Structure and dynamics of water in crowded environments slows down peptide conformational changes
Structure and dynamics of water in crowded environments slows down peptide conformational changes
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DOI：
10.1063/1.4891465
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发表时间：
2014-07-28
影响因子：
4.4
通讯作者：
Rao, Francesco
中科院分区：
文献类型：
--
作者：
Lu, Cheng;Prada-Gracia, Diego;Rao, Francesco
与传统的体外实验或模拟相比，细胞内的大分子浓度很高。为了表征拥挤对无序多肽热力学和动力学的影响，通过改变模拟框中相同的弱相互作用多肽的数量，在不同浓度下进行了分子动力学模拟。我们发现，拥挤的存在对整体热力学的影响不是很大。另一方面，多肽的构象动力学被发现受到强烈的影响，导致在较大的浓度下显著减慢。观察到较高浓度的多肽之间的长寿命水桥表明，溶剂在改变的多肽动力学中扮演着重要的角色。我们的结果加强了水在分子拥挤中的积极作用的想法，这一效应预计与受大溶剂暴露区域影响的问题相关，例如在内在无序的蛋白质中。(C)2014 AIP出版有限责任公司。
The concentration of macromolecules inside the cell is high with respect to conventional in vitro experiments or simulations. In an effort to characterize the effects of crowding on the thermodynamics and kinetics of disordered peptides, molecular dynamics simulations were run at different concentrations by varying the number of identical weakly interacting peptides inside the simulation box. We found that the presence of crowding does not influence very much the overall thermodynamics. On the other hand, peptide conformational dynamics was found to be strongly affected, resulting in a dramatic slowing down at larger concentrations. The observation of long lived water bridges between peptides at higher concentrations points to a nontrivial role of the solvent in the altered peptide kinetics. Our results reinforce the idea for an active role of water in molecular crowding, an effect that is expected to be relevant for problems influenced by large solvent exposure areas like in intrinsically disordered proteins. (C) 2014 AIP Publishing LLC.