1] Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA. [2] Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA.
1] Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA. [2] Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA. [3] Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA.
Nat Protoc. 2014 Jan;9(1):156-70. doi: 10.1038/nprot.2013.172. Epub 2013 Dec 19.
Metals have vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules in which metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal-binding environments. The CheckMyMetal (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal-binding sites in macromolecular structures using parameters derived from 7,350 metal-binding sites observed in a benchmark data set of 2,304 high-resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal-binding sites, as well as how it can alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal-binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the ANTICIPATED RESULTS section. CMM was designed for a broad audience--biomedical researchers studying metal-containing proteins and nucleic acids--but it is equally well suited for structural biologists validating new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure with 2-5 metal sites and a few hundred amino acids.
金属在生物大分子的机制和结构中都起着至关重要的作用。然而，在蛋白质数据库（PDB）中，存在大量金属含量大分子的结构，其中金属被错误识别和/或建模不当。这表明需要一种诊断工具来识别和纠正金属结合环境的此类建模问题。CheckMyMetal（CMM）服务器（http://csgid.org/csgid/metal_sites/）是一种复杂而用户友好的基于网络的方法，用于使用从 2304 个高分辨率晶体结构的基准数据集观察到的 7350 个金属结合位点中得出的参数来评估大分子结构中的金属结合位点。该方案概述了如何使用 CMM 服务器检测金属结合位点结构中的几何和其他不规则性，以及如何提醒研究人员注意金属分配中的潜在错误。该方案还为通过修改金属结合环境和/或在 PDB 文件中重新定义金属身份来纠正有问题的站点提供了实用的指导方针。在预期结果部分描述了几个导致有意义结果的示例。CMM 是为广大研究金属结合蛋白和核酸的生物医学研究人员设计的，但它同样适合在建模或精修过程中验证新结构的结构生物学家。CMM 服务器以 PDB 格式的含金属大分子结构坐标作为输入，对于具有 2-5 个金属位点和几百个氨基酸的典型蛋白质结构，响应时间在几秒钟内。
