Acquisition of Unix Computer Cluster for Molecular Dynamics Simulation Calculations

项目总结 针对NOT-GM-22-017，特别关注通知：行政补编 为精选NIGMS资助的奖项购买设备，我们申请资金来升级我们的本地Unix 2012年购买的计算群集，以及计算所需的GPU节点 家长奖助金上的描述。我们的家长助学金旨在理解非封闭式的形成 细胞器和凝集物。许多较小规模的计算都会出现，并因写入而受到阻碍 超级计算提案。由于中的更改，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，热焓 与熵驱动力的对比，溶解极限和相变的基础 与凝聚体的形成有关。1我们还研究了 组成/序列依赖性和蛋白质无序性2对这些蛋白的形成和稳定性的影响 装配。设计治疗靶点，促进或抑制组成蛋白或 生物分子凝聚体中的核酸需要详细了解分子作用力 驱动它们形成或溶解的物质。我们将考虑与细胞信号传递相关的混合模型 由五肽GGXGG、GGpXGG和GXGXG组成，其中X是丝氨酸、苏氨酸、 和酪氨酸，以模拟凝析油形成的组成依赖关系。我们还将研究 线粒体Cox17蛋白，其紊乱程度由生理条件控制。 这种60aa蛋白质是测试我们从小五肽模型研究中获得的洞察力的理想系统。

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.