Wilson Matthew S, Landau David P
Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA.
Phys Rev E. 2021 Aug;104(2-2):025303. doi: 10.1103/PhysRevE.104.025303.
The HP model, a coarse-grained protein representation with only hydrophobic (H) and polar (P) amino acids, has already been extensively studied on the simple cubic (SC) lattice. However, this geometry severely restricts possible bond angles, and a simple improvement is to instead use the face-centered cubic (fcc) lattice. In this paper, the density of states and ground state energies are calculated for several benchmark HP sequences on the fcc lattice using the replica-exchange Wang-Landau algorithm and a powerful set of Monte Carlo trial moves. Results from the fcc lattice proteins are directly compared with those obtained from a previous lattice protein folding study with a similar methodology on the SC lattice. A thermodynamic analysis shows comparable folding behavior between the two lattice geometries, but with a greater rate of hydrophobic-core formation persisting into lower temperatures on the fcc lattice.
HP模型是一种仅包含疏水（H）和极性（P）氨基酸的粗粒度蛋白质表示法，已经在简单立方（SC）晶格上得到了广泛研究。然而，这种几何结构严重限制了可能的键角，一种简单的改进方法是改用面心立方（fcc）晶格。在本文中，使用复制交换Wang-Landau算法和一组强大的蒙特卡罗试验移动，计算了fcc晶格上几个基准HP序列的态密度和基态能量。将fcc晶格蛋白质的结果与之前在SC晶格上采用类似方法进行的晶格蛋白质折叠研究结果直接进行比较。热力学分析表明，两种晶格几何结构之间的折叠行为具有可比性，但在fcc晶格上，疏水核心形成的速率在较低温度下持续更高。
