Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnæus University, Kalmar, 39182, Sweden; Linnæus University Centre of Excellence "Biomaterials Chemistry", Kalmar, 3912, Sweden.
Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece.
Arch Biochem Biophys. 2019 Mar 30;664:76-88. doi: 10.1016/j.abb.2019.01.033. Epub 2019 Feb 1.
The application of molecular dynamics simulations to study the folding and dynamics of peptides has attracted a lot of interest in the last couple of decades. Following the successful prediction of the folding of several proteins using molecular simulation, foldable peptides emerged as a favourable system mainly due to their application in improving protein structure prediction methods and in drug design studies. However, their performance is inherently linked to the accuracy of the empirical force fields used in the simulations, whose optimisation and validation is of paramount importance. Here we review the most important findings in the field of molecular peptide simulations and highlight the significant advancements made over the last twenty years. Special reference is made on the simulation of disordered peptides and the remaining challenge to find a force field able to describe accurately their conformational landscape.
在过去的几十年里，分子动力学模拟在研究肽的折叠和动力学方面的应用引起了广泛关注。在成功地使用分子模拟预测了几种蛋白质的折叠之后，可折叠肽作为一种有利的系统出现，主要是因为它们在改进蛋白质结构预测方法和药物设计研究中的应用。然而，它们的性能本质上与模拟中使用的经验力场的准确性有关，因此优化和验证这些力场至关重要。本文综述了分子肽模拟领域的最重要发现，并强调了过去二十年取得的重大进展。特别提到了无序肽的模拟以及寻找能够准确描述其构象景观的力场的仍然存在的挑战。
