MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

分子图形和模拟部分研究的问题 使用几种理论技术的生物学意义：分子 动力学、分子力学、建模、从头计算分析 分子结构和分子图形。这些技术已经被 在过去的一年里，它应用于各种大分子系统。 与艾滋病蛋白质研究有关的具体项目包括： -HIV-1蛋白酶/配体复合体的活性部位分析 --HIV-1蛋白酶作用机制的研究 -对HIV-1 gp120中与合胞体相关的V3环进行建模 形成 -创建指示SI/NSI倾向的V3循环序列数据库 -HIV-1逆转录酶的结构和活性 HIV-1整合酶的分子动力学模拟 其他应用于生物医学感兴趣的分子的研究使用分子 预测多肽功能或结构的动力学模拟 和蛋白质。这些项目包括： -对中间丝(IF)蛋白质进行建模 -鉴定与人MHC DR1结合的多肽 -模拟大型病毒复合体--人鼻病毒14(HRV14) 基础研究正在进行中，以更好地了解 大分子系统。这些项目包括以下方面的研究： -温度和水合作用对蛋白质动力学的影响 -检查蛋白质的非谐性，二面体转变的作用 葡萄球菌核酸酶的分子动力学模拟：比较 使用核磁共振数据 -大系统的谐和分析 DNA的分子动力学模拟研究：B-Z结 -用QM/MM技术阐明溶菌酶的作用机制 -用QM/MM技术阐明核糖核酸酶A的作用机制 -溶菌酶的模拟研究 -DPPC双层膜和单层膜的表面张力-面积等温线 -醇还原酶催化还原机理的研究 QM/MM方法

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