COMPUTATIONAL METHODS FOR STUDYING PROTEIN DYNAMICS BY ESR & NMR

点击翻译按钮获取中文摘要

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. We have developed new models and software for analyzing the ESR and NMR data from protein 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. When coupled with the slowly relaxing local structure (SRLS) model, the multifrequency fit outputs the local dynamics and ordering of the tether connecting the probe to the protein as well as the overall tumbling rate of the whole protein complex. This approach has been applied to the study of the dynamic properties of T4 lysozyme spin labeled at several sites. A systematic analysis of the ESR spectra measured at different temperatures adds additional spectral resolution to the fitting parameters. Special focus has been placed on a comparison of the dynamics and ordering parameters amongst different sites. We have used these results to design new experiments, which allow an effective separation of different modes of motions. We are also upgrading the SRLS model to include three modes of motion, which is a better approximation of the complex protein dynamics. In the second part of this subproject, we have formulated the SRLS model within the context of NMR relaxation theory to analyze protein 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 dynamical analysis. This approach has been successfully applied to the dynamics analyses of a few protein systems. It is currently being extended to the calculation of the cross terms of NMR spectral density.