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 have been applied to a wide variety of macromolecular systems within the past year. Specific projects related to the study of AIDS proteins include: -Analysis of the active site of HIV-1 protease/ligand complexes -Investigation of the mechanism of action of HIV-1 protease -Modelling the V3 loop in HIV-1 gp120 correlating with syncytium formation -Creating a database of V3 loop sequences indicating SI/NSI propensities -Structure and activity of HIV-1 reverse transcriptase -Molecular dynamics simulation of HIV-1 Integrase Other research applied to molecules of biomedical interest uses molecular dynamics simulations to predict the function or structures of peptides and proteins. Such projects include: -Modeling intermediate filament (IF) proteins -Identification of peptides which bind to human MHC DR1 -Simulation of a large virus complex, human rhinovirus 14 (HRV14) Basic research is underway to provide a better understanding of macromolecular systems. The projects include studies of: -Temperature and hydration effects on protein dynamics -Examining protein anharmonicity, the role of dihedral transitions -Molecular dynamics simulations of staphylococcal nuclease: comparison with NMR Data -Harmonic analysis of large systems -Molecular dynamics simulation studies of DNA: The B-Z junction -The mechanism of lysozyme elucidated by QM/MM techniques -The mechanism of ribonuclease A elucidated by QM/MM techniques -Simulation study of lysozyme -Surface tension - area isotherms of DPPC bilayers and monolayers -The study of the catalytic mechanism of aldus reductase reduction using QM/MM methods