ASSESSMENT OF MULTI-MICROSECOND SIMULATIONS OF INTRINSICALLY DISORDERED PROTEIN

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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. The objective of this proposal is to extend state-of-the-art NMR based trajectory assessment protocols to microsecond ensembles calculated for intrinsically disordered proteins (IDPs). This work will enable a rigorous assessment of the timescale of protein dynamics encoded in the best current force fields and the restrictions to their amplitudes. This project will also allow access to high resolution ensembles of IDPs, which are currently intractable to calculate with commercial software on single-laboratory clusters. IDPs have emerged as critical components of cellular systems, contributing to cell signaling and human disease. A better understanding of their physico-chemical properties is imperative as the very discovery of IDPs has transformed scientists' view of the relationship between protein structure and function. While our in-house computational infrastructure is sufficient for short (< 1 ?s) simulations of globular proteins, we lack the local resources necessary to perform all atom explicit solvent simulations of intrinsically disordered proteins. I request 50,000 CPU-hours to calculate approximately 40 ?s total simulation time of all atom explicit solvent trajectories of the C-terminal tail of human FCP1 (residues 930-961) using the AMBER99SB force field. FCP1 is chosen as a model system because of its critical role in promoting RNA polymerase II recycling following the termination of transcription. AMBER99SB will be used due to my past success using this force field to model a variety of NMR parameters with trajectories of well folded proteins. My laboratory's ever growing body of in-house collected experimental NMR data for the protein FCP1 and its complex with the TFIIF heavy chain protein RAP74 will facilitate quantitative ensemble assessment and validation of the ultra-long trajectories computed using established protocols. This project will yield immediate benefit to the broader IDP community because FCP1 is representative of the large number of IDPs that transition to a more ordered conformation upon binding other macromolecules. This makes this project an ideal opportunity to generate atomistic ensembles for all states involved in a folding-upon-binding system with known biological significance, therefore allowing us unprecedented mechanistic insight into the binding event.