NMR explorations of biomolecular systems with rapid conformational exchanges

Abstract

Biomolecules such as proteins and oligosaccharides undergo dynamic conformational exchanges, which are relevant to regulation of biologically functional processes as typified by molecular recognition. Nuclear magnetic resonance (NMR) spectroscopy provides useful approaches to characterize the conformational dynamics of biomolecules over a broad range of time scales. However, detailed characterizations of individual conformers are inherently challenging for those biomolecules that exhibit rapid conformational interconversions. Here we describe several NMR strategies to deal with dynamic conformational equilibria and ensembles using monomeric and dimeric ubiquitin (Ub) and the oligosaccharide moieties of gangliosides as model molecules. A specific Ub conformer could be enriched using high pressure combined with a single amino acid substitution. Introducing a covalent linkage constrained the conformational states of a Ub dimer. NMR spectroscopy was also useful for validating molecular dynamics simulations of highly flexible oligosaccharides. These methods provided for detailed determinations of dynamic conformational exchanges that involve minor conformational species.