Journal
JOURNAL OF BIOMOLECULAR NMR
Volume 23, Issue 2, Pages 139-150Publisher
SPRINGER
DOI: 10.1023/A:1016359412284
Keywords
aggregation; anisotropy; exchange; hydrodynamic calculations; protein dimer; protein NMR; relaxation; rotational diffusion
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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 T-1/T-2 values is described. For most proteins, the value of the atomic element radius ranges between 2.8 Angstrom and 3.8 Angstrom with a distribution centered at 3.3 Angstrom. 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 T-1/T-2 values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.
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