RESTMD-CHARMM simulation of the Chk2/PP2A interaction in DNA repair

DNA 修复中 Chk2/PP2A 相互作用的 RESTMD-CHARMM 模拟

• 批准号: 7927089
• 负责人: Shanadeen C Begay
• 金额: $ 3.69万
• 依托单位: BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7927089
• 关键词: Acids; Advanced Malignant Neoplasm; Algorithms; Amino Acids; Benchmarking; Binding; Boston; CHEK2 gene; Cancer Center; Chemistry; Collaborations; Communities; Complex; DNA Damage; DNA Repair; Data; Dissociation; Effectiveness; Genetic Processes; Goals; Laboratories; Maps; Mechanics; Mediating; Modeling; Molecular; Molecular Biology; Mutation; National Cancer Institute; Phosphoric Monoester Hydrolases; Phosphorylation; Predisposition; Protein phosphatase; Research; Research Institute; Sampling; Signal Transduction; Simulate; Strategic Planning; Temperature; Testing; Universities; base; cancer care; computational chemistry; human CHEK1 protein; insight; malignant breast neoplasm; molecular dynamics; response; simulation; therapeutic target

DESCRIPTION (provided by applicant): The goal of this project is to simulate conformational changes caused by phosporylation during the interaction of cell cycle checkpoint kinase, CHK2), with Protein Phosphatase 2A (PP2A) to elucidate signaling mechanisms during the DMA damage response. The research may identify therapeutic targets as outlined in the National Cancer Institute Strategic Plan. This interdisciplinary project is a collaboration between the Keyes laboratory, Boston University (computational chemistry) and the Monteiro laboratory, H. Lee Moffitt Cancer Center & Research Institute (molecular biology). The project has four specific aims. Aim 1 - Formulate, implement, and build a robust algorithm to sample the binding energy landscape of CHK2 and PP2A (Year 1). The Replica Exchange Statistical Temperature Molecular Dynamics (RESTMD) algorithm, which was derived in the Keyes laboratory, will be integrated into the Chemistry at HARvard Macromolecular Mechanics (CHARMM) package by adapting the original replica exchange module (Dr. Robert Best, University of Cambridge). To ascertain effectiveness, the RESTMD-CHARMM will be benchmarked against other sampling algorithms. Aim 2 - Model CHK2's SQ/TQ region (Years 2&3). Using RESTMD-CHARMM, the CHK2's unstructured domain will be modeled to determine the structural basis of the CHK2-PP2A interaction. The final package, data, and results will be made widely available to the biophysical community. Aim 3 - Identify the ammo acid residues of PP2A B' that mediate the interaction (Years 2&3). A large region of PP2A B'a (aa89-322) has been experimentally determined as the minimal binding region to CHK2. In order to narrow down the residues in binding, we will perform molecular dynamic analysis to generate a prediction of the amino acid residues involved. We will validate the prediction of the minimal region by experimentally testing mutations of the target amino acid residues. Aim 4 - Simulate the molecular binding of CHK2 and PP2A to determine the extent to which DNA damage-induced phosphorylation modulates complex formation and dissociation (Year 3). The CHK2-PP2A complex dissociates following DNA damage. Using the RESTMD-CHARMM package, the CHK2-PP2A energy landscape will be mapped. The molecular dynamics simulation will be compared to experimental data provided by the Monteiro laboratory. This research will advance cancer care by providing unprecedented insights into the fundamental genetic processes and determinants of breast cancer susceptibility.

描述（由申请人提供）：本项目的目标是模拟细胞周期检查点激酶（CHK 2）与蛋白磷酸酶2A（PP 2A）相互作用期间磷酸化引起的构象变化，以阐明DMA损伤反应期间的信号传导机制。这项研究可能会确定国家癌症研究所战略计划中概述的治疗靶点。这个跨学科的项目是波士顿大学凯斯实验室（计算化学）和蒙泰罗实验室，H。Lee Moffitt癌症中心和研究所（分子生物学）。该项目有四个具体目标。目标1 -制定，实施和构建一个强大的算法来采样CHK 2和PP 2A的结合能景观（第1年）。在Keyes实验室中推导出的交换温度统计分子动力学（RESTMD）算法将通过调整原始的复制交换模块（剑桥大学的Robert Best博士）集成到哈佛大学化学大分子力学（CHARMM）软件包中。为了确定有效性，将根据其他抽样算法对RESTMD-CHARMM进行基准测试。目标2 -CHK 2型的SQ/TQ区域（第2年和第3年）。使用RESTMD-CHARMM，将对CHK 2的非结构化结构域进行建模，以确定CHK 2-PP 2A相互作用的结构基础。最终的数据包、数据和结果将广泛提供给生物物理界。目的3 -鉴定介导相互作用的PP 2 A B'的氨基酸残基（第2年和第3年）。PP 2A B 'a（aa 89 -322）的大区域已通过实验确定为与CHK 2的最小结合区域。为了缩小结合中的残基，我们将进行分子动力学分析以预测所涉及的氨基酸残基。我们将通过实验测试目标氨基酸残基的突变来验证最小区域的预测。目的4 -模拟CHK 2和PP 2A的分子结合，以确定DNA损伤诱导的磷酸化调节复合物形成和解离的程度（第3年）。CHK 2-PP 2A复合物在DNA损伤后解离。使用RESTMD-CHARMM包，将绘制CHK 2-PP 2A能源景观。分子动力学模拟将与蒙泰罗实验室提供的实验数据进行比较。这项研究将通过对乳腺癌易感性的基本遗传过程和决定因素提供前所未有的见解来推进癌症护理。