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学科主题: 理论物理学
题名: Toward Investigating Protein Folding Using the Combination of Computer Simulation and Spectroscopy
作者: Zhuang W(庄巍)
会议文集: Scientific Program & Show Guide
会议名称: American Physical Society March Meeting 2011
会议日期: 2011-3-21
出版日期: 2011
会议地点: 达拉斯
其他题名: 结合计算机模拟和光谱理论研究蛋白质折叠机理
通讯作者: 庄巍
出版者: 待补充
出版地: 待补充
合作性质: 分会口头报告
部门归属: 1107
主办者: 美国物理学会
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.
英文摘要: 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.
内容类型: 会议论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/116035
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:American Physical Society March Meeting 2011. 达拉斯. 2011-3-21.
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