Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
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DOI：
10.1126/science.282.5389.740
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发表时间：
1998-10-23
期刊：
影响因子：
56.9
通讯作者：
Kollman, PA
中科院分区：
文献类型：
--
作者：
Duan, Y;Kollman, PA
经典分子动力学在并行计算机上的实现提高了效率，使蛋白质折叠的模拟与水的显式表示为1微秒，约两个数量级长比最长的模拟蛋白质在水中报告的日期。从绒毛蛋白头片段亚结构域的未折叠状态开始，在初始阶段发生疏水性塌陷和螺旋形成，随后发生构象重新调整。一个边缘稳定的状态，它具有约150纳秒的寿命，一个有利的溶剂化自由能，并显示出显着的相似性的原生结构，观察到两个途径，这种状态已经被发现。
An implementation of classical molecular dynamics on parallel computers of increased efficiency has enabled a simulation of protein folding with explicit representation of water for 1 microsecond, about two orders of magnitude Longer than the Longest simulation of a protein in water reported to date. Starting with an unfolded state of villin headpiece subdomain, hydrophobic collapse and helix formation occur in an initial phase, followed by conformational readjustments. A marginally stable state, which has a Lifetime of about 150 nanoseconds, a favorable solvation free energy, and shows significant resemblance to the native structure, is observed; two pathways to this state have been found.