Folding of model polypeptide sequences consisting of 50 and 150 amino-acid residues with the alanine and glycine repeat was explored using Langevin dynamics techniques at different values of the viscosity of a virtual medium. The starting conformations corresponded to a totally extended chain structure. The change in the dissipative properties of the medium was simulated under varying parameters of the Langevin thermostat. It is shown that there is a sufficiently high and threshold sensitivity of the result of chain folding to the viscosity of the medium. The folding of the considered polypeptide sequences when the viscosity of the medium is already on the order of viscosity of liquefied gases occurs mainly in alpha-helical conformations. With a decrease in the effective viscosity of the medium below the critical value, disordered structures are formed. It is noteworthy that in a virtual environment energy effects are not an unambiguous criterion for determining conformation as a result of folding of the polypeptide chain. The observed effects of viscosity, which lead to the correlation of conformational motions due to the action of dissipative forces and the selection of possible conformational relaxation paths of the chain, directly affect the folding result in accordance with the predictions of the analytic theory.

中文翻译：

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介质粘度对 (AlaGly)25 和 (AlaGly)75 多肽二级结构形成的分子动力学的影响

使用朗之万动力学技术在虚拟介质的不同粘度值下探索由 50 和 150 个氨基酸残基组成的模型多肽序列与丙氨酸和甘氨酸重复序列的折叠。起始构象对应于完全延伸的链结构。在朗之万恒温器的不同参数下模拟介质耗散特性的变化。结果表明，链折叠结果对介质粘度有足够高的阈值敏感性。当介质的粘度已经接近液化气体的粘度时，所考虑的多肽序列的折叠主要发生在α-螺旋构象中。随着介质的有效粘度降低到临界值以下，形成无序结构。值得注意的是，在虚拟环境中，能量效应并不是确定多肽链折叠结果的构象的明确标准。根据解析理论的预测，观察到的粘度效应会导致由于耗散力的作用和链的可能构象松弛路径的选择而导致构象运动的相关性，直接影响折叠结果。