Computing infrared spectra of proteins using the exciton model

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

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: Nov 21, 2016
• 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
• Contract Date: Nov 3, 2016