THE DYNAMICS AND PATHOLOGIES OF MOLECULAR MOTORS

分子马达的动力学和病理学

基本信息

  • 批准号:
    7723365
  • 负责人:
  • 金额:
    $ 0.05万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2008
  • 资助国家:
    美国
  • 起止时间:
    2008-08-01 至 2009-07-31
  • 项目状态:
    已结题

项目摘要

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The realization that many essential functions of living cells are performed by nanoscale motors consisting of protein complexes has given rise to an intense effort to understand their mechanisms. We focus on F1 ATPase and DNA polymerase I, two very different molecular motors of fundamental importance in biology. We propose to perform atomic-scale simulations to obtain information not available from experiment. The research will lead to a deeper understanding of the function of these motors and in the case of DNA polymerase, show how malfunction is prevented. F1 ATPase, the smallest biological rotary motor, is composed of seven units, six of which (alpha3beta3) form a spherical globular construct around a central shaft, the gamma subunit, which rotates 1000/sec as a result of ATP hydrolysis in the catalytic beta subunits; when an applied torque rotates the g subunit in the reverse direction, the motor synthesizes ATP, its normal function in the cell. Our previous studies investigated the pathway of the conformational change and the nature of the mechanical coupling. The essential next step is to evaluate the coupling between the chemical steps (hydrolysis or synthesis of ATP) and the subunit conformations on the rotational pathway. Free energy simulations will be used to find the conformations that favor hydrolysis or synthesis. That such conformations exist is an essential aspect of this remarkable motor, which makes possible efficient synthesis or hydrolysis of ATP, depending on the direction of the rotation of the g subunit. Given these conformations, combined quantum mechanical/molecular mechanical simulations will be performed to evaluate the free energy barrier of the reaction and elucidate the origin of the catalytic rate enhancement. DNA polymerases are responsible for the accurate copying of genetic information from one cell generation to the next. Our previous studies have determined the details of the translocation step, an essential part of the motor function. It occurs after the addition of a base to the primer strand, so as to position the polymerase on the DNA for adding the next base. The results of this analysis will make possible exploration of the mechanism by which mismatches in DNA (i.e., critical errors that can cause cancer) stall DNA replication, a mechanism by which the essential high fidelity is achieved. Known crystal structures of the polymerase I bound to DNA with mismatched bases make possible simulations to determine the effect of these on the translocation step. In addition, based on a new single molecule experiment, the effect of mismatches on slowing the fingers closing transition will be explored. Finally, again using known crystal structures, free energy simulations will be performed to determine the effect of mismatches on the configuration of the active site. The results will complement our analysis of normal DNA replication by providing an understanding of certain pathologies. This is of considerable medical importance, as well being of interest itself and a subject of intense experimental research. Two very different, but important motors are included in the same proposal because the complementarity of the research will make the results all the more meaningful. The research in both areas requires multiple closely related simulations, which can be done most efficiently in parallel. Moreover, since specific details of subsequent calculations depend critically on the previous results, it is essential also to perform these simulations rapidly with fast turn-around. Given the large size of the systems under investigation (on the order of 180,000 particles for F1 ATPase and 140,000 for DNA polymerase I complex), a state-of-the-art supercomputer will be essential not only for large-scale production following the standard paradigm, but also as a research tool intimately coupled to the computational design.
该子项目是利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者(PI)可能从另一个NIH来源获得了主要资金, 因此可以在其他CRISP条目中表示。所列机构为 研究中心,而研究中心不一定是研究者所在的机构。 活细胞的许多基本功能是由蛋白质复合物组成的纳米级马达执行的,这一认识引起了人们对理解其机制的强烈努力。我们专注于F1 ATP酶和DNA聚合酶I,两个非常不同的分子马达在生物学中的根本重要性。我们建议进行原子尺度的模拟,以获得从实验中无法获得的信息。这项研究将导致对这些马达功能的更深入理解,并在DNA聚合酶的情况下,展示如何防止故障。F1 ATP酶是最小的生物旋转马达,由七个单元组成,其中六个(α 3 β 3)形成围绕中心轴的球形球状结构,γ亚基,由于催化β亚基中的ATP水解而以1000/秒的速度旋转;当施加扭矩使g亚基反向旋转时,马达合成ATP,其在细胞中的正常功能。我们以前的研究探讨了构象变化的途径和机械耦合的性质。重要的下一步是评估化学步骤(ATP的水解或合成)和旋转途径上的亚基构象之间的耦合。自由能模拟将被用来找到有利于水解或合成的构象。这种构象的存在是这个非凡马达的一个重要方面,它使ATP的有效合成或水解成为可能,这取决于g亚基的旋转方向。鉴于这些构象,结合量子力学/分子力学模拟将进行评估的自由能垒的反应,并阐明的起源的催化速率增强。DNA聚合酶负责将遗传信息从一代细胞精确复制到下一代细胞。我们以前的研究已经确定了易位步骤的细节,这是运动功能的重要组成部分。它发生在将碱基添加到引物链之后,以便将聚合酶定位在DNA上用于添加下一个碱基。这种分析的结果将使探索DNA中的错配(即,可能导致癌症的关键错误)阻止DNA复制,这是一种实现基本高保真度的机制。已知的聚合酶I的晶体结构与错配碱基的DNA结合,使得可能的模拟,以确定这些对易位步骤的影响。此外,基于一个新的单分子实验,将探讨失配对减慢手指闭合跃迁的影响。最后,再次使用已知的晶体结构,进行自由能模拟以确定错配对活性位点构型的影响。这些结果将通过提供对某些病理的理解来补充我们对正常DNA复制的分析。这是相当重要的医学,以及感兴趣的本身和一个主题的激烈的实验研究。两个非常不同,但重要的发动机被包括在同一提案中,因为研究的互补性将使结果更有意义。这两个领域的研究都需要多个密切相关的模拟,这些模拟可以最有效地并行进行。此外,由于后续计算的具体细节严重依赖于先前的结果,因此也必须快速执行这些模拟。考虑到所研究系统的大尺寸(F1 ATP酶约为180,000个颗粒,DNA聚合酶I复合物约为140,000个颗粒),最先进的超级计算机不仅对于遵循标准范式的大规模生产至关重要,而且还作为与计算设计密切相关的研究工具。

项目成果

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Martin Karplus其他文献

Martin Karplus的其他文献

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{{ truncateString('Martin Karplus', 18)}}的其他基金

Modeling atomic structure of the EmrE multidrug pump to design inhibitor peptides
对 EmrE 多药泵的原子结构进行建模以设计抑制剂肽
  • 批准号:
    8839204
  • 财政年份:
    2014
  • 资助金额:
    $ 0.05万
  • 项目类别:
Modeling atomic structure of the EmrE multidrug pump to design inhibitor peptides
对 EmrE 多药泵的原子结构进行建模以设计抑制剂肽
  • 批准号:
    8681706
  • 财政年份:
    2014
  • 资助金额:
    $ 0.05万
  • 项目类别:
THE DYNAMICS AND PATHOLOGIES OF MOLECULAR MOTORS
分子马达的动力学和病理学
  • 批准号:
    7956224
  • 财政年份:
    2009
  • 资助金额:
    $ 0.05万
  • 项目类别:
SIMULATIONS OF BIOMOLECULES
生物分子模拟
  • 批准号:
    6411718
  • 财政年份:
    2000
  • 资助金额:
    $ 0.05万
  • 项目类别:
CONFORMATIONAL ANALYSIS OF RAS P21
RAS P21 的构象分析
  • 批准号:
    6221127
  • 财政年份:
    1999
  • 资助金额:
    $ 0.05万
  • 项目类别:
SIMULATIONS OF BIOMOLECULES
生物分子模拟
  • 批准号:
    6309539
  • 财政年份:
    1999
  • 资助金额:
    $ 0.05万
  • 项目类别:
SIMULATIONS OF BIOMOLECULES
生物分子模拟
  • 批准号:
    6319796
  • 财政年份:
    1999
  • 资助金额:
    $ 0.05万
  • 项目类别:
SIMULATION OF REACTION MECHANISM OF HAMMERHEAD RIBOZYME
锤头核酶反应机理的模拟
  • 批准号:
    6319770
  • 财政年份:
    1999
  • 资助金额:
    $ 0.05万
  • 项目类别:
SIMULATION OF PROTEIN FOLDING INTERMEDIATES USING MOLECULAR DYNAMICS
使用分子动力学模拟蛋白质折叠中间体
  • 批准号:
    6221121
  • 财政年份:
    1999
  • 资助金额:
    $ 0.05万
  • 项目类别:
SIMULATION OF BIOMOLECULES
生物分子模拟
  • 批准号:
    6295155
  • 财政年份:
    1998
  • 资助金额:
    $ 0.05万
  • 项目类别:
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