MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

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The Molecular Graphics and Simulation section studies problems of biological significance using several theoretical techniques: molecular dynamics, molecular mechanics, modeling, ab initio analysis of small molecule structure, and molecular graphics. These techniques are applied to a wide variety of macromolecular systems. Specific projects related to the study of AIDS proteins include: simulations of HIV-1 reverse transcriptase, analysis of inhibitor binding to the active site of HIV-1 protease, and investigation of the mechanism of action of HIV-1 protease. Other research applied to molecules of biomedical interest uses molecular dynamics simulations to predict function or structures of peptides and proteins. Such projects include: - Modeling Intermediate Filament (IF) Proteins - Identification of Peptides Which Bind to Human MHC DR1 - Structural Characterization of a Heme:Myoglobin Adduct Using Molecular Mechanics. Basic research is underway to provide a better understanding of macromolecular systems. The projects include studies of: - Temperature Effects on Protein Dynamics - The Effects of Hydration on Protein Dynamics - Molecular Dynamics Simulations on Staphylococcal Nuclease: Comparison with NMR Data - Harmonic Analysis of Large Systems - Modeling and Simulation of the Lipid Bilayers in Crystal and Gel Phases - Molecular Dynamics Simulation Studies of DNA: The B-z Junction - Examining Long-Range Deuterium Isotope Effects in C-13 NMR spectra - Solvent-Induced Forces Between Two Hydrophobic Groups - An Examination of Internal Friction in Proteins