Backbone additivity in the transfer model of protein solvation
Backbone additivity in the transfer model of protein solvation
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DOI：
10.1002/pro.378
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发表时间：
2010-05-01
期刊：
影响因子：
8
通讯作者：
Pettitt, B. Montgomery
中科院分区：
文献类型：
--
作者：
Hu, Char Y.;Kokubo, Hironori;Pettitt, B. Montgomery
通过计算测试了暗示肽主链转移自由能的可加性的转移模型。分子动力学模拟用于确定转移自由能 (Delta G(tr)) 随着带封端基团的寡甘氨酸链长的增加而变化的程度。通过对所有原子模型的模拟，计算了纯水和渗透剂溶液、2M 尿素和 2M 三甲胺 N-氧化物 (TMAO) 中不同长度的寡甘氨酸模型的溶剂化自由能，并确定了肽主链从水转移到渗透剂溶液的 Delta G(tr) 值。结果表明，转移自由能随着链长的增加而线性变化，证明了可加性原理，并提供了与实验相符的数值。在转移到尿素的情况下，肽主链转移自由能的贡献来自范德华相互作用，但在转移到TMAO溶液时则来自静电。这里使用的模拟允许计算待评估的更长寡甘氨酸模型的溶剂化和转移自由能，这比目前通过实验可能实现的模型要长。计算得出的肽主链单元转移自由能为 54 cal/mol/M，与实验测定的 43 cal/mol/M 相当。
The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (Delta G(tr)) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and Delta G(tr) values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of 54 cal/mol/M compares quite favorably with 43 cal/mol/M determined experimentally.