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Calculation of the infrared spectra of proteins

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Abstract

The CHARMM22 force field with associated partial charges is used to calculate the infrared spectra of a number of small proteins and some larger biothreat proteins. The calculated high-frequency region, from about 2,500 to 3,500 cm−1, is dominated by stretching modes of hydrogen bonded to other atoms, and is very similar in all proteins. There is a peak at 3,430 cm−1 whose intensity is predicted by these calculations to be a direct measure of arginine content. The calculated low-frequency THz region, up to 300 cm−1, is also very similar in all the proteins and just reflects the vibrational density of states in agreement with experimental results. Calculations show that the intermediate-frequency region between 500 and 1,200 cm−1 shows the greatest difference between individual proteins and is also the least affected by water absorption. However, to match experimental measurements in the amide region, it was necessary to reduce the hydrogen partial charges.

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Acknowledgments

We thank the Defense Threat Reduction Agency Grant HDTRA-08-0040 for financial support. We thank Saravana Prakash Thirumuruganandham for discussions and Stephanie Cope for her experimental measurement of the IR spectrum of lysozyme (Fig. 1).

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  1. Department of Physics, Arizona State University, Tempe, AZ, 85287, USA

    Adam J. Mott & Peter Rez

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  1. Adam J. Mott
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  2. Peter Rez
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Correspondence to Peter Rez.

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Mott, A.J., Rez, P. Calculation of the infrared spectra of proteins. Eur Biophys J 44, 103–112 (2015). https://doi.org/10.1007/s00249-014-1005-6

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  • DOI: https://doi.org/10.1007/s00249-014-1005-6

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