title: NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion.
abstract: NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca(2+)-free) state of calbindin D(9k). Calculations are performed in an expanding reference frame so as to discriminate between the effects of short- and long-range motions. This approach reveals that the dominant contributions to the order parameters are short-range. Longer-range contributions are limited to specific sites, many of which have been recognized in previous studies of correlated motions. These sites are identified on the basis of an effective reorientational number, n ( eff ). Not only does this parameter identify sites of short- and long-range motion, it also provides a way of evaluating the separability condition that is key to the Lipari-Szabo model-free method. When analyzed in conjunction with the Prompers-Brüschweiler separability index, the n ( eff ) values indicate that longer-range motions play a more prominent role in apo calbindin than they do in ubiquitin.
authors.affiliation: Department of Chemistry and Physical Sciences, College of Mount St. Joseph, Cincinnati, OH 45233, USA. eric_johnson@mail.msj.edu
authors.forename: Eric
authors.initials: E
authors.lastname: Johnson
mesh_terms: D064026:Calbindins; D009038:Motion; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D064030:S100 Calcium Binding Protein G / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry*; D014961:X-Ray Diffraction
chemical_list: D064026:Calbindins; D064030:S100 Calcium Binding Protein G; D025801:Ubiquitin