Sikorski Andrzej, Romiszowski Piotr
Department of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
J Mol Model. 2007 Feb;13(2):327-33. doi: 10.1007/s00894-006-0147-6. Epub 2006 Sep 15.
A coarse-grained model of polypeptide chains confined in a slit formed by two parallel impenetrable surfaces was studied. The chains were flexible heteropolymers (polypeptides) built of two kinds of united atoms-hydrophobic and hydrophilic. The positions of the united atoms were restricted to the vertices of a [310] lattice. The force field consisted of a rigorous excluded volume, a long-distance potential between a pair of amino-acid residues and a local preference for forming secondary structure (helices). The properties of the chains were studied at a wide range of temperatures from good to bad solvent conditions. Monte-Carlo simulations were carried out using the algorithm based on the chain's local changes of conformation and employing the Replica Exchange technique. The influence of the chain length, the distances between the confining surfaces, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that the presence of the confinement chain complicates the process of the chain collapse to low-temperature structures. For some conditions, one can find a rapid decrease of chain size and a second transition indicated by the rapid decrease of the total energy of the system.
研究了一种限制在由两个平行不可穿透表面形成的狭缝中的多肽链粗粒化模型。这些链是由两种联合原子（疏水和亲水）构建的柔性杂聚物（多肽）。联合原子的位置被限制在[310]晶格的顶点。力场包括严格的排除体积、一对氨基酸残基之间的长程势以及形成二级结构（螺旋）的局部偏好。在从良溶剂条件到不良溶剂条件的广泛温度范围内研究了链的性质。使用基于链构象局部变化的算法并采用复制交换技术进行了蒙特卡罗模拟。研究了链长、限制表面之间的距离、温度和力场对链的尺寸和结构的影响。结果表明，受限链的存在使链坍缩成低温结构的过程变得复杂。在某些条件下，可以发现链尺寸的快速减小以及由系统总能量的快速减小所表明的第二次转变。
