TARGETING PROTEIN INTERACTIONS AND DESIGNING CHIMERIC PROTEINS

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 开发治疗药物以破坏癌症途径中的蛋白质-蛋白质相互作用和细菌毒力是基于结构的药物设计中的一个新兴战略。提出了一种系统的方法来1)识别蛋白质-蛋白质界面的热点残基；2)评估可能针对这样的界面的潜在化合物的数据库。管道的第一阶段利用分子动力学结合泊松-玻尔兹曼表面积计算(MM/PBSA)来确定界面上的临界残留物。管道的第二阶段应用虚拟对接技术，从现成的独特化合物的大型数据库中筛选候选抑制剂。管道的最后阶段使用热力学背景下的MM/PBSA技术，以进一步评估作为铅抑制剂的选定候选对象。部分管道的初步测试和应用取得了良好的结果，并为进一步测试、开发和应用ErbB受体和细菌双组分Phop系统提供了动力。我们要求计算能力来促进我们的研究，因为这些计算的密集性质。设计能够抵抗热变性和蛋白质降解的蛋白质是一个具有挑战性的问题。在自然界中，蛋白质序列仅限于天然产生的20种氨基酸及其翻译后修饰的组合。结合非天然氨基酸和半刚性多肽仿制技术为设计采用稳定的预定折叠的蛋白质提供了独特的可能性，使蛋白质工程成为现实。我们需要计算资源来研究预组织在提高蛋白质热稳定性中的作用。我们最初对一个28个残基的蛋白质进行的分子动力学模拟表明，经典的MD模拟缺乏做出有意义的熔化温度预测所需的样本。我们建议使用副本交换分子动力学模拟来加强采样，并生成系综轨迹，用于分析系统的温度依赖行为。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Developing therapeutics to disrupt protein-protein interactions in cancer pathways and bacterial virulence is an emerging strategy in structure-based drug design. A systematic method is proposed to 1) identify hot-spot residues an protein-protein interface; 2) evaluate a database of potential compounds that may target such an interface. The first stage of the pipeline utilizes molecular dynamics in combination with Poisson-Boltzmann surface area calculations (MM/PBSA) to identify critical residues at the interface. The second stage of the pipeline applies virtual docking techniques to screen for candidate inhibitors from a large database of unique compounds that are readily available. The last stage of the pipeline uses the MM/PBSA technique in a thermodynamic context to further evaluate the selected candidates as lead inhibitors. Preliminary testing and application of parts of the pipeline yielded promising results and provided motivations to further test, develop, and apply the pipeline on the ErbB receptors and the bacterial two-component PhoP system. We are requesting computational power to facilitate in our research because the intensive nature of these calculations. Designing proteins that are resistant to thermal denaturation and proteolytic degradation is a challenging problem. In nature, protein sequences are limited to combinations of the naturally occurring 20 amino acids and their post-translational modifications. Incorporation of non-natural amino acids and semi-rigid peptidomimetics provides unique possibilities for designing proteins that adopt a stable predetermined fold, allowing protein engineering to become a reality. We are request computational resources to study the role of pre-organization in enhancing the thermal stability of proteins. Our initial molecular dynamics simulations on a 28-residue protein shows than classical MD simulations lack the sampling required to make meaningful predictions of melting temperature. We proposed to use replica exchange molecular dynamics simulations to enhance sampling and to generate an ensemble trajectories that will be analyzed for temperature dependent behavior of the system.