Noguti T, Go N
Computation Center, Faculty of Engineering, Kyushu University, Fukuoka, Japan.
Proteins. 1989;5(2):125-31. doi: 10.1002/prot.340050206.
Differences in atom packing are studied in the minimum energy conformations derived from the record of the Monte Carlo simulation of conformational fluctuation in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations observed among the minima which are found in the previous paper are accompanied by rearrangement of atom packing. Spatial locations of the local deformations in the three-dimensional folded structure are also studied. It is found that the local deformations are distributed in space in several clusters in the folded structure. The size and location of the clusters characterize the respective fluctuations of the first and the second levels observed in the simulation. In the fluctuations of the first level local deformations, each of which usually involves a few side chains and one main chain local segment, are thermally exited independently of each other near the surface of the molecule. The observed fluctuation of the second level involves a cooperative deformation involving many side chains and local main chain segments all in one cluster, which goes though the core of the molecule. The collective local deformations observed both in the first and second levels are plastic in the sense that they are accompanied with rearrangement of atom packing.
在球状蛋白质牛胰蛋白酶抑制剂天然状态下构象波动的蒙特卡罗模拟记录所衍生的最低能量构象中，研究了原子堆积的差异。结果发现，在前一篇论文中发现的极小值之间观察到的局部变形伴随着原子堆积的重新排列。还研究了三维折叠结构中局部变形的空间位置。结果发现，局部变形在折叠结构中以几个簇的形式分布在空间中。簇的大小和位置表征了模拟中观察到的第一级和第二级各自的波动。在第一级局部变形的波动中，每个局部变形通常涉及几个侧链和一个主链局部片段，它们在分子表面附近彼此独立地热激发。观察到的第二级波动涉及一个协同变形，该变形涉及一个簇中的许多侧链和局部主链片段，贯穿分子的核心。在第一级和第二级中观察到的集体局部变形在某种意义上是可塑性的，因为它们伴随着原子堆积的重新排列。
