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: Analysis of soluble active site of HIV-1 protease inhibitors - 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: - 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: - Simulation of Nucleic Acids and NA/protein complexes - Temperature and hydration effects on protein dynamics - Molecular dynamics simulations of staphylococcal nuclease: comparison with NMR Data - 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 - The study of the catalytic mechanism of aldose reductase using QM/MM methods - Gel phase simulations of DPPC lipid bilayer, comparison with experiment - DNA/protein interactions: the sex-determining region of the human chromosome - Modeling the hammerhead ribozyme-substrate complex system - Examining Leucine Zipper Motifs