Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy
Abstract 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.
- Content Type Journal Article
- DOI 10.1007/s10858-010-9452-6
- Authors
- Alexander N. Volkov, Department of Molecular and Cellular Interactions, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Marcellus Ubbink, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
- Nico A. J. van Nuland, Department of Molecular and Cellular Interactions, VIB, Pleinlaan 2, 1050 Brussels, Belgium
Source: Journal of Biomolecular NMR