New Methods and Applications for the Dynamic Characterization of Proteins by the Combination of NMR Spectroscopy and Computer Simulations

Florida State University, Tallahassee FL

Investigators

Abstract

The objective of this research is to study protein dynamics by nuclear magnetic resonance (NMR) and computational approaches. NMR relaxation parameters are now routinely measured for the protein backbone, but less so for protein side chains. While side-chain relaxation studies have mainly focused on methyl group relaxation, the majority of side-chain carbon atoms belong to methylene moieties. If not partially deuterated, dipole-dipole cross correlations generally make their relaxation behavior and their interpretation difficult. New relaxation experiments are developed that efficiently suppress dipole-dipole cross-correlated relaxation in fully carbon-labeled proteins. The relaxation data will be interpreted in terms of reorientational eigenmode dynamics (RED) analysis that integrates NMR relaxation data with molecular dynamics simulations for studying motional correlation effects in the ns and sub-ns time scale range. Until recently, slower time-scale dynamics of proteins in the hundreds of ns to ms range have been very hard to assess for spins that do not show exchange broadening. The advent of residual dipolar couplings is now opening up this time window for comprehensive experimental investigations. By applying and improving the recently introduced model-free approach that uses dipolar coupling data in a variety of alignment media with different alignment tensors, protein dynamics on these slower time scales will be investigated for the protein backbone as well as for the side chains. The dynamics information will be retrieved in the form of averaged spherical harmonics that define an order parameter as well as the anisotropy of motion. Realistic analytical motional models will be developed to characterize motions of local protein fragments as well as collective motions involving amino-acid groups and whole secondary structural elements. Structural dynamics of proteins play an important role in biochemical processes. Detailed information on protein dynamics at an atomic level is of fundamental importance for understanding their function. The overall goal of this research is the exploration and development of new experimental and computational methods for a comprehensive description of complex protein dynamics on widely different time scales and to demonstrate their applicability to biologically relevant systems.