THEORETICAL INVESTIGATIONS OF DNA POLYMERASES

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。子项目及 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。 ErbB家族受体介导的信号传导激活多层网络，介导导致细胞增殖、分化和迁移的关键途径。我们提出的目标是在两个尺度上应用建模工具：（1）原子和显式溶剂化系统的生物分子动力学，伞形采样和自由能扰动，用于在原子分辨率下研究ErbB激酶的调节过程。(2)与ErbB受体内化和运输有关的膜变形的弹性膜模拟。项目一：采用自由能微扰（FEP）模拟研究由于关键残基突变以及由于ErbB 1激酶活性和非活性构象中的配体结合引起的自由能变化。项目二：描绘自由能景观和结构表征的分子途径，描述了野生型ErbB 1和ErbB 4受体酪氨酸激酶二聚体系统的非活性和活性构象之间的过渡。项目三：使用粗粒模型和热力学积分计算中尺度高度弯曲膜中蛋白质介导的膜变形的自由能。模拟研究将与宾夕法尼亚大学马克·莱蒙教授实验室的合作实验协同进行。实验工作将包括X射线晶体学，定点诱变，以及细胞信号分析。

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. ErbB family receptor-mediated signaling activates a multi-layered network mediating crucial pathways leading to cell proliferation, differentiation, and migration. Our proposed objective is to apply modeling tools at two scales: (1) biomolecular dynamics on atomistic and explicitly solvated systems, umbrella sampling, and free energy perturbation, for studying at atomic resolution, the regulatory processes in the ErbB kinases. (2) Elastic membrane simulations of membrane deformations to relate to ErbB receptor internalization and trafficking. Project 1: Employ Free Energy Perturbation (FEP) simulations to study the free energy changes due to mutations of key residues and due to ligand binding in active and inactive conformations of ErbB1 kinase. Project 2: Delineate the free energy landscape and structurally characterize the molecular pathway that describes the transition between the inactive and active conformations in wildtype ErbB1 and ErbB4 receptor tyrosine kinase dimer systems. Project 3: Compute the free energies of protein-mediated membrane deformations in highly curved membranes at the mesoscale using coarse-grained models and thermodynamic integration. The simulation studies will be synergistic with collaborative experiments done in Professor Mark Lemmon's lab at Penn. The experimental work will include X-ray crystallography, site-directed mutagenesis, as well as cellular signaling assays.