Chapter 7. Protein Interaction: A Closer Look at the ‘Structure-Dynamics-Function’ Triad

  1. Igor A. Kaltashov and
  2. Stephen J. Eyles

Published Online: 27 JAN 2005

DOI: 10.1002/0471705179.ch7

Mass Spectrometry in Biophysics: Conformation and Dynamics of Biomolecules

Mass Spectrometry in Biophysics: Conformation and Dynamics of Biomolecules

How to Cite

Kaltashov, I. A. and Eyles, S. J. (2005) Protein Interaction: A Closer Look at the ‘Structure-Dynamics-Function’ Triad, in Mass Spectrometry in Biophysics: Conformation and Dynamics of Biomolecules, John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/0471705179.ch7

Author Information

  1. University of Massachusetts at Amherst, USA

Publication History

  1. Published Online: 27 JAN 2005
  2. Published Print: 6 APR 2005

Book Series:

  1. Wiley-Interscience Series in Mass Spectrometry

Book Series Editors:

  1. Dominic M. Desiderio2 and
  2. Nico M. M. Nibbering3

Series Editor Information

  1. 2

    Departments of Neurology and Biochemistry, University of Tennessee Health Science Center, USA

  2. 3

    Vrije Universiteit Amsterdam, The Netherlands

ISBN Information

Print ISBN: 9780471456025

Online ISBN: 9780471705178



  • protein binding;
  • protein interaction;
  • binding and dynamics;
  • enzymatic reactions;
  • enzyme-substrate complex;
  • enzymatic center;
  • substrate analog;
  • inhibition;
  • allostery


In the preceding three chapters we have discussed various mass spectrometry-based techniques to study biomolecular higher order structure and dynamics under a variety of conditions. Characterization of protein structure and dynamics is often key to understanding how these macromolecules carry out their “duties” via a sophisticated web of interactions with each other, other biopolymers and small organic and inorganic ligands. We have already discussed several qualitative examples of how both structure and dynamics govern protein-protein interaction. In this chapter we will consider several mass spectrometry-based methods that can be used to extract quantitative information on protein-ligand interaction. We will first consider several approaches to measuring protein-small ligand binding energy. Particular attention will be paid to complexes that are unstable in the gas phase. We will then proceed to discuss various methods that are used to obtain quantitative information on protein-protein interactions. The remainder of the chapter will discuss advanced uses of mass spectrometry to characterize dynamics of multiprotein assemblies and its role in modulating protein function. Two specific examples that will be considered include both large-scale dynamics (such as transient unfolding, as well as intrinsic disorder) and relatively small-scale “long-distance” motions (allosteric effects).