Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model

	Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model
	Song, Jian 1,2; Zhuang, Wei 2; Han, KL ; Zhang, X ; Yang, MJ
刊名	protein conformational dynamics
	2014
卷号	805 页码:199-220
关键词	Protein folding/unfolding Markov state model Folding intermediates Two dimensional infrared spectroscopy Fluorescence spectroscopy
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.
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
收录类别	BSCI ; SCI
语种	英语
WOS记录号	WOS:000350417100010
公开日期	2016-05-09
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/145781]
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.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
推荐引用方式 GB/T 7714	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.