Karasawa T, Tabuchi K, Fumoto M, Yasukawa T
Material System Engineering, Faculty of Technology, Tokyo University of Agriculture and Technology, Japan.
Comput Appl Biosci. 1993 Jun;9(3):243-51. doi: 10.1093/bioinformatics/9.3.243.
A model system is proposed to simulate the folding processes of proteins during thermal annealing. This system consists of four subsystems: (i) the pearl necklace model with isotropic inter-residue interactions; (ii) the extended pearl necklace model with anisotropic interaction potentials; (iii) molten globule phase dynamics; and (iv) final generation of the three-dimensional structure of a given protein. In this paper results obtained with the pearl necklace model are reported. This model consists of spherical elements and virtual bonds of 3.8 A in length and is intended to simulate dynamical processes at relatively high temperature where entropic terms play a dominant role. Inter-residue interactions are composed of spherical soft repulsive potentials and hydrophobic interactions inherent to respective residues. A simulation of folding processes of BPTI starting from the fully extended conformation indicated that intermediates, even at early stages of folding, are not randomly coiled but assume organized structures that resemble, to some extent, the native conformation.
提出了一个模型系统来模拟蛋白质在热退火过程中的折叠过程。该系统由四个子系统组成：(i) 具有各向同性残基间相互作用的珍珠项链模型；(ii) 具有各向异性相互作用势的扩展珍珠项链模型；(iii) 熔球态动力学；以及(iv) 给定蛋白质三维结构的最终生成。本文报道了用珍珠项链模型获得的结果。该模型由球形单元和长度为3.8 Å的虚拟键组成，旨在模拟熵项起主导作用的相对高温下的动力学过程。残基间相互作用由球形软排斥势和各个残基固有的疏水相互作用组成。从完全伸展构象开始对BPTI折叠过程的模拟表明，即使在折叠的早期阶段，中间体也不是随机卷曲的，而是呈现出在某种程度上类似于天然构象的有组织结构。
