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Computing infrared spectra of proteins using the exciton model

Husseini, FS; Robinson, D; Hunt, NT; Parker, AW; Hirst, JD; (2017) Computing infrared spectra of proteins using the exciton model. Journal of Computational Chemistry , 38 (16) pp. 1362-1375. 10.1002/jcc.24674. Green open access

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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.

Type: Article
Title: Computing infrared spectra of proteins using the exciton model
Open access status: An open access version is available from UCL Discovery
DOI: 10.1002/jcc.24674
Publisher version: http://doi.org/10.1002/jcc.24674
Language: English
Additional information: Copyright © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Keywords: two‐dimensional infrared spectroscopy, protein, molecular dynamics simulation
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
URI: https://discovery-pp.ucl.ac.uk/id/eprint/10055530
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