Quantitative Redox Biology

描述(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的测序。这带来了一场革命，使研究人员能够通过全新的工具获得关于细胞蛋白质、功能和人类健康问题的信息。这一突飞猛进的进步的主要原因是信息丰富、可广泛获取的基因组和蛋白质数据库。然而，为了充分利用这些新的科学方法，仍然必须确定蛋白质、脂类、核酸以及存在于细胞和组织中的许多瞬时和准稳定物种的绝对定量范围。此外，这一信息必须与所有相关物种的反应动力学相结合，特别是代谢的瞬时物种，如活性氧和氮物种。因此，我们建议在这项拟议的研究中通过四个关键的具体目标来解决氧化还原生物学中的这些关键问题。在SA 1和SA 2中，我们将通过实验确定这些浓度范围以及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，我们将启动将三类信息汇编到一套公开可用的数据库中。这将包括：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)每个物种一系列反应的动力学速率常数；以及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。这些模型将以集中参数(仅与时间相关)、一维或更高空间维度的形式提供，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的置信度的近似值。这些最初的模型将侧重于线粒体附近的物种运输，将与SA 3中开发的数据库一起公开使用。随着实验验证的继续，社区可以扩展数据库和模型，以改进对细胞和组织氧化还原环境的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信息，指导动物实验的设计，最大限度地减少它们的使用，并制定临床方案，以实现最大限度的成功。 UCR部分 维克多·G·罗杰斯博士已经搬到了加州大学河滨分校。有了现代通信系统，我们定期开会讨论我们正在进行的项目。有了Skype，我们可以非常轻松地免费召开会议。他平均每年会花1.0个月的时间在这个项目上。他的努力将集中在具体目标4上，即开发模型化氧化还原体的模块化数学算法。他在运动和运输过程建模方面拥有丰富的专业知识。他还将与斯里尼瓦森教授和比特纳教授合作设计数据库，以便与数学建模无缝连接。他还将监督UCR的一名TBN研究生，负责建模系统的日常开发。项目说明： 人们刚刚意识到，氧化还原生物化学是细胞基础生物学的核心。在这项工作中，我们建议将处于氧化还原生物化学核心的物种的热力学、动力学和浓度信息收集到公共可用的数据库中：抗氧化剂、还原剂、抗氧化酶和蛋白质，以及瞬时和准稳定自由基和相关氧化剂。我们将构建并提供数学模型，以使用这些信息来了解氧化还原环境如何与细胞生物学和人类健康问题联系起来；这些模型可以指导实验设计，以最大限度地减少动物的使用，并最大限度地成功开发针对人类健康问题的新疗法。

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.