Computing infrared spectra of proteins using the exciton model

Husseini, FS, Robinson, D ORCID: https://orcid.org/0000-0003-2760-7163, Hunt, NT, Parker, AW and Hirst, JD, 2017. Computing infrared spectra of proteins using the exciton model. Journal of Computational Chemistry, 38 (16), pp. 1362-1375. ISSN 0192-8651

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Abstract

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I region, using an exciton approach, in which a local mode basis of carbonyl stretches is considered. The role of solvent in shifting the Amide I band (by 30 to 50 cm−1) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations.

Item Type:	Journal article
Publication Title:	Journal of Computational Chemistry
Creators:	Husseini, F.S., Robinson, D., Hunt, N.T., Parker, A.W. and Hirst, J.D.
Publisher:	John Wiley
Date:	15 June 2017
Volume:	38
Number:	16
ISSN:	0192-8651
Identifiers:	Number Type 10.1002/jcc.24674 DOI
Divisions:	Schools > School of Science and Technology
Record created by:	Linda Sullivan
Date Added:	09 Mar 2017 14:14
Last Modified:	09 Jun 2017 14:13
URI:	https://irep.ntu.ac.uk/id/eprint/30343

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