Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier.
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier.
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DOI：
10.1093/bioinformatics/btac159
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发表时间：
2022-05-13
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提出了一种新的动态群落识别器(DCI)，该识别器依靠高斯弹性网络模型产生的蛋白质残基动态互相关来识别蛋白质内表现出运动的残基簇。展示了包括GPCRs在内的各种蛋白质的一些群落的例子。它是一种工具，可以立即简化和澄清任何给定蛋白质最基本的功能运动部分。蛋白质通常可以细分为几组残基，这些残基作为群落移动。这些通常是密集排列的局部亚结构，但在某些情况下，可能是物理上相距较远的残基，被鉴定为在同一群落内。每种蛋白质的这些群落的集合是运动的部分。这些整体的组织方式有助于理解功能动力学和变构的许多方面。DCI可以更直接地了解功能，包括酶的活性、跨膜的作用以及由于突变或配体结合而导致的群落结构的变化。DCI服务器可在网站(https://dci.bb.iastate.edu/).)上免费获得补充数据可在生物信息学在线上获得。寨卡病毒NS5蛋白(PDB ID：5M2Z)的三个社区。每一种颜色都代表着一个独特的社区及其运动。
A new dynamic community identifier (DCI) is presented that relies upon protein residue dynamic cross-correlations generated by Gaussian elastic network models to identify those residue clusters exhibiting motions within a protein. A number of examples of communities are shown for diverse proteins, including GPCRs. It is a tool that can immediately simplify and clarify the most essential functional moving parts of any given protein. Proteins usually can be subdivided into groups of residues that move as communities. These are usually densely packed local sub-structures, but in some cases can be physically distant residues identified to be within the same community. The set of these communities for each protein are the moving parts. The ways in which these are organized overall can aid in understanding many aspects of functional dynamics and allostery. DCI enables a more direct understanding of functions including enzyme activity, action across membranes and changes in the community structure from mutations or ligand binding. The DCI server is freely available on a web site (https://dci.bb.iastate.edu/). Supplementary data are available at Bioinformatics online. Three communities for Zika virus NS5 protein (PDB ID: 5M2Z). Each color represents a unique community with its motions.