Abstract
The broad amide I band in the infrared spectrum of peptides and proteins is accurately simulated with the coupled oscillator model of Miyazawa. Formulas for modeling the geometry-dependent interactions between peptide groups needed to reproduce the amide I contour for a peptide or protein of known structure are given. The accuracy and utility of this approach are suggested through several examples for which protein structure cannot be acquired by standard high-resolution technologies.
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Acknowledgements
We thank Prof. Tim Keiderling for productive discussions about the effects of extended β-sheet structures on the amide I contour. We thank Dr. Carol Flach for a critical reading of the MS. The writing of this chapter was supported in part from the US Public Health Service NIH/NIAID program project award AI083222 Program Project “Collectins and Innate Defense against Inhaled Pathogens” (9/1/09-8/31/11), PI, Barbara Seaton, Boston University; sub award to RM. We thank Prof. B. Seaton for permission to use Fig. 2.9.
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Brauner, J.W., Mendelsohn, R. (2012). A Quantitative Reconstruction of the Amide I Contour in the IR Spectra of Peptides and Proteins: From Structure to Spectrum. In: Fabian, H., Naumann, D. (eds) Protein Folding and Misfolding. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22230-6_2
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