This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.Developing therapeutics to disrupt protein-protein interactions in cancer pathways and bacterial virulence is an emerging strategy in structure-based drug design. A systematic method is proposed to 1) identify hot-spot residues an protein-protein interface; 2) evaluate a database of potential compounds that may target such an interface. The first stage of the pipeline utilizes molecular dynamics in combination with Poisson-Boltzmann surface area calculations (MM/PBSA) to identify critical residues at the interface. The second stage of the pipeline applies virtual docking techniques to screen for candidate inhibitors from a large database of unique compounds that are readily available. The last stage of the pipeline uses the MM/PBSA technique in a thermodynamic context to further evaluate the selected candidates as lead inhibitors. Preliminary testing and application of parts of the pipeline yielded promising results and provided motivations to further test, develop, and apply the pipeline on the ErbB receptors and the bacterial two-component PhoP system. We are requesting computational power to facilitate in our research because the intensive nature of these calculations. Designing proteins that are resistant to thermal denaturation and proteolytic degradation is a challenging problem. In nature, protein sequences are limited to combinations of the naturally occurring 20 amino acids and their post-translational modifications. Incorporation of non-natural amino acids and semi-rigid peptidomimetics provides unique possibilities for designing proteins that adopt a stable predetermined fold, allowing protein engineering to become a reality. We are request computational resources to study the role of pre-organization in enhancing the thermal stability of proteins. Our initial molecular dynamics simulations on a 28-residue protein shows than classical MD simulations lack the sampling required to make meaningful predictions of melting temperature. We proposed to use replica exchange molecular dynamics simulations to enhance sampling and to generate an ensemble trajectories that will be analyzed for temperature dependent behavior of the system.
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