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模块化蛋白质和DNA发夹的力-伸长曲线理论

Theory of force-extension curves for modular proteins and DNA hairpins.

作者信息

Bonilla L L, Carpio A, Prados A

机构信息

G. Millán Institute, Fluid Dynamics, Nanoscience and Industrial Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain.

Departamento de Matemática Aplicada, Universidad Complutense de Madrid, 28040 Madrid, Spain.

出版信息

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 May;91(5):052712. doi: 10.1103/PhysRevE.91.052712. Epub 2015 May 26.

Abstract

We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest-neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices.

摘要

我们研究了一个描述模块化蛋白质、核酸以及由多个单个单元或模块组成的其他生物分子的力-伸长曲线的模型。在介观描述层面,系统的构型由每个单元的伸长量给出。系统自由能包括每个单元的双阱势以及它们之间的弹性近邻相互作用。使自由能最小化可得出系统的平衡性质,而其动力学由伸长量的(过阻尼)朗之万方程给出,其中摩擦和噪声幅度由涨落耗散定理相关联。我们关于平衡和动态情况的结果,包括在力或长度控制下系统力-伸长曲线的解析和数值描述,并且与生物分子的实际实验非常吻合。我们的结论也适用于其他由多个亚稳单元组成的物理系统,例如存储系统或半导体超晶格。

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