EMT: Study of Transmembrane Proteins for Biomolecular Logic & Storage

I.科学价值：设计和构建纳米级计算和存储元件的能力是当今生物模拟设备工程最有趣的挑战之一。其他挑战包括在信息处理应用中将蛋白质用作高效的生物分子机器，对蛋白质结构-功能关系的系统研究，改变、保持和探测生物分子机器状态的能力，以及帮助此类实验工作的模拟工具的开发和传播。这个新兴的计算模型和技术(EMT)团队热衷于接受这些挑战，并提议研究跨膜蛋白(离子动力ATP酶)作为生物分子状态机的使用，严格检查它们的结构、功能和性能，以期建立能够进行逻辑运算和存储的计算状态机。在现有工具和经验的基础上，受跨膜蛋白作为仿生分子机器测试蓝图的潜力的激励，该团队将从基础和应用工程的角度研究Na+/K+ATPase的电生理反应、原子结构和热力学效率，在每个阶段提出并解决关于它们作为活性纳米结构用于计算的关键问题。提案团队包括一个来自俄亥俄大学的协同研究小组，他们汇集了离子动力跨膜蛋白研究的关键技能和背景。首先，我们将对Na/K泵进行稳态和暂态测量，并通过电学和光学手段研究通过定点突变改变的泵的结构和功能。这将使我们能够识别、分离和研究与蛋白质的给定逻辑状态相对应的特定泵构象。其次，我们将利用扫描隧道显微镜(STM)获得突变的南瓜蛋白的高分辨率图像(这是以前从未尝试过的)。这将导致更好地从结构上理解本研究和整个生物工程界所需的离子传输机制。第三，我们将通过建模和仿真工作支持实验研究。我们将解决的具体问题包括：1)泵循环的哪些状态对于计算任务是最容易获得和最有用的？2)我们如何通过电学、光学(使用荧光)或STM-蛋白质相互作用来“读出”和“写入”这样的逻辑状态？3)基于运输蛋白质的计算的热力学极限和效率是什么？4)STM原子成像和操纵技术如何帮助理解运输蛋白质，特别是钠/钾泵的结构-功能问题？5)如何传播现有的数值工具，如分子动力学模拟器，并开发新的紧凑型模拟器来指导基于蛋白质的生物分子机器设计？这些问题是可以通过强大的实验技术和我们团队中发现的模拟专业知识的独特组合来解决的小问题样本。ii.更广泛的影响：科学工作将涉及来自表面物理、生物科学和工程学三个不同学术领域的研究生和博士后研究员，以实现共同的跨学科应用。这些合作将通过出版物、公开和专业陈述来广泛传播研究成果。在本地方面，为了应对俄亥俄州东南部不合标准的煤粉污染和经济/教育环境，以及促进多元化和性别/种族平等，我们建议开展外展和教育活动，让私人投资机构直接参与，通过广泛的讲座和科学博览会项目，将纳米生物科学教育带到乡村和市中心的学校，其中重点介绍纳米生物科学和工程的发展。为了对更广泛的公众产生影响，包括俄亥俄州东南部、肯塔基州北部和西弗吉尼亚州西部的阿巴拉契亚社区，我们将定期向俄亥俄大学公共广播/电视台WOUB的科学节目捐款，并为他们的学生作家提供经济支持和实习机会。所有支持这项提议的学生都将参加NSF资助的暑期学校项目，并将成为NanoHub计算纳米技术合作伙伴的用户，学术人员将传播关于运输蛋白质设备的研究结果，确保从这一合作中获得的结果为NSF/NIH支持的仿生科学计划带来最大好处，特别是通过伊利诺伊大学厄巴纳-香槟分校贝克曼研究所的外部合作者。

I. Scientific Merit: The ability to design and construct nanoscale computing and memory elements is one of the most interesting challenges for bio-mimetic device engineering today. Additional challenges include the use of proteins as efficient bio-molecular machines in information processing applications, the systematic study of protein structure-function relationships, the ability to change, retain and probe states of bio-molecular machines, and the development and dissemination of simulation tools to assist such experimental efforts. This Emerging Models and Technologies for Computation (EMT) team eagerly accepts these challenges and proposes to investigate the use of transmembrane proteins (ion-motive ATP-ases) as bio-molecular statemachines, critically examining their structure, function and performance with a view to building computational state machines capable of logic operations and storage. Building on the existing tools and experience, and motivated by the potential of transmembrane proteins as tested blueprints for biomimetic molecular machines,the team will investigate the electrophysiological response, atomic structure and thermodynamic efficiency of the Na+/K+ ATPase from both fundamental and applied engineering points of view, at each stage asking and addressing key questions regarding their use as active nanostructures for computation.The proposal team includes a synergistic group of researchers from Ohio University who bring together the skills and background crucial for the study of ion motive transmembrane proteins. First, we will perform steady-state and transient measurements on the Na/K pump and investigate the structure and function by electrical and optical means of pumps altered by site-directed mutagenesis. This will allow us to identify, isolate and study specific pump conformations corresponding to a given logic state of the protein. Second, we will utilize a scanning tunneling microscope (STM) to obtain high-resolution images of mutated pumpproteins (which has never been attempted before). This will lead to better structural understanding of the mechanism of ion transport needed by both this study and the bio-engineering community as a whole. Third, we will support the experimental studies with modeling and simulation efforts. Specific issues we will address will include: 1) which states of the pump cycle are the most accessible and useful for computing tasks? 2) Howdo we 'read out' and 'write in' such logic states either electrically, optically (using fluorescence) or by means of STM-protein interactions? 3) What are the thermodynamic limits and efficiency for transport protein based computing? 4) How can STM atomic imaging and manipulation techniques aid in the understanding of structure-function questions of transport proteins in general and the Na/K pump in particular? and 5) How can we disseminate existing numerical tools such as molecular dynamics simulators and develop new compact simulators to guide protein based bio-molecular machine design? These questions are a small sample of issues addressable through the unique combination of powerful experimental techniques and simulation expertise found in our team.II. Broader Impacts: The scientific work will involve both graduate and undergraduate students and postdoctoral fellows from three distinct academic fields, surface physics, biological sciences and engineering for a common interdisciplinary application. These collaborations will result in broad dissemination of the research outcomes via publications, public and professional presentations. Locally, to counter the sub-standard coalstrickeneconomical/educational climate of Southeastern Ohio and to promote diversity and gender/racial equity, we propose outreach and educational activities that will involve the direct participation of the PIs in bringing nano-bio science education to rural and inner-city schools through broadly accessible presentations and science fair projects in which developments in nano-bio science and engineering are highlighted. To provide an impactfor the broader public, including Appalachian communities of southeastern Ohio, northern Kentucky and western West Virginia, we will regularly contribute to science programs on OhioU's public radio/TV station WOUB and provide financial support and internship opportunities for their student writers. All students to be supported with this proposal will participate in NSF-funded Summer School-programs and will become users of NanoHub partnership in computational nanotechnology, and the academic personnel will disseminatefindings on transport protein devices, ensuring that results obtained from this collaboration produces maximum benefits for NSF/NIH-supported biomimetic science initiatives, especially through external collaborators at Beckman Institute, University of Illinois at Urbana-Champaign.