Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States.
Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
J Phys Chem B. 2020 Nov 5;124(44):9852-9861. doi: 10.1021/acs.jpcb.0c08091. Epub 2020 Oct 27.
Molecular dynamics simulations of the villin headpiece subdomain HP36 have been carried out to examine relations between rates of vibrational energy transfer across non-covalently bonded contacts and equilibrium structural fluctuations, with focus on van der Waals contacts. Rates of energy transfer across van der Waals contacts vary inversely with the variance of the contact length, with the same constant of proportionality for all nonpolar contacts of HP36. A similar relation is observed for hydrogen bonds, but the proportionality depends on contact pairs, with hydrogen bonds stabilizing the α-helices all exhibiting the same constant of proportionality, one that is distinct from those computed for other polar contacts. Rates of energy transfer across van der Waals contacts are found to be up to 2 orders of magnitude smaller than rates of energy transfer across polar contacts.
已对 villin 头部亚结构域 HP36 进行了分子动力学模拟，以研究非共价键合接触处振动能量转移速率与平衡结构波动之间的关系，重点研究了范德华接触。范德华接触处能量转移的速率与接触长度的方差成反比，所有 HP36 的非极性接触都具有相同的比例常数。氢键也存在类似的关系，但比例取决于接触对，氢键稳定 α-螺旋，所有氢键都具有相同的比例常数，与计算得到的其他极性接触的常数不同。范德华接触处的能量转移速率比极性接触处的能量转移速率低 2 个数量级。
