THEORETICAL INVESTIGATIONS OF DNA POLYMERASES

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。 ERb受体家族激活了一个多层网络，介导了细胞增殖、分化、迁移和新陈代谢的关键途径，以响应许多相关的激活生长因子。因此，从分子的角度定量描述受体的激活，以及网络中蛋白质-蛋白质相互作用产生的信号转导，对于确定抑制剂敏感性和耐药性的来源都是必不可少的。配体诱导的胞外区二聚化和激活的过程现在已经很清楚了。这种配体诱导的二聚化事件是如何偶联并导致细胞内酪氨酸激酶域的激活的，最近的研究才出现。在我们的实验室，我们建议进行多尺度模拟，以帮助确定ERb家族RTK的药物敏感性突变的作用、原因和意义。我们试图通过计算研究Erb RTK的激活模式，以及突变场景如何改变激活机制。因此，我们的结果将有助于识别结构性活性突变，并将有助于制定一种范式，以了解ERb家族RTK对小分子抑制剂的依赖(和敏感性)。我们的研究结果将对小分子治疗抑制策略的优化产生重大影响。主要目标是描绘自由能格局和结构特征，描述在完全原子化、显式溶剂化的野生型ErbB1(EGFR)受体酪氨酸激酶(RTK)二聚体系统中描述非活性构象和活性构象之间转换的分子途径，并研究随后ErbB1催化底物酪氨酸磷酸化的途径。我们提出的工作分为四个项目：(A)经典MD项目，(B)伞采样项目，(C)过渡路径采样项目，和(D)QMMM模拟项目。模拟结果将通过与宾夕法尼亚大学Mark Lemmon实验室的合作得到验证，方法是通过计算识别对所描述的分子途径至关重要的新突变，并验证它们在细胞实验中的作用。

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. The Erb family of receptors activates a multi-layered network mediating crucial pathways leading to cell proliferation, differentiation, migration, and metabolism, in response to many related activating growth factors. Thus, a quantitative description of the receptor activation from a molecular perspective, as well as the signal transduction resulting form protein-protein interactions in networks, are both essential to pin-down the origin of inhibitor sensitivity and drug resistance. The process of ligand-induced dimerization and activation of the extracellular domain is now well understood. Precisely how this ligand-induced dimerization event is coupled to, and leads to, activation of the intracellular tyrosine kinase domain is only now emerging from recent studies. In our laboratory, we propose to carry out multiscale simulations to help identify the role, cause, and significance of drug sensitizing mutations of the Erb family RTKs. We seek to computationally study the modes of activation of Erb RTKs, and how the mutation landscape alters the activation mechanism. Our results will thus serve to identify constitutively active mutants, and will help formulate a paradigm to understand the Erb family RTK dependence (and sensitivity) to small molecule inhibitors. The outcome of our studies will significantly impact the optimization of small molecule therapeutic inhibition strategies. The overarching goal is to delineate the free energy landscape and structurally characterize the molecular pathway that describes the transition between the inactive and active conformations in a fully atomistic, explicitly solvated wildtype ErbB1 (EGFR) receptor tyrosine kinase (RTK) dimer system and to study the pathway for the subsequent ErbB1 catalyzed phosphorylation of substrate tyrosines. Our proposed efforts are categorized into four projects: Project (a) Classical MD, Project (b) Umbrella Sampling, Project (c) Transition Path Sampling, and Project (d) QMMM Simulations. The simulation results will be validated through a collaboration with Mark Lemmon's lab at Penn by computationally identifying new mutations that are crucial to the delineated molecular pathway and verifying their role in the cellular experiments.