PROTEIN DYNAMICS FROM NMR WITH IMPROVED STOCHASTIC MODELS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. NMR is a powerful method for elucidating protein dynamics. A useful dynamic probe is the 15N-1H bond vector, which engages in both the global reorientation of the protein and local site-specific motions. The commonly used data analysis method is model-free (MF), where the global and local motions are assumed decoupled, and features of local geometry are simplified. We found that the experimental 15N relaxation data are sensitive to mode-coupling and general features of local geometry. These elements are inherent to the Slowly Relaxing Local Structure (SRLS) approach of Freed et al., which we have applied to NMR spin relaxation in proteins. The SRLS model expresses the dynamic coupling between the N-H bond, which typically relaxes at a faster rate, RL, and its immediate (internal) protein surroundings, which typically relax at a slower rate, RC. The coupling materializes through a potential, U/kT, which represents the spatial restrictions imposed by the protein at the site of the local motion of the N-H bond. By virtue of dynamical coupling the faster internal N-H dynamics readjusts itself to the changing orientation of the protein. Within the context of axial local potentials SRLS has been applied to a large number of proteins, in particular ligand-free and inhibitor-bound E. coli adenylate kinase (AKeco). This enzyme catalyzes the reaction ATP + AMP produces 2ADP. It is made up of three domains, two of which (LID and AMPbd) execute large amplitude catalysis-related segmental motions. Our study of ligand-free AKeco yielded the rate at which the domains AMPbd and LID move in solution. Our study of the complex of AKeco with the two-substrate-mimic inhibitor AP5A yielded dynamic elements akin to the transition state of the catalytic reaction. The methodology is being further developed within the context of non-axial local potentials, which requires the calculations of the cross spectral densities.