NDLI: Understanding the Signatures of Secondary-Structure Elements in Proteins with Raman Optical Activity Spectroscopy

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Understanding the Signatures of Secondary-Structure Elements in Proteins with Raman Optical Activity Spectroscopy

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Luber, Sandra Jacob, Christoph R. Reiher, Markus
Description	Author Affiliation: Jacob CR ( ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland. christoph.jacob@phys.chem.ethz.ch)
Abstract	A prerequisite for the understanding of functional molecules like proteins is the elucidation of their structure under reaction conditions. Chiral vibrational spectroscopy is one option for this purpose, but provides only indirect access to this structural information. By first-principles calculations, we investigate how Raman optical activity (ROA) signals in proteins are generated and how signatures of specific secondary-structure elements arise. As a first target we focus on helical motifs and consider polypeptides consisting of twenty alanine residues to represent α-helical and $3_{10}-helical$ secondary-structure elements. Although ROA calculations on such large molecules have not been carried out before, our main goal is the stepwise reconstruction of the ROA signals. By analyzing the calculated ROA spectra in terms of rigorously defined localized vibrations, we investigate in detail how total band intensities and band shapes emerge. We find that the total band intensities can be understood in terms of the reconstructed localized vibrations on individual amino acid residues. Two different basic mechanisms determining the total band intensities can be established, and it is explained how structural changes affect the total band intensities. The band shapes can be rationalized in terms of the coupling between the localized vibrations on different residues, and we show how different band shapes arise as a consequence of different coupling patterns. As a result, it is demonstrated for the chiral variant of Raman spectroscopy how collective vibrations in proteins can be understood in terms of well-defined localized vibrations. Based on our calculations, we extract characteristic ROA signatures of α helices and of $3_{10}-helices,$ which our analysis directly relates to differences in secondary structure.
ISSN	09476539
e-ISSN	15213765
Journal	Chemistry - A European Journal
Issue Number	48
Volume Number	15
Language	English
Publisher	Wiley-VCH;ChemPubSoc Europe
Publisher Date	2009-12-14
Publisher Place	Germany
Access Restriction	Open
Subject Keyword	Peptides Chemistry Protein Structure, Secondary Proteins Models, Molecular Protein Conformation Quantum Theory Spectrum Analysis, Raman Research Support, Non-U.S. Gov't
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Catalysis

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