Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide
Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide
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DOI：
10.1002/qua.21553
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发表时间：
2008-04-01
影响因子：
2.2
通讯作者：
Lovas, Sandor
中科院分区：
文献类型：
--
作者：
Hatfield, Marcus P. D.;Palermo, Nicholas Y.;Lovas, Sandor
在BHandHLYP/cc-pVTZ理论水平上，采用3种不同的加帽策略和密度泛函量子化学计算方法，研究了禽胰多肽疏水核内Pro 5-Thr 6-Tyr 7-Pro 8复合物与Phe 20相互作用能的准确性.最准确的测定结果来自α-氨基的乙酰化和α-羰基的甲基酰胺化，相对偏差小于10%。α-氨基的氢化与α-羰基被氢取代的组合以及α-氨基的氢化与α-羰基的甲基化的组合不太准确，导致高达35%的相对偏差。加帽方法的选择取决于多肽系统的结构特征、所需的准确度和可用的计算资源。(c)2007 Wiley Periodicals，Inc.
The accuracy of the determination of the energy of interaction between Phe20 and the Pro5-Thr6-Tyr7-Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. The most accurate determination resulted from acetylation of the a-amino group combined with methyl amidation of the a-carbonyl group, with relative deviations less than 10%. Combinations of hydrogenation of the a-amino group with the replacement of the a-carbonyl group with a hydrogen and the hydrogenation of the a-amino group with methylation of the a-carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy, and the available computational resources. (c) 2007 Wiley Periodicals, Inc.