Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra

Mensch, C., Barron, L. D. and Johannessen, C. (2016) Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra. Physical Chemistry Chemical Physics, 18(46), pp. 31757-31768. (doi: 10.1039/c6cp05862k) (PMID:27841400)

Abstract

In the past few decades, Raman optical activity (ROA) spectroscopy has been shown to be very sensitive to the solution structure of peptides and proteins. A major and urgent challenge remains the need to make detailed assignments of experimental ROA patterns and relate those to the solution structure adopted by the protein. In the past few years, theoretical developments and implementations of ROA theory have made it possible to use quantum chemical methods to compute the ROA spectra of peptides. In this work, a large database of ROA spectra of peptide model structures describing the allowed backbone conformations of proteins was systematically calculated and used to make unprecedented detailed assignments of experimental ROA patterns to the conformational elements of the peptide in solution. By using a similarity index to compare an experimental spectrum to the database spectra (2902 theoretical spectra), the conformational preference of the peptide in solution can be assigned to a very specific region in the Ramachandran space. For six (poly)peptides this approach was validated and gives excellent agreement between experiment and theory. Additionally, hydrogen/deuterium exchanged structures and the conformational dependence of the amide modes in Raman spectra can be analysed using the new database. The excellent agreement between experiment and theory demonstrates the power of the newly developed database as a tool to study Raman and ROA patterns of peptides and proteins. The interpretation of experimental ROA patterns of different proteins published in the scientific literature is discussed based on the spectral trends observed in the database.

• Item Type: Articles
• Additional Information: The authors acknowledge the financial support provided by the Flemish Community, the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship of C. M., the University of Ghent (IOF Advanced TT) for the purchase of the ChiralRAMAN spectrometer and the Flemish Super Computing Centre (VSC) financed by the Flemish government and the Hercules Foundation.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Barron, Professor Laurence and Johannessen, Dr Christian
• Authors: Mensch, C., Barron, L. D., and Johannessen, C.
• College/School: College of Science and Engineering > School of Chemistry
• Journal Name: Physical Chemistry Chemical Physics
• Publisher: Royal Society of Chemistry
• ISSN: 1463-9076
• ISSN (Online): 1463-9084
• Published Online: 26 October 2016
• Copyright Holders: Copyright © 2016 The Owner Societies
• First Published: First published in Physical Chemistry Chemical Physics 18(46): 31757-31768
• Publisher Policy: Reproduced in accordance with the publisher copyright policy