title: Computing infrared spectra of proteins using the exciton model.
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. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
authors.affiliation: School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
authors.forename: Fouad S
authors.initials: FS
authors.lastname: Husseini
authors.affiliation: School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Robinson
authors.affiliation: Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, Scotland, United Kingdom.
authors.forename: Neil T
authors.initials: NT
authors.lastname: Hunt
authors.affiliation: STFC Rutherford Appleton Laboratory, Central Laser Facility, Harwell Campus, Didcot, OX11 0QX, United Kingdom.
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Parker
authors.affiliation: School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Hirst
mesh_terms: D000577:Amides / Q000737:chemistry; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013055:Spectrophotometry, Infrared / Q000379:methods; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D011506:Proteins; D012997:Solvents; D014867:Water
keywords: molecular dynamics simulation; protein; two-dimensional infrared spectroscopy