EMT: Study of Transmembrane Proteins for Biomolecular Logic & Storage

EMT：跨膜蛋白的生物分子逻辑研究

• 批准号: 0622158
• 负责人: Savas Kaya
• 金额: --
• 依托单位: Ohio University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2010-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0622158&HistoricalAwards=false
• 关键词: EMT; Study; Transmembrane; Proteins; Biomolecular

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.

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仿生器件工程最有趣的挑战之一。其他的挑战包括使用蛋白质作为有效的生物分子机器在信息处理应用，蛋白质结构功能关系的系统研究，改变的能力，保持和探测状态的生物分子机器，和模拟工具的开发和传播，以协助这种实验的努力。这个新兴的计算模型和技术（EMT）团队热切地接受这些挑战，并提出研究使用跨膜蛋白（离子动力ATP酶）作为生物分子状态机，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。基于现有的工具和经验，并受到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+ ATP酶的电生理反应，原子结构和热力学效率，在每一个阶段，提出并解决有关其作为计算活性纳米结构使用的关键问题。该提案小组包括一个来自俄亥俄州大学的研究人员协同小组，他们汇集了技能和背景对于离子运动跨膜蛋白的研究至关重要。首先，我们将对Na/K泵进行稳态和瞬态测量，并通过定点诱变改变泵的电学和光学手段研究其结构和功能。这将使我们能够识别，分离和研究对应于蛋白质的给定逻辑状态的特定泵构象。其次，我们将利用扫描隧道显微镜（STM）获得突变泵蛋白的高分辨率图像（以前从未尝试过）。这将导致更好地理解本研究和整个生物工程界所需的离子传输机制的结构。第三，我们将通过建模和模拟工作支持实验研究。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最容易访问和有用？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)基于转运蛋白的计算的热力学极限和效率是什么？4)STM原子成像和操作技术如何帮助理解一般转运蛋白的结构-功能问题，特别是Na/K泵？以及5）我们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，以指导基于蛋白质的生物分子机器设计？这些问题是通过我们团队中强大的实验技术和模拟专业知识的独特组合可解决的问题的一小部分。更广泛的影响：科学工作将涉及来自三个不同学术领域的研究生和本科生以及博士后研究员，表面物理学，生物科学和工程学，用于共同的跨学科应用。这些合作将导致通过出版物，公众和专业演讲广泛传播研究成果。在当地，以应对低于标准的coalstrickeneconomic/教育气候的东南部俄亥俄州，并促进多样性和性别/种族平等，我们提出的推广和教育活动，将涉及直接参与的PI将纳米生物科学教育，农村和内城学校通过广泛访问的演示文稿和科学博览会项目，其中纳米生物科学和工程的发展是突出的。为了提供更广泛的公众，包括东南部俄亥俄州，北方肯塔基州和西弗吉尼亚州西部的阿巴拉契亚社区的影响，我们将定期促进俄亥俄州的公共广播/电视台WOUB的科学节目，并为他们的学生作家提供财政支持和实习机会。所有的学生将支持这项建议将参加NSF资助的暑期学校计划，并将成为计算纳米技术的NanoHub伙伴关系的用户，学术人员将传播关于运输蛋白设备的发现，确保从这种合作中获得的结果为NSF/NIH支持的仿生科学计划带来最大的利益，特别是通过贝克曼研究所的外部合作者，伊利诺伊大学香槟分校。