Snow Christopher D, Zagrovic Bojan, Pande Vijay S
Department of Chemistry and Biophysics Program, Stanford University, Stanford, California 94305-5080, USA.
J Am Chem Soc. 2002 Dec 11;124(49):14548-9. doi: 10.1021/ja028604l.
Using over 75 mus of molecular dynamics simulation, we have generated several thousand folding simulations of the 20-residue Trp cage at experimental temperature and solvent viscosity. A total of 116 independent folding simulations reach RMSDcalpha values below 3 A RMSDcalpha, some as close as 1.4 A RMSDcalpha. We estimate a folding time of 5.5+/-3.5 mus, a rate that is in reasonable agreement with experimental kinetics. Finally, we characterize both the folded and unfolded ensemble under native conditions and note that the average topology of the unfolded ensemble is very similar to the topology of the native state.
通过超过75微秒的分子动力学模拟，我们在实验温度和溶剂粘度下对20个残基的色氨酸笼进行了数千次折叠模拟。总共116次独立的折叠模拟达到了均方根偏差（RMSDα）值低于3埃，有些甚至接近1.4埃。我们估计折叠时间为5.5±3.5微秒，这一速率与实验动力学结果合理相符。最后，我们表征了天然条件下的折叠态和未折叠态系综，并注意到未折叠态系综的平均拓扑结构与天然态的拓扑结构非常相似。
