Computer Simulation of Protein Structure and Dynamics

蛋白质结构和动力学的计算机模拟

• 批准号: 9820779
• 负责人: Sebastian Doniach
• 金额: $ 27万
• 依托单位: Stanford University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-08-15 至 2002-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9820779&HistoricalAwards=false
• 关键词: Computer; Simulation; Protein; Structure; Dynamics

This is a two-part project for the study of biomolecular dynamics using computer simulation. In the first part the time-dependence of the molecular motion of a protein in the multi-nanosecond range will be simulated using a multiple time step Langevin dynamics alogorithm to model experiments which measure how proteins move on time scales varying from a few nanoseconds to many tens of nanoseconds. NMR measurements and fast optical spectroscopy measurements following a laser pulse which gives the protein a shock will be considered. In the second part of the project, protein folding will be examined by fixing the beginning (unfolded) and ending (folded) conformations and examining various reaction paths leading from the unfolded to the folded conformation. The aim of the research is to study the kinds of folding trajectories which occur as the number of time steps allowed between the unfolded and folded states is increased.

这是一个由两部分组成的项目，用于使用计算机模拟研究生物分子动力学。 在第一部分中，将使用多时间步长朗之万动力学算法来模拟蛋白质在多纳秒范围内的分子运动的时间依赖性，以模拟测量蛋白质如何在从几纳秒到几十纳秒的时间尺度上移动的实验。 将考虑在激光脉冲后对蛋白质进行冲击的核磁共振测量和快速光谱测量。 在该项目的第二部分中，将通过固定开始（展开）和结束（折叠）构象并检查从展开构象到折叠构象的各种反应路径来检查蛋白质折叠。 该研究的目的是研究随着展开状态和折叠状态之间允许的时间步数增加而发生的折叠轨迹的类型。