Influence of the hydrodynamic interaction on kinetics and thermodynamics of minimal protein models
Influence of the hydrodynamic interaction on kinetics and thermodynamics of minimal protein models
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DOI：
10.1143/jpsj.71.3069
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发表时间：
2002-12-01
影响因子：
1.7
通讯作者：
Hiwatari, Y
中科院分区：
文献类型：
--
作者：
Baumketner, A;Hiwatari, Y
本文研究了最小蛋白质模型中流体动力学相互作用对折叠过程的影响。在最小模型中，整个蛋白质残基（或残基组）在简化的水平上由相互作用的珠子表示。在粘性介质中，例如水，珠粒受到流体动力学相互作用：当其中一个珠粒开始运动时，速度场会对所有剩余的珠粒施加力。这种有效的相互作用是占在我们的模拟中通过的M-Prager迁移率张量。我们考虑了两种类型的链分子，β发夹和α螺旋，旨在代表蛋白质的最常见的二级结构元素。利用布朗动力学模拟研究了所考察模型的几何和动力学性质。结果表明，流体动力学相互作用对蛋白质折叠过程的影响取决于其天然状态的几何形状。就β蛋白而言，流体动力学相互作用降低了塌陷和折叠转变的温度。在动力学上，折叠时间的温度依赖性具有最小值的位置显著地向较低温度移动，并且最小折叠时间本身增长2倍。对于α螺旋，流体动力学相互作用既不影响其热力学也不影响其动力学。我们推测，所观察到的β和α蛋白行为的差异与这些蛋白折叠的不同机制有关。
In this paper we study the influence of the hydrodynamic interaction on the folding process in minimal protein models. In minimal models entire protein residues (or groups of residues) are represented at a simplified level by interacting beads. In a viscous medium such as water the beads are subject to the hydrodynamic interaction: when one of the beads is set in motion incited thereby velocity field exert force on all the remaining beads. This effective interaction is accounted for in our simulations through the Rome-Prager mobility tensor. We considered two types of chain molecules, a beta hairpin and an alpha helix, designed to represent the proteins' most common secondary structure elements. Both thermodynamical and dynamical properties of the examined models were studied by using Brownian dynamics simulations. It was found that the effect of the hydrodynamic interaction on the folding process of a protein depends on the geometry of its native state. In the case of the beta protein the hydrodynamic interaction lowers the temperature of collapse and folding transitions. Kinetically, the position at which the temperature dependence of the folding time has a minimum is shifted significantly towards lower temperatures and the minimal folding time itself grows by a factor of 2. As to the alpha helix, the hydrodynamic interaction affects neither its thermodynamics nor kinetics. We speculate that the observed difference in the behaviour of beta and alpha proteins is connected with the differing mechanisms by which these proteins fold.