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学科主题物理化学
Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach
Zhuang, Wei1; Cui, Raymond Z.2; Silva, Daniel-Adriano2; Huang, Xuhui2; Zhuang W(庄巍); Huang XH(黄旭辉)
刊名JOURNAL OF PHYSICAL CHEMISTRY B
2011-05-12
ISSN1520-6106
DOI10.1021/jp109592b
115期:18页:5415-5424
收录类别SCI
文章类型Article
部门归属11
项目归属1107
产权排名1,1
WOS标题词Science & Technology ; Physical Sciences
类目[WOS]Chemistry, Physical
研究领域[WOS]Chemistry
关键词[WOS]NONLINEAR-INFRARED-SPECTROSCOPY ; PROTEIN-FOLDING PROBLEM ; HYDROGEN-BOND DYNAMICS ; FREE-ENERGY LANDSCAPE ; AMIDE-I ; VIBRATIONAL SPECTROSCOPY ; 2D IR ; N-METHYLACETAMIDE ; BETA-SHEET ; MOLECULAR SIMULATION
英文摘要Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach; We proposed a computational protocol of simulating the T-jump peptide unfolding experiments and the related transient IR and two-dimensional IR (2DIR) spectra based on the Markov state model (MSM) and nonlinear exciton propagation (NEP) methods. MSMs partition the conformation space into a set of nonoverlapping metastable states, and we can calculate spectra signal for each of these states using the 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. We show that results from MSMs constructed from a large number of simulations have a much better agreement with the equilibrium experimental 2DIR spectra compared to that generated from straightforward MID simulations starting from the folded state. This indicates that a sufficient sampling of important relevant conformational states is critical for calculating the accurate spectroscopic observables. 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 not only provides a justification for our protocol, but also provides the physical insight of the underlying spectroscopic observables. The protocol we developed has the potential to be extended to simulate a wide range of fast triggering plus optical detection experiments for biomolecules.
语种英语
WOS记录号WOS:000290127100039
引用统计
被引频次:52[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/115429
专题中国科学院大连化学物理研究所
通讯作者Zhuang W(庄巍); Huang XH(黄旭辉)
作者单位1.Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Liaoning, Peoples R China
2.Hong Kong Univ Sci & Technol, Dept Chem, Kowloon, Hong Kong, Peoples R China
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Zhuang, Wei,Cui, Raymond Z.,Silva, Daniel-Adriano,et al. Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2011,115(18):5415-5424.
APA Zhuang, Wei,Cui, Raymond Z.,Silva, Daniel-Adriano,Huang, Xuhui,庄巍,&黄旭辉.(2011).Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach.JOURNAL OF PHYSICAL CHEMISTRY B,115(18),5415-5424.
MLA Zhuang, Wei,et al."Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach".JOURNAL OF PHYSICAL CHEMISTRY B 115.18(2011):5415-5424.
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