RUI: Atomistic Modeling of Membrane Proteins

标题：RUI：膜蛋白的原子建模许多蛋白质在细胞膜环境中发挥其功能。在这个项目中，研究者将使用计算机建模来检查脂质对细胞膜内蛋白质结构和相互作用的影响。这项工作的重点是视紫红质，这种蛋白质参与了视觉过程的第一步，也是一类重要的膜蛋白的模型。本项目将对本科生进行培训。除了学习计算机模拟方法外，学生还将向校园社区以及国家和地区科学会议展示他们的成果。这些演讲将为他们作为科学研究人员的职业生涯做好准备，并将为未来的科学专业学生展示令人兴奋的机会。通过将分子建模技术从研究实验室转移到化学课程，在本科教学期间，该机构的所有科学专业都将受到影响。本研究的主要研究工具是分子动力学（MD）计算机模拟。具体项目包括：(1)研究脂质介导的蛋白质-蛋白质相互作用作为脂质类型的功能，重点是多不饱和；(2)从结构、动力学和热力学参数方面表征与跨膜蛋白相关的脂质环；(3)研究视黄质-视蛋白相互作用作为视紫红质光循环的功能，以了解蛋白质和配体之间的相互控制程度；(4)改进改良视网膜配体的CHARMM力场，以支持其激动剂作用的研究。该项目由生物科学理事会分子和细胞生物科学部的分子生物物理集群和数学与物理科学理事会化学部的化学理论、模型和计算方法项目共同资助。

Title: RUI: Atomistic Modeling of Membrane ProteinsMany proteins carry out their function within the environment of the cellular membrane. In this project, the investigator will use computer modeling to examine the effect of lipids on the structure and interactions of proteins contained within the cellular membrane. The membrane protein that will be the focus of this work is Rhodopsin, the protein involved in the first steps of the vision process and one that serves as a model for an important class of membrane proteins. Undergraduate students will be trained in this project. In addition to learning computer simulation methods, students will present their results to the campus community and at national and regional scientific meetings. These presentations will prepare them for careers as scientific researchers and will demonstrate exciting opportunities available to prospective science majors. All science majors at the institution will be impacted during undergraduate instruction through the transfer of molecular modeling techniques from the research laboratory to the chemistry curriculum.The primary research tool for this investigation is molecular dynamics (MD) computer simulation. Specific projects include: (1) studies of lipid mediated protein-protein interaction as a function of lipid type with a focus on polyunsaturation, (2) characterization of the annulus of lipids associated with transmembrane proteins in terms of structural, dynamic, and thermodynamic parameters, (3) investigation of retinal-opsin interactions as a function of the Rhodopsin photocycle to understand the extent of reciprocal control between protein and ligand, and (4) refinement of the CHARMM force field for modified retinal ligands to support investigations of their role as agonists. This project is jointly funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Chemical Theory, Models and Computational Methods Program in the Division of Chemistry in the Directorate of Mathematical and Physical Sciences.