Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR.
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.
Bernadó
Pau
P
Departament de Química Orgànica, Universitat de Barcelona, Spain.
García de la Torre
José
J
Pons
Miquel
M
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
D009587:Nitrogen Isotopes; D011506:Proteins