title: Influence of the fluctuations of the alignment tensor on the analysis of the structure and dynamics of proteins using residual dipolar couplings.
abstract: It has been suggested that the fluctuations of the alignment tensor can affect the results of procedures for characterizing the structure and the dynamics of proteins using residual dipolar couplings. We show here that the very significant fluctuations of the steric alignment tensor caused by the dynamics of proteins can be safely ignored when they do not correlate with those of the bond vectors. A detailed analysis of these correlations in the protein ubiquitin reveals that their effects are negligible for the analysis of backbone motions within secondary structure elements, but also that they may be significant in turns, loops and side chains, especially for bond vectors that have small residual dipolar couplings. Our results suggest that methods that explicitly consider the motions of the alignment tensor will be needed to study the large-scale structural fluctuations that take place on the millisecond timescale, which are often important for the biological function of proteins, from residual dipolar coupling measurements.
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. xs210@cam.ac.uk
authors.forename: X
authors.initials: X
authors.lastname: Salvatella
authors.forename: B
authors.initials: B
authors.lastname: Richter
authors.forename: M
authors.initials: M
authors.lastname: Vendruscolo
mesh_terms: D003198:Computer Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D013329:Structure-Activity Relationship; D025801:Ubiquitin / Q000737:chemistry
chemical_list: D011506:Proteins; D025801:Ubiquitin