CDI-Type II: Discovery of Biophysical Mechanisms Inducing Signaling and Cytotoxicity: An Experimental Approach Enabled by Cyber Tools

PI：Christina Chan，Michael Feig和Amadeu SumInstitution：Michigan州立大学提案编号：0941055智力功绩。该项目旨在将分子生物学、生物物理学和细胞研究与分子建模相结合，以提供对由多个相互作用过程组成的复杂生物系统的变革性理解。对于该项目，PI计划研究内质网跨膜蛋白激酶/核糖核酸内切酶（IRE 1），其响应未折叠蛋白反应（UPR）而被激活。这对许多疾病具有广泛的影响，因为已知UPR在癌症、病毒感染和许多其他疾病中被激活。这项研究首次开发了一个多尺度模型来整合跨膜蛋白的各个结构域，以了解棕榈酸酯如何激活蛋白质，代表了一种创新的多尺度方法来收集，处理和解释从分子到细胞水平的数据。在脂肪酸中，饱和脂肪酸，即，棕榈酸盐通常是最具细胞毒性的。饱和脂肪酸已被证明会导致许多类型细胞的细胞死亡，并且是与各种疾病相关的风险因素。转型/创新。这个项目将提供跨膜蛋白激酶的一般理解急需的洞察力。的发现将依赖于生物物理事件的计算分析以及生物学，化学，物理学和工程学的综合工具。这种方法将提供洞察力，将补充和帮助解释和分析细胞功能，信号和毒性的宏观测量，并最终设计策略，以控制或预防细胞损伤和调节脂肪酸诱导的细胞信号。计算和实验方法依赖于分子水平上的发现，通过分子建模和分子生物学的结合，推动生物化学和信号转导研究。虽然细胞反应的生物化学和信号转导研究是必要的，但细胞过程的复杂性阻碍了对实验结果的清晰解释和理解。因此，这些研究的设计和工程将由分子过程的计算结果驱动。这种方法代表了一种用于合理调查脂肪酸对细胞的生物物理效应的网络使能方法。因此，这项研究对饱和脂肪酸如何参与多种疾病以及目前靶向抑制跨膜激酶的药物治疗的疗效具有影响。更广泛的影响。这里进行的研究集中在与膜和蛋白质的生物物理相互作用，作为棕榈酸酯诱导的细胞功能改变导致细胞毒性或细胞死亡的潜在机制之一。生物物理概念在这个问题上的应用是一种新的方法，这种方法在很大程度上被忽视了，有利于生物化学和信号传导过程。从教育的角度来看，该项目将为学生提供广泛的接触机会，整合来自不同领域的知识基础，并应用定量工具来研究非传统工程问题。PI在实验室中支持（女性和少数民族）高中生和本科生。PI将继续争取高中和本科学生的帮助，以获得在夏季的初步结果。本科生和高中生为实验室的研究生提供了一个机会，使他们在获得传统研究经验的同时沿着获得监督经验。对于高中和本科生，目标是鼓励他们通过接触实验室研究经验来追求工程和科学事业。PI已经并将继续开发新的课程，其中包括研究开发和研究结果。除了在科学会议上口头介绍和在学术期刊上发表文章等传统方式外，还将通过网络传播所制定的方法。

PI: Christina Chan, Michael Feig and Amadeu SumInstitution: Michigan State University Proposal Number: 0941055 Intellectual Merit. This project aims to integrate molecular biology, biophysics, and cellular studies with molecular modeling to provide a transformative understanding of complex biological systems comprised of multiple interacting processes. Specifically for this project the PIs plan to study the endoplasmic reticulum transmembrane protein kinase/endoribonuclease (IRE1), which is activated in response to the Unfolded Protein Response (UPR). This has broad implications on a number of diseases, since UPR is known to be activated in cancers, viral infection and many other diseases. This study is a first at developing a multi-scale model to integrate the various domains of the transmembrane protein to understand how palmitate activates the protein, representing an innovative, multi-scale approach to gather, process, and interpret data from the molecular to the cellular level. Among the fatty acids, saturated fatty acids, i.e., palmi-tate, are typically the most cytotoxic. Saturated fatty acids have been shown to cause cell death in many types of cells and be risk factors associated with a variety of diseases. Transformation/Innovation. This project will provide much needed insight into the general understanding of transmembrane protein kinases. The findings of will rely on computational analysis of biophysical events as well as integrating tools from biology, chemistry, physics, and engineering. This approach will provide insight that will complement and aid in the interpretation and analysis of macroscopic measurements of cellular function, signaling and toxicity, and eventual design of strategies to control or prevent cell damage and modulate cell signaling induced by fatty acids. The computational and experimental approaches rely on the findings at the molecular levels, through a combination of molecular modeling and molecular biology, to drive the bio-chemical and signaling transduction studies. While the biochemical and signaling studies of the cellular responses are necessary, the complexity of cellular processes hinders a clear interpretation and understanding of the experimental results. As such, design and engineering of these studies will be driven by computational findings of the molecular processes. This approach represents a cyber enabled methodology for a rational investigation of the biophysical effects of fatty acids on cells. Therefore, this study has implications on how saturated fatty acids may be involved in multiple diseases as well as on the efficacy of current drug therapies that are targeted to inhibit transmembrane kinases. Broader Impact. The studies pursued here are centered on biophysical interactions with membranes and proteins as one of the underlying mechanisms behind palmitate-induced alterations in cellular function leading to cytotoxicity or death of cells. The application of bio-physical concepts to this problem is a novel approach that has been largely overlooked in favor of biochemical and signaling processes. From an educational standpoint, this project will provide a broad exposure to the students with an opportunity to integrate the knowledge base from vastly differing fields and to apply quantitative tools to investigate non-traditional engineering problems. The PIs have supported both (female and minority) high school and undergraduate students in the laboratory. The PIs will continue to enlist the help of high school and undergraduate students to obtain preliminary results during the summer months. The undergraduate and high school students provide an opportunity for the graduate students in the lab to gain supervisory experience along with their traditional research experience. For the high school and undergraduate students, the goal is to encourage them to pursue careers in engineering and science by exposing them to hands-on laboratory research experiences. The PIs have and will continue to develop new courses that incorporate the research development and findings. The methodology developed will be disseminated through the web, in addition to traditional modes, such as oral presentations at scientific meetings and publications in scholarly journals.