COMPUTATION OF THE TWO-DIMENSIONAL POTENTIAL OF MEAN FORCE SURFACE OF AQUIFEX A

AQUIFEX A 平均力面二维势的计算

• 批准号: 7956231
• 负责人: MING LEI
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956231
• 关键词: Algorithms; Binding; Biomedical Research; Catalysis; Chemicals; Computer Retrieval of Information on Scientific Projects Database; Enzymes; Free Energy; Funding; Goals; Grant; High Performance Computing; Homologous Gene; Institution; Ligands; Maps; Methods; Molecular Conformation; Motion; Mutagenesis; Mutation; Protocols documentation; Reaction; Research; Research Personnel; Resources; Sampling; Simulate; Source; Structure; Surface; United States National Institutes of Health; Weight; Work; adenylate kinase; base; conformational conversion; inhibitor/antagonist; inorganic phosphate; simulation; two-dimensional

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. Adenylate kinase (AK) catalyzes the transfer of one phosphate group from ATP to AMP, producing two ADP as end products. Previously, the Kern's group determined that the conformational transition between the open and the closed states, rather than the chemical catalysis, is the rate limiting step of the reaction. Our main goal of this project is to determine the transition state structure(s) between the two states. The enzyme is made up of three domains: the core, the ATP and the AMP lid. In our previous work we have simulated Aquifex aeolicus adenylate kinase (AAK) in its ligand free form and in its inhibitor bound form. In both simulations, the motion of the ATP lid is independent of the motion of the AMP lid. Therefore a two-dimensional (2D) potential of mean force (PMF) computation is necessary to map the free energy landscape of the enzyme, rather than the one dimensional PMF computations carried out by other groups on AK homologues. Based on our previous simulation work, we have defined two geometrical angles between the centers of mass of selected groups of residues to be the two reaction coordinates. We have used the umbrella sampling algorithm to sample the conformations at some of the grid points between the two states. We need more CPU power to finish the simulations on the remaining grid points, and also to extend the trajectories on the grid points that are already sampled. Once all these simulations are completed, we will use weighted histogram analysis method (WHAM) to construct the 2D PMF surface. From the 2D PMF surface, we will first compute the free energy difference between the open and the closed states. Such a value has been experimentally determined by Kern's group. A direct comparison between the computed and the experimental values will be used to justify the computation protocol. We will also pinpoint the transition state structure(s), and the key interactions present in the transition state structure(s) and not in either the open or the closed state. We will then predict the mutations of which residues influence the transition rate between the two states. These predictions can then be further testified by experimental mutagenesis studies.

这个子项目是许多研究子项目中的一个 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。 腺苷酸激酶（AK）催化一个磷酸基团从ATP转移到AMP，产生两个ADP作为终产物。以前，克恩小组确定，开放和封闭状态之间的构象转变，而不是化学催化，是反应的速率限制步骤。我们这个项目的主要目标是确定两个状态之间的过渡态结构。该酶由三个结构域组成：核心，ATP和AMP盖子。在我们以前的工作中，我们模拟了风产液菌腺苷酸激酶（AAK）在其配体的自由形式和在其抑制剂结合的形式。在两个模拟中，ATP盖的运动独立于AMP盖的运动。因此，二维（2D）的平均力（PMF）计算的潜力是必要的映射的自由能景观的酶，而不是一维的PMF计算进行的AK同系物。基于我们以前的模拟工作，我们已经定义了两个几何角度之间的质量中心的选定组的残基的两个反应坐标。我们已经使用了伞形采样算法来采样两个状态之间的一些网格点处的构象。我们需要更多的CPU能力来完成剩余网格点上的模拟，并扩展已经采样的网格点上的轨迹。一旦所有这些模拟完成后，我们将使用加权直方图分析方法（WHAM）来构建二维PMF表面。从2D PMF表面，我们将首先计算开态和闭态之间的自由能差。这个值是由克恩小组通过实验确定的。计算值和实验值之间的直接比较将用于证明计算协议。我们还将查明过渡态结构，以及过渡态结构中存在的关键相互作用，而不是开放或封闭状态。然后我们将预测哪些残基的突变会影响两种状态之间的转变速率。这些预测，然后可以进一步证实实验诱变研究。