MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

生物大分子的分子动力学模拟

• 批准号: 3774966
• 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/3774966
• 关键词: HIV envelope protein gp120; RNA directed DNA polymerase; X ray crystallography; chemical models; computer data analysis; computer simulation; deuterium; endopeptidases; human immunodeficiency virus 1; intermediate filaments; intermolecular interaction; lipid bilayer membrane; macromolecule; major histocompatibility complex; model design /development; molecular dynamics; myoglobin; nuclear magnetic resonance spectroscopy; physical model; protein structure function; temperature

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-1 reverse transcriptase, analysis of inhibitor binding to the active site of HIV-1 protease, and 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: - Modeling Intermediate Filament (IF) Proteins - Identification of Peptides Which Bind to Human MHC DR1 - Structural Characterization of a Heme:Myoglobin Adduct Using Molecular Mechanics. Basic research is underway to provide a better understanding of macromolecular systems. The projects include studies of: - Temperature Effects on Protein Dynamics - The Effects of Hydration on Protein Dynamics - Molecular Dynamics Simulations on Staphylococcal Nuclease: Comparison with NMR Data - Harmonic Analysis of Large Systems - Modeling and Simulation of the Lipid Bilayers in Crystal and Gel Phases - Molecular Dynamics Simulation Studies of DNA: The B-z Junction - Examining Long-Range Deuterium Isotope Effects in C-13 NMR spectra - Solvent-Induced Forces Between Two Hydrophobic Groups - An Examination of Internal Friction in Proteins

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。这些技术被应用于 到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-1逆转录酶的模拟，抑制物结合分析 HIV-1蛋白水解酶的活性部位及其作用机制的研究 HIV-1蛋白酶的作用。 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： -对中间丝(IF)蛋白质建模 -鉴定与人MHC DR1结合的多肽 -用分子方法表征血红素：肌红蛋白加合物的结构 机械师。 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： -温度对蛋白质动力学的影响 -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：比较 使用核磁共振数据 -大系统的简谐分析 晶体和凝胶中类脂双层膜的建模与仿真 阶段 DNA的分子动力学模拟研究：B-z结 -在C-13核磁共振谱中检查长程氚同位素效应 -两个疏水基团之间的溶剂诱导力 --蛋白质内耗的研究