MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

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The Molecular Graphics and Simulation Section studies problems of biologica 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: - Analysis of the active site of HIV-1 protease/ligand complexes - Investigation of the mechanism of action of HIV-1 protease - Design of an anthrax related toxin activated by 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: - Examining the mechanism of beta-lactamases using MD and QM/MM methods - Identification of peptides which bind to human MHC DR1 - Modeling intermediate filament (IF) proteins - Simulation of a large virus complex, human rhino virus 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 - DNA/protein interactions: the sex-determining region of the human chromosome - 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 - Surface tension area isotherms of DPPC bilayers and monolayers - The study of the catalytic mechanism of aldose reductase, using QM/MM methods - Gel phase simulations of DPPC lipid bilayer (comparison with experiment)