DICP OpenIR
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
Source PublicationJOURNAL OF PHYSICAL CHEMISTRY A
2013-07-25
DOI10.1021/jp400625a
Volume117Issue:29Pages:6256-6263
Indexed BySCI
SubtypeArticle
WOS HeadingsScience & Technology ; Physical Sciences
WOS SubjectChemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS Research AreaChemistry ; Physics
WOS Keyword2-DIMENSIONAL INFRARED-SPECTROSCOPY ; FREE-ENERGY LANDSCAPE ; PROTEIN-FOLDING PROBLEM ; AMIDE-I ; MOLECULAR-DYNAMICS ; VIBRATIONAL SPECTROSCOPY ; TRANSITION-STATE ; WATER ; CONFORMATION ; MINIMIZATION
AbstractWe 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.
Language英语
WOS IDWOS:000322503200042
Citation statistics
Cited Times:5[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/137731
Collection中国科学院大连化学物理研究所
Affiliation1.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
Recommended Citation
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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