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Computing infrared spectra of proteins using the exciton model

Husseini, Fouad S.; Robinson, David; Hunt, Neil T.; Parker, Anthony W.; Hirst, J.D.

Authors

Fouad S. Husseini

David Robinson

Neil T. Hunt

Anthony W. Parker



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.

Citation

Husseini, F. S., Robinson, D., Hunt, N. T., Parker, A. W., & Hirst, J. (in press). Computing infrared spectra of proteins using the exciton model. Journal of Computational Chemistry, 38(16), https://doi.org/10.1002/jcc.24674

Journal Article Type Article
Acceptance Date Oct 29, 2016
Online Publication Date Nov 21, 2016
Deposit Date Nov 3, 2016
Publicly Available Date Mar 28, 2024
Journal Journal of Computational Chemistry
Print ISSN 0192-8651
Electronic ISSN 1096-987X
Publisher Wiley
Peer Reviewed Peer Reviewed
Volume 38
Issue 16
DOI https://doi.org/10.1002/jcc.24674
Keywords Two-dimensional Infrared Spectroscopy, Protein, Molecular Dynamics Simulation
Public URL https://nottingham-repository.worktribe.com/output/827564
Publisher URL http://onlinelibrary.wiley.com/doi/10.1002/jcc.24674/full

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