A geometrical framework for thinking about proteins.

IF 3.2 4区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-08-10 DOI:10.1002/prot.26567

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

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Abstract

We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise attraction that assembles these building blocks, while respecting their individual symmetries. Instead of seeking to mimic the complexity of proteins, we look for a simple abstraction of reality that yet captures the essence of proteins. We employ analytic calculations and detailed Monte Carlo simulations to explore some consequences of our theory. The predictions of our approach are in accord with experimental data. Our framework provides a rationalization for understanding the common characteristics of proteins. Our results show that the free energy landscape of a globular protein is pre-sculpted at the backbone level, sequences and functionalities evolve in the fixed backdrop of the folds determined by geometry and symmetry, and that protein structures are unique in being simultaneously characterized by stability, diversity, and sensitivity.

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一个思考蛋白质的几何框架。

我们提出了一个基于对称和几何的蛋白质模型。利用数学和物理的基本概念，我们导出了离散螺旋和片状的几何形状。我们假设一个相容的溶剂介导的紧急成对吸引力，组装这些积木，同时尊重他们的个体对称性。我们不是试图模仿蛋白质的复杂性，而是寻找一种简单的现实抽象，但又能抓住蛋白质的本质。我们使用分析计算和详细的蒙特卡罗模拟来探索我们的理论的一些结果。我们方法的预测与实验数据是一致的。我们的框架为理解蛋白质的共同特征提供了一种合理化。我们的研究结果表明，球形蛋白质的自由能结构在骨干水平上被预先雕刻，序列和功能在由几何形状和对称性决定的褶皱的固定背景下进化，蛋白质结构同时具有稳定性、多样性和敏感性的独特特征。

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.