Quantitative Redox Biology

描述（由申请人提供）：上个世纪生物学的主要成就之一是人类基因组测序。这带来了一场革命，使研究人员能够利用全新的工具获得有关细胞蛋白质、功能和人类健康问题的信息。信息丰富且可广泛获取的基因组和蛋白质数据库是这些技术飞速发展的主要原因。然而，为了充分利用这些新的科学方法，仍然有必要确定细胞和组织中存在的蛋白质、脂质、核酸和许多瞬时和准稳定物种的绝对定量范围。此外，这些信息必须与所有相关物种的反应动力学相结合，特别是代谢的瞬态物种，例如活性氧和活性氮物种。因此，我们建议在本研究中通过四个关键的特定目标来解决这些氧化还原生物学中的关键问题。在SA 1和SA 2中，我们将通过实验确定这些浓度范围和所需的动力学和热力学信息，并将其与文献中的数据相结合。在SA 3中，我们将开始在一组公开可用的数据库中组装三类信息。这些将包括：a)定义细胞/组织氧化还原环境的所有相关物种的绝对浓度（拷贝数）-这将包括抗氧化酶和蛋白质，小分子抗氧化剂或酶底物，以及ROS/RNS；B)每种物质的一系列反应的动力学速率常数；c)所有相关氧化还原对的热力学参数。在第四个SA中，我们将开发初始的确定性或随机数学模型，利用这些参数来预测细胞和组织的生物状态和生物功能。这些模型将以集总参数（仅依赖于时间）、一维或更高的空间维度形式提供，以反映手头特定动态系统的复杂性。在模型内，将提供模型可预测性置信度的近似值。这些最初的模型将关注线粒体附近的物种运输，将与sa3中开发的数据库一起公开使用。随着实验验证的继续，数据库和模型都可以被社区扩展，以改进细胞和组织氧化还原环境变化如何改变其基本生物学的表示和预测。这些数据库和数学模型中的信息将提供指导动物实验设计的信息，最大限度地减少它们的使用，并制定临床方案以最大限度地提高成功率。

DESCRIPTION (provided by applicant): One of the major accomplishments in biology of the last century has been the sequencing of the human genome. This has brought about a revolution, allowing researchers to gain information on cellular proteins, function, and human health issues with entirely new tools. The principal reasons for the whirlwind of advances are the information-rich and broadly accessible genome- and protein-databases. However, in order to fully utilize these new scientific approaches, it remains imperative that the absolute quantitation range of the proteins, lipids, nucleic acids, and the many transient and quasi-stable species present in cells and tissues are determined. In addition, this information must be coupled to the dynamics of the reactions of all relevant species, especially the transient species of metabolism, e.g. reactive oxygen and nitrogen species. Therefore, we propose to address these critical issues in redox biology in this proposed research through four critical Specific Aims. In SA 1 and 2 we will experimentally determine these concentration ranges and needed kinetic and thermodynamic information and couple this with data in the literature. In SA 3 we will initiate the assembly of three categories of information in a publicly available set of databases. These will include: a) absolute concentrations (copy number) of all relevant species that define the redox environment of a cell/tissue -- this will include antioxidant enzymes and proteins, small molecule antioxidants or enzyme substrates, and ROS/RNS; b) the kinetic rate constants for the array of reactions for each species; and c) the thermodynamic parameters for all relevant redox couples. In the fourth SA we will develop initial deterministic or stochastic mathematical models that utilize these parameters to predict the biological state and biological functioning of cells and tissues. These models will be available as lumped-parameter (time-dependent only), 1-D or higher spatial dimension forms to reflect the complexity of the specific dynamic system at hand. Within the model, approximations of the confidence in the models predictability will be provided. These initial models, which will focus on species transport near the mitochondrion, will be publicly available for use in conjunction with the databases developed in SA 3. As experimental verification continues, both the databases and models can be expanded upon by the community to improve representation and prediction of how changes in the redox environment of cells and tissue change their basic biology. The information in these databases and the mathematical models will provide information that can guide the design of animal experiments, minimizing their use, and the development of clinical protocols to maximize success. UCR PORTION Dr. Victor G. Rodgers has moved to the University of California at Riverside. With modern systems of communication we have regular meetings to discuss our ongoing projects. With Skype we are able to conference very easily at no cost. He will on average devote 1.0 months/yr of his effort to the project. His efforts will be focused on Specific Aim 4, the development of modular mathematical algorithms to model the redoxome. He has extensive expertise in modeling kinetic and transport processes. He will also work with Professors Srinivason and Buettner to design the data bases so that there is a seamless interface with the mathematical modeling. He will also oversee a TBN graduate student at UCR that will be responsible for the day-to-day development of the modeling systems.Project Narrative: It is just now being realized that redox biochemistry is at the heart of the basic biology of the cell. In this work we propose to gather into publicly available databases thermodynamic, kinetic, and concentration information on the species at the heart of this redox biochemistry: antioxidants, reducing agents, antioxidant enzymes and proteins, as well as the transient and quasi-stable free radicals and related oxidants. We will construct and make available mathematical models to use this information to understand how the redox environment connects to cell biology and issues of human health; the models can guide experimental design to minimize the use of animals and maximize success in developing new treatments for human health problems.