MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

生物大分子的分子动力学模拟

• 批准号: 3752812
• 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/3752812
• 关键词: RNA directed DNA polymerase; bacterial proteins; chemical hydration; chemical models; computer data analysis; computer simulation; endopeptidases; enzyme mechanism; human immunodeficiency virus 1; intermediate filaments; intermolecular interaction; lipid bilayer membrane; macromolecule; major histocompatibility complex; model design /development; molecular dynamics; nuclear magnetic resonance spectroscopy; nuclease; physical model; protease inhibitor; protein structure function; temperature; virus protein

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.

分子图形学和模拟部分研究的问题， 生物学意义，使用几种理论技术：分子 动力学，分子力学，建模，从头算分析 分子结构和分子图形。这些技术应用于 各种各样的大分子系统。 与艾滋病蛋白质研究有关的具体项目包括： HIV-I逆转录酶模拟，抑制剂结合分析 对HIV-1蛋白酶活性位点的修饰，并探讨其作用机制 HIV-1蛋白酶的作用。 应用于生物医学感兴趣的分子的其他研究使用分子 动态模拟来预测肽的功能或结构， proteins.这些项目包括： - 中间丝蛋白质建模 - 与人MHC DR 1结合的肽的鉴定 - HIV-1中与合胞体形成相关的V3环的建模 - 大型病毒复合体的模拟 正在进行基础研究，以更好地了解 大分子系统这些项目包括研究： - 温度对蛋白质动力学的影响 - 水合作用对蛋白质动力学的影响 - 蛋白质的非谐性和二面角跃迁的作用 - 葡萄球菌核酸酶分子动力学模拟的比较 核磁共振数据 - 大系统谐波分析 - 晶体相和凝胶相脂质双层的建模与模拟 - DNA B-Z结的分子动力学模拟研究 - 溶菌酶作用机理的量子力学/分子力学研究 机械（QM/MM）技术 - 用QM/MM技术阐明了核糖核酸酶A的作用机理。