Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin
Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin
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蛋白质与水接触时能量转移率的变化与同二聚血红蛋白的平衡结构波动
DOI：
10.1021/acs.jpcb.9b11413
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Leitner, David M.
中科院分区：
文献类型：
--
作者：
Reid, Korey M.;Yamato, Takahisa;Leitner, David M.
本文用分子动力学模拟方法研究了非键合接触的振动能量转移速率与平衡结构涨落之间的关系，重点研究了蛋白质-水接触的振动能量转移速率与平衡结构涨落之间的关系。的缩放与平衡波动的接触长度的能量转移速率被发现持有以及为残基和血红素之间的接触，在界面和17个界面水分子的簇在未配位状态的HbI，以及配位状态，其中集群包含平均11个水分子。在这两种状态下，能量转移的速率也被发现满足扩散关系。在每个球内，极性接触的比例与早期肌红蛋白分析中发现的相似。熵与每个球内的极性接触的动力学和血红素和水簇之间的接触被发现后，连接增加。能量交换网络（EENs）的配体和unliganded状态从模拟中得到的也提出和讨论。能量传输网络，通过非键合接触传输能量的HbI，称为非键合网络（NBNs），确定从EEN和比较的两个状态。
Molecular dynamics simulations of the homodimeric hemoglobin fromScapharca inaequivalvis(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.