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 propose to use the multi-microsecond capabilities of ANTON to harvest one or more spontaneous transitions between the active and inactive conformations of the signaling protein NtrC using unbiased molecular dynamics. The resulting trajectory will be analyzed to identify intramolecular interactions that stabilize the transition. These findings will be directly tested by experiments performed in the lab of one the PI's (D. Kern). Specifically, site directed mutagenesis will be used to create mutant NtrC proteins for which the computationally identified interactions are disabled;transition rates for these mutant proteins will be compared to those for wild type. Significant differences in transition rates will confirm the computational predictions. By taking advantage of this close integration between computation and experiment, the proposed simulations on ANTON will significantly advance the understanding of conformational transitions in NtrC, and the mechanisms that underlie transitions among folded protein states in general.
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