SIMULATIONS OF BIOMOLECULES

生物分子模拟

• 批准号: 6411718
• 负责人: Martin Karplus
• 金额: $ 1.29万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-12-01 至 2001-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6411718
• 关键词: biological products; biomedical resource; computers; enzymes; structural biology; technology /technique

The aim of the proposed research is to use computation methods to increase the understanding of the dynamics and function of biomolecules. The essential conformational change in the control protein EFTu will be studied by normal mode analysis and molecular dynamics. All-atom explicit solvent simulations of lysozyme and of structurally related proteins will be performed to explore the origin of the differences in the native state dynamics and in the unfolding behavior. Discontinuous molecular dynamics simulations with simplified protein models will be used to examine the full potential energy surface and dynamics involoved in folding and unfolding. To obtain a deeper understanding of enzyme catalysis, the potential of mean force along the reaction path and the dynamics of the reaction will be calculated for lysozyme, xylose isomerase, hammerhead ribozyme and nitrogenase.

拟议研究的目的是使用计算方法来 增加对的动力和功能的理解 生物分子。对照中的本质构象变化 蛋白质EFTU将通过简正波分析和分子研究 动力学。溶菌酶和溶菌酶的全原子显式溶剂模拟 结构上相关的蛋白质将被用来探索起源 在原生状态动力学和在展开中的差异 行为。非连续分子动力学模拟 简化的蛋白质模型将被用来检验全部潜力。 参与折叠和展开的能量面和动力学。至 对酶催化有了更深入的了解， 反应路径上的平均作用力和反应动力学 将计算出溶菌酶、木糖异构酶、锤头状核酶 和固氮酶。