Biophysical Effects of Reversible Lipid Modification of Integral Membrane Proteins

越来越多的证据表明，整体膜蛋白（约占人体蛋白质的30%）通过脂质修饰来维持其健康的生物学功能。然而，脂化如何调节膜蛋白的功能尚不清楚。本项目将揭示脂质修饰对这些整体膜蛋白的影响。利用计算机建模和模拟，该项目将研究由于脂质附着而导致的蛋白质结构变化。该项目还将研究该蛋白与其他整体膜蛋白的相互作用，以及在存在和不存在附着脂质的情况下其生物活性的变化。该项目涉及多个学科的概念，包括化学、生物、物理、数学和计算机科学，为培养不同学术背景的学生提供了一个极好的机会。该项目将通过基于队列的方法为本科生提供科学培训，该方法将让5-10名本科生组成的团队参与为期10周的暑期研究项目。该项目将侧重于招募和更好地为少数族裔学生进入研究生院做准备。学生将具备研究经验、基础知识和专业技能，以成功过渡到STEM学科的博士课程。这个研究项目的动机是缺乏关于脂质和蛋白质相互作用的分子生物物理学知识——生命的结构和功能主力。重点将是棕榈酰化，棕榈酸通过硫酯键与蛋白质的半胱氨酸残基共价连接。棕榈酰链的添加通过改变特定的蛋白质-蛋白质和蛋白质-脂质相互作用来调节蛋白质的动力学和生物学功能。该项目将(i)描述棕榈酰化对蛋白质结构的影响，使用全原子模拟来研究添加棕榈酰链在蛋白质中引入的结构和化学不对称性；（ii）通过多尺度模拟计算棕榈酰化对蛋白质-脂质动力学的影响，以阐明在仿生细胞和亚细胞膜环境中棕榈酰化在几十微秒和几十纳米内的蛋白质动力学；（iii）通过应用新开发和验证的蛋白质关联能量景观（PANEL）方法来捕获蛋白质组装，评估棕榈酰化对蛋白质功能的影响。获得的结果将通过与实验研究小组的数据共享合作得到验证。使用广泛的计算工具包和生物信息学方法进行体外实验将建立棕榈酰化膜蛋白在其脂质景观中的基本结构-功能和动力学方面。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

There is growing evidence that integral membrane proteins, which represent approximately 30% of the proteins in the human body, undergo lipid modifications to maintain their healthy biological function. However, how lipidation regulates the function of the membrane proteins is not well understood. This project will uncover the effect of lipid modification on these integral membrane proteins. Using computer modeling and simulations, the project will study the changes in protein structure due to the attachment of the lipid. The project will also examine the interaction of the protein with other integral membrane proteins and the change in their biological activity in the presence and absence of the attached lipid. The project involves concepts from many disciplines, including chemistry, biology, physics, mathematics, and computer science, and provides an excellent opportunity to train students with different academic backgrounds. The project will provide scientific training to undergraduate students through a cohort-based approach that will engage a team of 5–10 undergraduates in a ten-week summer research project. The project will focus on recruiting and better preparing underrepresented minority students for graduate school. Students will be equipped with research experiences, fundamental knowledge, and professional skills to successfully transition to doctoral programs in STEM disciplines.This research project is motivated by a lack of knowledge pertaining to the molecular biophysics of the interplay of lipids and proteins—the structural and functional workhorses of life. The focus will be on palmitoylation, the covalent attachment of palmitic acid to a protein's cysteine residue via a thioester bond. The addition of palmitoyl chain(s) regulates a protein's dynamics and biological function by altering specific protein-protein and protein-lipid interactions. The project will (i) characterize the impact of palmitoylation on protein's structure using all-atom simulations to investigate the structural and chemical asymmetry introduced in proteins by the addition of palmitoyl chains; (ii) compute the influence of palmitoylation on protein-lipid dynamics via multiscale simulations to elucidate palmitoylated protein dynamics over tens of microseconds, and tens of nanometers in biomimetic cellular and subcellular membrane environments; and (iii) evaluate the consequence of palmitoylation on protein function via the application of the newly developed and validated protein association energy landscape (PANEL) method to capture protein assembly. Results obtained will be verified by data-sharing collaborations with experimental research groups. The use of an extensive computational toolkit and bioinformatics approaches with in vitro experiments will establish the fundamental structural-functional and dynamical aspects of palmitoylated membrane proteins in their lipid landscapes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.