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Stochastic conformational pumping: a mechanism for free-energy transduction by molecules.
Annual Review of Biophysics ( IF 12.4 ) Pub Date : 2011-03-01 , DOI: 10.1146/annurev-biophys-042910-155355
R Dean Astumian 1
Affiliation  

Proteins and other macromolecules can act as molecular machines that convert energy from one form to another through cycles of conformational transitions. In a macroscopically fluctuating environment or at the single-molecule level, the probability for a molecule to be in any state j fluctuates, and the probability current from any other state i to state j is given as the sum of a steady-state current and a pumped current, I(ij)=I(ss)(ij)+F(ij)dP(j)/dt, where F(ij) is the fraction of the fluctuating current into and out of state j coming directly from state i, and dP(j)/dt is the rate of change of the probability for the molecule to be in state j. If the fluctuations arise from an equilibrium source, microscopic reversibility guarantees that the time average of the pumped current is zero. If, however, the fluctuations arise due to the action of a nonequilibrium source, the time average of the pumped current is not in general zero and can be opposite in sign to the steady-state current. The pumped current provides a mechanism by which fluctuations, whether generated externally or arising from an internal nonequilibrium chemical reaction, can do electrical, mechanical, or chemical work on a system by coupling into the equilibrium conformational transitions of a protein. In this review I examine work elaborating the mechanism of stochastic pumping and also discuss a thermodynamically consistent approach for modeling the effects of dynamic disorder on enzymes and other proteins.

中文翻译:

随机构象泵浦:分子自由能转导的机制。

蛋白质和其他大分子可以充当分子机器,通过构象转变循环将能量从一种形式转换为另一种形式。在宏观波动的环境中或在单分子水平上,分子处于任何状态j的概率发生波动,并且从其他状态i到状态j的电流的概率为稳态电流和泵浦电流,I(ij)= I(ss)(ij)+ F(ij)dP(j)/ dt,其中F(ij)是进入和离开状态j的直接来自状态j的波动电流的分数i和dP(j)/ dt是分子处于状态j的概率变化率。如果波动来自平衡源,则微观可逆性可确保泵浦电流的时间平均值为零。但是,如果 波动是由于非平衡源的作用而引起的,抽运电流的时间平均值通常不为零,并且其符号可能与稳态电流相反。泵浦的电流提供了一种机制,通过这种机制,无论是外部产生的波动还是内部非平衡化学反应产生的波动,都可以通过耦合到蛋白质的平衡构象转变来对系统进行电,机械或化学作用。在这篇综述中,我研究了阐明随机泵送机理的工作,还讨论了一种热力学一致的方法,该方法可以对酶和其他蛋白质的动态失调的影响进行建模。泵浦的电流提供了一种机制,通过这种机制,无论是外部产生的波动还是内部非平衡化学反应产生的波动,都可以通过耦合到蛋白质的平衡构象转变来对系统进行电,机械或化学作用。在这篇综述中,我研究了阐明随机泵送机理的工作,还讨论了一种热力学一致的方法,用于对酶和其他蛋白质的动态失调的影响进行建模。泵浦电流提供了一种机制,通过这种机制,无论是外部产生的波动还是内部非平衡化学反应产生的波动,都可以通过耦合到蛋白质的平衡构象转变来对系统进行电,机械或化学作用。在这篇综述中,我研究了阐明随机泵送机理的工作,还讨论了一种热力学一致的方法,用于对酶和其他蛋白质的动态失调的影响进行建模。
更新日期:2011-05-05
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