Abstract Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different proteinā??protein complexes.
- Content Type Journal Article
- DOI 10.1007/s10858-010-9409-9
- Authors
- Fabien Ferrage, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA
- Kaushik Dutta, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA
- Alexander Shekhtman, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA
- David Cowburn, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA
Source: Journal of Biomolecular NMR