Computing infrared spectra of proteins using the exciton model
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 measuremen...
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| Format: | Article |
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Wiley
2016
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| Online Access: | https://eprints.nottingham.ac.uk/38384/ |
| _version_ | 1848795599787261952 |
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| author | Husseini, Fouad S. Robinson, David Hunt, Neil T. Parker, Anthony W. Hirst, J.D. |
| author_facet | Husseini, Fouad S. Robinson, David Hunt, Neil T. Parker, Anthony W. Hirst, J.D. |
| author_sort | Husseini, Fouad S. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T19:34:39Z |
| format | Article |
| id | nottingham-38384 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:34:39Z |
| publishDate | 2016 |
| publisher | Wiley |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-383842020-05-04T18:20:26Z https://eprints.nottingham.ac.uk/38384/ Computing infrared spectra of proteins using the exciton model Husseini, Fouad S. Robinson, David Hunt, Neil T. Parker, Anthony W. Hirst, J.D. 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. Wiley 2016-11-21 Article PeerReviewed Husseini, Fouad S., Robinson, David, Hunt, Neil T., 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 Two-dimensional Infrared Spectroscopy Protein Molecular Dynamics Simulation http://onlinelibrary.wiley.com/doi/10.1002/jcc.24674/full doi:10.1002/jcc.24674 doi:10.1002/jcc.24674 |
| spellingShingle | Two-dimensional Infrared Spectroscopy Protein Molecular Dynamics Simulation Husseini, Fouad S. Robinson, David Hunt, Neil T. Parker, Anthony W. Hirst, J.D. Computing infrared spectra of proteins using the exciton model |
| title | Computing infrared spectra of proteins using the exciton model |
| title_full | Computing infrared spectra of proteins using the exciton model |
| title_fullStr | Computing infrared spectra of proteins using the exciton model |
| title_full_unstemmed | Computing infrared spectra of proteins using the exciton model |
| title_short | Computing infrared spectra of proteins using the exciton model |
| title_sort | computing infrared spectra of proteins using the exciton model |
| topic | Two-dimensional Infrared Spectroscopy Protein Molecular Dynamics Simulation |
| url | https://eprints.nottingham.ac.uk/38384/ https://eprints.nottingham.ac.uk/38384/ https://eprints.nottingham.ac.uk/38384/ |