for RNA structures. This chapter describes the tools and techniques our research group and our collaborators have developed over the years to help RNA structural biologists both evaluate and achieve better accuracy. Expert analysis of large, high-resolution, quality-conscious RNA datasets provides the fundamental information that enables automated methods for robust and efficient error diagnosis in validating RNA structures at all resolutions. The even more crucial goal of correcting the diagnosed outliers has steadily developed toward highly effective, computationally based techniques. Automation enables solving complex issues in large RNA structures, but cannot circumvent the need for thoughtful examination of local details, and so we also provide some guidance for interpreting and acting on the results of current structure validation for RNA.

Authors
Jain, S; Richardson, DC; Richardson, JS
MLA Citation
Jain, S, Richardson, DC, and Richardson, JS. "Computational Methods for RNA Structure Validation and Improvement." Methods in enzymology 558 (January 2015): 181-212.
Website
http://hdl.handle.net/10161/10807
PMID
26068742
Source
epmc
Published In
Methods in Enzymology
Volume
558
Publish Date
2015
Start Page
181
End Page
212
DOI
10.1016/bs.mie.2015.01.007

Computational Methods for RNA Structure Validation and Improvement

© 2015 Elsevier Inc.With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. To make clean biological interpretations from three-dimensional structures, it is imperative to have high-quality, accurate RNA crystal structures available, and the community has thoroughly embraced that goal. However, due to the many degrees of freedom inherent in RNA structure (especially for the backbone), it is a significant challenge to succeed in building accurate experimental models for RNA structures. This chapter describes the tools and techniques our research group and our collaborators have developed over the years to help RNA structural biologists both evaluate and achieve better accuracy. Expert analysis of large, high-resolution, quality-conscious RNA datasets provides the fundamental information that enables automated methods for robust and efficient error diagnosis in validating RNA structures at all resolutions. The even more crucial goal of correcting the diagnosed outliers has steadily developed toward highly effective, computationally based techniques. Automation enables solving complex issues in large RNA structures, but cannot circumvent the need for thoughtful examination of local details, and so we also provide some guidance for interpreting and acting on the results of current structure validation for RNA.

Authors
Jain, S; Richardson, DC; Richardson, JS
MLA Citation
Jain, S, Richardson, DC, and Richardson, JS. "Computational Methods for RNA Structure Validation and Improvement." Methods in Enzymology (2015).
Source
scival
Published In
Methods in Enzymology
Publish Date
2015
DOI
10.1016/bs.mie.2015.01.007

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.

Authors
Kapral, GJ; Jain, S; Noeske, J; Doudna, JA; Richardson, DC; Richardson, JS
MLA Citation
Kapral, GJ, Jain, S, Noeske, J, Doudna, JA, Richardson, DC, and Richardson, JS. "New tools provide a second look at HDV ribozyme structure, dynamics and cleavage." Nucleic acids research 42.20 (November 2014): 12833-12846.
Website
http://hdl.handle.net/10161/10808
PMID
25326328
Source
epmc
Published In
Nucleic Acids Research
Volume
42
Issue
20
Publish Date
2014
Start Page
12833
End Page
12846
DOI
10.1093/nar/gku992

Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity.

The Staphylococcus aureus virulence factor staphylococcal protein A (SpA) is a major contributor to bacterial evasion of the host immune system, through high-affinity binding to host proteins such as antibodies. SpA includes five small three-helix-bundle domains (E-D-A-B-C) separated by conserved flexible linkers. Prior attempts to crystallize individual domains in the absence of a binding partner have apparently been unsuccessful. There have also been no previous structures of tandem domains. Here we report the high-resolution crystal structures of a single C domain, and of two B domains connected by the conserved linker. Both structures exhibit extensive multiscale conformational heterogeneity, which required novel modeling protocols. Comparison of domain structures shows that helix1 orientation is especially heterogeneous, coordinated with changes in side chain conformational networks and contacting protein interfaces. This represents the kind of structural plasticity that could enable SpA to bind multiple partners.

Authors
Deis, LN; Pemble, CW; Qi, Y; Hagarman, A; Richardson, DC; Richardson, JS; Oas, TG
MLA Citation
Deis, LN, Pemble, CW, Qi, Y, Hagarman, A, Richardson, DC, Richardson, JS, and Oas, TG. "Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity." Structure (London, England : 1993) 22.10 (October 2014): 1467-1477.
Website
http://hdl.handle.net/10161/11167
PMID
25295398
Source
epmc
Published In
Structure
Volume
22
Issue
10
Publish Date
2014
Start Page
1467
End Page
1477
DOI
10.1016/j.str.2014.08.014

Biophysical highlights from 54 years of macromolecular crystallography.

The United Nations has declared 2014 the International Year of Crystallography, and in commemoration, this review features a selection of 54 notable macromolecular crystal structures that have illuminated the field of biophysics in the 54 years since the first excitement of the myoglobin and hemoglobin structures in 1960. Chronological by publication of the earliest solved structure, each illustrated entry briefly describes key concepts or methods new at the time and key later work leveraged by knowledge of the three-dimensional atomic structure.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Biophysical highlights from 54 years of macromolecular crystallography." Biophysical journal 106.3 (February 2014): 510-525. (Review)
PMID
24507592
Source
epmc
Published In
Biophysical Journal
Volume
106
Issue
3
Publish Date
2014
Start Page
510
End Page
525
DOI
10.1016/j.bpj.2014.01.001

The statistical conformation of a highly flexible protein: Small-angle x-ray scattering of S. aureus protein A

Summary Staphylococcal protein A (SpA) is a multidomain protein consisting of five globular IgG binding domains separated by a conserved six- to nine-residue flexible linker. We collected SAXS data on the N-terminal protein-binding half of SpA (SpA-N) and constructs consisting of one to five domain modules in order to determine statistical conformation of this important S. aureus virulence factor. We fit the SAXS data to a scattering function based on a new polymer physics model, which provides an analytical description of the SpA-N statistical conformation. We describe a protocol for systematically determining the appropriate level of modeling to fit a SAXS data set based on goodness of fit and whether the addition of parameters improves it. In the case of SpA-N, the analytical polymer physics description provides a depiction of the statistical conformation of a flexible protein that, while lacking atomistic detail, properly reflects the information content of the data. © 2014 Elsevier Ltd.

Authors
Capp, JA; Hagarman, A; Richardson, DC; Oas, TG
MLA Citation
Capp, JA, Hagarman, A, Richardson, DC, and Oas, TG. "The statistical conformation of a highly flexible protein: Small-angle x-ray scattering of S. aureus protein A." Structure 22.8 (2014): 1184-1195.
Website
http://hdl.handle.net/10161/11168
Source
scival
Published In
Structure
Volume
22
Issue
8
Publish Date
2014
Start Page
1184
End Page
1195
DOI
10.1016/j.str.2014.06.011

Crystallographic model validation: from diagnosis to healing.

Model validation has evolved from a passive final gatekeeping step to an ongoing diagnosis and healing process that enables significant improvement of accuracy. A recent phase of active development was spurred by the worldwide Protein Data Bank requiring data deposition and establishing Validation Task Force committees, by strong growth in high-quality reference data, by new speed and ease of computations, and by an upswing of interest in large molecular machines and structural ensembles. Progress includes automated correction methods, concise and user-friendly validation reports for referees and on the PDB websites, extension of error correction to RNA and error diagnosis to ligands, carbohydrates, and membrane proteins, and a good start on better methods for low resolution and for multiple conformations.

Authors
Richardson, JS; Prisant, MG; Richardson, DC
MLA Citation
Richardson, JS, Prisant, MG, and Richardson, DC. "Crystallographic model validation: from diagnosis to healing." Curr Opin Struct Biol 23.5 (October 2013): 707-714. (Review)
PMID
24064406
Source
pubmed
Published In
Current Opinion in Structural Biology
Volume
23
Issue
5
Publish Date
2013
Start Page
707
End Page
714
DOI
10.1016/j.sbi.2013.06.004

Studying and polishing the PDB's macromolecules.

Macromolecular crystal structures are among the best of scientific data, providing detailed insight into these complex and biologically important molecules with a relatively low level of error and subjectivity. However, there are two notable problems with getting the most information from them. The first is that the models are not perfect: there is still opportunity for improving them, and users need to evaluate whether the local reliability in a structure is up to answering their question of interest. The second is that protein and nucleic acid molecules are highly complex and individual, inherently handed and three-dimensional, and the cooperative and subtle interactions that govern their detailed structure and function are not intuitively evident. Thus there is a real need for graphical representations and descriptive classifications that enable molecular 3D literacy. We have spent our career working to understand these elegant molecules ourselves, and building tools to help us and others determine and understand them better. The Protein Data Bank (PDB) has of course been vital and central to this undertaking. Here we combine some history of our involvement as depositors, illustrators, evaluators, and end-users of PDB structures with commentary on how best to study and draw scientific inferences from them.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Studying and polishing the PDB's macromolecules." Biopolymers 99.3 (March 2013): 170-182. (Review)
PMID
23023928
Source
pubmed
Published In
Biopolymers
Volume
99
Issue
3
Publish Date
2013
Start Page
170
End Page
182
DOI
10.1002/bip.22108

Crystallographic model validation: From diagnosis to healing

Model validation has evolved from a passive final gatekeeping step to an ongoing diagnosis and healing process that enables significant improvement of accuracy. A recent phase of active development was spurred by the worldwide Protein Data Bank requiring data deposition and establishing Validation Task Force committees, by strong growth in high-quality reference data, by new speed and ease of computations, and by an upswing of interest in large molecular machines and structural ensembles. Progress includes automated correction methods, concise and user-friendly validation reports for referees and on the PDB websites, extension of error correction to RNA and error diagnosis to ligands, carbohydrates, and membrane proteins, and a good start on better methods for low resolution and for multiple conformations. © 2013 Elsevier Ltd.

Authors
Richardson, JS; Prisant, MG; Richardson, DC
MLA Citation
Richardson, JS, Prisant, MG, and Richardson, DC. "Crystallographic model validation: From diagnosis to healing." Current Opinion in Structural Biology 23.5 (2013): 707-714.
Source
scival
Published In
Current Opinion in Structural Biology
Volume
23
Issue
5
Publish Date
2013
Start Page
707
End Page
714
DOI
10.1016/j.sbi.2013.06.004

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

UNLABELLED: We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that are induced by mutations to the protein sequence; (2) modeling of proteins and ligands as ensembles of low-energy structures to better approximate binding affinity; and (3) a globally optimal protein design search, guaranteeing that the computational predictions are optimal with respect to the input model. Here, we illustrate the importance of these three characteristics. We then describe OSPREY, a protein redesign suite that implements our protein design algorithms. OSPREY has been used prospectively, with experimental validation, in several biomedically relevant settings. We show in detail how OSPREY has been used to predict resistance mutations and explain why improved flexibility, ensembles, and provability are essential for this application. AVAILABILITY: OSPREY is free and open source under a Lesser GPL license. The latest version is OSPREY 2.0. The program, user manual, and source code are available at www.cs.duke.edu/donaldlab/software.php. CONTACT: osprey@cs.duke.edu.

Authors
Gainza, P; Roberts, KE; Georgiev, I; Lilien, RH; Keedy, DA; Chen, C-Y; Reza, F; Anderson, AC; Richardson, DC; Richardson, JS; Donald, BR
MLA Citation
Gainza, P, Roberts, KE, Georgiev, I, Lilien, RH, Keedy, DA, Chen, C-Y, Reza, F, Anderson, AC, Richardson, DC, Richardson, JS, and Donald, BR. "OSPREY: protein design with ensembles, flexibility, and provable algorithms." Methods Enzymol 523 (2013): 87-107.
PMID
23422427
Source
pubmed
Published In
Methods in Enzymology
Volume
523
Publish Date
2013
Start Page
87
End Page
107
DOI
10.1016/B978-0-12-394292-0.00005-9

Doing molecular biophysics: finding, naming, and picturing signal within complexity.

A macromolecular structure, as measured data or as a list of coordinates or even on-screen as a full atomic model, is an extremely complex and confusing object. The underlying rules of how it folds, moves, and interacts as a biological entity are even less evident or intuitive to the human mind. To do science on such molecules, or to relate them usefully to higher levels of biology, we need to start with a natural history that names their features in meaningful ways and with multiple representations (visual or algebraic) that show some aspect of their organizing principles. The two of us have jointly enjoyed a highly varied and engrossing career in biophysical research over nearly 50 years. Our frequent changes of emphasis are tied together by two threads: first, by finding the right names, visualizations, and methods to help both ourselves and others to better understand the 3D structures of protein and RNA molecules, and second, by redefining the boundary between signal and noise for complex data, in both directions-sometimes identifying and promoting real signal up out of what seemed just noise, and sometimes demoting apparent signal into noise or systematic error. Here we relate parts of our scientific and personal lives, including ups and downs, influences, anecdotes, and guiding principles such as the title theme.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Doing molecular biophysics: finding, naming, and picturing signal within complexity." Annu Rev Biophys 42 (2013): 1-28.
PMID
23451888
Source
pubmed
Published In
Annual Review of Biophysics
Volume
42
Publish Date
2013
Start Page
1
End Page
28
DOI
10.1146/annurev-biophys-083012-130353

Invited review: Studying and polishing the PDB's macromolecules

Macromolecular crystal structures are among the best of scientific data, providing detailed insight into these complex and biologically important molecules with a relatively low level of error and subjectivity. However, there are two notable problems with getting the most information from them. The first is that the models are not perfect: there is still opportunity for improving them, and users need to evaluate whether the local reliability in a structure is up to answering their question of interest. The second is that protein and nucleic acid molecules are highly complex and individual, inherently handed and three-dimensional, and the cooperative and subtle interactions that govern their detailed structure and function are not intuitively evident. Thus there is a real need for graphical representations and descriptive classifications that enable molecular 3D literacy. We have spent our career working to understand these elegant molecules ourselves, and building tools to help us and others determine and understand them better. The Protein Data Bank (PDB) has of course been vital and central to this undertaking. Here we combine some history of our involvement as depositors, illustrators, evaluators, and end-users of PDB structures with commentary on how best to study and draw scientific inferences from them. © 2012 Wiley Periodicals, Inc.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Invited review: Studying and polishing the PDB's macromolecules." Biopolymers 99.3 (2013): 170-182.
Source
scival
Published In
Biopolymers
Volume
99
Issue
3
Publish Date
2013
Start Page
170
End Page
182
DOI
10.1002/bip.22108

Advances, interactions, and future developments in the CNS, phenix, and rosetta structural biology software Systems

Allosteric propagation results in communication between distinct sites in the protein structure; it also encodes specific effects on cellular pathways, and in this way it shapes cellular response. One example of long-range effects is binding of morphogens to cell surface receptors, which initiates a cascade of protein interactions that leads to genome activation and specific cellular action. Allosteric propagation results from combinations of multiple factors, takes place through dynamic shifts of conformational ensembles, and affects the equilibria of macromolecular interactions. Here, we (a) emphasize the well-known yet still underappreciated role of allostery in conveying explicit signals across large multimolecular assemblies and distances to specify cellular action; (b) stress the need for quantitation of the allosteric effects; and finally, (c) propose that each specific combination of allosteric effectors along the pathway spells a distinct function. The challenges are colossal; the inspiring reward will be predicting function, misfunction, and outcomes of drug regimes. Copyright © 2013 by Annual Reviews.

Authors
Adams, PD; Baker, D; Brunger, AT; Das, R; Maio, FD; Read, RJ; Richardson, DC; Richardson, JS; Terwilliger, TC
MLA Citation
Adams, PD, Baker, D, Brunger, AT, Das, R, Maio, FD, Read, RJ, Richardson, DC, Richardson, JS, and Terwilliger, TC. "Advances, interactions, and future developments in the CNS, phenix, and rosetta structural biology software Systems." Annual Review of Biophysics 42.1 (2013): 265-287.
PMID
23451892
Source
scival
Published In
Annual Review of Biophysics
Volume
42
Issue
1
Publish Date
2013
Start Page
265
End Page
287
DOI
10.1146/annurev-biophys-083012-130253

The zen of model anomalies - Correct most of them. Treasure the meaningful valid few. Live serenely with the rest!

Historically, validation has been considered primarily as a gatekeeping function done at the end of a structure solution. Currently, the most interesting and important part of validation is the opportunity to correct diagnosed errors, provided mainly by local as opposed to global criteria, and available to you throughout the crystallographic process. Elsewhere in this book, you will hear about up-to-date methods in the data and model-to-data aspects of validation. This chapter addresses model validation and model improvement, first about current best-practice methodology (as done on the MolProbity website and elsewhere), and second about some important developments to anticipate in the near future. Model validation has three primary parts: (a) geometry (bond lengths and angles, planarity, chirality), (b) conformation (rotamers, Ramachandran, ring pucker, RNA backbone conformers), (c) and sterics (clashes, H-bonds, packing). All of these both enhance and must be considered along with the information from electron density. The model criteria are primarily local, but their rate of occurrence can also be summarized as a global score. © 2013 Springer Science+Business Media Dordrecht.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "The zen of model anomalies - Correct most of them. Treasure the meaningful valid few. Live serenely with the rest!." NATO Science for Peace and Security Series A: Chemistry and Biology (2013): 1-10.
Source
scival
Published In
NATO Science for Peace and Security Series A: Chemistry and Biology
Publish Date
2013
Start Page
1
End Page
10
DOI
10.1007/978-94-007-6232-9-1

“The plot” thickens: More data, more dimensions, more uses

© 2013 by World Scientific Publishing Co. Pte. Ltd. All rights reserved.The scientific history of the Ramachandran plot is reviewed, emphasizing relationships to the title theme and to trends in current research. The growth and quality of macromolecular structure data have enabled the understanding of relationships with further variables and the application to an ever-widening set of uses such as prediction, simulation, design, motif identification, and structure validation and improvement. Then a current research example is explored, using a new dataset of 8000 selected protein chains and >1.5 million quality-filtered residues. The new Ramachandran plots show an unprecedented level of detail, allow the valid addition of more subcategories and more dimensions, and point the way toward the feasibility of an essentially complete and robust treatment of torsional conformation in the near future.

Authors
Richardson, JS; Keedy, DA; Richardson, DC
MLA Citation
Richardson, JS, Keedy, DA, and Richardson, DC. "“The plot” thickens: More data, more dimensions, more uses." (January 1, 2012): 46-61. (Chapter)
Source
scopus
Publish Date
2012
Start Page
46
End Page
61
DOI
10.1142/9789814449144_0004

The role of local backrub motions in evolved and designed mutations.

Amino acid substitutions in protein structures often require subtle backbone adjustments that are difficult to model in atomic detail. An improved ability to predict realistic backbone changes in response to engineered mutations would be of great utility for the blossoming field of rational protein design. One model that has recently grown in acceptance is the backrub motion, a low-energy dipeptide rotation with single-peptide counter-rotations, that is coupled to dynamic two-state sidechain rotamer jumps, as evidenced by alternate conformations in very high-resolution crystal structures. It has been speculated that backrubs may facilitate sequence changes equally well as rotamer changes. However, backrub-induced shifts and experimental uncertainty are of similar magnitude for backbone atoms in even high-resolution structures, so comparison of wildtype-vs.-mutant crystal structure pairs is not sufficient to directly link backrubs to mutations. In this study, we use two alternative approaches that bypass this limitation. First, we use a quality-filtered structure database to aggregate many examples for precisely defined motifs with single amino acid differences, and find that the effectively amplified backbone differences closely resemble backrubs. Second, we directly apply a provably-accurate, backrub-enabled protein design algorithm to idealized versions of these motifs, and discover that the lowest-energy computed models match the average-coordinate experimental structures. These results support the hypothesis that backrubs participate in natural protein evolution and validate their continued use for design of synthetic proteins.

Authors
Keedy, DA; Georgiev, I; Triplett, EB; Donald, BR; Richardson, DC; Richardson, JS
MLA Citation
Keedy, DA, Georgiev, I, Triplett, EB, Donald, BR, Richardson, DC, and Richardson, JS. "The role of local backrub motions in evolved and designed mutations." PLoS Comput Biol 8.8 (2012): e1002629-.
PMID
22876172
Source
pubmed
Published In
PLoS computational biology
Volume
8
Issue
8
Publish Date
2012
Start Page
e1002629
DOI
10.1371/journal.pcbi.1002629

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Traditional methods for macromolecular refinement often have limited success at low resolution (3.0-3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a reference-model method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a Ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from non-redundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered Rfree and a decreased gap between Rwork and Rfree. © International Union of Crystallography 2012.

Authors
Headd, JJ; Echols, N; Afonine, PV; Grosse-Kunstleve, RW; Chen, VB; Moriarty, NW; Richardson, DC; Richardson, JS; Adams, PD
MLA Citation
Headd, JJ, Echols, N, Afonine, PV, Grosse-Kunstleve, RW, Chen, VB, Moriarty, NW, Richardson, DC, Richardson, JS, and Adams, PD. "Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution." Acta Crystallographica Section D: Biological Crystallography 68.4 (2012): 381-390.
PMID
22505258
Source
scival
Published In
Acta Crystallographica Section D
Volume
68
Issue
4
Publish Date
2012
Start Page
381
End Page
390
DOI
10.1107/S0907444911047834

Graphical tools for macromolecular crystallography in PHENIX

A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified. © 2012 International Union of Crystallography Printed in Singapore-all rights reserved.

Authors
Echols, N; Grosse-Kunstleve, RW; Afonine, PV; Bunkóczi, G; Chen, VB; Headd, JJ; McCoy, AJ; Moriarty, NW; Read, RJ; Richardson, DC; Richardson, JS; Terwilliger, TC; Adams, PD
MLA Citation
Echols, N, Grosse-Kunstleve, RW, Afonine, PV, Bunkóczi, G, Chen, VB, Headd, JJ, McCoy, AJ, Moriarty, NW, Read, RJ, Richardson, DC, Richardson, JS, Terwilliger, TC, and Adams, PD. "Graphical tools for macromolecular crystallography in PHENIX." Journal of Applied Crystallography 45.3 (2012): 581-586.
PMID
22675231
Source
scival
Published In
Journal of Applied Crystallography
Volume
45
Issue
3
Publish Date
2012
Start Page
581
End Page
586
DOI
10.1107/S0021889812017293

The Phenix software for automated determination of macromolecular structures

X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. © 2011 Elsevier Inc.

Authors
Adams, PD; Afonine, PV; Bunkóczi, G; Chen, VB; Echols, N; Headd, JJ; Hung, L-W; Jain, S; Kapral, GJ; Kunstleve, RWG; McCoy, AJ; Moriarty, NW; Oeffner, RD; Read, RJ; Richardson, DC; Richardson, JS; Terwilliger, TC; Zwart, PH
MLA Citation
Adams, PD, Afonine, PV, Bunkóczi, G, Chen, VB, Echols, N, Headd, JJ, Hung, L-W, Jain, S, Kapral, GJ, Kunstleve, RWG, McCoy, AJ, Moriarty, NW, Oeffner, RD, Read, RJ, Richardson, DC, Richardson, JS, Terwilliger, TC, and Zwart, PH. "The Phenix software for automated determination of macromolecular structures." Methods 55.1 (2011): 94-106.
PMID
21821126
Source
scival
Published In
Methods
Volume
55
Issue
1
Publish Date
2011
Start Page
94
End Page
106
DOI
10.1016/j.ymeth.2011.07.005

Alternate states of proteins revealed by detailed energy landscape mapping

What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR describes structure in solution but using less data. NMR structures display more variability, but is this because crystal contacts are absent or because of fewer data constraints? Here we report unexpected insight into this issue obtained through analysis of detailed protein energy landscapes generated by large-scale, native-enhanced sampling of conformational space with Rosetta@home for 111 protein domains. In the absence of tightly associating binding partners or ligands, the lowest-energy Rosetta models were nearly all < 2.5 Å CαRMSD from the experimental structure; this result demonstrates that structure prediction accuracy for globular proteins is limited mainly by the ability to sample close to the native structure. While the lowest-energy models are similar to deposited structures, they are not identical; the largest deviations are most often in regions involved in ligand, quaternary, or crystal contacts. For ligand binding proteins, the low energy models may resemble the apo structures, and for oligomeric proteins, the monomeric assembly intermediates. The deviations between the low energy models and crystal structures largely disappear when landscapes are computed in the context of the crystal lattice or multimer. The computed low-energy ensembles, with tight crystal-structure-like packing in the core, but more NMR-structure-like variability in loops, may in some cases resemble the native state ensembles of proteins better than individual crystal or NMR structures, and can suggest experimentally testable hypotheses relating alternative states and structural heterogeneity to function. © 2010 Elsevier Ltd. All rights reserved.

Authors
Tyka, MD; Keedy, DA; André, I; Dimaio, F; Song, Y; Richardson, DC; Richardson, JS; Baker, D
MLA Citation
Tyka, MD, Keedy, DA, André, I, Dimaio, F, Song, Y, Richardson, DC, Richardson, JS, and Baker, D. "Alternate states of proteins revealed by detailed energy landscape mapping." Journal of Molecular Biology 405.2 (2011): 607-618.
PMID
21073878
Source
scival
Published In
Journal of Molecular Biology
Volume
405
Issue
2
Publish Date
2011
Start Page
607
End Page
618
DOI
10.1016/j.jmb.2010.11.008

MolProbity: all-atom structure validation for macromolecular crystallography.

MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

Authors
Chen, VB; Arendall, WB; Headd, JJ; Keedy, DA; Immormino, RM; Kapral, GJ; Murray, LW; Richardson, JS; Richardson, DC
MLA Citation
Chen, VB, Arendall, WB, Headd, JJ, Keedy, DA, Immormino, RM, Kapral, GJ, Murray, LW, Richardson, JS, and Richardson, DC. "MolProbity: all-atom structure validation for macromolecular crystallography." Acta Crystallogr D Biol Crystallogr 66.Pt 1 (January 2010): 12-21.
PMID
20057044
Source
pubmed
Published In
Acta Crystallographica Section D
Volume
66
Issue
Pt 1
Publish Date
2010
Start Page
12
End Page
21
DOI
10.1107/S0907444909042073

Phenix.model-vs-data: A high-level tool for the calculation of crystallographic model and data statistics

phenix.model-vs-data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed. © 2010 International Union of Crystallography Printed in Singapore - all rights reserved.

Authors
Afonine, PV; Grosse-Kunstleve, RW; Chen, VB; Headd, JJ; Moriarty, NW; Richardson, JS; Richardson, DC; Urzhumtsev, A; Zwart, PH; Adams, PD
MLA Citation
Afonine, PV, Grosse-Kunstleve, RW, Chen, VB, Headd, JJ, Moriarty, NW, Richardson, JS, Richardson, DC, Urzhumtsev, A, Zwart, PH, and Adams, PD. "Phenix.model-vs-data: A high-level tool for the calculation of crystallographic model and data statistics." Journal of Applied Crystallography 43.4 (2010): 669-676.
PMID
20648263
Source
scival
Published In
Journal of Applied Crystallography
Volume
43
Issue
4
Publish Date
2010
Start Page
669
End Page
676
DOI
10.1107/S0021889810015608

PHENIX: A comprehensive Python-based system for macromolecular structure solution

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How-ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo-graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

Authors
Adams, PD; Afonine, PV; Bunkóczi, G; Chen, VB; Davis, IW; Echols, N; Headd, JJ; Hung, L-W; Kapral, GJ; Grosse-Kunstleve, RW; McCoy, AJ; Moriarty, NW; Oeffner, R; Read, RJ; Richardson, DC; Richardson, JS; Terwilliger, TC; Zwart, PH
MLA Citation
Adams, PD, Afonine, PV, Bunkóczi, G, Chen, VB, Davis, IW, Echols, N, Headd, JJ, Hung, L-W, Kapral, GJ, Grosse-Kunstleve, RW, McCoy, AJ, Moriarty, NW, Oeffner, R, Read, RJ, Richardson, DC, Richardson, JS, Terwilliger, TC, and Zwart, PH. "PHENIX: A comprehensive Python-based system for macromolecular structure solution." Acta Crystallographica Section D: Biological Crystallography 66.2 (2010): 213-221.
PMID
20124702
Source
scival
Published In
Acta Crystallographica Section D
Volume
66
Issue
2
Publish Date
2010
Start Page
213
End Page
221
DOI
10.1107/S0907444909052925

KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program.

Proper visualization of scientific data is important for understanding spatial relationships. Particularly in the field of structural biology, where researchers seek to gain an understanding of the structure and function of biological macromolecules, it is important to have access to visualization programs which are fast, flexible, and customizable. We present KiNG, a Java program for visualizing scientific data, with a focus on macromolecular visualization. KiNG uses the kinemage graphics format, which is tuned for macromolecular structures, but is also ideal for many other kinds of spatially embedded information. KiNG is written in cross-platform, open-source Java code, and can be extended by end users through simple or elaborate "plug-in" modules. Here, we present three such applications of KiNG to problems in structural biology (protein backbone rebuilding), bioinformatics of high-dimensional data (e.g., protein sidechain chi angles), and classroom education (molecular illustration). KiNG is a mature platform for rapidly creating and capitalizing on scientific visualizations. As a research tool, it is invaluable as a test bed for new methods of visualizing scientific data and information. It is also a powerful presentation tool, whether for structure browsing, teaching, direct 3D display on the web, or as a method for creating pictures and videos for publications. KiNG is freely available for download at http://kinemage.biochem.duke.edu.

Authors
Chen, VB; Davis, IW; Richardson, DC
MLA Citation
Chen, VB, Davis, IW, and Richardson, DC. "KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program." Protein Sci 18.11 (November 2009): 2403-2409.
PMID
19768809
Source
pubmed
Published In
Protein Science
Volume
18
Issue
11
Publish Date
2009
Start Page
2403
End Page
2409
DOI
10.1002/pro.250

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.

Misfit sidechains in protein crystal structures are a stumbling block in using those structures to direct further scientific inference. Problems due to surface disorder and poor electron density are very difficult to address, but a large class of systematic errors are quite common even in well-ordered regions, resulting in sidechains fit backwards into local density in predictable ways. The MolProbity web site is effective at diagnosing such errors, and can perform reliable automated correction of a few special cases such as 180 degrees flips of Asn or Gln sidechain amides, using all-atom contacts and H-bond networks. However, most at-risk residues involve tetrahedral geometry, and their valid correction requires rigorous evaluation of sidechain movement and sometimes backbone shift. The current work extends the benefits of robust automated correction to more sidechain types. The Autofix method identifies candidate systematic, flipped-over errors in Leu, Thr, Val, and Arg using MolProbity quality statistics, proposes a corrected position using real-space refinement with rotamer selection in Coot, and accepts or rejects the correction based on improvement in MolProbity criteria and on chi angle change. Criteria are chosen conservatively, after examining many individual results, to ensure valid correction. To test this method, Autofix was run and analyzed for 945 representative PDB files and on the 50S ribosomal subunit of file 1YHQ. Over 40% of Leu, Val, and Thr outliers and 15% of Arg outliers were successfully corrected, resulting in a total of 3,679 corrected sidechains, or 4 per structure on average. Summary Sentences: A common class of misfit sidechains in protein crystal structures is due to systematic errors that place the sidechain backwards into the local electron density. A fully automated method called "Autofix" identifies such errors for Leu, Val, Thr, and Arg and corrects over one third of them, using MolProbity validation criteria and Coot real-space refinement of rotamers.

Authors
Headd, JJ; Immormino, RM; Keedy, DA; Emsley, P; Richardson, DC; Richardson, JS
MLA Citation
Headd, JJ, Immormino, RM, Keedy, DA, Emsley, P, Richardson, DC, and Richardson, JS. "Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place." J Struct Funct Genomics 10.1 (March 2009): 83-93.
PMID
19002604
Source
pubmed
Published In
Journal of Structural and Functional Genomics
Volume
10
Issue
1
Publish Date
2009
Start Page
83
End Page
93
DOI
10.1007/s10969-008-9045-8

KinImmerse: Macromolecular VR for NMR ensembles.

BACKGROUND: In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience - to enhance intuition and communicate excitement - rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. METHODS: The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. RESULTS: In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs). CONCLUSION: The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis.

Authors
Block, JN; Zielinski, DJ; Chen, VB; Davis, IW; Vinson, EC; Brady, R; Richardson, JS; Richardson, DC
MLA Citation
Block, JN, Zielinski, DJ, Chen, VB, Davis, IW, Vinson, EC, Brady, R, Richardson, JS, and Richardson, DC. "KinImmerse: Macromolecular VR for NMR ensembles. (Published online)" Source Code Biol Med 4 (February 17, 2009): 3-.
PMID
19222844
Source
pubmed
Published In
Source Code for Biology and Medicine
Volume
4
Publish Date
2009
Start Page
3
DOI
10.1186/1751-0473-4-3

Recent developments in phasing and structure refinement for macromolecular crystallography

Central to crystallographic structure solution is obtaining accurate phases in order to build a molecular model, ultimately followed by refinement of that model to optimize its fit to the experimental diffraction data and prior chemical knowledge. Recent advances in phasing and model refinement and validation algorithms make it possible to arrive at better electron density maps and more accurate models. © 2009 Elsevier Ltd.

Authors
Adams, PD; Afonine, PV; Grosse-Kunstleve, RW; Read, RJ; Richardson, JS; Richardson, DC; Terwilliger, TC
MLA Citation
Adams, PD, Afonine, PV, Grosse-Kunstleve, RW, Read, RJ, Richardson, JS, Richardson, DC, and Terwilliger, TC. "Recent developments in phasing and structure refinement for macromolecular crystallography." Current Opinion in Structural Biology 19.5 (2009): 566-572.
PMID
19700309
Source
scival
Published In
Current Opinion in Structural Biology
Volume
19
Issue
5
Publish Date
2009
Start Page
566
End Page
572
DOI
10.1016/j.sbi.2009.07.014

The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.

For template-based modeling in the CASP8 Critical Assessment of Techniques for Protein Structure Prediction, this work develops and applies six new full-model metrics. They are designed to complement and add value to the traditional template-based assessment by the global distance test (GDT) and related scores (based on multiple superpositions of Calpha atoms between target structure and predictions labeled "Model 1"). The new metrics evaluate each predictor group on each target, using all atoms of their best model with above-average GDT. Two metrics evaluate how "protein-like" the predicted model is: the MolProbity score used for validating experimental structures, and a mainchain reality score using all-atom steric clashes, bond length and angle outliers, and backbone dihedrals. Four other new metrics evaluate match of model to target for mainchain and sidechain hydrogen bonds, sidechain end positioning, and sidechain rotamers. Group-average Z-score across the six full-model measures is averaged with group-average GDT Z-score to produce the overall ranking for full-model, high-accuracy performance. Separate assessments are reported for specific aspects of predictor-group performance, such as robustness of approximately correct template or fold identification, and self-scoring ability at identifying the best of their models. Fold identification is distinct from but correlated with group-average GDT Z-score if target difficulty is taken into account, whereas self-scoring is done best by servers and is uncorrelated with GDT performance. Outstanding individual models on specific targets are identified and discussed. Predictor groups excelled at different aspects, highlighting the diversity of current methodologies. However, good full-model scores correlate robustly with high Calpha accuracy.

Authors
Keedy, DA; Williams, CJ; Headd, JJ; Arendall, WB; Chen, VB; Kapral, GJ; Gillespie, RA; Block, JN; Zemla, A; Richardson, DC; Richardson, JS
MLA Citation
Keedy, DA, Williams, CJ, Headd, JJ, Arendall, WB, Chen, VB, Kapral, GJ, Gillespie, RA, Block, JN, Zemla, A, Richardson, DC, and Richardson, JS. "The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models." Proteins 77 Suppl 9 (2009): 29-49.
PMID
19731372
Source
pubmed
Published In
Proteins: Structure, Function and Bioinformatics
Volume
77 Suppl 9
Publish Date
2009
Start Page
29
End Page
49
DOI
10.1002/prot.22551

Algorithm for backrub motions in protein design.

MOTIVATION: The Backrub is a small but kinematically efficient side-chain-coupled local backbone motion frequently observed in atomic-resolution crystal structures of proteins. A backrub shifts the C(alpha)-C(beta) orientation of a given side-chain by rigid-body dipeptide rotation plus smaller individual rotations of the two peptides, with virtually no change in the rest of the protein. Backrubs can therefore provide a biophysically realistic model of local backbone flexibility for structure-based protein design. Previously, however, backrub motions were applied via manual interactive model-building, so their incorporation into a protein design algorithm (a simultaneous search over mutation and backbone/side-chain conformation space) was infeasible. RESULTS: We present a combinatorial search algorithm for protein design that incorporates an automated procedure for local backbone flexibility via backrub motions. We further derive a dead-end elimination (DEE)-based criterion for pruning candidate rotamers that, in contrast to previous DEE algorithms, is provably accurate with backrub motions. Our backrub-based algorithm successfully predicts alternate side-chain conformations from < or = 0.9 A resolution structures, confirming the suitability of the automated backrub procedure. Finally, the application of our algorithm to redesign two different proteins is shown to identify a large number of lower-energy conformations and mutation sequences that would have been ignored by a rigid-backbone model. AVAILABILITY: Contact authors for source code.

Authors
Georgiev, I; Keedy, D; Richardson, JS; Richardson, DC; Donald, BR
MLA Citation
Georgiev, I, Keedy, D, Richardson, JS, Richardson, DC, and Donald, BR. "Algorithm for backrub motions in protein design." Bioinformatics 24.13 (July 1, 2008): i196-i204.
PMID
18586714
Source
pubmed
Published In
Bioinformatics
Volume
24
Issue
13
Publish Date
2008
Start Page
i196
End Page
i204
DOI
10.1093/bioinformatics/btn169

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).

A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle delta epsilon zeta alpha beta gamma delta combinations empirically found favorable for the sugar-to-sugar "suite" unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for delta epsilon zeta and a lowercase letter for alpha beta gamma delta, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.

Authors
Richardson, JS; Schneider, B; Murray, LW; Kapral, GJ; Immormino, RM; Headd, JJ; Richardson, DC; Ham, D; Hershkovits, E; Williams, LD; Keating, KS; Pyle, AM; Micallef, D; Westbrook, J; Berman, HM; RNA Ontology Consortium,
MLA Citation
Richardson, JS, Schneider, B, Murray, LW, Kapral, GJ, Immormino, RM, Headd, JJ, Richardson, DC, Ham, D, Hershkovits, E, Williams, LD, Keating, KS, Pyle, AM, Micallef, D, Westbrook, J, Berman, HM, and RNA Ontology Consortium, . "RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)." RNA 14.3 (March 2008): 465-481.
PMID
18192612
Source
pubmed
Published In
RNA (New York, N.Y.)
Volume
14
Issue
3
Publish Date
2008
Start Page
465
End Page
481
DOI
10.1261/rna.657708

RNABC: Forward kinematics to reduce all-atom steric clashes in RNA backbone

Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes ( 0.4 Å overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations. Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%). For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is available from http://kinemage.biochem.duke.edu . © 2007 Springer-Verlag.

Authors
Wang, X; Kapral, G; Murray, L; Richardson, D; Richardson, J; Snoeyink, J
MLA Citation
Wang, X, Kapral, G, Murray, L, Richardson, D, Richardson, J, and Snoeyink, J. "RNABC: Forward kinematics to reduce all-atom steric clashes in RNA backbone." Journal of Mathematical Biology 56.1-2 (2008): 253-278.
PMID
17401565
Source
scival
Published In
Journal of Mathematical Biology
Volume
56
Issue
1-2
Publish Date
2008
Start Page
253
End Page
278
DOI
10.1007/s00285-007-0082-x

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

Authors
Davis, IW; Leaver-Fay, A; Chen, VB; Block, JN; Kapral, GJ; Wang, X; Murray, LW; Arendall, WB; Snoeyink, J; Richardson, JS; Richardson, DC
MLA Citation
Davis, IW, Leaver-Fay, A, Chen, VB, Block, JN, Kapral, GJ, Wang, X, Murray, LW, Arendall, WB, Snoeyink, J, Richardson, JS, and Richardson, DC. "MolProbity: all-atom contacts and structure validation for proteins and nucleic acids." Nucleic Acids Res 35.Web Server issue (July 2007): W375-W383.
PMID
17452350
Source
pubmed
Published In
Nucleic Acids Research
Volume
35
Issue
Web Server issue
Publish Date
2007
Start Page
W375
End Page
W383
DOI
10.1093/nar/gkm216

Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 Å resolution

The hypothetical protein PF0899 is a 95-residue peptide from the hyperthermophilic archaeon Pyrococcus furiosus that represents a gene family with six members. P. furiosus ORF PF0899 has been cloned, expressed and crystallized and its structure has been determined by the Southeast Collaboratory for Structural Genomics (http://www.secsg.org). The structure was solved using the SCA2Structure pipeline from multiple data sets and has been refined to 1.85 Å against the highest resolution data set collected (a presumed gold derivative), with a crystallographic R factor of 21.0% and Rfree of 24.0%. The refined structure shows some structural similarity to a wedge-shaped domain observed in the structure of the major capsid protein from bacteriophage HK97, suggesting that PF0899 may be a structural protein. © International Union of Crystallography 2007.

Authors
Kelley, L-LC; Dillard, BD; Tempel, W; Chen, L; Shaw, N; Lee, D; Newton, MG; Sugar, FJ; Jr, FEJ; Lee, HS; Shah, C; III, FLP; Adams, MWW; Richardson, JS; Richardson, DC; Liu, Z-J; Wang, B-C; Rose, J
MLA Citation
Kelley, L-LC, Dillard, BD, Tempel, W, Chen, L, Shaw, N, Lee, D, Newton, MG, Sugar, FJ, Jr, FEJ, Lee, HS, Shah, C, III, FLP, Adams, MWW, Richardson, JS, Richardson, DC, Liu, Z-J, Wang, B-C, and Rose, J. "Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 Å resolution." Acta Crystallographica Section F: Structural Biology and Crystallization Communications 63.7 (2007): 549-552.
PMID
17620707
Source
scival
Published In
Acta Crystallographica Section F
Volume
63
Issue
7
Publish Date
2007
Start Page
549
End Page
552
DOI
10.1107/S1744309107024049

Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: A component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon

The open-reading frame PF0895 in the genome of the hyperthermophilic archaeon, Pyrococcus furiosus, encodes a 206-residue protein (MR 23,152). The structure of the recombinant protein was solved by single isomorphous replacement with anomalous scattering (SIRAS) using a mercury derivative. It has been refined to 1.70 Å with a crystallographic R and Rfree values of 19.7% and 22.3%, respectively. The PF0895 structure is similar to those of the ATP binding cassettes observed in the ABC transporter family. However, bioinformatics and molecular analyses indicate that PF0895 is not part of the expected five-gene operon that encodes a typical prokaryotic solute-binding ABC transporter. Rather, transcriptional profiling data show that PF0895 is part of a novel four-gene operon (PF0895-PF0896-PF0897-PF0897.1) where only PF0895 has homologs in other organisms. Interestingly, from genome analysis, P. furiosus itself contains a second version of this complex, encoded by PF1090-PF1093. From the structural studies we can only conclude that one of the subunits of this novel membrane complex, PF0895, and its homolog PF1090, likely bind a purine nucleotide. PF0895 is therefore predicted to be part of a membrane-bound multiprotein complex unrelated to ABC transporters that is so far unique to P. furiosus. It appears to play a role in the stress response, as its expression is down regulated when the organism is subjected to cold-shock, where cells are transferred from 95°C, near the optimal growth temperature, to 72°C, near the minimal growth temperature. The related PF1090-containing operon is unaffected by cold-shock and is independently regulated. © 2007 Springer Science+Business Media B.V.

Authors
Gerwe, B; Kelley, L-LC; Dillard, BD; Lai, T; Liu, Z-J; Tempel, W; Chen, L; Habel, J; Lee, D; Jr, FEJ; Sugar, FJ; Richardson, JS; Richardson, DC; Newton, MG; Wang, B-C; Adams, MWW; Rose, JP
MLA Citation
Gerwe, B, Kelley, L-LC, Dillard, BD, Lai, T, Liu, Z-J, Tempel, W, Chen, L, Habel, J, Lee, D, Jr, FEJ, Sugar, FJ, Richardson, JS, Richardson, DC, Newton, MG, Wang, B-C, Adams, MWW, and Rose, JP. "Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: A component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon." Journal of Structural and Functional Genomics 8.1 (2007): 1-10.
PMID
17932790
Source
scival
Published In
Journal of Structural and Functional Genomics
Volume
8
Issue
1
Publish Date
2007
Start Page
1
End Page
10
DOI
10.1007/s10969-007-9026-3

The backrub motion: how protein backbone shrugs when a sidechain dances.

Surprisingly, the frozen structures from ultra-high-resolution protein crystallography reveal a prevalent, but subtle, mode of local backbone motion coupled to much larger, two-state changes of sidechain conformation. This "backrub" motion provides an influential and common type of local plasticity in protein backbone. Concerted reorientation of two adjacent peptides swings the central sidechain perpendicular to the chain direction, changing accessible sidechain conformations while leaving flanking structure undisturbed. Alternate conformations in sub-1 angstroms crystal structures show backrub motions for two-thirds of the significant Cbeta shifts and 3% of the total residues in these proteins (126/3882), accompanied by two-state changes in sidechain rotamer. The Backrub modeling tool is effective in crystallographic rebuilding. For homology modeling or protein redesign, backrubs can provide realistic, small perturbations to rigid backbones. For large sidechain changes in protein dynamics or for single mutations, backrubs allow backbone accommodation while maintaining H bonds and ideal geometry.

Authors
Davis, IW; Arendall, WB; Richardson, DC; Richardson, JS
MLA Citation
Davis, IW, Arendall, WB, Richardson, DC, and Richardson, JS. "The backrub motion: how protein backbone shrugs when a sidechain dances." Structure 14.2 (February 2006): 265-274.
PMID
16472746
Source
pubmed
Published In
Structure
Volume
14
Issue
2
Publish Date
2006
Start Page
265
End Page
274
DOI
10.1016/j.str.2005.10.007

RNA backbone rotamers--finding your way in seven dimensions.

Despite the importance of local structural detail for a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been recalcitrant to analysis. There are too many variable dihedral angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor and all-atom-steric clashes) to the backbone dihedral angle distributions from a selected 8636 residue RNA database. With noise levels significantly decreased, clear signal appears for the underlying angle preferences. We analyse the multidimensional backbone dihedral distributions within sugar-to-sugar 'suites' rather than chemical residues due to the greater base interaction and steric interdependence within the suite. The final result is a small library of RNA backbone rotamers, each represented by a data cluster in seven-dimensional dihedral space, which should provide valid conformations for nearly all RNA backbones encountered in experimental structures. We are in the process of improving that library, and developing tools and applications for it in structure determination and analysis.

Authors
Murray, LJW; Richardson, JS; Arendall, WB; Richardson, DC
MLA Citation
Murray, LJW, Richardson, JS, Arendall, WB, and Richardson, DC. "RNA backbone rotamers--finding your way in seven dimensions." Biochem Soc Trans 33.Pt 3 (June 2005): 485-487.
PMID
15916548
Source
pubmed
Published In
Biochemical Society transactions
Volume
33
Issue
Pt 3
Publish Date
2005
Start Page
485
End Page
487
DOI
10.1042/BST0330485

Assessment of molecular construction in undergraduate biochemistry

Molecular visualization is used by instructors to enhance the student's learning, although few assessments are available to validate this belief. The first performance assessment showed that lecture and lab effectively communicated several core concepts in protein biochemistry. The purpose of the current study was to build on White's study and investigate what biochemistry students learned from the process of actually constructing annotated graphic images of biological macromolecule using experimentally solved coordinate sets from the protein data bank along with the related primary literature. The survey data showed a positive effect on student attitudes about learning various aspects of protein structure, especially higher-order structural concepts.

Authors
Booth, D; Jr, RCB; Sirochman, R; Richardson, DC; Richardson, JS; Weiner, SW; Farwell, M; Putnam-Evans, C
MLA Citation
Booth, D, Jr, RCB, Sirochman, R, Richardson, DC, Richardson, JS, Weiner, SW, Farwell, M, and Putnam-Evans, C. "Assessment of molecular construction in undergraduate biochemistry." Journal of Chemical Education 82.12 (2005): 1854-1858.
Source
scival
Published In
Journal of Chemical Education
Volume
82
Issue
12
Publish Date
2005
Start Page
1854
End Page
1858

The high-throughput protein-to-structure pipeline at SECSG

Using a high degree of automation, the crystallography core at the Southeast Collaboratory for Structural Genomics (SECSG) has developed a high-throughput protein-to-structure pipeline. Various robots and automation procedures have been adopted and integrated into a pipeline that is capable of screening 40 proteins for crystallization and solving four protein structures per week. This pipeline is composed of three major units: crystallization, structure determination/validation and crystallomics. Coupled with the protein-production cores at SECSG, the protein-to-structure pipeline provides a two-tiered approach for protein production at SECSG In tier 1, all protein samples supplied by the protein-production cores pass through the pipeline using standard crystallization screening and optimization procedures. The protein targets that failed to yield diffraction-quality crystals (resolution better than 3.0 Å) become tier 2 or salvaging targets. The goal of tier 2 target salvaging, carried out by the crystallomics core, is to produce the target proteins with increased purity and homogeneity, which would render them more likely to yield well diffracting crystals. This is performed by alternative purification procedures and/or the introduction of chemical modifications to the proteins (such as tag removal, methylation, surface mutagenesis, selenomethionine labelling etc.). Details of the various procedures in the pipeline for protein crystallization, target salvaging, data collection/processing and high-throughput structure determination/validation, as well as some examples, are described. © 2005 International Union of Crystallography - all rights reserved.

Authors
Liu, Z-J; Tempel, W; Ng, JD; Lin, D; Shah, AK; Chen, L; Horanyi, PS; Habel, JE; Kataeva, IA; Xu, H; Yang, H; Chang, JC; Huang, L; Chang, S-H; Zhou, W; Lee, D; Praissman, JL; Zhang, H; Newton, MG; Rose, JP; Richardson, JS; Richardson, DC; Wang, B-C
MLA Citation
Liu, Z-J, Tempel, W, Ng, JD, Lin, D, Shah, AK, Chen, L, Horanyi, PS, Habel, JE, Kataeva, IA, Xu, H, Yang, H, Chang, JC, Huang, L, Chang, S-H, Zhou, W, Lee, D, Praissman, JL, Zhang, H, Newton, MG, Rose, JP, Richardson, JS, Richardson, DC, and Wang, B-C. "The high-throughput protein-to-structure pipeline at SECSG." Acta Crystallographica Section D: Biological Crystallography 61.6 (2005): 679-684.
PMID
15930619
Source
scival
Published In
Acta Crystallographica Section D
Volume
61
Issue
6
Publish Date
2005
Start Page
679
End Page
684
DOI
10.1107/S0907444905013132

Away from the edge II: In-house Se-SAS phasing with chromium radiation

Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray radiation opens a new possibility for phasing a protein with data collected in-house and has led to several successful examples of de novo structure solution using only weak anomalous scatterers such as sulfur. To further reduce data-collection time and make SAS phasing more robust, it is natural to combine selenomethionine-derivatized protein (SeMet protein) with Cr Kα radiation to take advantage of the larger anomalous scattering signal from selenium (f″ = 2.28 e-) compared with sulfur (f″ = 1.14 e-). As reported herein, the crystal structure of a putative chorismate mutase from Clostridium thermocellum was determined using Se-SAS with Cr Kα radiation. Each protein molecule contains eight selenomethionine residues in 148 amino-acid residues, providing a calculated Bijvoet ratio of about 3.5% at the Cr Kα wavelength. A single data set to 2.2 Å resolution with approximately ninefold redundancy was collected using an imaging-plate detector coupled with a Cr source. Structure solution, refinement and deposition to the Protein Data Bank were performed within 9 h of the availability of the scaled diffraction data. The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography. © 2005 International Union of Crystallography - all rights reserved.

Authors
Xu, H; Yang, C; Chen, L; Kataeva, IA; Tempel, W; Lee, D; Habel, JE; Nguyen, D; Pflugrath, JW; Ferrara, JD; III, WBA; Richardson, JS; Richardson, DC; Liu, Z-J; Newton, MG; Rose, JP; Wang, B-C
MLA Citation
Xu, H, Yang, C, Chen, L, Kataeva, IA, Tempel, W, Lee, D, Habel, JE, Nguyen, D, Pflugrath, JW, Ferrara, JD, III, WBA, Richardson, JS, Richardson, DC, Liu, Z-J, Newton, MG, Rose, JP, and Wang, B-C. "Away from the edge II: In-house Se-SAS phasing with chromium radiation." Acta Crystallographica Section D: Biological Crystallography 61.7 (2005): 960-966.
PMID
15983419
Source
scival
Published In
Acta Crystallographica Section D
Volume
61
Issue
7
Publish Date
2005
Start Page
960
End Page
966
DOI
10.1107/S0907444905010644

A test of enhancing model accuracy in high-throughput crystallography.

The high throughput of structure determination pipelines relies on increased automation and, consequently, a reduction of time spent on interactive quality control. In order to meet and exceed current standards in model accuracy, new approaches are needed for the facile identification and correction of model errors during refinement. One such approach is provided by the validation and structure-improvement tools of the MOL: PROBITY: web service. To test their effectiveness in high-throughput mode, a large subset of the crystal structures from the SouthEast Collaboratory for Structural Genomics (SECSG) has used protocols based on the MOL: PROBITY: tools. Comparison of 29 working-set and 19 control-set SECSG structures shows that working-set outlier scores for updated Ramachandran-plot, sidechain rotamer, and all-atom steric criteria have been improved by factors of 5- to 10-fold (relative to the control set or to a Protein Data Bank sample), while quality of covalent geometry, R(work), R(free), electron density and difference density are maintained or improved. Some parts of this correction process are already fully automated; other parts involve manual rebuilding of conformations flagged by the tests as trapped in the wrong local minimum, often altering features of functional significance. The ease and effectiveness of this technique shows that macromolecular crystal structures from either traditional or high-throughput determinations can feasibly reach a new level of excellence in conformational accuracy and reliability.

Authors
Arendall, WB; Tempel, W; Richardson, JS; Zhou, W; Wang, S; Davis, IW; Liu, Z-J; Rose, JP; Carson, WM; Luo, M; Richardson, DC; Wang, B-C
MLA Citation
Arendall, WB, Tempel, W, Richardson, JS, Zhou, W, Wang, S, Davis, IW, Liu, Z-J, Rose, JP, Carson, WM, Luo, M, Richardson, DC, and Wang, B-C. "A test of enhancing model accuracy in high-throughput crystallography." J Struct Funct Genomics 6.1 (2005): 1-11.
PMID
15965733
Source
pubmed
Published In
Journal of Structural and Functional Genomics
Volume
6
Issue
1
Publish Date
2005
Start Page
1
End Page
11
DOI
10.1007/s10969-005-3138-4

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.

MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules and can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. The results are reported in multiple forms: as overall numeric scores, as lists, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown on-line in the KiNG viewer. This service is available free to all users at http://kinemage.biochem.duke.edu.

Authors
Davis, IW; Murray, LW; Richardson, JS; Richardson, DC
MLA Citation
Davis, IW, Murray, LW, Richardson, JS, and Richardson, DC. "MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes." Nucleic Acids Res 32.Web Server issue (July 1, 2004): W615-W619.
PMID
15215462
Source
pubmed
Published In
Nucleic Acids Research
Volume
32
Issue
Web Server issue
Publish Date
2004
Start Page
W615
End Page
W619
DOI
10.1093/nar/gkh398

Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin

Authors
Tempel, W; Liu, Z-J; Schubot, FD; Shah, A; Weinberg, MV; Jr, FEJ; III, WBA; Adams, MWW; Richardson, JS; Richardson, DC; Rose, JP; Wang, B-C
MLA Citation
Tempel, W, Liu, Z-J, Schubot, FD, Shah, A, Weinberg, MV, Jr, FEJ, III, WBA, Adams, MWW, Richardson, JS, Richardson, DC, Rose, JP, and Wang, B-C. "Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin." Proteins: Structure, Function and Genetics 57.4 (2004): 878-882.
PMID
15468318
Source
scival
Published In
Proteins: Structure, Function and Genetics
Volume
57
Issue
4
Publish Date
2004
Start Page
878
End Page
882
DOI
10.1002/prot.20280

RNA backbone is rotameric.

Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor, and all-atom steric clashes) to the backbone torsion angle distributions from an 8,636-residue RNA database. With noise levels greatly reduced, clear signal appears for the underlying angle preferences. Half-residue torsion angle distributions for alpha-beta-gamma and for delta-epsilon-zeta are plotted and contoured in 3D; each shows about a dozen distinct peaks, which can then be combined in pairs to define complete RNA backbone conformers. Traditional nucleic acid residues are defined from phosphate to phosphate, but here we use a base-to-base (or sugar-to-sugar) division into "suites" to parse the RNA backbone repeats, both because most backbone steric clashes are within suites and because the relationship of successive bases is both reliably determined and conformationally important. A suite conformer has seven variables, with sugar pucker specified at both ends. Potential suite conformers were omitted if not represented by at least a small cluster of convincing data points after application of quality filters. The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures.

Authors
Murray, LJW; Arendall, WB; Richardson, DC; Richardson, JS
MLA Citation
Murray, LJW, Arendall, WB, Richardson, DC, and Richardson, JS. "RNA backbone is rotameric." Proc Natl Acad Sci U S A 100.24 (November 25, 2003): 13904-13909.
PMID
14612579
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
100
Issue
24
Publish Date
2003
Start Page
13904
End Page
13909
DOI
10.1073/pnas.1835769100

Structure validation by Cα geometry: φ,ψ and Cβ deviation

Geometrical validation around the Cα is described, with a new Cβ measure and updated Ramachandran plot. Deviation of the observed Cβ atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cβ deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new φ,ψ plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and nonprePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the γ-turn conformation near +75°,-60°, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the γ-turn H-bond. Favored and allowed φ,ψ regions are also defined for Pro, pre. Pro, and Gly (important because Gly φ,ψ angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of α-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (httpd/www.cryst. bioc.cam.ac.uk/rampage). © 2003 Wiley-Liss, Inc.

Authors
Lovell, SC; Davis, IW; III, WBA; Bakker, PIWD; Word, JM; Prisant, MG; Richardson, JS; Richardson, DC
MLA Citation
Lovell, SC, Davis, IW, III, WBA, Bakker, PIWD, Word, JM, Prisant, MG, Richardson, JS, and Richardson, DC. "Structure validation by Cα geometry: φ,ψ and Cβ deviation." Proteins: Structure, Function and Genetics 50.3 (2003): 437-450.
PMID
12557186
Source
scival
Published In
Proteins: Structure, Function and Genetics
Volume
50
Issue
3
Publish Date
2003
Start Page
437
End Page
450
DOI
10.1002/prot.10286

New tools and data for improving structures, using all-atom contacts.

Authors
Richardson, JS; Bryan, WA; Richardson, DC
MLA Citation
Richardson, JS, Bryan, WA, and Richardson, DC. "New tools and data for improving structures, using all-atom contacts." Methods Enzymol 374 (2003): 385-412.
PMID
14696383
Source
pubmed
Published In
Methods in Enzymology
Volume
374
Publish Date
2003
Start Page
385
End Page
412

Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation.

The fact that natural beta-sheet proteins are usually soluble but that fragments or designs of beta structure usually aggregate suggests that natural beta proteins must somehow be designed to avoid this problem. Regular beta-sheet edges are dangerous, because they are already in the right conformation to interact with any other beta strand they encounter. We surveyed edge strands in a large sample of all-beta proteins to tabulate features that could protect against further beta-sheet interactions. beta-barrels, of course, avoid edges altogether by continuous H-bonding around the barrel cylinder. Parallel beta-helix proteins protect their beta-sheet ends by covering them with loops of other structure. beta-propeller and single-sheet proteins use a combination of beta-bulges, prolines, strategically placed charges, very short edge strands, and loop coverage. beta-sandwich proteins favor placing an inward-pointing charged side chain on one of the edge strands where it would be buried by dimerization; they also use bulges, prolines, and other mechanisms. One recent beta-hairpin design has a constrained twist too great for accommodation into a larger beta-sheet, whereas some beta-sheet edges are protected by the bend and reverse twist produced by an Lbeta glycine. All free edge strands were seen to be protected, usually by several redundant mechanisms. In contrast, edge strands that natively form beta H-bonded dimers or rings have long, regular stretches without such protection. These results are relevant to understanding how proteins may assemble into beta-sheet amyloid fibers, and they are especially applicable to the de novo design of beta structure. Many edge-protection strategies used by natural proteins are beyond our current abilities to constrain by design, but one possibility stands out as especially useful: a single charged side chain near the middle of what would ordinarily be the hydrophobic side of the edge beta strand. This minimal negative-design strategy changes only one residue, requires no backbone distortion, and is easy to design. The accompanying paper [Wang, W. & Hecht, M. H. (2002) Proc. Natl. Acad. Sci. USA 99, 2760-2765] makes use of the inward-pointing charge strategy with great success, turning highly aggregated beta-sandwich designs into soluble monomers.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation." Proc Natl Acad Sci U S A 99.5 (March 5, 2002): 2754-2759.
PMID
11880627
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
99
Issue
5
Publish Date
2002
Start Page
2754
End Page
2759
DOI
10.1073/pnas.052706099

Teaching molecular 3-D literacy

Authors
Richardson, DC; Richardson, JS
MLA Citation
Richardson, DC, and Richardson, JS. "Teaching molecular 3-D literacy." Biochemistry and Molecular Biology Education 30.1 (2002): 21-26.
Source
scival
Published In
Biochemistry and Molecular Biology Education
Volume
30
Issue
1
Publish Date
2002
Start Page
21
End Page
26
DOI
10.1002/bmb.2002.494030010005

Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry

Authors
Jr, RCB; Booth, D; Sirochman, R; Richardson, J; Richardson, D
MLA Citation
Jr, RCB, Booth, D, Sirochman, R, Richardson, J, and Richardson, D. "Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry." Journal of Chemical Education 79.5 (2002): 551--.
Source
scival
Published In
Journal of Chemical Education
Volume
79
Issue
5
Publish Date
2002
Start Page
551-

Exploring steric constraints on protein mutations using MAGE/PROBE.

When planning a mutation to test some hypothesis, one crucial question is whether the new side chain is compatible with the existing structure; only if it is compatible can the interpretation of mutational results be straightforward. This paper presents a simple way of using the sensitive geometry of all-atom contacts (including hydrogens) to answer that question. The interactive MAGE/PROBE system lets the biologist explore conformational space for the mutant side chain, with an interactively updated kinemage display of its all-atom contacts to the original structure. The Autobondrot function in PROBE systematically explores that same conformational space, outputting contact scores at each point, which are then contoured and displayed. These procedures are applied here in two types of test cases, with known mutant structures. In ricin A chain, the ability of a neighboring glutamate to rescue activity of an active-site mutant is modeled successfully. In T4 lysozyme, six mutations to Leu are analyzed within the wild-type background structure, and their Autobondrot score maps correctly predict whether or not their surroundings must shift significantly in the actual mutant structures; interactive examination of contacts for the conformations involved explains which clashes are relieved by the motions. These programs are easy to use, are available free for UNIX or Microsoft Windows operating systems, and should be of significant help in choosing good mutation experiments or in understanding puzzling results.

Authors
Word, JM; Bateman, RC; Presley, BK; Lovell, SC; Richardson, DC
MLA Citation
Word, JM, Bateman, RC, Presley, BK, Lovell, SC, and Richardson, DC. "Exploring steric constraints on protein mutations using MAGE/PROBE." Protein Sci 9.11 (November 2000): 2251-2259.
PMID
11152136
Source
pubmed
Published In
Protein Science
Volume
9
Issue
11
Publish Date
2000
Start Page
2251
End Page
2259
DOI
10.1110/ps.9.11.2251

The penultimate rotamer library.

All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of chi angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389-408.

Authors
Lovell, SC; Word, JM; Richardson, JS; Richardson, DC
MLA Citation
Lovell, SC, Word, JM, Richardson, JS, and Richardson, DC. "The penultimate rotamer library." Proteins 40.3 (August 15, 2000): 389-408.
PMID
10861930
Source
pubmed
Published In
Proteins: Structure, Function and Bioinformatics
Volume
40
Issue
3
Publish Date
2000
Start Page
389
End Page
408

SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics.

Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical short helices, we here proceed by an extensive redesign of the ROP protein. A fully symmetrical SymROP sequence derived from ROP was chosen by modeling ideal-geometry side chains, including hydrogens, while maintaining the "goodness-of-fit" of side-chain packing by calculating all-atom contact surfaces with the Reduce and Probe programs. To estimate the probable extent of backbone movement and side-chain mobility, restrained molecular dynamics simulations were compared for candidate sequences and controls, including substitution of Abu for all or half the core Ala residues. The resulting 17-residue designed sequence is 41% identical to the relevant regions in ROP. SymROP is intended for construction by the Template Assembled Synthetic Proteins approach, to control the bundle topology, to use short helices, and to allow blocked termini and unnatural amino acids. ROP protein has been a valuable system for studying helical protein structure because of its simplicity and regularity within a structure large enough to have a real hydrophobic core. The SymROP design carries that simplicity and regularity even further.

Authors
Grell, D; Richardson, JS; Richardson, DC; Mutter, M
MLA Citation
Grell, D, Richardson, JS, Richardson, DC, and Mutter, M. "SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics." J Mol Graph Model 18.3 (June 2000): 290-310.
PMID
11021545
Source
pubmed
Published In
Journal of Molecular Graphics and Modelling
Volume
18
Issue
3
Publish Date
2000
Start Page
290
End Page
310

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

The technique of small-probe contact dot surfaces is described as a method for calculating and displaying the detailed atomic contacts inside or between molecules. It allows one both to measure and to visualize directly the goodness-of-fit of packing interactions. It requires both highly accurate structures and also the explicit inclusion of all hydrogen atoms and their van der Waals interactions. A reference dataset of 100 protein structures was chosen on the basis of resolution (1.7 A or better), crystallographic R-value, non-homology, and the absence of any unusual problems. Hydrogen atoms were added in standard geometry and, where needed, with rotational optimization of OH, SH, and NH+3 positions. Side-chain amide orientations were corrected where required by NH van der Waals clashes, as described in the accompanying paper. It was determined that, in general, methyl groups pack well in the default staggered conformation, except for the terminal methyl groups of methionine residues, which required rotational optimization. The distribution of serious clashes (i.e. non-H-bond overlap of >/=0.4 A) was studied as a function of resolution, alternate conformations, and temperature factor (B), leading to the decision that packing and other structural features would not be analyzed for residues in 'b' alternate conformations or with B-factors of 40 or above. At the level of the fine details analyzed here, structural accuracy improves quite significantly over the range from 1.7 to 1.0 A resolution. These high-resolution structures show impressively well-fitted packing interactions, with some regions thoroughly interdigitated and other regions somewhat sparser. Lower-resolution structures or model structures could undoubtedly be improved in accuracy by the incorporation of this additional information: for example, nucleic acid structures in non-canonical conformations are often very accurate for the bases and much less reliable for the backbone, whose conformation could be specified better by including explicit H atom geometry and contacts. The contact dots are an extremely sensitive method of finding problem areas, and often they can suggest how to make improvements. They can also provide explanations for structural features that have been described only as empirical regularities, which is illustrated by showing that the commonest rotamer of methionine (a left-handed spiral, with all chi values near -60 degrees) is preferred because it provides up to five good H atom van der Waals contacts. This methodology is thus applicable in two different ways: (1) for finding and correcting errors in structure models (either experimental or theoretical); and (2) for analyzing interaction patterns in the molecules themselves.

Authors
Word, JM; Lovell, SC; LaBean, TH; Taylor, HC; Zalis, ME; Presley, BK; Richardson, JS; Richardson, DC
MLA Citation
Word, JM, Lovell, SC, LaBean, TH, Taylor, HC, Zalis, ME, Presley, BK, Richardson, JS, and Richardson, DC. "Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms." J Mol Biol 285.4 (January 29, 1999): 1711-1733.
PMID
9917407
Source
pubmed
Published In
Journal of Molecular Biology
Volume
285
Issue
4
Publish Date
1999
Start Page
1711
End Page
1733
DOI
10.1006/jmbi.1998.2400

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.

Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 A resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln "flips", this process included rotation of OH, SH, NH3+, and methionine methyl H atoms, flip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide flips (or N and C identity for His flips), no non-H atoms were shifted. Even in these very high-quality structures, about 20 % of the Asn/Gln side-chains required a 180 degrees flip to optimize H-bonding and/or to avoid NH2 clashes with neighboring atoms (incorporating a conservative score penalty which, for marginal cases, favors the assignment in the original coordinate file). The programs Reduce, Probe, and Mage provide not only a suggested amide orientation, but also a numerical score comparison, a categorization of the marginal cases, and a direct visualization of all relevant interactions in both orientations. Visual examination allowed confirmation of the raw score assignment for about 40 % of those Asn/Gln flips placed within the "marginal" penalty range by the automated algorithm, while uncovering only a small number of cases whose automated assignment was incorrect because of special circumstances not yet handled by the algorithm. It seems that the H-bond and the atomic-clash criteria independently look at the same structural realities: when both criteria gave a clear answer they agreed every time. But consideration of van der Waals clashes settled many additional cases for which H-bonding was either absent or approximately equivalent for the two main alternatives. With this extra information, 86 % of all side-chain amide groups could be oriented quite unambiguously. In the absence of further experimental data, it would probably be inappropriate to assign many more than this. Some of the remaining 14 % are ambiguous because of coordinate error or inadequacy of the theoretical model, but the great majority of ambiguous cases probably occur as a dynamic mix of both flip states in the actual protein molecule. The software and the 100 coordinate files with all H atoms added and optimized and with amide flips corrected are publicly available.

Authors
Word, JM; Lovell, SC; Richardson, JS; Richardson, DC
MLA Citation
Word, JM, Lovell, SC, Richardson, JS, and Richardson, DC. "Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation." J Mol Biol 285.4 (January 29, 1999): 1735-1747.
PMID
9917408
Source
pubmed
Published In
Journal of Molecular Biology
Volume
285
Issue
4
Publish Date
1999
Start Page
1735
End Page
1747
DOI
10.1006/jmbi.1998.2401

Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.

Previous rotamer libraries showed little significant clustering for asparagine chi2 or glutamine chi3 values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at /=0.4 A). All H atoms were added and optimized, and amide orientation was flipped by 180 degrees if required by H bonding or atomic clashes. A side chain was included only if its amide orientation was clearly determined and if no atom had a B factor >/=40, alternate conformation, or severe clash; that selection process yielded 1,490 Asn and 863 Gln side chains. Clear clustering was observed for Asn chi2 and Gln chi3 (except when Gln chi2 is trans). For Gln, five major and four minor rotamers cover 87% of examples. For Asn, there are seven backbone-independent rotamers covering 94% of examples plus rotamers specified for strictly alpha-helical, beta, and left-handed (+phi) Asn. Although the strongest influence on chi angles is avoidance of atomic clashes (especially with the NH2 hydrogens), some Asn or Gln rotamers are influenced by favorable van der Waals contacts and others by specific local H-bond patterns.

Authors
Lovell, SC; Word, JM; Richardson, JS; Richardson, DC
MLA Citation
Lovell, SC, Word, JM, Richardson, JS, and Richardson, DC. "Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering." Proc Natl Acad Sci U S A 96.2 (January 19, 1999): 400-405.
PMID
9892645
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
96
Issue
2
Publish Date
1999
Start Page
400
End Page
405

Puzzle pieces defined: locating common packing units in tertiary protein contacts.

Puzzle pieces are defined as small packing units which make up the unique tertiary interactions in proteins. Anti-parallel and perpendicular helix-helix contacts were broken down into basic puzzle-piece pairs in order to study the traits of such contacts: their limited geometry, preferred residue involvement, residue conformation and other common constraints. These traits can then be used for continued comparison of other protein structures, improving models of and designing proteins de novo and, in time, predicting 3D structure from primary sequence. Results from a small (100 proteins) database of anti-parallel helix-helix contacts and from preliminary work on a large database (600 proteins) of perpendicular helix-helix contacts are presented.

Authors
Gernert, KM; Thomas, BD; Plurad, JC; Richardson, JS; Richardson, DC; Bergman, LD
MLA Citation
Gernert, KM, Thomas, BD, Plurad, JC, Richardson, JS, Richardson, DC, and Bergman, LD. "Puzzle pieces defined: locating common packing units in tertiary protein contacts." Pac Symp Biocomput (1996): 331-349.
PMID
9390242
Source
pubmed
Published In
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Publish Date
1996
Start Page
331
End Page
349

The Alacoil: a very tight, antiparallel coiled-coil of helices.

The Alacoil is an antiparallel (rather than the usual parallel) coiled-coil of alpha-helices with Ala or another small residue in every seventh position, allowing a very close spacing of the helices (7.5-8.5 A between local helix axes), often over four or five helical turns. It occurs in two distinct types that differ by which position of the heptad repeat is occupied by Ala and by whether the closest points on the backbone of the two helices are aligned or are offset by half a turn. The aligned, or ROP, type has Ala in position "d" of the heptad repeat, which occupies the "tip-to-tip" side of the helix contact where the C alpha-C beta bonds point toward each other. The more common offset, or ferritin, type of Alacoli has Ala in position "a" of the heptad repeat (where the C alpha-C beta bonds lie back-to-back, on the "knuckle-touch" side of the helix contact), and the backbones of the two helices are offset vertically by half a turn. In both forms, successive layers of contact have the Ala first on one and then on the other helix. The Alacoil structure has much in common with the coiled-coils of fibrous proteins or leucine zippers: both are alpha-helical coiled-coils, with a critical amino acid repeated every seven residues (the Leu or the Ala) and a secondary contact position in between. However, Leu zippers are between aligned, parallel helices (often identical, in dimers), whereas Alacoils are between antiparallel helices, usually offset, and much closer together. The Alacoil, then, could be considered as an "Ala anti-zipper." Leu zippers have a classic "knobs-into-holes" packing of the Leu side chain into a diamond of four residues on the opposite helix; for Alacoils, the helices are so close together that the Ala methyl group must choose one side of the diamond and pack inside a triangle of residues on the other helix. We have used the ferritin-type Alacoil as the basis for the de novo design of a 66-residue, coiled helix hairpin called "Alacoilin." Its sequence is: cmSPDQWDKE AAQYDAHAQE FEKKSHRNng TPEADQYRHM ASQY QAMAQK LKAIANQLKK Gsetcr (with "a" heptad positions underlined and nonhelical parts in lowercase), which we will produce and test for both stability and uniqueness of structure.

Authors
Gernert, KM; Surles, MC; Labean, TH; Richardson, JS; Richardson, DC
MLA Citation
Gernert, KM, Surles, MC, Labean, TH, Richardson, JS, and Richardson, DC. "The Alacoil: a very tight, antiparallel coiled-coil of helices." Protein Sci 4.11 (November 1995): 2252-2260.
PMID
8563621
Source
pubmed
Published In
Protein Science
Volume
4
Issue
11
Publish Date
1995
Start Page
2252
End Page
2260
DOI
10.1002/pro.5560041102

An algorithm for smoothly tessellating beta-sheet structures in proteins.

An algorithm is presented for tiling the surface of beta-sheet structures, smoothed both along the strands and perpendicular to them. The algorithm is intended for creating graphical representations of beta structure within the three-dimensional context of proteins. This article presents sufficient detail to allow a programmer with some knowledge of protein structure to implement the tiling algorithm. Several examples of its use are illustrated.

Authors
Bergman, LD; Richardson, JS; Richardson, DC
MLA Citation
Bergman, LD, Richardson, JS, and Richardson, DC. "An algorithm for smoothly tessellating beta-sheet structures in proteins." J Mol Graph 13.1 (February 1995): 36-58.
PMID
7794833
Source
pubmed
Published In
Journal of Molecular Graphics
Volume
13
Issue
1
Publish Date
1995
Start Page
36
End Page
58

Defining, computing, and visualizing molecular interfaces

A parallel, analytic approach for defining and computing the inter- and intra-molecular interfaces in three dimensions is described. The molecular interface surfaces are derived from approximations to the power-diagrams over the participating molecular units. For a given molecular interface our approach can generate a family of interface surfaces parametrized by α and β, where α is the radius of the solvent molecule (also known as the probe-radius) and β is the interface radius that defines the size of the molecular interface. Molecular interface surfaces provide biochemists with a powerful tool to study surface complementarity and to efficiently characterize the interactions during a protein-substrate docking. The complexity of our algorithm for molecular environments is O(nk log2 k), where n is the number of atoms in the participating molecular units and k is the average number of neighboring atoms - a constant, given α and β.

Authors
Varshney, A; Jr, FPB; Richardson, DC; Wright, WV; Manocha, D
MLA Citation
Varshney, A, Jr, FPB, Richardson, DC, Wright, WV, and Manocha, D. "Defining, computing, and visualizing molecular interfaces." Proceedings of the IEEE Visualization Conference (1995): 36-43.
Source
scival
Published In
Proceedings of the IEEE Visualization Conference
Publish Date
1995
Start Page
36
End Page
43

The tyrosine corner: a feature of most Greek key beta-barrel proteins.

The Tyr corner is a conformation in which a tyrosine (residue "Y") near the beginning or end of an antiparallel beta-strand makes an H bond from its side-chain OH group to the backbone NH and/or CO of residue Y - 3, Y - 4, or Y - 5 in the nearby connection. The most common "classic" case is a delta 4 Tyr corner (more than 40 examples listed), in which the H bond is to residue Y - 4 and the Tyr chi 1 is near -60 degrees. Y - 2 is almost always a glycine, whose left-handed beta or very extended beta conformation helps the backbone curve around the Tyr ring. Residue Y - 3 is in polyproline II conformation (often Pro), and residue Y - 5 is usually a hydrophobic (often Leu) that packs next to the Tyr ring. The consensus sequence, then, is LxPGxY, where the first x (the H-bonding position) is hydrophilic. Residues Y and Y - 2 both form narrow pairs of beta-sheet H-bonds with the neighboring strand. delta 5 Tyr corners have a 1-residue insertion between the Gly and Tyr, forming a beta-bulge. One protein family has a delta 4 corner formed by a His rather than a Tyr, and several examples use Trp in place of Tyr. For almost all these cases, the protein or domain is a Greek key beta-barrel structure, the Tyr corner ends a Greek key connection, and it is well-conserved in related proteins. Most low-twist Greek key beta-barrels have 1 Tyr corner. "Reverse" delta 4 Tyr corners (H bonded to Y + 4) and other variants are described, all less common and less conserved. It seems likely that the more classic Tyr corners (delta 4, delta 5, and delta 3 Tyr, Trp, or His) contribute to the stability of a Greek key connection over a hairpin connection, and also that they may aid in the process of folding up Greek key structures.

Authors
Hemmingsen, JM; Gernert, KM; Richardson, JS; Richardson, DC
MLA Citation
Hemmingsen, JM, Gernert, KM, Richardson, JS, and Richardson, DC. "The tyrosine corner: a feature of most Greek key beta-barrel proteins." Protein Sci 3.11 (November 1994): 1927-1937.
PMID
7703839
Source
pubmed
Published In
Protein Science
Volume
3
Issue
11
Publish Date
1994
Start Page
1927
End Page
1937
DOI
10.1002/pro.5560031104

Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein.

How an amino acid sequence encodes the information necessary for a protein to adopt a unique tertiary structure remains unresolved. We are addressing this problem by designing "from scratch" protein molecules that will adopt predetermined three-dimensional structures. Based on this strategy, two identical four-stranded beta-sheets were designed to dimerize and form a beta-sandwich protein, called betadoublet. A synthetic gene encoding half the beta-sandwich protein was expressed in Escherichia coli, and the protein was purified to homogeneity. Biophysical characterization of betadoublet in aqueous solution demonstrated that the disulfide formed between the two sheets and that the dimer was a compact unaggregated globular protein, consisting predominantly of beta-sheet and stable to thermal denaturation. It has some backbone amide protons whose exchange is slow enough to be measured by NMR but binds more of the dye 1-anilinonaphthalene-8-sulfonate than a well-folded protein.

Authors
Quinn, TP; Tweedy, NB; Williams, RW; Richardson, JS; Richardson, DC
MLA Citation
Quinn, TP, Tweedy, NB, Williams, RW, Richardson, JS, and Richardson, DC. "Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein." Proc Natl Acad Sci U S A 91.19 (September 13, 1994): 8747-8751.
PMID
8090717
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
91
Issue
19
Publish Date
1994
Start Page
8747
End Page
8751

Kinemages--simple macromolecular graphics for interactive teaching and publication.

Authors
Richardson, DC; Richardson, JS
MLA Citation
Richardson, DC, and Richardson, JS. "Kinemages--simple macromolecular graphics for interactive teaching and publication." Trends Biochem Sci 19.3 (March 1994): 135-138.
PMID
8203021
Source
pubmed
Published In
Trends in Biochemical Sciences
Volume
19
Issue
3
Publish Date
1994
Start Page
135
End Page
138

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions. Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrange-multiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded beta-ribbon into an approximate beta-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and (2) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed.

Authors
Surles, MC; Richardson, JS; Richardson, DC; Brooks, FP
MLA Citation
Surles, MC, Richardson, JS, Richardson, DC, and Brooks, FP. "Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system." Protein Sci 3.2 (February 1994): 198-210. (Review)
PMID
8003957
Source
pubmed
Published In
Protein Science
Volume
3
Issue
2
Publish Date
1994
Start Page
198
End Page
210
DOI
10.1002/pro.5560030205

VIEW-An exploratory molecular visualization system with user-definable interaction sequences

VIEW is an exploratory visualization system for studying the structures of molecules. The systems supports a high degree of complex user interaction with the image. Visualization are constructed by selecting drawing tools from a library. Each tool uses parameters obtained from interactive selection of on-screen geometry by the user, and from a molecular database.

Authors
Bergman, LD; Richardson, JS
MLA Citation
Bergman, LD, and Richardson, JS. "VIEW-An exploratory molecular visualization system with user-definable interaction sequences." Proc ACM SIGGRAPH 93 Conf Comput Graphics (1993): 117-126.
Source
scival
Published In
Proc ACM SIGGRAPH 93 Conf Comput Graphics
Publish Date
1993
Start Page
117
End Page
126

A COMMON ARCH STRUCTURE IN BETA SANDWICH PROTEINS - THE TYROSINE TURN

Authors
HEMMINGSEN, JM; RICHARDSON, JS; RICHARDSON, DC
MLA Citation
HEMMINGSEN, JM, RICHARDSON, JS, and RICHARDSON, DC. "A COMMON ARCH STRUCTURE IN BETA SANDWICH PROTEINS - THE TYROSINE TURN." PROTEIN ENGINEERING 6 (1993): 104-104.
Source
wos-lite
Published In
Protein Engineering
Volume
6
Publish Date
1993
Start Page
104
End Page
104

STRUCTURAL CHARACTERISTICS OF FELIX, A DESIGNED PROTEIN

Authors
GERNERT, KM; RICHARDSON, JS; RICHARDSON, DC
MLA Citation
GERNERT, KM, RICHARDSON, JS, and RICHARDSON, DC. "STRUCTURAL CHARACTERISTICS OF FELIX, A DESIGNED PROTEIN." PROTEIN ENGINEERING 6 (1993): 114-114.
Source
wos-lite
Published In
Protein Engineering
Volume
6
Publish Date
1993
Start Page
114
End Page
114

Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992.

Looking at proteins is an active process of interpretation and selection, emphasizing some features and deleting others. Multiple representations are needed, for such purposes as showing motions or conveying both the chain connectivity and the three-dimensional shape simultaneously. In studying and comparing protein structures, ideas are suggested about the determinants of tertiary structure and of folding (e.g., that Greek key beta barrels may fold up two strands at a time). The design and synthesis of new proteins "from scratch" provides a route toward the experimental testing of such ideas. It has also been a fruitful new perspective from which to look at structures, requiring such things as statistics on very narrowly defined structural categories and explicit attention to "negative design" criteria that actively block unwanted alternatives (e.g., reverse topology of a helix bundle, or edge-to-edge aggregation of beta sheets). Recently, the field of protein design has produced a rather unexpected general result: apparently we do indeed know enough to successfully design proteins that fold into approximately correct structures, but not enough to design unique, native-like structures. The degree of order varies considerably, but even the best designed material shows multiple conformations by NMR, more similar to a "molten globule" folding intermediate than to a well ordered native tertiary structure. In response to this conclusion, we are now working on systems that test useful questions with approximate structures (such as determining which factors most influence the choice of helix-bundle topology) and also analyzing how natural proteins achieve unique core conformations (e.g., for side chains on the interior side of a beta sheet, illustrated in the kinemages).

Authors
Richardson, JS; Richardson, DC; Tweedy, NB; Gernert, KM; Quinn, TP; Hecht, MH; Erickson, BW; Yan, Y; McClain, RD; Donlan, ME
MLA Citation
Richardson, JS, Richardson, DC, Tweedy, NB, Gernert, KM, Quinn, TP, Hecht, MH, Erickson, BW, Yan, Y, McClain, RD, and Donlan, ME. "Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992." Biophys J 63.5 (November 1992): 1185-1209. (Review)
PMID
1477272
Source
pubmed
Published In
Biophysical Journal
Volume
63
Issue
5
Publish Date
1992
Start Page
1185
End Page
1209

The kinemage: a tool for scientific communication.

A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared and specified by the author(s) of a journal article, in order to better communicate ideas that depend on three-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program, such as the one described here (called MAGE), which presently runs on Macintosh computers. A utility (called PREKIN) helps authors prepare the kinemages. Kinemages are being implemented under the auspices of the Innovative Technology Fund.

Authors
Richardson, DC; Richardson, JS
MLA Citation
Richardson, DC, and Richardson, JS. "The kinemage: a tool for scientific communication." Protein Sci 1.1 (January 1992): 3-9.
PMID
1304880
Source
pubmed
Published In
Protein Science
Volume
1
Issue
1
Publish Date
1992
Start Page
3
End Page
9
DOI
10.1002/pro.5560010102

De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence.

The protein Felix was designed de novo to fold into an antiparallel four-helix bundle of specific topology. Its sequence of 79 amino acid residues is not homologous to any known protein sequence, but is "native-like" in that it is nonrepetitive and contains 19 of the 20 naturally occurring amino acids. Felix has been expressed from a synthetic gene cloned in Escherichia coli, and the protein has been purified to homogeneity. Physical characterization of the purified protein indicates that Felix (i) is monomeric in solution, (ii) is predominantly alpha-helical, (iii) contains a designed intramolecular disulfide bond linking the first and fourth helices, and (iv) buries its single tryptophan in an apolar environment and probably in close proximity with the disulfide bond. These physical properties rule out several alternative structures and indicate that Felix indeed folds into approximately the designed three-dimensional structure.

Authors
Hecht, MH; Richardson, JS; Richardson, DC; Ogden, RC
MLA Citation
Hecht, MH, Richardson, JS, Richardson, DC, and Ogden, RC. "De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence." Science 249.4971 (August 24, 1990): 884-891.
PMID
2392678
Source
pubmed
Published In
Science
Volume
249
Issue
4971
Publish Date
1990
Start Page
884
End Page
891

The de novo design of protein structures.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "The de novo design of protein structures." Trends Biochem Sci 14.7 (July 1989): 304-309. (Review)
PMID
2672455
Source
pubmed
Published In
Trends in Biochemical Sciences
Volume
14
Issue
7
Publish Date
1989
Start Page
304
End Page
309

Amino acid preferences for specific locations at the ends of alpha helices.

A definition based on alpha-carbon positions and a sample of 215 alpha helices from 45 different globular protein structures were used to tabulate amino acid preferences for 16 individual positions relative to the helix ends. The interface residue, which is half in and half out of the helix, is called the N-cap or C-cap, whichever is appropriate. The results confirm earlier observations, such as asymmetrical charge distributions in the first and last helical turn, but several new, sharp preferences are found as well. The most striking of these are a 3.5:1 preference for Asn at the N-cap position, and a preference of 2.6:1 for Pro at N-cap + 1. The C-cap position is overwhelmingly dominated by Gly, which ends 34 percent of the helices. Hydrophobic residues peak at positions N-cap + 4 and C-cap - 4.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Amino acid preferences for specific locations at the ends of alpha helices." Science 240.4859 (June 17, 1988): 1648-1652.
PMID
3381086
Source
pubmed
Published In
Science
Volume
240
Issue
4859
Publish Date
1988
Start Page
1648
End Page
1652

Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal.

The DNA-binding helix pairs in gene repressor and activator proteins were compared with other approximately perpendicular pairs of adjacent helices in the known protein structures. Two other examples of closely matching conformations were found in cytochrome c peroxidase (residues 153-174) and in ribosomal L7/L12 protein (residues 68-89). Another group of such offset "lap-joints" are the Ca-binding "EF hand" structures, which bind a positive rather than a negative ligand. The EF hands turn out to match the DNA-binding motifs quite well (outside of the loop) if their sequence direction is reversed. This conformation is thus not as unusual as had been thought, but may have a more generalized role in ion binding and occasionally occur in a purely structural role.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal." Proteins 4.4 (1988): 229-239.
PMID
2855370
Source
pubmed
Published In
Proteins: Structure, Function and Bioinformatics
Volume
4
Issue
4
Publish Date
1988
Start Page
229
End Page
239
DOI
10.1002/prot.340040402

Erratum: Amino acid preferences for specific locations at the ends of α helices (Science (1988) (1648))

Authors
Richardson, J; Richardson, D
MLA Citation
Richardson, J, and Richardson, D. "Erratum: Amino acid preferences for specific locations at the ends of α helices (Science (1988) (1648))." Science 242.4886 (1988): 1624--.
Source
scival
Published In
Science
Volume
242
Issue
4886
Publish Date
1988
Start Page
1624-

The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase

Isolated hemoprotein subunits of Escherichia coli NADPH:sulfite reductase catalyze the 6-electron reduction of SO32- to S2-. The prosthetic groups of the hemoprotein, a siroheme and a Fe4S4 cluster, have been shown by spectroscopy to be tightly coupled. We have crystallized the isolated hemoprotein subunits and produced a 3-Å electron density map by x-ray crystallography. A single heavy atom derivative and the native anomalous scattering (from the protein's 5 Fe and several S) were used to calculate the phases. In the electron density map, the cluster has a geometry similar to other Fe4S4 clusters. Both the cluster and the siroheme are found near the surface of the protein. The siroheme and the Fe4S4 cluster pack next to each other in the structure, apparently with a common ligand, consistent with a cysteine Sγ, share by the siroheme Fe and one of the cluster Fe. The distance from the siroheme Fe to the center of the cluster is 5.5 Å and the distance from the siroheme Fe to the nearest Fe is 4.4 Å. The edge of the siroheme macrocycle appears to be in Van der Waals contact with a cubane S atom of the cluster. The sixth coordination position of the siroheme Fe appears unoccupied and is quite exposed to the solvent. Some possible implications of the proposed structure on the role of the bridged siroheme-Fe4S4 cluster in catalysis are discussed.

Authors
McRee, DE; Richardson, DC; Richardson, JS; Siegel, LM
MLA Citation
McRee, DE, Richardson, DC, Richardson, JS, and Siegel, LM. "The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase." Journal of Biological Chemistry 261.22 (December 1, 1986): 10277-10281.
Source
scopus
Published In
The Journal of biological chemistry
Volume
261
Issue
22
Publish Date
1986
Start Page
10277
End Page
10281

The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase.

Isolated hemoprotein subunits of Escherichia coli NADPH:sulfite reductase catalyze the 6-electron reduction of SO2-3 to S2-. The prosthetic groups of the hemoprotein, a siroheme and a Fe4S4 cluster, have been shown by spectroscopy to be tightly coupled. We have crystallized the isolated hemoprotein subunits and produced a 3-A electron density map by x-ray crystallography. A single heavy atom derivative and the native anomalous scattering (from the protein's 5 Fe and several S) were used to calculate the phases. In the electron density map, the cluster has a geometry similar to other Fe4S4 clusters. Both the cluster and the siroheme are found near the surface of the protein. The siroheme and the Fe4S4 cluster pack next to each other in the structure, apparently with a common ligand, consistent with a cysteine S gamma, shared by the siroheme Fe and one of the cluster Fe. The distance from the siroheme Fe to the center of the cluster is 5.5 A and the distance from the siroheme Fe to the nearest cluster Fe is 4.4 A. The edge of the siroheme macrocycle appears to be in Van der Waals contact with a cubane S atom of the cluster. The sixth coordination position of the siroheme Fe appears unoccupied and is quite exposed to the solvent. Some possible implications of the proposed structure on the role of the bridged siroheme-Fe4S4 cluster in catalysis are discussed.

Authors
McRee, DE; Richardson, DC; Richardson, JS; Siegel, LM
MLA Citation
McRee, DE, Richardson, DC, Richardson, JS, and Siegel, LM. "The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase." J Biol Chem 261.22 (August 5, 1986): 10277-10281.
PMID
3525540
Source
pubmed
Published In
The Journal of biological chemistry
Volume
261
Issue
22
Publish Date
1986
Start Page
10277
End Page
10281

Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli.

Crystals of the acyl carrier protein of Escherichia coli have been grown and analyzed by X-ray diffraction. The crystals grow in space group C2 with unit cell dimensions a = 46.8 A, b = 52.1 A, c = 47.3 A and beta = 93.2 degrees. An isomorphous derivative, HgCl2, has been identified and characterized.

Authors
McRee, DE; Richardson, JS; Richardson, DC
MLA Citation
McRee, DE, Richardson, JS, and Richardson, DC. "Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli." J Mol Biol 182.3 (April 5, 1985): 467-468.
PMID
3892013
Source
pubmed
Published In
Journal of Molecular Biology
Volume
182
Issue
3
Publish Date
1985
Start Page
467
End Page
468

Interpretation of electron density maps.

Authors
Richardson, JS; Richardson, DC
MLA Citation
Richardson, JS, and Richardson, DC. "Interpretation of electron density maps." Methods Enzymol 115 (1985): 189-206.
PMID
3841180
Source
pubmed
Published In
Methods in Enzymology
Volume
115
Publish Date
1985
Start Page
189
End Page
206

Protein engineering: Design and synthesis of a protein

Authors
Unson, CG; Erickson, BW; Richardson, DC; Richardson, JS
MLA Citation
Unson, CG, Erickson, BW, Richardson, DC, and Richardson, JS. "Protein engineering: Design and synthesis of a protein." Federation Proceedings 43.6 (1984): no.-2457.
Source
scival
Published In
Federation Proceedings
Volume
43
Issue
6
Publish Date
1984
Start Page
no.
End Page
2457

Structure and mechanism of copper, zinc superoxide dismutase.

Copper, zinc superoxide dismutase (SOD) catalyses the very rapid two-step dismutation of the toxic superoxide radical (O-2) to molecular oxygen and hydrogen peroxide through the alternate reduction and oxidation of the active-site copper. We report here that after refitting and further refinement of the previous 2 A structure of SOD2, analysis of the new model and its calculated molecular surface shows an extensive surface topography of sequence-conserved residues stabilized by underlying tight packing and H-bonding. There is a single, highly complementary position for O-2 to bind to both the Cu(II) and activity-important Arg 141 with correct geometry; two water molecules form a ghost of the superoxide in this position. The geometry and molecular surface of the active site, together with biochemical data, suggest a specific model for the enzyme mechanism.

Authors
Tainer, JA; Getzoff, ED; Richardson, JS; Richardson, DC
MLA Citation
Tainer, JA, Getzoff, ED, Richardson, JS, and Richardson, DC. "Structure and mechanism of copper, zinc superoxide dismutase." Nature 306.5940 (November 17, 1983): 284-287.
PMID
6316150
Source
pubmed
Published In
Nature
Volume
306
Issue
5940
Publish Date
1983
Start Page
284
End Page
287

Electrostatic recognition between superoxide and copper, zinc superoxide dismutase.

Electrostatic forces have been implicated in a variety of biologically important molecular interactions including drug orientation by DNA, protein folding and assembly, substrate binding and catalysis and macromolecular complementarity with inhibitors, drugs and hormones. To examine enzyme-substrate interactions in copper, zinc superoxide dismutase (SOD), we developed a method for the visualization and analysis of an enzyme's three-dimensional electrostatic vector field that allows the contributions of specific residues to be identified. We report here that the arrangement of electrostatic charges in SOD promotes productive enzyme-substrate interaction through substrate guidance and charge complementarity: sequence-conserved residues create an extensive electrostatic field that directs the negatively charged superoxide (O-2) substrate to the highly positive catalytic binding site at the bottom of the active-site channel. Dissection of the electrostatic potential gradient indicated the relative contributions of individual charged residues: Lys 134 and Glu 131 seem to have important roles in directing the long-range approach of O-2, while Arg 141 has local orienting effects. The reported methods of analysis may have general application for the elucidation of intermolecular recognition processes.

Authors
Getzoff, ED; Tainer, JA; Weiner, PK; Kollman, PA; Richardson, JS; Richardson, DC
MLA Citation
Getzoff, ED, Tainer, JA, Weiner, PK, Kollman, PA, Richardson, JS, and Richardson, DC. "Electrostatic recognition between superoxide and copper, zinc superoxide dismutase." Nature 306.5940 (November 17, 1983): 287-290.
PMID
6646211
Source
pubmed
Published In
Nature
Volume
306
Issue
5940
Publish Date
1983
Start Page
287
End Page
290

Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.

Authors
Tainer, JA; Getzoff, ED; Beem, KM; Richardson, JS; Richardson, DC
MLA Citation
Tainer, JA, Getzoff, ED, Beem, KM, Richardson, JS, and Richardson, DC. "Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase." J Mol Biol 160.2 (September 15, 1982): 181-217.
PMID
7175933
Source
pubmed
Published In
Journal of Molecular Biology
Volume
160
Issue
2
Publish Date
1982
Start Page
181
End Page
217

Preliminary X-ray diffraction studies on the hemoprotein subunit of Escherichia coli sulfite reductase.

Authors
McRee, DE; Richardson, DC
MLA Citation
McRee, DE, and Richardson, DC. "Preliminary X-ray diffraction studies on the hemoprotein subunit of Escherichia coli sulfite reductase." J Mol Biol 154.1 (January 5, 1982): 179-180.
PMID
7042979
Source
pubmed
Published In
Journal of Molecular Biology
Volume
154
Issue
1
Publish Date
1982
Start Page
179
End Page
180

"Active" conformation of an inactive semi-synthetic ribonuclease-S.

Authors
Taylor, HC; Richardson, DC; Richardson, JS; Wlodawer, A; Komoriya, A; Chaikes, IM
MLA Citation
Taylor, HC, Richardson, DC, Richardson, JS, Wlodawer, A, Komoriya, A, and Chaikes, IM. ""Active" conformation of an inactive semi-synthetic ribonuclease-S." J Mol Biol 149.2 (June 25, 1981): 313-317.
PMID
7310884
Source
pubmed
Published In
Journal of Molecular Biology
Volume
149
Issue
2
Publish Date
1981
Start Page
313
End Page
317

The beta bulge: a common small unit of nonrepetitive protein structure.

A beta bulge is a region between two consecutive beta-type hydrogen bonds which includes two residues (positions 1 and 2) on one strand opposite a single residue (position x) on the other strand. Compared to regular beta structure, a beta bulge puts the usual alternation of side-chain direction out of register on one of the strands, introduces a slight bend in the beta sheet, and locally accentuates the usual right-handed strand twist. Almost all beta bulges are between antiparallel strands, usually between a narrow rather than a wide pair of hydrogen bonds. Ninety-one examples are listed. The two commonest types are the "classic" beta bulge, with position 1 in approximately alpha-helical conformation, and the "G1" beta bulge, with a required glycine at position 1 in approximately left-handed alpha-helical conformation, G1 bulges almost always occur in combination with a type II tight turn. The functional roles of beta bulges probably include compensating for the effects of a single-residue insertion or deletion within beta structure and providing the strong local twist required for form closed beta barrel structures.

Authors
Richardson, JS; Getzoff, ED; Richardson, DC
MLA Citation
Richardson, JS, Getzoff, ED, and Richardson, DC. "The beta bulge: a common small unit of nonrepetitive protein structure." Proc Natl Acad Sci U S A 75.6 (June 1978): 2574-2578.
PMID
275827
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
75
Issue
6
Publish Date
1978
Start Page
2574
End Page
2578

Metal sites of copper-zinc superoxide dismutase.

Silver-copper and silver-cobalt proteins have been prepared in which Ag+ resides in the native copper site of superoxide dismutase and either Cu2+ of Co2+ reside in the zinc site. The electron paramagnetic resonance (EPR) spectrum of the copper and the visible absorption spectrum of the cobalt greatly resemble those of either Cu4 of Cu2,Cu2,Co2 proteins, respectively, in which the copper of the native copper sites has been reduced. It was found that, unlike cyanide, azide anion would not perturb the EPR spectrum of Ag2,Cu2 protein. Since azide produces the same perturbation upon the EPR spectrum of native and Cu2 proteins, it must bind to the copper and not the zinc of superoxide dismutase. A model of the metal sites of the enzyme has been fitted to a 3-A electron-density map using an interactive molecular graphics display. The model shows that histidine-61, which appears to bind both copper and zinc, does not lie in the plane of the copper and its three other histidine ligands, but occupies a position intermediate between planar and axial. This feature probably accounts for the rhombicity of the EPR spectrum and the activity of the enzyme.

Authors
Beem, KM; Richardson, DC; Rajagopalan, KV
MLA Citation
Beem, KM, Richardson, DC, and Rajagopalan, KV. "Metal sites of copper-zinc superoxide dismutase." Biochemistry 16.9 (May 3, 1977): 1930-1936.
PMID
192282
Source
pubmed
Published In
Biochemistry
Volume
16
Issue
9
Publish Date
1977
Start Page
1930
End Page
1936

Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies.

Authors
Beem, KM; Richardson, JS; Richardson, DC
MLA Citation
Beem, KM, Richardson, JS, and Richardson, DC. "Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies." J Mol Biol 105.2 (August 5, 1976): 327-332.
PMID
787536
Source
pubmed
Published In
Journal of Molecular Biology
Volume
105
Issue
2
Publish Date
1976
Start Page
327
End Page
332

Similarity of three-dimensional structure between the immunoglobulin domain and the copper, zinc superoxide dismutase subunit.

Authors
Richardson, JS; Richardson, DC; Thomas, KA; Silverton, EW; Davies, DR
MLA Citation
Richardson, JS, Richardson, DC, Thomas, KA, Silverton, EW, and Davies, DR. "Similarity of three-dimensional structure between the immunoglobulin domain and the copper, zinc superoxide dismutase subunit." J Mol Biol 102.2 (April 5, 1976): 221-235.
PMID
1271464
Source
pubmed
Published In
Journal of Molecular Biology
Volume
102
Issue
2
Publish Date
1976
Start Page
221
End Page
235

Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase.

Authors
Richardson, JS; Thomas, KA; Richardson, DC
MLA Citation
Richardson, JS, Thomas, KA, and Richardson, DC. "Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase." Biochem Biophys Res Commun 63.4 (April 21, 1975): 986-992.
PMID
1169067
Source
pubmed
Published In
Biochemical and Biophysical Research Communications
Volume
63
Issue
4
Publish Date
1975
Start Page
986
End Page
992

Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands.

An electron density map at 3 angstrom resolution has been calculated for Cu2+, Zn2+ superoxide dismutase from bovine erythrocytes, and the course of the main chain has been traced. The dominant structural feature is an 8-stranded barrel of antiparallel beta-pleated sheet. There is one very short helical section and two long loops of non-repetitive structure. The Cu and Zn are bound between the loops and one side of the beta barrel and are about 6 Angstrom apart, with a common histidine ligand. The Cu has four histidine ligands in a somewhat distorted square plane, and the Zn has three histidines and an aspartate in approximately tetrahedral arrangement. The two coppers of a dimer are about 34 Angstrom apart. The two subunits have essentially the same conformation and have an extensive contact area that mainly involves hydrophobic side chain interactions. The overall folding pattern of the polypeptide chain is very similar to that of an immunoglobulin domain.

Authors
Richardson, J; Thomas, KA; Rubin, BH; Richardson, DC
MLA Citation
Richardson, J, Thomas, KA, Rubin, BH, and Richardson, DC. "Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands." Proc Natl Acad Sci U S A 72.4 (April 1975): 1349-1353.
PMID
1055410
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
72
Issue
4
Publish Date
1975
Start Page
1349
End Page
1353

The crystal structure of bovine Cu2+,Zn2+ superoxide dismutase at 5.5-A resolution.

Authors
Thomas, KA; Rubin, BH; Bier, CJ; Richardson, JS; Richardson, DC
MLA Citation
Thomas, KA, Rubin, BH, Bier, CJ, Richardson, JS, and Richardson, DC. "The crystal structure of bovine Cu2+,Zn2+ superoxide dismutase at 5.5-A resolution." J Biol Chem 249.17 (September 10, 1974): 5677-5683.
PMID
4472353
Source
pubmed
Published In
The Journal of biological chemistry
Volume
249
Issue
17
Publish Date
1974
Start Page
5677
End Page
5683

Two crystal forms of bovine superoxide dismutase.

Authors
Richardson, DC; Bier, CJ; Richardson, JS
MLA Citation
Richardson, DC, Bier, CJ, and Richardson, JS. "Two crystal forms of bovine superoxide dismutase." J Biol Chem 247.19 (October 10, 1972): 6368-6369.
PMID
4675640
Source
pubmed
Published In
The Journal of biological chemistry
Volume
247
Issue
19
Publish Date
1972
Start Page
6368
End Page
6369

A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing.

Authors
Arnone, A; Bier, CJ; Cotton, FA; Day, VW; Hazen, EE; Richardson, DC; Yonath, A; Richardson, JS
MLA Citation
Arnone, A, Bier, CJ, Cotton, FA, Day, VW, Hazen, EE, Richardson, DC, Yonath, A, and Richardson, JS. "A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing." J Biol Chem 246.7 (April 10, 1971): 2302-2316.
PMID
5555571
Source
pubmed
Published In
The Journal of biological chemistry
Volume
246
Issue
7
Publish Date
1971
Start Page
2302
End Page
2316

The extracellular nuclease of Staphylococcus aureus: structures of the native enzyme and an enzyme-inhibitor complex at 4 A resolution.

Independent 4 A electron density maps calculated for the extracellular nuclease of Staphylococcus aureus (based on data from three heavy-atom derivatives) and for a nuclease-thymidine-3',5'-diphosphate-calcium ion complex (based on a single isomorphous derivative) show about 60 per cent of the chain resolved, including 3(1/2) turns of helix. The pyrimidine ring of the inhibitor fits into a pocket in the enzyme and appears to be parallel to the ring of a tyrosyl residue. Conformational changes can be observed between the nuclease and the nuclease-inhibitor complex, but the two structures seem to be identical over most of the molecule.

Authors
Arnone, A; Bier, CJ; Cotton, FA; Hazen, EE; Richardson, DC; Richardson, JS
MLA Citation
Arnone, A, Bier, CJ, Cotton, FA, Hazen, EE, Richardson, DC, and Richardson, JS. "The extracellular nuclease of Staphylococcus aureus: structures of the native enzyme and an enzyme-inhibitor complex at 4 A resolution." Proc Natl Acad Sci U S A 64.2 (October 1969): 420-427.
PMID
5261023
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
64
Issue
2
Publish Date
1969
Start Page
420
End Page
427

Molecular Structure and Bonding in Diethylenetriaminechromium Tricarbonyl: The Cr(0) and Approximate Mn(0) Radii

Authors
Cotton, FA; Richardson, DC
MLA Citation
Cotton, FA, and Richardson, DC. "Molecular Structure and Bonding in Diethylenetriaminechromium Tricarbonyl: The Cr(0) and Approximate Mn(0) Radii." Inorganic Chemistry 5.11 (November 1966): 1851-1854.
Source
crossref
Published In
Inorganic Chemistry
Volume
5
Issue
11
Publish Date
1966
Start Page
1851
End Page
1854
DOI
10.1021/ic50045a003

Crystalline extracellular nuclease of Staphylococcus aureus.

Authors
Cotton, FA; Hazen, EE; Richardson, DC
MLA Citation
Cotton, FA, Hazen, EE, and Richardson, DC. "Crystalline extracellular nuclease of Staphylococcus aureus." J Biol Chem 241.19 (October 10, 1966): 4389-4390.
PMID
5922963
Source
pubmed
Published In
The Journal of biological chemistry
Volume
241
Issue
19
Publish Date
1966
Start Page
4389
End Page
4390

A Spectrophotometric Study of Equilibria Involving Mononuclear Chromium(VI) Species in Solutions of Various Acids

Authors
Haight, GP; Richardson, DC; Coburn, NH
MLA Citation
Haight, GP, Richardson, DC, and Coburn, NH. "A Spectrophotometric Study of Equilibria Involving Mononuclear Chromium(VI) Species in Solutions of Various Acids." Inorganic Chemistry 3.12 (December 1964): 1777-1780.
Source
crossref
Published In
Inorganic Chemistry
Volume
3
Issue
12
Publish Date
1964
Start Page
1777
End Page
1780
DOI
10.1021/ic50022a028
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Research Areas:

  • Biophysics
  • Computer Graphics
  • Crystallography, X-Ray
  • Databases, Nucleic Acid
  • Databases, Protein
  • Hepatitis Delta Virus
  • Hydrogen
  • Nucleic Acid Conformation
  • Protein Engineering
  • Protein Structure, Tertiary
  • RNA
  • RNA Cleavage
  • RNA, Catalytic
  • Software
  • Superoxide Dismutase
  • User-Computer Interface
  • X-Ray Diffraction