COMPUTATIONAL METHODS FOR STUDYING PROTEIN AND DNA DYNAMICS BY ESR & NMR

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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. We have developed new models and software for analyzing the ESR and NMR data from macromolecules such as protein and DNA systems. In the ESR context, the new software allows a simultaneous fit of ESR spectra at different frequencies to enhance the spectral resolution to the various fitting parameters. It also allows for dynamic exchanges between conformers. When coupled with the slowly relaxing local structure (SRLS) model, the multi frequency fit outputs the local dynamics and ordering of the tether connecting the spin label to the macromolecule as well as the overall tumbling rate of the whole macromolecule complex. This approach has been applied to the study of the dynamic properties of T4 lysozyme spin labeled at several mutant sites. Currently we are conducting a more comprehensive study of T4 lysozyme dynamics at more mutant sites and more frequencies in different solvents. We are adding new features to our fitting programs. These features include (1) an asymmetric diffusion tensor for the internal motion of the spin label and (2) an internal diffusion tilt with all three Euler angles. In the second part of this subproject, we have formulated the SRLS model within the context of NMR relaxation theory to analyze macromolecule dynamics. An important assumption of the widely used model free (MF) theory in the protein NMR community is the decoupling between the two modes of motions. The dynamical coupling of the overall protein tumbling and the local motion is an important step forward towards our understanding of the protein dynamics. This approach has been successfully applied to the dynamics analyses of a few protein systems, and will be used in a NMR study by Dr David Fushman, University of Maryland, to analyze the overall and inter-domain motions in dual-domain (di-ubiquitin) system.