II. Geometrical framework for thinking about globular proteins: The power of poking.

IF 3.2 4区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-08-21 DOI:10.1002/prot.26566

Tatjana Škrbić, Achille Giacometti, Trinh X Hoang, Amos Maritan, Jayanth R Banavar

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Abstract

Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed a consistent approach for understanding the formation of the two key common building blocks of helices and sheets as well as the compatible assembly of secondary structures into the tertiary structure through the notion of poking pairwise interactions. Here we benchmark our predictions with a detailed analysis of structural data of over 4000 proteins from the Protein Data Bank. We also present the results of detailed computer simulations of a simplified model demonstrating a pre-sculpted free energy landscape, determined by geometry and symmetry, comprising numerous minima corresponding to putative native state structures. We explore the consequences of our model. Our results suggest that symmetry and geometry are a powerful guide to capture the simplicity underlying protein complexity.

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2。思考球形蛋白质的几何框架：戳的力量。

最近，我们提出了一个理解蛋白质结构的框架，该框架基于牵手或触摸物体的简单结构可以用来合理化球状蛋白质的共同特征。我们开发了一种一致的方法来理解螺旋和薄片这两个关键的共同构建块的形成，以及通过戳戳成对相互作用的概念将二级结构兼容地组装到三级结构中。在这里，我们通过对蛋白质数据库中超过4000种蛋白质的结构数据的详细分析来对我们的预测进行基准测试。我们还展示了一个简化模型的详细计算机模拟结果，该模型展示了一个预先雕刻的自由能景观，由几何和对称性决定，包括与假定的自然状态结构相对应的许多最小值。我们探索我们的模型的结果。我们的研究结果表明，对称和几何是捕捉蛋白质复杂性背后的简单性的有力指南。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Proteins-Structure Function and Bioinformatics 生物-生化与分子生物学

CiteScore

5.90

自引率

3.40%

发文量

172

审稿时长

3 months

期刊介绍： PROTEINS : Structure, Function, and Bioinformatics publishes original reports of significant experimental and analytic research in all areas of protein research: structure, function, computation, genetics, and design. The journal encourages reports that present new experimental or computational approaches for interpreting and understanding data from biophysical chemistry, structural studies of proteins and macromolecular assemblies, alterations of protein structure and function engineered through techniques of molecular biology and genetics, functional analyses under physiologic conditions, as well as the interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates. Research in protein and peptide biochemistry directed toward synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function, is also within the scope of PROTEINS. In addition to full-length reports, short communications (usually not more than 4 printed pages) and prediction reports are welcome. Reviews are typically by invitation; authors are encouraged to submit proposed topics for consideration.