Integrated computational approach to the analysis of NMR relaxation in proteins: application to ps-ns main chain 15N-1H and global dynamics of the Rho GTPase binding domain of plexin-B1.

ABSTRACT: An integrated computational methodology for interpreting NMR spin relaxation in proteins has been developed. It combines a two-body coupled-rotator stochastic model with a hydrodynamics-based approach for protein diffusion, together with molecular dynamics based calculations for the evaluation of the coupling potential of mean force. The method is applied to ¹⁵N relaxation of N-H bonds in the Rho GTPase binding (RBD) domain of plexin-B1, which exhibits intricate internal mobility. Bond vector dynamics are characterized by a rhombic local ordering tensor, S, with principal values S₀² and S₂², and an axial local diffusion tensor, D₂, with principal values D(2,||) and D(2,⊥). For α-helices and β-sheets we find that S₀² ~ -0.5 (strong local ordering), -1.2 < S₂² < -0.8 (large S tensor anisotro

SUBMITTER: Zerbetto M 

PROVIDER: S-EPMC3079214 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature