Reid Lauren M, Guzzetti Ileana, Svensson Tor, Carlsson Anna-Carin, Su Wu, Leek Tomas, von Sydow Lena, Czechtizky Werngard, Miljak Marija, Verma Chandra, De Maria Leonardo, Essex Jonathan W
School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
Bioinformatics Institute (ASTAR) 30 Biolpolis Street Matrix 138671 Singapore.
Chem Sci. 2022 Jan 20;13(7):1957-1971. doi: 10.1039/d1sc03496k. eCollection 2022 Feb 16.
Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.
了解内在无序蛋白质和肽（IDP）在各种生物环境中的构象集合对于理解它们在蛋白质组中的机制和功能作用至关重要，这有助于更深入地了解多种疾病并开发潜在的治疗方法。为了确定分子模拟是否能够生成准确的IDP构象集合，我们使用溶质标度副本交换（REST2）探索了PLP肽（蛋白脂质膜蛋白的一个内在无序区域）在水性和模拟膜溶剂中的结构景观，并研究了四种力场（ff14SB、ff14IDPSFF、CHARMM36和CHARMM36m）重现文献圆二色性（CD）数据的能力。还展示了变温（VT）氢和旋转框架Overhauser效应光谱（ROESY）核磁共振（NMR）实验的结果，这些结果与从模拟和CD获得的结构观察结果一致。我们还将最佳模拟方案应用于TP2和ONEG（分别为一种细胞穿透肽（CPP）和一种阴性对照肽），以深入了解可能导致它们观察到的膜穿透能力差异的结构差异。在测试的力场中，我们发现CHARMM36和CHARMM36m最适合IDP研究，并准确预测了随着从水性溶剂转变为模拟膜溶剂，PLP肽从无序到螺旋的构象转变。我们还确定了TP2在模拟膜溶剂中的α螺旋结构，并参考先前关于该肽的文献讨论了这一观察结果的机制意义。根据这些结果，我们建议使用CHARMM36m和REST2方案来研究特定环境下的IDP构象。我们相信该模拟方案将允许研究在不同生物环境中经历构象转变的多种IDP。
