Reid Korey M, Yamato Takahisa, Leitner David M
Department of Chemistry , University of Nevada, Reno , 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 Feb 20;124(7):1148-1159. doi: 10.1021/acs.jpcb.9b11413. Epub 2020 Feb 10.
Molecular dynamics simulations of the homodimeric hemoglobin from (HbI) have been carried out to examine relations between rates of vibrational energy transfer across nonbonded contacts and equilibrium structural fluctuations, with emphasis on protein-water contacts. The scaling of rates of energy transfer with equilibrium fluctuations of the contact length is found to hold up well for contacts between residues and hemes at the interface and the cluster of 17 interface water molecules in the unliganded state of HbI, as well as for the liganded state, for which the cluster contains on average 11 water molecules. In both states, the rate of energy transfer is also found to satisfy a diffusion relation. Within each globule, the scaling for polar contacts is similar to that found in an earlier analysis of myoglobin. Entropy associated with dynamics of polar contacts within each globule and with contacts between the hemes and water cluster is found to increase upon ligation. Energy exchange networks (EENs) for liganded and unliganded states obtained from the simulations are also presented and discussed. Energy transport networks through which nonbonded contacts transport energy in HbI, referred to as nonbonded networks (NBNs), are determined from the EENs and compared for the two states.
对（HbI）的同二聚体血红蛋白进行了分子动力学模拟，以研究非键接触间振动能量转移速率与平衡结构波动之间的关系，重点关注蛋白质 - 水接触。研究发现，对于HbI未结合状态下界面处残基与血红素之间以及17个界面水分子簇的接触，以及对于平均含有11个水分子的结合状态下的接触，能量转移速率与接触长度平衡波动的标度关系都能很好地成立。在两种状态下，还发现能量转移速率满足扩散关系。在每个球蛋白内，极性接触的标度与早期对肌红蛋白的分析结果相似。发现每个球蛋白内极性接触动力学以及血红素与水簇之间接触的熵在结合时会增加。还展示并讨论了从模拟中获得的结合态和未结合态的能量交换网络（EENs）。从EENs确定了HbI中非键接触传输能量的能量传输网络，称为非键网络（NBNs），并对两种状态进行了比较。
