<br>Cys.sqlite：蛋白质数据库中半胱氨酸二硫键综合分析的结构化信息方法,Journal of Chemical Information and Modeling

当前位置： X-MOL 学术 › J. Chem. Inf. Model. › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

Cys.sqlite：蛋白质数据库中半胱氨酸二硫键综合分析的结构化信息方法
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2019-01-29 00:00:00 , DOI: 10.1021/acs.jcim.8b00950
Theodore L Fobe _{1,

2} , Andrei Kazakov ₃ , Demian Riccardi ₃

Affiliation

半胱氨酸是一种多面氨基酸，是许多蛋白质结构和功能的核心。两个半胱氨酸之间形成的二硫键通过强共价键和围绕键的扭转（能量上倾向于±90°）来限制蛋白质构象。在本研究中，我们将超过 30 000 个蛋白质数据库文件 (PDBx/mmCIF) 转换为单个文件，即 SQLite 数据库 (Cys.sqlite)。数据库模式旨在容纳氧化和还原半胱氨酸的结构信息，并保留必要的蛋白质元数据以建立信息和生物来源。 Cys.sqlite 包含超过 95 000 条肽链和 500 000 个半胱氨酸（700 000 个结构构象异构体）；使用所有可用的实验方法解析的结构中存在超过 265 000 个半胱氨酸二硫键构象。根据序列同一性截断、实验方法和二硫键的能量学分析结构信息。我们发现，随着实验信息变得有限并且建模的影响变得更加明显，观察到的平均应变人为地增加。这里提供的数据库和分析可用于改进已知含有一个或多个二硫键的实验的生物结构的细化。

"点击查看英文标题和摘要"

Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank

Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90°. In this study, we transform over 30 000 Protein Databank files (PDBx/mmCIFs) into a single file, the SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information on both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance. Cys.sqlite contains over 95 000 peptide chains and 500 000 cysteines (700 000 structural conformers); there are over 265 000 cysteine disulfide bond conformations from structures solved with all available experimental methods. The structural information is analyzed with respect to sequence identity cutoff, the experimental method, and energetics of the disulfide. We find that as the experimental information becomes limiting and the influence of modeling becomes more pronounced, the observed average strain increases artificially. The database and analyses presented here can be used to improve the refinement of biological structures from experiments that are known to contain one or more disulfide bonds.

更新日期：2019-01-29

点击分享查看原文

点击收藏

公开下载

阅读更多本刊新发论文本刊介绍/投稿指南