Acquisition of Unix Computer Cluster for Molecular Dynamics Simulation Calculations

购置 Unix 计算机集群用于分子动力学模拟计算

• 批准号: 10799081
• 负责人: Bernard MONTGOMERY PETTITT
• 金额: $ 5万
• 依托单位: UNIVERSITY OF TEXAS MED BR GALVESTON
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10799081
• 关键词: Administrative Supplement; Award; Cell physiology; Computing Methodologies; Dependence; Diagnostic; Disease; Funding; Future; Mitochondria; Modeling; Molecular; National Institute of General Medical Sciences; Nucleic Acids; Organelles; Pathologic; Phase Transition; Physical condensation; Physiological; Proteins; Role; Serine; Signal Transduction; Solubility; Study models; Supercomputing; System; Testing; Therapeutic; Thermodynamics; Threonine; Tyrosine; Writing; cluster computing; computer cluster; design; driving force; equipment acquisition; insight; interest; molecular dynamics; nervous system disorder; parent grant; public health relevance; response; therapeutic target

PROJECT SUMMARY In response to NOT-GM-22-017, Notice of Special Interest: Administrative Supplements for Equipment Purchases for Select NIGMS-Funded Awards, we request funds to upgrade our local Unix compute cluster, which was purchased in 2012, with GPU nodes that are needed for the calculations described on the parent grant. Our parent grant aims to understand the formation of non-enveloped organelles and condensates. Many calculations of smaller size arise and are hampered by writing supercomputing proposals. The current nodes are nearly impossible to maintain due to changes in hardware compatibility. Our calculations focus on deciphering the thermodynamic manifold, enthalpic versus entropic driving forces, underlying the solubility limit and consequent phase transition associated with the formation of condensates.1 We also investigate the role of compositional/sequence dependencies and protein disorder2 on the formation and stability of these assemblies. Design of therapeutic targets that promote or inhibit formation of component proteins or nucleic acids in biomolecular condensates requires a detailed understanding of the molecular forces that drive their formation or dissolution. We will consider model mixtures relevant to cell signaling consisting of pentapeptides GGXGG, GGpXGG, and GXGXG systems, where X is serine, threonine, and tyrosine, to model the compositional dependency on condensate formation. We will also study the mitochondrial Cox17 protein where the level of disorder is controlled by physiological conditions.3 This 60 aa protein is an ideal system to test our insights from the small pentapeptide model studies.

项目概要 针对 NOT-GM-22-017，特别关注通知：行政补充 为选择 NIGMS 资助的奖项购买设备，我们请求资金来升级我们本地的 Unix 计算集群，2012年购买，带有计算所需的GPU节点 父母补助金中描述。我们的家长资助旨在了解非包络的形成 细胞器和凝聚物。许多较小规模的计算出现并受到写作的阻碍 超级计算提案。由于变化，当前节点几乎无法维护 硬件兼容性。我们的计算重点是破译热力学流形、焓 与熵驱动力，溶解度极限和随之而来的相变的基础 与冷凝物的形成有关。1我们还研究了 组成/序列依赖性和蛋白质无序2对其形成和稳定性的影响 组件。设计促进或抑制成分蛋白形成的治疗靶点或 生物分子凝聚物中的核酸需要详细了解分子力 推动它们的形成或分解。我们将考虑与细胞信号传导相关的模型混合物 由五肽GGXGG、GGpXGG和GXGXG系统组成，其中X是丝氨酸、苏氨酸， 和酪氨酸，以模拟冷凝物形成的成分依赖性。我们也会学习 线粒体 Cox17 蛋白，其紊乱水平由生理条件控制。3 这种 60 个氨基酸的蛋白质是测试我们从小型五肽模型研究中获得的见解的理想系统。

项目成果

Contributions of higher-order proximal distribution functions to solvent structure around proteins.

高阶近端分布函数对蛋白质周围溶剂结构的贡献。

• 发表时间: 2021-09-14
• 作者: Yousefi, Razie;Lynch, Gillian C;Galbraith, Madeline;Pettitt, B Montgomery
• 通讯作者: Pettitt, B Montgomery

The Effects of Flexibility on dsDNA-dsDNA Interactions.

灵活性对 dsDNA-dsDNA 相互作用的影响。

• 发表时间: 2022-05-07
• 作者: Chen, Chuanying;Pettitt, B Montgomery
• 通讯作者: Pettitt, B Montgomery

Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide.

亲水水合和分子内相互作用在十丙氨酸肽螺旋-螺旋转变和螺旋-螺旋组装的热力学中的重要性。

• 发表时间: 2016-01-14
• 作者: Tomar, Dheeraj S;Weber, Valéry;Pettitt, B Montgomery;Asthagiri, D
• 通讯作者: Asthagiri, D

Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15.

分子内相互作用克服水合作用，驱动 Gly15 的塌陷转变。

• 发表时间: 2017-08-31
• 作者: Asthagiri, D;Karandur, Deepti;Tomar, Dheeraj S;Pettitt, B Montgomery
• 通讯作者: Pettitt, B Montgomery

Mobility of Histidine Side Chains Analyzed with 15N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions.

使用 15N NMR 弛豫和互相关数据分析组氨酸侧链的迁移率：深入了解锌指-DNA 相互作用。

• 发表时间: 2019
• 作者: Kemme, Catherine A;Luu, Ross H;Chen, Chuanying;Pletka, Channing C;Pettitt, B Montgomery;Iwahara, Junji
• 通讯作者: Iwahara, Junji