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
文献类型：期刊论文
| 作者 | Zhuang, Wei1; Cui, Raymond Z.2; Silva, Daniel-Adriano2; Huang, Xuhui2 |
| 刊名 | journal of physical chemistry b
 |
| 出版日期 | 2011-05-12 |
| 卷号 | 115期号:18页码:5415-5424 |
| ISSN号 | 1520-6106 |
| 产权排序 | 1,1 |
| 通讯作者 | 庄巍 ; 黄旭辉 |
| 中文摘要 | 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 |
| 英文摘要 | 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. |
| WOS标题词 | science & technology ; physical sciences |
| 学科主题 | 物理化学 |
| 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 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000290127100039 |
| 公开日期 | 2012-07-09 |
| 源URL | [http://159.226.238.44/handle/321008/115429]  |
| 专题 | 大连化学物理研究所_中国科学院大连化学物理研究所 |
| 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 |
| 推荐引用方式 GB/T 7714 | 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.(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. |
入库方式： OAI收割
来源：大连化学物理研究所
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