Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Roy, Santanu; Lessing, Joshua; Meisl, Georg; Ganim, Ziad; Tokmakoff, Andrei; Knoester, Jasper; Jansen, Thomas L. C.

doi:doi:10.1063/1.3665417

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We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D₂O and compare with experimental observations.

Article Outline

INTRODUCTION
THEORY AND METHODS
1. Electrostatic map for proline
2. Dihedral map for proline
3. TCC map
VALIDATION OF THE MAP
1. Experiments
2. Simulations
3. Results and discussion
CONCLUSIONS

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KEYWORDS and PACS

Keywords

infrared spectra, molecular biophysics, molecular configurations, proteins, spectrochemical analysis, vibrations

PACS

87.14.ef

Peptides
87.15.B-

Structure of biomolecules
87.15.hp

Conformational changes
87.15.M-

Spectra of biomolecules

ARTICLE DATA

Digital Object Identifier

http://dx.doi.org/10.1063/1.3665417

PUBLICATION DATA

ISSN

0021-9606 (print)

1089-7690 (online)

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$abstract.society.value is a Member of CrossRef

American Institute of Physics

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