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Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model
Song, Jian1,2; Zhuang, Wei2; Han, KL; Zhang, X; Yang, MJ
关键词Protein Folding/unfolding Markov State Model Folding Intermediates Two Dimensional Infrared Spectroscopy Fluorescence Spectroscopy
刊名PROTEIN CONFORMATIONAL DYNAMICS
2014
DOI10.1007/978-3-319-02970-2_9
805页:199-220
收录类别BSCI ; SCI
文章类型Article
WOS标题词Science & Technology ; Life Sciences & Biomedicine
类目[WOS]Biology ; Medicine, Research & Experimental
研究领域[WOS]Life Sciences & Biomedicine - Other Topics ; Research & Experimental Medicine
关键词[WOS]MOLECULAR-DYNAMICS SIMULATIONS ; CIRCULAR-DICHROISM SPECTRA ; X-RAY-SCATTERING ; VIBRATIONAL SPECTROSCOPY ; SECONDARY STRUCTURE ; PROTEINS ; INTERMEDIATE ; AGGREGATION ; ABSORPTION ; CONFORMATION
英文摘要Optical spectroscopic tools are used to monitor protein folding/unfolding dynamics after a fast triggering such as the laser induced temperature jump. These techniques provide new opportunities for comparison between theory and simulations and atom-level understanding protein folding mechanism. However, the direct comparison still face two main challenges: a gap between folding relevant timescales (microseconds or above) and length of molecular dynamics simulations (typically tens to hundreds of nanoseconds), and difficulty in directly calculating spectroscopic observables from simulation configurations. Markov State Model (MSM) approach is one of the most powerful means which can increase simulations timescale up to microsecond or even millisecond. We address progress on modeling infrared and fluorescence spectroscopic signals of temperature jump induced unfolding dynamics for a few small proteins. The harmoniousness between experiment and theoretical can both improve our understanding of protein folding mechanisms and provide direct validation of those theoretical models.
语种英语
WOS记录号WOS:000350417100010
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文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/145781
专题中国科学院大连化学物理研究所
作者单位1.HeNan Normal Univ, Dept Phys, Xinxiang 453003, Peoples R China
2.Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China
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Song, Jian,Zhuang, Wei,Han, KL,et al. Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model[J]. PROTEIN CONFORMATIONAL DYNAMICS,2014,805:199-220.
APA Song, Jian,Zhuang, Wei,Han, KL,Zhang, X,&Yang, MJ.(2014).Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model.PROTEIN CONFORMATIONAL DYNAMICS,805,199-220.
MLA Song, Jian,et al."Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model".PROTEIN CONFORMATIONAL DYNAMICS 805(2014):199-220.
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