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学科主题: 物理化学
题名: Toward Investigating Protein Folding Using the Combination of Computer Simulation and Spectroscopy
作者: Zhuang W(庄巍)
会议名称: International Symposium on Theoretical and Computational Chemistry –2010:High Performance Computing Simulations
会议日期: 2010-12-05
出版日期: 2010-12-05
会议地点: 中国
其他题名: 利用计算机模拟与光谱相结合来观测蛋白质折叠
通讯作者: 庄巍
部门归属: 十一室
主办者: 中国科学院超级计算中心; 哈尔滨理工大学
摘要: Protein folding is an important problem that is attracting scientists from a wide range of disciplines. One of the major challenges comes from the gap between the experimental and the theoretical studies. We proposed a computational protocol of simulating the T-jump peptide unfolding experiments and the related transient IR and 2DIR spectra based on the Markov State Model (MSM) and Nonlinear Exciton Propagation (NEP) methods. MSMs partition the conformation space into a set of non-overlapping metastable states, and we can calculate spectra signal for each of these states using NEP method. Thus the overall spectroscopic observable for a given system is simply the sum of spectra of different metastable states weighted by their populations. Simulated spectra based on MSM have a much better agreement with the equilibrium experimental 2DIR spectra compared to MD simulations starting from the folded state. MSMs are also capable of simulating the unfolding relaxation dynamics upon the temperature jump. The agreement of the simulation using MSMs and NEP with the experiment provides a justification for our protocol as well as a physical insight underlying the spectroscopic observables.
语种: 中文
内容类型: 会议论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/114358
Appears in Collections:中国科学院大连化学物理研究所_会议论文

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Recommended Citation:
Zhuang W. Toward Investigating Protein Folding Using the Combination of Computer Simulation and Spectroscopy[C]. 见:International Symposium on Theoretical and Computational Chemistry –2010:High Performance Computing Simulations. 中国. 2010-12-05.
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