title: Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR.
abstract: HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C(alpha)-H vectors in a rigid protein structure starting from an atomic level representation. Thus HYDRONMR can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results. HYDRONMR contains a single adjustable parameter, the atomic element radius. A protocol to determine the value that gives the best agreement between calculated and experimental T1/T2 values is described. For most proteins, the value of the atomic element radius ranges between 2.8 A and 3.8 A with a distribution centered at 3.3 A. Deviations from the usual range towards larger values are associated to aggregation in several proteins. Deviations to lower values may be related to large-scale motions or inappropriate model structures. If the average structure is correct, deviations between experimental T1/T2 values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.
authors.affiliation: Departament de Química Orgànica, Universitat de Barcelona, Spain.
authors.forename: Pau
authors.initials: P
authors.lastname: Bernadó
authors.forename: José
authors.initials: J
authors.lastname: García de la Torre
authors.forename: Miquel
authors.initials: M
authors.lastname: Pons
mesh_terms: D000465:Algorithms; D016880:Anisotropy; D008958:Models, Molecular; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D009587:Nitrogen Isotopes; D011506:Proteins