National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), GKVK Campus, Bellary Road, Bengaluru, Karnataka 560065, India.
The University of Trans-Disciplinary Health Sciences and Technology (TDU), #74/2, Jarakabande Kaval, Post Attur, Via Yelahanka, Bengaluru, Karnataka 560064, India.
Database (Oxford). 2022 Mar 1;2022. doi: 10.1093/database/baac005.
Disulphide bonds are stabilizing crosslinks in proteins and serve to enhance their thermal stability. In proteins that are small and rich in disulphide bonds, they could be the major determining factor for the choice of conformational state since their constraints on appropriate backbone conformation can be substantial. Such crosslinks and their positional conservation could itself enable protein family and functional association. Despite the importance of the field, there is no comprehensive database on disulphide crosslinks that is available to the public. Herein we provide information on disulphides in DSDBASE2.0, an updated and significantly expanded database that is freely available, fully annotated and manually curated database on native and modelled disulphides. The web interface also provides several useful computational tools that have been specifically developed for proteins containing disulphide crosslinks. The modelling of disulphide crosslinks is performed using stereochemical criteria, coded within our Modelling of Disulphides in Proteins (MODIP) algorithm. The inclusion of modelled disulphides potentially enhances the loop database substantially, thereby permitting the recognition of compatible polypeptide segments that could serve as templates for immediate modelling. The DSDBASE2.0 database has been updated to include 153,944 PDB entries, 216,096 native and 20,153,850 modelled disulphide bond segments from PDB January 2021 release. The current database also provides a resource to user-friendly search for multiple disulphide bond containing loops, along with annotation of their function using GO and subcellular localization of the query. Furthermore, it is possible to obtain the three-dimensional models of disulphide-rich small proteins using an independent algorithm, RANMOD, that generates and examines random, but allowed backbone conformations of the polypeptide. DSDBASE2.0 still remains the largest open-access repository that organizes all disulphide bonds of proteins on a single platform. The database can be accessed from http://caps.ncbs.res.in/dsdbase2.
二硫键是蛋白质中的稳定交联键，可增强其热稳定性。在富含二硫键且体积较小的蛋白质中，由于对合适的骨架构象有很大的限制作用，它们可能是决定构象状态选择的主要因素。这些交联键及其位置的保守性本身可以使蛋白质家族和功能发生关联。尽管该领域非常重要，但目前还没有可供公众使用的关于二硫键交联的综合数据库。在此，我们提供了 DSDBASE2.0 中二硫键的相关信息，这是一个经过更新和显著扩展的免费公共数据库，对天然和建模的二硫键进行了全面注释和人工整理。该网络界面还提供了几个专门为含有二硫键交联的蛋白质开发的有用计算工具。二硫键的建模是使用立体化学标准进行的，这些标准编码在我们的蛋白质中二硫键建模（MODIP）算法中。建模二硫键的加入可以大大增强环数据库，从而允许识别可作为模板立即建模的相容多肽片段。DSDBASE2.0 数据库已更新，包含 153944 个 PDB 条目、216096 个天然二硫键和 20153850 个来自 PDB 2021 年 1 月版的建模二硫键片段。当前数据库还提供了一个方便用户的资源，用于搜索多个含有二硫键的环，并使用 GO 和查询的亚细胞定位对其功能进行注释。此外，还可以使用独立的 RANMOD 算法获取富含二硫键的小蛋白质的三维模型，该算法生成并检查多肽的随机但允许的骨架构象。DSDBASE2.0 仍然是组织在单个平台上所有蛋白质中二硫键的最大开放访问数据库。该数据库可从 http://caps.ncbs.res.in/dsdbase2 访问。
