Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA.
J Comput Chem. 2022 Jul 5;43(18):1229-1236. doi: 10.1002/jcc.26887. Epub 2022 May 11.
Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. The results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.
多肽与肽不同，酰胺键可以更频繁地采用顺式和反式构象。两种构象之间的转变需要克服一个大的能量障碍，使得传统的分子模拟难以充分访问顺式和反式结构。本文提出了一种复制交换方法，该方法允许酰胺键的轻松旋转，并与高温副本有效地连接。该方法仅需要三个副本（一个在感兴趣的温度和哈密顿量下，第二个具有偏置二面角势的高温副本，以及第三个将它们连接起来），以克服酰胺键采样问题，并增强其他坐标的采样。结果表明，对于短肽寡聚物，构象可以从全顺式到全反式变化，平均顺/反式比取决于侧链和势模型。
