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Modeling the Thermal Unfolding 2DIR Spectra of a beta-Hairpin Peptide Based on the Implicit Solvent MD Simulation
Wu, Tianmin1; Yang, Lijiang3; Zhang, Ruiting2; Shao, Qiang4; Zhuang, Wei2
刊名JOURNAL OF PHYSICAL CHEMISTRY A
2013-07-25
DOI10.1021/jp400625a
117期:29页:6256-6263
收录类别SCI
文章类型Article
WOS标题词Science & Technology ; Physical Sciences
类目[WOS]Chemistry, Physical ; Physics, Atomic, Molecular & Chemical
研究领域[WOS]Chemistry ; Physics
关键词[WOS]2-DIMENSIONAL INFRARED-SPECTROSCOPY ; FREE-ENERGY LANDSCAPE ; PROTEIN-FOLDING PROBLEM ; AMIDE-I ; MOLECULAR-DYNAMICS ; VIBRATIONAL SPECTROSCOPY ; TRANSITION-STATE ; WATER ; CONFORMATION ; MINIMIZATION
英文摘要We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a beta-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.
语种英语
WOS记录号WOS:000322503200042
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被引频次:5[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/321008/137731
专题中国科学院大连化学物理研究所
作者单位1.Univ Sci & Technol China, Dept Chem Phys, Hefei 230026, Peoples R China
2.Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China
3.Peking Univ, Beijing Natl Lab Mol Sci, Coll Chem & Mol Engn, Beijing 100871, Peoples R China
4.Shanghai Inst Mat Med, Shanghai 201203, Peoples R China
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GB/T 7714
Wu, Tianmin,Yang, Lijiang,Zhang, Ruiting,et al. Modeling the Thermal Unfolding 2DIR Spectra of a beta-Hairpin Peptide Based on the Implicit Solvent MD Simulation[J]. JOURNAL OF PHYSICAL CHEMISTRY A,2013,117(29):6256-6263.
APA Wu, Tianmin,Yang, Lijiang,Zhang, Ruiting,Shao, Qiang,&Zhuang, Wei.(2013).Modeling the Thermal Unfolding 2DIR Spectra of a beta-Hairpin Peptide Based on the Implicit Solvent MD Simulation.JOURNAL OF PHYSICAL CHEMISTRY A,117(29),6256-6263.
MLA Wu, Tianmin,et al."Modeling the Thermal Unfolding 2DIR Spectra of a beta-Hairpin Peptide Based on the Implicit Solvent MD Simulation".JOURNAL OF PHYSICAL CHEMISTRY A 117.29(2013):6256-6263.
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