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，从头算，小分子分析 分子结构和分子图形。这些技术是 适用于多种大分子体系。 与艾滋病蛋白质研究有关的具体项目包括： HIV-1蛋白酶抑制剂的可溶性活性部位分析 HIV-1蛋白酶作用机制的研究。 其他应用于生物医学感兴趣的分子的研究使用分子 用动力学模拟预测多肽的功能或结构 蛋白质。这些项目包括： -使用MD和QM/MM检查β-内酰胺酶的机制 方法 -鉴定与人MHC DR1结合的多肽 -对中间丝(IF)蛋白质进行建模 -模拟大型病毒复合体--人类犀牛病毒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： -核酸和NA/蛋白质复合体的模拟 -温度和水合作用对蛋白质动力学的影响 -葡萄球菌核酸酶的分子动力学模拟： 与核磁共振数据的对比 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 -醛糖还原酶催化机理的研究 QM/MM方法 -DPPC脂质双层的凝胶相模拟，与 实验 -DNA/蛋白质相互作用：人类性别决定区域 染色体 -对锤头状核酶-底物复合系统进行建模 -检查亮氨酸拉链图案

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