Abe H, Wako H
Department of Natural Sciences, Nishinippon Institute of Technology, Fukuoka 800-0394, Japan.
Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jul;74(1 Pt 1):011913. doi: 10.1103/PhysRevE.74.011913. Epub 2006 Jul 18.
Folding and unfolding simulations of three-dimensional lattice proteins were analyzed using a simplified statistical mechanical model in which their amino acid sequences and native conformations were incorporated explicitly. Using this statistical mechanical model, under the assumption that only interactions between amino acid residues within a local structure in a native state are considered, the partition function of the system can be calculated for a given native conformation without any adjustable parameter. The simulations were carried out for two different native conformations, for each of which two foldable amino acid sequences were considered. The native and non-native contacts between amino acid residues occurring in the simulations were examined in detail and compared with the results derived from the theoretical model. The equilibrium thermodynamic quantities (free energy, enthalpy, entropy, and the probability of each amino acid residue being in the native state) at various temperatures obtained from the simulations and the theoretical model were also examined in order to characterize the folding processes that depend on the native conformations and the amino acid sequences. Finally, the free energy landscapes were discussed based on these analyses.
利用一个简化的统计力学模型对三维晶格蛋白质的折叠与解折叠模拟进行了分析，该模型明确纳入了它们的氨基酸序列和天然构象。使用这个统计力学模型，在仅考虑天然状态下局部结构内氨基酸残基之间相互作用的假设下，对于给定的天然构象，无需任何可调参数即可计算系统的配分函数。针对两种不同的天然构象进行了模拟，每种构象考虑了两个可折叠的氨基酸序列。详细检查了模拟中出现的氨基酸残基之间的天然和非天然接触，并与理论模型得出的结果进行了比较。还检查了从模拟和理论模型获得的不同温度下的平衡热力学量（自由能、焓、熵以及每个氨基酸残基处于天然状态的概率），以表征依赖于天然构象和氨基酸序列的折叠过程。最后，基于这些分析讨论了自由能景观。
