Kolinski A, Ilkowski B, Skolnick J
Department of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
Biophys J. 1999 Dec;77(6):2942-52. doi: 10.1016/S0006-3495(99)77127-4.
Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on the Metropolis sampling scheme, and Entropy Sampling Monte Carlo (ESMC), were applied in a study of a high-resolution lattice model of the C-terminal fragment of the B1 domain of protein G. The results provide a detailed description of folding dynamics and thermodynamics and agree with recent experimental findings (. Nature. 390:196-197). In particular, it was found that the folding is cooperative and has features of an all-or-none transition. Hairpin assembly is usually initiated by turn formation; however, hydrophobic collapse, followed by the system rearrangement, was also observed. The denatured state exhibits a substantial amount of fluctuating helical conformations, despite the strong beta-type secondary structure propensities encoded in the sequence.
可能具有一些球状蛋白特征的小肽能够为蛋白质折叠问题提供重要见解。两种模拟方法,基于 metropolis 抽样方案的蒙特卡罗动力学(MCD)和熵抽样蒙特卡罗(ESMC),被应用于对蛋白质 G 的 B1 结构域 C 末端片段的高分辨率晶格模型的研究中。结果提供了折叠动力学和热力学的详细描述,并与最近的实验结果相符(《自然》。390:196 - 197)。特别地,发现折叠是协同的,具有全或无转变的特征。发夹组装通常由转角形成引发;然而,也观察到了疏水塌缩,随后是系统重排。尽管序列中编码了强烈的β型二级结构倾向,但变性状态仍表现出大量波动的螺旋构象。