Cooperativity in amide hydrogen bonding chains. Relation between energy, position, and H-bond chain length in peptide and protein folding models
Cooperativity in amide hydrogen bonding chains. Relation between energy, position, and H-bond chain length in peptide and protein folding models
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DOI：
10.1021/jp0365209
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发表时间：
2003-12-04
影响因子：
2.9
通讯作者：
Dannenberg, JJ
中科院分区：
文献类型：
--
作者：
Kobko, N;Dannenberg, JJ
对于含有 2 至 15 个单体单元的氢键甲酰胺直链，各个氢键能量已在 B3LYP/D95** 水平上计算。对最强氢键（最靠近 15-甲酰胺链中心的氢键）的协同效应接近二聚体的 200%。协同相互作用远远超出了静电相互作用的预期。使用成对最近邻势不能轻易地对计算出的氢键焓的巨大变化进行建模。从 DFT 计算中获得的能量数据已使用基于链长 (n) 和氢键类型 (k) 的参数进行经验拟合，氢键类型 (k) 对应于链中氢键的位置（k = 1 表示末端，2 表示倒数第二个氢键等）。每种类型 (k) 的氢键都渐近地接近该类型特有的极限相互作用能。随着 k 变大，该类型的初始氢键变得更加稳定，但对该类型的合作贡献变得更少。讨论了结果对于改进肽结构和蛋白质折叠建模的实用性。
The individual H-bond energies have been calculated at the B3LYP/D95** level for linear chains of H-bonding formamides containing from 2 to 15 monomeric units. The cooperative effect upon the strongest H-bonds (those nearest the center of the 15-formamide chain) approaches 200% that of the dimer. The cooperative interaction far exceeds that expected for electrostatic interactions. The large variation in the calculated H-bonding enthalpies cannot readily be modeled using pairwise nearest-neighbor potentials. The energetic data obtained from the DFT calculations have been empirically fit using parameters based upon the chain length (n) and the H-bond type (k) which corresponds to the position of the H-bond in the chain (k = 1 for terminal, 2 for penultimate H-bonds, etc.). Each type (k) of H-bond asymptotically approaches a limiting interaction energy specific for that type. As k becomes larger, the initial H-bond for that type becomes more stable, but the cooperative contribution to that type becomes less. The results are discussed with respect to their utility for improving the modeling of peptide structure and protein folding.