A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

doi:10.1107/S2059798315022408

Title: A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

Journal Article · Fri Jan 01 04:00:00 UTC 2016 · Acta Crystallographica. Section D. Structural Biology

DOI: https://doi.org/10.1107/S2059798315022408 · OSTI ID:1378757

Moriarty, Nigel W. ^[1]; Tronrud, Dale E. ^[2]; Adams, Paul D. ^[3]; Karplus, P. Andrew ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences
Oregon State Univ., Corvallis, OR (United States). Dept. of Biochemistry and Biophysics
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering

Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1378757

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Issue: 1 Vol. 72; ISSN 2059-7983; ISSN ACSDAD

Publisher:: IUCrCopyright Statement

Country of Publication:: United States

Language:: English

References (16)

Conformational transitions and geometry differences between low-energy conformers of N -acetyl- N ′-methyl alanineamide: An ab initio study at the 4-21G level with gradient relaxed geometries : CONFORMATIONAL TRANSITIONS Schäfer, Lothar; Klimkowski, V. J.; Momany, Frank A. Biopolymers, Vol. 23, Issue 11 https://doi.org/10.1002/bip.360231115	journal	November 1984
Experimentally observed conformation-dependent geometry and hidden strain in proteins Karplus, P. Andrew Protein Science, Vol. 5, Issue 7 https://doi.org/10.1002/pro.5560050719	journal	July 1996
Conformation Dependence of Backbone Geometry in Proteins Berkholz, Donald S.; Shapovalov, Maxim V.; Dunbrack, Roland L. Structure, Vol. 17, Issue 10 https://doi.org/10.1016/j.str.2009.08.012	journal	October 2009
Proteins Do Not Have Strong Spines After All Dauter, Zbigniew; Wlodawer, Alexander Structure, Vol. 17, Issue 10 https://doi.org/10.1016/j.str.2009.09.002	journal	October 2009
Predictions of protein backbone structural parameters from first principles: Systematic comparisons of calculated N-C(.alpha.)-C' angles with high-resolution protein crystallographic results Jiang, Xiaoqin; Cao, Ming; Teppen, Brian The Journal of Physical Chemistry, Vol. 99, Issue 26 https://doi.org/10.1021/j100026a014	journal	June 1995
Ab initio studies of molecular geometries. 27. Optimized molecular structures and conformational analysis of N.alpha.-acetyl-N-methylalaninamide and comparison with peptide crystal data and empirical calculations Scarsdale, J. N.; Van Alsenoy, C.; Klimkowski, V. J. Journal of the American Chemical Society, Vol. 105, Issue 11 https://doi.org/10.1021/ja00349a010	journal	June 1983
The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W. Journal of Applied Crystallography, Vol. 35, Issue 1 https://doi.org/10.1107/S0021889801017824	journal	January 2002
A short history of SHELX Sheldrick, George M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122 https://doi.org/10.1107/S0108767307043930	journal	December 2007
An efficient general-purpose least-squares refinement program for macromolecular structures Tronrud, D. E.; Ten Eyck, L. F.; Matthews, B. W. Acta Crystallographica Section A Foundations of Crystallography, Vol. 43, Issue 4 https://doi.org/10.1107/S0108767387099124	journal	July 1987
A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions Karplus, P. Andrew; Shapovalov, Maxim V.; Dunbrack, Roland L. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 3 https://doi.org/10.1107/S0907444908002333	journal	February 2008
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins Tronrud, Dale E.; Berkholz, Donald S.; Karplus, P. Andrew Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 7 https://doi.org/10.1107/S0907444910019207	journal	June 2010
A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution Tronrud, Dale E.; Karplus, P. Andrew Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 8 https://doi.org/10.1107/S090744491102292X	journal	July 2011
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D. FEBS Journal, Vol. 281, Issue 18 https://doi.org/10.1111/febs.12860	journal	June 2014

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Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations Jiang, Zhongming; Biczysko, Malgorzata; Moriarty, Nigel W. Proteins: Structure, Function, and Bioinformatics, Vol. 86, Issue 3 https://doi.org/10.1002/prot.25451	journal	January 2018
Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach Malliavin, Thérèse E.; Mucherino, Antonio; Lavor, Carlile Journal of Chemical Information and Modeling, Vol. 59, Issue 10 https://doi.org/10.1021/acs.jcim.9b00215	journal	August 2019
Systematic exploration of protein conformational space using a Distance Geometry approach Malliavin, Thérèse E.; Mucherino, Antonio; Lavor, Carlile Journal of Chemical Information and Modeling https://doi.org/10.1101/650903	journal	August 2019
An editor for the generation and customization of geometry restraints Moriarty, Nigel W.; Draizen, Eli J.; Adams, Paul D. Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2 https://doi.org/10.1107/s2059798316016570	journal	February 2017
Strategies for carbohydrate model building, refinement and validation Agirre, Jon Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2 https://doi.org/10.1107/s2059798316016910	journal	February 2017
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/s2059798319011471	journal	October 2019
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix Moriarty, Nigel W.; Janowski, Pawel A.; Swails, Jason M. Acta Crystallographica Section D Structural Biology, Vol. 76, Issue 1 https://doi.org/10.1107/s2059798319015134	journal	January 2020
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43042	text	January 2019

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59 BASIC BIOLOGICAL SCIENCES
Phenix
covalent geometry restraints
crystallographic refinement
protein structure
validation

Title: A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

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References (16)

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