Modeling and Theory of Biomolecular Association

生物分子关联的建模和理论

基本信息

  • 批准号:
    0919586
  • 负责人:
  • 金额:
    $ 35.39万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Standard Grant
  • 财政年份:
    2009
  • 资助国家:
    美国
  • 起止时间:
    2009-09-01 至 2013-08-31
  • 项目状态:
    已结题

项目摘要

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).The association of ligand and protein is of fundamental importance in biology, playing roles in functions as diverse as immunity, metabolism, signaling, and cognition. Recent advances on Brownian dynamics and continuum simulation methods provide powerful tools to study diffusion in biomolecular systems, but they are mostly restricted to systems that are near the limit of diffusion-control one-step association processes. For more complicated processes, such as two-step association processes that involve short-range interactions and conformational changes of ligands and proteins, existing methods may not be reliable enough to study the association pathways and predict the rate constants. This project will develop new computer simulation tools and theoretical models to study the two-step binding processes. This work will be carried out in three integrated steps: First, new multi-scale methods, combining Brownian dynamics simulation methods and continuum simulation methods to study ligand-protein encounters and association rate constants will be developed. Second, the new codes will be modified for field programmable gate arrays (FPGAs). Notably, FPGAs are new hardware code accelerators that can largely speedup the calculations. Third, free energy profile of binding pathways, energy barriers and kinetic and thermodynamic properties of ligand-receptor association and dissociation will be computed by several widely used molecular simulation packages and methods to be developed. The PI will integrate the research activities with education at different levels. The training of young scientists, including graduate students, undergraduates, as well as postdoctoral fellows, will be a central focus of the PI's group. The PI strongly encourages undergraduates from underrepresented groups in science to participate in the research. Local high school students will also have the opportunity to gain research experience in the PI's lab through a variety of programs at the PI's institution. The PI will distribute all codes developed in this project.
该奖项是根据2009年美国复苏和再投资法案(公法111 - 5)资助的。配体和蛋白质的结合在生物学中具有根本的重要性,在免疫,代谢,信号传导和认知等多种功能中发挥作用。布朗动力学和连续模拟方法的最新进展为研究生物分子系统中的扩散提供了强有力的工具,但它们大多局限于接近扩散控制一步缔合过程极限的系统。对于更复杂的过程,例如涉及配体和蛋白质的短程相互作用和构象变化的两步缔合过程,现有方法可能不足以可靠地研究缔合途径和预测速率常数。本计画将开发新的电脑模拟工具与理论模型,以研究两步结合的过程。这项工作将在三个综合步骤进行:第一,新的多尺度方法,结合布朗动力学模拟方法和连续模拟方法来研究配体-蛋白质的遭遇和缔合速率常数将被开发。第二,新的代码将被修改为现场可编程门阵列(FPGA)。值得注意的是,FPGA是新的硬件代码加速器,可以大大加快计算速度。第三,结合途径的自由能分布、配体-受体缔合和解离的能垒以及动力学和热力学性质将通过几种广泛使用的分子模拟软件包和待开发的方法来计算。PI将把研究活动与各级教育结合起来。青年科学家的培训,包括研究生,本科生,以及博士后研究员,将是PI小组的中心重点。PI强烈鼓励来自科学界代表性不足群体的本科生参与研究。当地高中学生也将有机会通过PI机构的各种计划在PI的实验室获得研究经验。PI将分发本项目中开发的所有代码。

项目成果

期刊论文数量(0)
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Chia-en Chang其他文献

Chia-en Chang的其他文献

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{{ truncateString('Chia-en Chang', 18)}}的其他基金

Development and Application of Multi-scale Modeling to Biomolecular Association
生物分子关联多尺度建模的发展与应用
  • 批准号:
    1932984
  • 财政年份:
    2019
  • 资助金额:
    $ 35.39万
  • 项目类别:
    Standard Grant
CAREER: Development and Application of Multi-scale Modeling for Biomolecular Association
职业:生物分子关联多尺度模型的开发和应用
  • 批准号:
    1350401
  • 财政年份:
    2014
  • 资助金额:
    $ 35.39万
  • 项目类别:
    Continuing Grant

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