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-I reverse transcriptase, analysis of inhibitor binding to the active site of HIV-l protease, and investigation of the mechanism of action of HIV-l 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 that bind to human MHC DR1 - Modeling the V3 loop in HIV-1 correlating with syncytium formation - Simulation of a large virus complex Basic research is underway to provide a better understanding of macromolecular systems. The projects include studies of: - Temperature effects on protein dynamics - Effects of hydration on protein dynamics - Protein anharmonicity and the role of dihedral transitions - Molecular dynamics simulations on Staphylococcal nuclease: comparison with NMR data - Harmonic analysis of large systems - Modeling and simulation of lipid bilayers in crystal and gel phases - Molecular dynamics simulation studies of DNA: the B-Z junction - The mechanism of lysozyme elucidated by quantum mechanical/molecular mechanical (QM/MM) techniques - The mechanism of ribonuclease A elucidated by QM/MM techniques.
