Overall protein structure quality assessment using hydrogen-bonding parameters.

IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-08-01 Epub Date: 2023-07-11 DOI:10.1107/S2059798323005077
Pavel V Afonine, Oleg V Sobolev, Nigel W Moriarty, Thomas C Terwilliger, Paul D Adams
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Abstract

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.

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利用氢键参数评估蛋白质结构的整体质量。
在低分辨率下完善原子模型通常是一项具有挑战性的任务。这主要是因为实验数据不够详细,无法用原子模型来描述。为了使细化工作切实可行,并确保细化后的原子模型具有几何意义,需要使用额外的信息,如对拉马钱德兰图分布或残基侧链旋转态的限制。然而,使用拉马钱德兰图或旋转体状态作为细化目标会削弱这些工具的验证能力。因此,寻找其他未被使用或难以用作细化目标的模型验证标准是可取的。氢键是塑造和维持蛋白质结构的重要非共价相互作用之一。这些相互作用可以通过供氢原子和受氢原子的特定几何形状来表征。对蛋白质数据库中经过质量过滤的高分辨率蛋白质模型进行的系统分析显示,这些几何结构具有独特而保守的分布。在此,我们将展示如何将这些信息用于原子模型验证。
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来源期刊
Acta Crystallographica. Section D, Structural Biology
Acta Crystallographica. Section D, Structural Biology BIOCHEMICAL RESEARCH METHODSBIOCHEMISTRY &-BIOCHEMISTRY & MOLECULAR BIOLOGY
CiteScore
4.50
自引率
13.60%
发文量
216
期刊介绍: Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.
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Making the most of an abundance of data. Peter Main (1939-2024). Photosystem II: light-dependent oscillation of ligand composition at its active site. The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1. Improving macromolecular structure refinement with metal-coordination restraints.
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