Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches,The Journal of Physical Chemistry B

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Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2021-09-10 , DOI: 10.1021/acs.jpcb.1c02424
Narendar Kolimi ₁ , Ashok Pabbathi ₁ , Nabanita Saikia ₁ , Feng Ding ₁ , Hugo Sanabria ₁ , Joshua Alper _{1,

2}

Affiliation

Out-of-equilibrium processes are ubiquitous across living organisms and all structural hierarchies of life. At the molecular scale, out-of-equilibrium processes (for example, enzyme catalysis, gene regulation, and motor protein functions) cause biological macromolecules to sample an ensemble of conformations over a wide range of time scales. Quantifying and conceptualizing the structure–dynamics to function relationship is challenging because continuously evolving multidimensional energy landscapes are necessary to describe nonequilibrium biological processes in biological macromolecules. In this perspective, we explore the challenges associated with state-of-the-art experimental techniques to understanding biological macromolecular function. We argue that it is time to revisit how we probe and model functional out-of-equilibrium biomolecular dynamics. We suggest that developing integrated single-molecule multiparametric force–fluorescence instruments and using advanced molecular dynamics simulations to study out-of-equilibrium biomolecules will provide a path towards understanding the principles of and mechanisms behind the structure–dynamics to function paradigm in biological macromolecules.

中文翻译：

不平衡的生物物理化学：多维、集成的单分子方法的案例

不平衡过程在生物体和生命的所有结构层次中无处不在。在分子尺度上，不平衡过程（例如，酶催化、基因调控和运动蛋白功能）导致生物大分子在广泛的时间尺度上对一组构象进行采样。量化和概念化结构-动力学与功能的关系具有挑战性，因为不断演变的多维能量景观对于描述生物大分子中的非平衡生物过程是必要的。从这个角度来看，我们探讨了与最先进的实验技术相关的挑战，以了解生物大分子功能。我们认为，是时候重新审视我们如何探索和模拟功能失衡的生物分子动力学了。我们建议开发集成的单分子多参数力-荧光仪器并使用先进的分子动力学模拟来研究失衡的生物分子，这将为理解生物大分子结构-动力学到功能范式背后的原理和机制提供一条途径。

更新日期：2021-09-23

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