Theory and Modeling of Biomolecules and their Interactions - Equipment Supplement

生物分子及其相互作用的理论和建模 - 设备补充

基本信息

批准号：
10580491
负责人：
CHARLES L BROOKS
金额：
$ 22.1万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-02-01 至 2024-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10580491
关键词：
Acids Actin-Binding Protein Address Aging Area Award Big Data Biological Biomedical Research CREBBP gene Chemicals Collaborations Communities Computational algorithm Computer Simulation Computer software Development Docking Environment Enzymes Equilibrium Equipment Evolution Fibroblast Growth Factor Flavins Free Energy GTP-Binding Proteins Genetic Transcription Goals Homologous Protein Interleukins Ligand Binding Ligands Longevity MED25 gene Malignant Neoplasms Maps Mediating Mediation Menin Methodology Methods Mixed Function Oxygenases Modeling Molecular Pharmaceutical Preparations Pharmacologic Substance Phosphotransferases Process Productivity Proteins Protocols documentation Research Signal Transduction Statistical Mechanics Structure Testing Thermodynamics Transcriptional Activation Update Work algorithm development base computational platform computer infrastructure design innovation insight instrumentation interdisciplinary approach models and simulation molecular dynamics novel protonation receptor sensor simulation small molecule software development software infrastructure theories tool

项目摘要

Project Summary/Abstract The establishment of tools from statistical mechanics and computer simulation that enable the exploration of biological molecules and their interactions are central to discovery within biomedical research. This proposal supports ongoing efforts in this area, addressing challenges in theory and modeling, as well as strategically chosen collaborations on important biomedical questions that provide crucial tests of the approaches. Our development efforts include the exploration of receptor-ligand interactions and the thermodynamics of ligand binding to biological receptors through the development and application of novel methods of free energy simulations, docking and receptor-ligand interaction modeling. The continued refinement, hardening and application of methods of constant pH molecular dynamics to integrate the critical aspects of pH and protonation state changes in biomolecules and their ligands in molecular simulations and modeling is also part of ongoing work. Finally, software infrastructure, specifically the CHARMM simulation package, provides the framework for advancing our methodological approaches and enabling the broader community to explore biomedically motivated questions via its wide usage and distribution. We will continue the innovative implementation of methods and simulation approaches into this community standard software package. We will balance and drive our development efforts in the areas of free energy simulations, ligand – receptor docking and pH-mediated structure-function processes through strategic collaborations with experimental colleagues in the areas of: transcriptional activation based on small amphipathic molecules targeting co-activators from the CREB binding protein (KIX) and the AciD domain of Med25; key cancer targets such as menin-MLL; enzyme redesign and substrate scope expansion to better understand the evolution of function of a novel Flavin-dependent hydroxylase for chemical transformations important in the development of pharmaceuticals; pH-regulated sensors in kinase signaling associated with the G-protein from the tetrameric Gai protein; the pH-modulated switch for myristoylated histactophilin, an actin binding protein homolog with interleukin-1b and fibroblast growth factor. Finally, we will engage developers of big data applications of molecular simulations and the design and execution of robust user APIs to work with us toward advancing software development for large multi-scale simulations of cellular environments and automated workflows, through CHARMM-GUI, for simulation protocols. This requested supplement provides a critical update to the computational infrastructure needed for the developments and applications proposed as part of our R35 award. We have made significant efforts to map computational algorithms onto accelerated computing platforms (GPUs) and the proposed instrumentation will enable access to the latest of these platforms, replacing standard CPU and aging GPU platforms that are beyond their useful lifespan, thus facilitating the productivity of algorithm development and key biomedical applications.

项目概要/摘要建立统计力学和计算机模拟工具，使人们能够探索生物分子及其相互作用是生物医学研究发现的核心。支持该领域的持续努力，解决理论和建模以及战略方面的挑战选择在重要的生物医学问题上进行合作，为这些方法提供关键的测试。开发工作包括探索受体-配体相互作用和配体的热力学通过开发和应用新的自由能方法与生物受体结合模拟、对接和受体-配体相互作用建模。应用恒定 pH 分子动力学方法整合 pH 和质子化的关键方面分子模拟和建模中生物分子及其配体的状态变化也是正在进行的一部分最后，软件基础设施，特别是 CHARMM 仿真包，提供了框架。推进我们的方法论并使更广泛的社区能够探索生物医学通过其广泛使用和分发激发的问题我们将继续创新实施。我们将平衡和推动这个社区标准软件包的方法和模拟方法。我们在自由能模拟、配体-受体对接和 pH 介导领域的开发工作通过与实验同事在以下领域的战略合作来实现结构-功能过程：基于针对 CREB 结合的共激活剂的小两亲分子的转录激活蛋白质 (KIX) 和 Med25 的 AciD 结构域；例如 menin-MLL 酶重新设计和底物范围扩展，以更好地了解新型黄素依赖性功能的演变用于化学转化的羟化酶对于 pH 调节药物的开发非常重要；与四聚体 Gai 蛋白的 G 蛋白相关的激酶信号转导传感器；切换为肉豆蔻酰化亲组蛋白，一种与白细胞介素 1b 和成纤维细胞生长相关的肌动蛋白结合蛋白同源物最后，我们将聘请分子模拟和设计的大数据应用开发人员。执行强大的用户 API，与我们合作推进大型多尺度软件开发通过 CHARMM-GUI 模拟细胞环境和自动化工作流程，用于模拟协议。此请求的补充提供了对计算基础设施所需的关键更新作为 R35 奖项的一部分提出的开发和应用，我们在绘制地图方面付出了巨大的努力。加速计算平台（GPU）上的计算算法和所提出的仪器将允许访问最新的这些平台，取代超出标准的 CPU 和老化的 GPU 平台它们的使用寿命，从而提高算法开发和关键生物医学应用的生产力。