Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

doi:10.1088/1674-1056/25/1/018201

中国物理B ›› 2016, Vol. 25 ›› Issue (1): 18201-018201.doi: 10.1088/1674-1056/25/1/018201

所属专题： TOPICAL REVIEW — 8th IUPAP International Conference on Biological Physics

• TOPICAL REVIEW—8th IUPAP International Conference on Biological Physics • 上一篇下一篇

Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

Tianmin Wu (吴天敏), Tianjun Wang (王天骏), Xian Chen(陈娴), Bin Fang(方彬), Ruiting Zhang(张睿挺), Wei Zhuang(庄巍)

1. Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China;
2. State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian 116023, China

收稿日期:2015-04-29 出版日期:2016-01-05 发布日期:2016-01-05
通讯作者: Wei Zhuang E-mail:wzhuang@dicp.ac.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 21203178), the National Natural Science Foundation of China (Grant No. 21373201), the National Natural Science Foundation of China (Grant No. 21433014), the Science and Technological Ministry of China (Grant No. 2011YQ09000505), and “Strategic Priority Research Program” of the Chinese Academy of Sciences (Grant Nos. XDB10040304 and XDB100202002).

Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

Tianmin Wu (吴天敏)¹, Tianjun Wang (王天骏)², Xian Chen(陈娴)², Bin Fang(方彬)², Ruiting Zhang(张睿挺)², Wei Zhuang(庄巍)²

1. Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China;
2. State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian 116023, China

Received:2015-04-29 Online:2016-01-05 Published:2016-01-05
Contact: Wei Zhuang E-mail:wzhuang@dicp.ac.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 21203178), the National Natural Science Foundation of China (Grant No. 21373201), the National Natural Science Foundation of China (Grant No. 21433014), the Science and Technological Ministry of China (Grant No. 2011YQ09000505), and “Strategic Priority Research Program” of the Chinese Academy of Sciences (Grant Nos. XDB10040304 and XDB100202002).

摘要/Abstract

摘要：

We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GB^OBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide folding landscapes.

关键词: peptide, two-dimensional infrared spectra (2DIR), folding landscape, implicit solvent model

Abstract:

Key words: peptide, two-dimensional infrared spectra (2DIR), folding landscape, implicit solvent model

中图分类号: (Molecular dynamics simulation)

87.15.ap

87.15.M- (Spectra of biomolecules) 82.20.Wt (Computational modeling; simulation) 87.64.-t (Spectroscopic and microscopic techniques in biophysics and medical physics)

吴天敏, 王天骏, 陈娴, 方彬, 张睿挺, 庄巍. Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique[J]. 中国物理B, 2016, 25(1): 18201-018201.

Tianmin Wu (吴天敏), Tianjun Wang (王天骏), Xian Chen(陈娴), Bin Fang(方彬), Ruiting Zhang(张睿挺), Wei Zhuang(庄巍). Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique[J]. Chin. Phys. B, 2016, 25(1): 18201-018201.

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Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

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