MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

生物大分子的分子动力学模拟

• 批准号: 2571576
• 负责人: B R BROOKS
• 金额: --
• 依托单位: CENTER FOR INFORMATION TECHNOLOGY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/2571576
• 关键词: bacterial proteins; chemical hydration; computer graphics /printing; computer simulation; cytoskeletal proteins; enzyme structure; human immunodeficiency virus 1; intermediate filaments; intermolecular interaction; lipid bilayer membrane; macromolecule; model design /development; molecular dynamics; nuclear magnetic resonance spectroscopy; nucleic acid structure; physical model; protease inhibitor; protein structure function; temperature; virus protein

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)

分子图形和模拟部分研究生物制品的问题 使用多种理论技术的意义：分子动力学， 分子力学、建模、小分子从头算分析 结构和分子图形。 这些技术应用广泛 各种高分子体系。 与艾滋病蛋白研究相关的具体项目包括： - HIV-1蛋白酶/配体复合物活性位点分析 - HIV-1蛋白酶作用机制的研究 - 由 HIV-1 蛋白酶激活的炭疽相关毒素的设计 其他应用于生物医学分子的研究使用分子 动力学模拟来预测肽的功能或结构 蛋白质。此类项目包括： - 使用 MD 和 QM/MM 方法检查 β-内酰胺酶的机制 - 鉴定与人 MHC DR1 结合的肽 - 中间丝 (IF) 蛋白建模 - 模拟大型病毒复合体，人犀牛病毒14（HRV14） 基础研究正在进行中，以便更好地了解 大分子系统。 这些项目包括以下方面的研究： - 温度和水合对蛋白质动力学的影响 - 检查蛋白质的不和谐性、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 和 核磁共振数据 - DNA/蛋白质相互作用：人类的性别决定区域 染色体 - DNA 的分子动力学模拟研究：B-Z 连接 - 通过QM/MM技术阐明溶菌酶的机制 - 通过QM/MM技术阐明核糖核酸酶A的机制 - DPPC双层和单层的表面张力面积等温线 - 利用QM/MM研究醛糖还原酶的催化机制 方法 - DPPC 脂质双层的凝胶相模拟（与 实验）