Raman Spectroscopy of Proteins and Nucleoproteins

Daniel Nemecek1, Josef Stepanek2, George J. Thomas3

1 Central European Institute of Technology, Masaryk University , Brno, Czech Republic, 2 Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Prague, Czech Republic, 3 School of Biological Sciences, University of Missouri‐Kansas City, Kansas City, Missouri
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 17.8
DOI:  10.1002/0471140864.ps1708s71
Online Posting Date:  February, 2013
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Abstract

A protein Raman spectrum comprises discrete bands representing vibrational modes of the peptide backbone and its side chains. The spectral positions, intensities, and polarizations of the Raman bands are sensitive to protein secondary, tertiary, and quaternary structures and to side‐chain orientations and local environments. In favorable cases, the Raman spectrum serves as an empirical signature of protein three‐dimensional structure, intramolecular dynamics, and intermolecular interactions. Quantitative analysis of Raman spectral series can be further boosted by advanced statistical approaches of factor analysis that allow fitting of specific theoretical models while reducing the amount of analyzed data. Here, the strengths of Raman spectroscopy are illustrated by considering recent applications from the authors' work that address (1) subunit folding and recognition in assembly of the icosahedral bacteriophages, (2) orientations of subunit main chains and side chains in native filamentous viruses, (3) roles of cysteine hydrogen bonding in the folding, assembly, and function of virus structural proteins, and (4) structural determinants of protein/DNA recognition in gene regulatory complexes. Conventional Raman and polarized Raman techniques are surveyed. Curr. Protoc. Protein Sci. 71:17.8.1‐17.8.52. © 2013 by John Wiley & Sons, Inc.

Keywords: viral protein; virus assembly; DNA recognition; Raman spectroscopy; polarized Raman spectroscopy

     
 
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Table of Contents

  • Introduction
  • Nature of the Data
  • Experimental Design
  • Data Analysis
  • Applications to Assemblies of Viral Proteins
  • Applications to DNA‐Binding Proteins
  • Overview and Conclusions
  • Acknowledgments
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Literature Cited

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