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蛋白质结构的构建模块:物理学与生物学的交汇。

Building blocks of protein structures: Physics meets biology.

机构信息

Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA.

Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.

出版信息

Phys Rev E. 2021 Jul;104(1-1):014402. doi: 10.1103/PhysRevE.104.014402.

Abstract

The native state structures of globular proteins are stable and well packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry of the building blocks of protein structures-α helices and strands assembled into β sheets-with no adjustable parameters, no amino acid sequence information, and no chemistry. There is an almost perfect fit between the dictates of mathematics and physics and the rules of quantum chemistry. Protein evolution is facilitated by sequence-independent platforms, which can elaborate sequence-dependent functional diversity. Our work highlights the vital role of discreteness in life and may have implications for the creation of artificial life and on the nature of life elsewhere in the cosmos.

摘要

天然状态的球状蛋白质结构稳定且组装紧密,这表明在折叠条件下,蛋白质-溶剂相互作用不利于蛋白质分子内的相互作用。我们以此为指导原则,推导出蛋白质结构基本组成单位——无任何可调参数、无需氨基酸序列信息、也无需考虑化学性质的α 螺旋和β折叠——的构建块的几何形状。数学和物理学的规律与量子化学的规则之间几乎完美契合。序列独立的平台促进了蛋白质进化,使序列依赖的功能多样性成为可能。我们的工作强调了离散性在生命中的重要作用,这可能对人工生命的创造以及宇宙中其他生命的本质产生影响。

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