Overall protein structure quality assessment using hydrogen-bonding parameters

被引:3
|
作者
Afonine, Pavel V. [1 ]
Sobolev, Oleg V. [1 ]
Moriarty, Nigel W. [1 ]
Terwilliger, Thomas C. [2 ,3 ]
Adams, Paul D. [1 ,4 ]
机构
[1] Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA
[2] Los Alamos Natl Lab, Biosci Div, Mail Stop M888, Los Alamos, NM 87545 USA
[3] New Mexico Consortium, Los Alamos, NM 87544 USA
[4] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA
来源
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2023年 / 79卷
关键词
atomic model refinement; hydrogen bonds; crystallography; cryo-EM; validation; CRYO-EM; CRYSTALLOGRAPHIC REFINEMENT; VALIDATION; PHENIX; TOOLS; DICTIONARY; MOLPROBITY; RESTRAINTS; KNOWLEDGE; DOMAIN;
D O I
10.1107/S2059798323005077
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Atomic model refinement at low resolution is often a challenging task. This is mostly because the experimental data are not sufficiently detailed to be described by atomic models. To make refinement practical and ensure that a refined atomic model is geometrically meaningful, additional information needs to be used such as restraints on Ramachandran plot distributions or residue side-chain rotameric states. However, using Ramachandran plots or rotameric states as refinement targets diminishes the validating power of these tools. Therefore, finding additional model-validation criteria that are not used or are difficult to use as refinement goals is desirable. Hydrogen bonds are one of the important noncovalent interactions that shape and maintain protein structure. These interactions can be characterized by a specific geometry of hydrogen donor and acceptor atoms. Systematic analysis of these geometries performed for quality-filtered high-resolution models of proteins from the Protein Data Bank shows that they have a distinct and a conserved distribution. Here, it is demonstrated how this information can be used for atomic model validation.
引用
收藏
页码:684 / 693
页数:10
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