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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

基本信息

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
项目类别：
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

项目摘要

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.

项目摘要针对NOT-GM-22-017，特别关注通知：设备购买选择NIGMS资助的奖项，我们要求资金升级我们的本地Unix 计算集群，于2012年购买，具有计算所需的GPU节点在父母补助金上描述。我们的父母补助金旨在了解非包膜的形成细胞器和冷凝物。许多较小规模的计算出现，并受到写作的阻碍超级计算机的提案当前节点几乎不可能维护，因为硬件兼容性我们的计算重点是破译热力学流形，相对于熵驱动力，潜在的溶解度极限和随之而来的相变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紊乱2对这些的形成和稳定性的影响组件.设计促进或抑制组分蛋白质形成的治疗靶标，或生物分子凝聚物中的核酸需要对分子力有详细的了解驱动它们形成或分解的机制我们将考虑与细胞信号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，以模拟对冷凝物形成的组成依赖性。我们还将研究线粒体Cox 17蛋白，其中紊乱水平由生理条件控制。这60个氨基酸的蛋白质是一个理想的系统，以测试我们的见解，从小五肽模型研究。

项目成果

期刊论文数量（90）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace.

DOI：
10.1080/08927022.2015.1110583
发表时间：
2016
期刊：
Molecular simulation
影响因子：
2.1
作者：
Zhang C;Lai CL;Pettitt BM
通讯作者：
Pettitt BM

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。

DOI：
10.1021/acs.jpcb.9b03132
发表时间：
2019
期刊：
The journal of physical chemistry. B
影响因子：
0
作者：
Kemme,CatherineA;Luu,RossH;Chen,Chuanying;Pletka,ChanningC;Pettitt,BMontgomery;Iwahara,Junji
通讯作者：
Iwahara,Junji

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。