TARGETING PROTEIN INTERACTIONS AND DESIGNING CHIMERIC PROTEINS

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 开发治疗药物来破坏癌症途径和细菌毒力中的蛋白质-蛋白质相互作用是基于结构的药物设计中的新兴策略。提出了一种系统的方法，以1）确定热点残基的蛋白质-蛋白质界面; 2）评估数据库的潜在化合物，可能靶向这样的接口。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），以确定在界面上的关键残留物。管道的第二阶段应用虚拟对接技术，从一个易于获得的独特化合物的大型数据库中筛选候选抑制剂。管道的最后阶段在热力学背景下使用MM/PBSA技术，以进一步评估所选候选物作为铅抑制剂。部分管道的初步测试和应用取得了令人鼓舞的结果，并为进一步测试，开发和应用ErbB受体和细菌双组分PhoP系统的管道提供了动力。我们要求计算能力，以促进我们的研究，因为这些计算的密集性。设计耐热变性和蛋白水解降解的蛋白质是一个具有挑战性的问题。在自然界中，蛋白质序列限于天然存在的20个氨基酸及其翻译后修饰的组合。非天然氨基酸和半刚性肽模拟物的掺入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，从而使蛋白质工程成为现实。我们正在请求计算资源来研究预组织在增强蛋白质热稳定性中的作用。我们最初的28个残基的蛋白质的分子动力学模拟显示，比经典的MD模拟缺乏所需的采样，使有意义的预测熔化温度。我们建议使用副本交换分子动力学模拟，以提高采样，并产生一个合奏轨迹，将分析系统的温度依赖性行为。

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.