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

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

Abstract

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.

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

Received: 29 April 2015
Accepted manuscript online:

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

Fund:

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).

Corresponding Authors: Wei Zhuang
E-mail: wzhuang@dicp.ac.cn

Cite this article:

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 2016 Chin. Phys. B 25 018201

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

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