PROTEIN DYNAMICS FROM NMR WITH RHOMBIC LOCAL POTENTIALS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 5N-1H spin relaxation is a powerful method for elucidating protein backbone dynamics. In order to derive as much information as possible from the experimental data a theoretical approach is needed which matches the integrity of currently available data. We have shown that the slowly relaxing local structure (SRLS) approach is capable of accomplishing this. Dominant phenomena such as dynamical coupling between the local motion of the probe (e.g., N-H bond) and the global tumbling of the protein, and general features of local geometry, are explicitly included in SRLS. In recent work we have focused on the geometric aspects, in particular the symmetry of the mode-coupling potential, which reflects the local geometry about the 15N site. The symmetry of the potential depends on the symmetry of the local diffusion/local ordering frame, M, and the symmetry of the local director frame, C, which are illustrated below top. We found that the particular rhombic symmetry of the M frame is of the "nearly planar Ym-Ym" type, in agreement with the stereo-chemistry of the peptide plane and the N-H site. (crankshaft fluctuations and peptide-plane reorientation of adjacent carbon bonds in peptide backbone axis) are functionally important internal motions, which necessarily involve rhombic spatial restrictions, can be treated satisfactorily with SRLS whereas the model free approach is not able to explicitly allow for them. We found that a proper SRLS theory is required to discern such functionally important motions. We demonstrated this with examples of NMR relaxation data from adenylate kinase, calmodulin, binase and ribonuclease H. With mode-coupling and the local geometry properly accounted for, SRLS appears to match the quality of current 15N relaxation data in proteins. Thus SRLS provides insightful information on backbone dynamics which can be related directly to function.