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采用副本交换分子动力学对β发卡Trpzip4重折叠进行研究,结果表明,构象空间存在较大能垒时,副本交换分子动力学(REMD)表现出比分子动力学(MD)更优的抽样效率.288 K下,Trpzip4势能、骨架均方根偏差、溶剂可及表面积(SASA)在REMD中呈逐渐降低趋势.采样得到两种特定形态的低势能构象:β发卡和螺旋-卷曲.β发卡中,第3组氢键Asp46容易与Thr49形成氢键;转角Thr49的羟基(OH)倾向于与Asp46的羧基(COO-)或主链上的C=O形成氢键,强化了Asp46与Thr49的相互作用,导致转角形成折回弯度;与Thr49相比,Thr51的羟基倾向与水分子作用,甲基朝内,因此与Asp46的侧链作用微小.螺旋-卷曲中,吲哚环-甲基为主要疏水形式.Trpzip4在折叠成β发卡过程中,转角氢键影响整个β发卡构象的形成.转角氢键具有距离优势和强侧链相互作用,最先形成.
Coprecipitation of the Trpzip4 beta-hairpin was studied by replica exchange molecular dynamics. The results show that the replicon exchange molecular dynamics (REMD) shows better sampling efficiency than the molecular dynamics (MD) when there is a large energy barrier in the conformational space. At 288 K, Trpzip4 potential, skeletal root-mean-square deviation and solvent-accessible surface area (SASA) decreased gradually in REMD. Two specific morphological low-potential conformations were obtained by sampling: β-hairpin and spiral- Asp46 of group 3 easily forms hydrogen bonds with Thr49; the hydroxyl group (OH) of corner Thr49 tends to form hydrogen bonds with the carboxyl group (COO-) of Asp46 or C = O in the main chain, strengthening the interaction between Asp46 and Thr49 , Leading to the turning angle of the turn; Compared with Thr49, Thr51 hydroxyl tends to water molecules, methyl inward, and therefore the effect of side chain Asp46 tiny. Helix - curl, indole ring - methyl as the main hydrophobic form In the process of folding into beta hairpin, the corner hydrogen bond affects the formation of the whole β hairpin conformation.The corner hydrogen bond has distance advantage and strong side chain interaction, which is the first formation.