Understanding the role of membrane environment on membrane protein association and function

膜蛋白是细胞的守门人，在大多数生物功能中起着密切的作用。对膜环境如何调节膜蛋白结合的详细分子描述将为与生物医学、制药和太阳能收集等领域相关的生物过程提供基本见解。计算建模方法将被用来确定细胞膜对膜蛋白结合的影响。计算建模的优点是它可以表征膜蛋白的结合和解离动力学。本文研究的膜蛋白是海洋生态系统中微生物共同存在的蛋白质——变形紫红质（PR）。PR对这些微生物的生存至关重要，它们在碳循环中的作用可能直接影响海洋适应大气环境波动的能力。本项目旨在模拟改变细胞膜组成对PR功能及其与多组分复合物结合的影响。研究结果将有助于生物物理学界理解细胞膜环境与蛋白质功能之间的关系。除了培训研究生和本科生外，拟议的研究还将涉及西弗吉尼亚州主要本科院校的教授和学生。这些学生来自阿巴拉契亚地区，这是一个传统上在STEM领域代表性不足的地区。因此，该项目将建立长期关系，以增加学生对科学研究的参与，并鼓励他们在STEM领域从事职业。本项目的具体目标是表征变形紫质中质子泵浦的结构-功能关系，鉴定该蛋白寡聚过程中关键单体-单体相互作用，以及确定膜环境与寡聚之间的关系。几个分子动力学（MD）模拟方法将用于追求每个目标。确定PR活化的构象变化将阐明质子泵是如何发生的。表征膜组成与低聚化之间的关系将调和关于天然和非天然膜环境中PR低聚化的相互矛盾的假设。这也将有助于了解膜蛋白在诸如细菌内膜等系统中的相互作用。所获得的见解将为解释和设计洗涤剂膜蛋白实验提供一个总体框架，因为洗涤剂增溶是这些研究的实际方法。

Membrane proteins act as the gatekeepers of the cell, playing an intimate role in most biological functions. A detailed molecular description of how the membrane environment modulates association of membrane proteins will provide fundamental insights into biological processes that are linked to fields such as biomedicine, pharmaceuticals, and solar energy harvesting. Computational modeling approaches will be utilized to determine the effect of the cellular membrane on the association of membrane proteins. The advantage of computational modeling is that it can characterize the dynamics of association and dissociation of membrane proteins. The membrane protein to be studied is proteorhodopsin (PR), a protein common to microbial life in marine ecosystems. PR is a critical to survival of these microbes and their role in the carbon cycle may directly affect the ability of the ocean to accommodate fluctuations in the atmospheric environment. This project aims to model the effects of changing cell membrane composition on the function of PR and its association into multi-component complexes. Results will aid the biophysics community in their understanding of the relationship between cell membrane environment and protein function. In addition to training graduate and undergraduate students, the proposed research will involve professors and students from primarily undergraduate institutions in West Virginia. These students are from Appalachia, a traditionally underrepresented region in STEM fields. Thus, this project will develop long-term relationships for increasing student involvement in scientific research and encourage them to pursue careers in STEM fields.The specific objectives of this project are the characterization of the structure-function relationship of proton pumping in proteorhodopsin, the identification of key monomer-monomer interactions during oligomerization of this protein, and, determination of the relationship between membrane environment and oligomerization. Several molecular dynamics (MD) simulation approaches will be used to pursue each objective. Determination of conformational changes in PR activation will elucidate how proton pumping occurs. Characterization of the relationship between membrane composition and oligomerization will reconcile conflicting hypotheses on oligomerization of PR in native-like and non-native membrane environments. This will also contribute to knowledge of membrane protein interactions in systems such as bacterial inner membranes. Insights obtained will provide a general framework for interpretation and design of detergent-membrane protein experiments, since detergent solubilization is the de facto method for these studies.