THEORETICAL INVESTIGATIONS OF DNA POLYMERASES

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 ErbB家族受体介导的信号激活了一个多层网络，介导了导致细胞增殖、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、伞形采样和自由能微扰，用于在原子分辨率下研究ErbB激酶的调节过程。(2)与ErbB受体内化和转运有关的膜变形的弹性膜模拟。项目1：利用自由能微扰(FEP)模拟来研究ErbB1激酶活性构象和非活性构象中关键残基突变和配体结合引起的自由能变化。项目2：描绘自由能格局并从结构上描述描述野生型ErbB1和ErbB4受体酪氨酸激酶二聚体系统中非活性构象和活性构象之间转换的分子途径。项目3：使用粗粒模型和热力学积分，在中尺度上计算高度弯曲膜中蛋白质介导膜变形的自由能。模拟研究将与在宾夕法尼亚大学马克·莱蒙教授的实验室进行的合作实验协同进行。实验工作将包括X射线结晶学、定点突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. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.