Computing infrared spectra of proteins using the exciton model

Husseini, Fouad S. and Robinson, David and Hunt, Neil T. and Parker, Anthony W. and Hirst, J.D. (2016) Computing infrared spectra of proteins using the exciton model. Journal of Computational Chemistry, 38 (16). pp. 1362-1375. ISSN 1096-987X

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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 paper, we have studied nine structurally and spectroscopically well-characterised 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 band (by 30 to 50cm-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: Article
Keywords: Two-dimensional Infrared Spectroscopy, Protein, Molecular Dynamics Simulation
Schools/Departments: University of Nottingham, UK > Faculty of Science > School of Chemistry
Identification Number: 10.1002/jcc.24674
Depositing User: Bramwell, Roseanna
Date Deposited: 03 Nov 2016 11:27
Last Modified: 04 May 2017 15:01
URI: http://eprints.nottingham.ac.uk/id/eprint/38384

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