Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy.

TitleMapping the encounter state of a transient protein complex by PRE NMR spectroscopy.
Publication TypeJournal Article
Year of Publication2010
AuthorsVolkov, A., M. Ubbink, and N. A. J. van Nuland
JournalJ Biomol NMR
Date Published2010 Dec
KeywordsCytochrome-c Peroxidase, Cytochromes c, Electron Spin Resonance Spectroscopy, Mitochondria, Models, Molecular, Multiprotein Complexes, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Protein Conformation, Protein Interaction Mapping, Yeasts

Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). First, we describe a simple, general method to map out the spatial and temporal distributions of binding geometries constituting the Cc-CcP encounter state. We show that the spatiotemporal mapping provides a reliable estimate of the experimental coverage and, at higher coverage levels, allows to delineate the conformational space sampled by the minor species. To further refine the encounter state, we performed PRE-based ensemble simulations. The generated solutions reproduce well the experimental data and lie within the allowed regions of the encounter maps, confirming the validity of the mapping approach. The refined encounter ensembles are distributed predominantly in a region encompassing the dominant form of the complex, providing experimental proof for the results of classical theoretical simulations.

Alternate JournalJ. Biomol. NMR
PubMed ID21049303
PubMed Central IDPMC3235994