Simulating Protein Structures, Complexes, And Dynamics

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We have continued to develop, implement, and apply simulation methods in computational studies of the energetics and dynamics of biomolecular systems. We are working to refine a continuum description of macromolecular solvation in terms of polar, nonpolar, and solvent-structure effects. One manuscript has been submitted, and another is in preparation. We also model proteins based on homology and work to improve the generation and refinement of such models (Curr. Protein Pept. Sci., 2006; book chapter, in press). A paper discussing the prediction of side-chain conformations on protein surfaces is in press (Proteins Struct. Funct. Bioinform., in press). In collaboration with NCI, we built a model of the human fumarate hydratase homotetramer in a study of hereditary leiomyomatosis and renal cell cancer (J. Med. Genet., 2006). With NICHD, we studied the biological effect of a mutation in the human luteinizing hormone receptor with the aid of our homology model (Mol. Endocrinol., 2006). With NCI, we have been studying the interactions involved in kinase binding to Hsp90 (Mol. Cell. Biol., 2006). In collaboration with NIMH and NHLBI, we are preparing a manuscript describing reliable ways of determining the transition state of peripheral benzodiazepine receptor ligands that are utilized as probes for brain imaging. Quantum chemical calculations are being carried out to design inhibitors of Hsp90 and to establish a structure-activity relationship for A-beta amyloid probes. With NIDA, we are studying the structure-activity relationships of opioid-receptor ligands. With NICHD we are studying the dynamics and energetics of proteins involved in the synthesis of melatonin. In collaboration with NIDDK, we have worked to characterize the chemistry, thermodynamics, and spectroscopic properties of carbon nanotubes and their interactions with water (J. Chem. Phys., 2006).