Modelling carbon core metabolism in Bacillus subtilis - exploring the contribution of protein complexes in core carbon and nitrogen metabolism

在本提案中，我们的目标是将通过直接实验获得的数据与数学模型相结合，以寻求预测模型细菌中中心碳代谢的行为。生物学家和数学家之间的这种相互作用，使用系统级方法，为描述生物过程提供了潜在的强大工具。我们试图理解的系统是在被称为枯草芽孢杆菌的革兰氏+细菌模型中的中心碳代谢系统，即营养物质转化为能量的方式。枯草芽孢杆菌已经得到了很好的研究，因此作为一种非常适合细菌生理学研究的模式生物。在我们的联盟中，来自互补学科的生物学家和数学家聚集在一起，我们将专注于碳被这种生物体吸收的方式以及碳和氮代谢之间的相互作用。近年来，越来越清楚的是，生理学的许多关键方面不是由独立的酶调节的，而是由多组分复合物调节的。这项研究计划的核心是碳/氮同化过程中许多关键酶可能作为复合物发挥作用的方式。我们试图识别和验证代谢中的这些复合物。这些大分子复合物可能赋予由这些必需蛋白质催化的酶促反应特殊的性质。例如，在一个紧密相关的复合体中，维持催化碳/氮代谢生化途径中连续步骤的两种酶，可能会增加底物a通过中间产物B通过底物通道过程转化为产物C的速度。虽然似乎直觉上应该是这样，但这并没有得到明确的证明。此外，这些必需的蛋白质复合物可能会根据细胞的能量状态改变组成，这种可能性还有待探索。因此，通过一系列旨在识别关键复合物的实验，我们将评估通过界面区域诱变靶向破坏对生物体生命周期的影响。通过将来自各种来源的数据链输入旨在以数学方式描述代谢途径的计算机模型，我们可以使用该模型来形成关于系统变化可能产生的影响的假设，然后回到实验室来测试这些预测。我们的核心目标是描述关键的生化参数，这些参数定义了蛋白质之间的相互作用，以最强大的形式完成计算机模型，并确定关键复合物的三维结构，以便我们可以将细胞现象置于原子尺度上。

In this proposal, we aim to combine data obtained by direct experimentation with mathematical models that seek to predict the behaviour of central carbon metabolism in a model bacterium. This interplay between biologists and mathematicians, using a systems level approach, provides a potentially powerful tool for characterising biological processes. The system that we seek to understand is that of central carbon metabolism - the means by which nutrients are converted into energy - in the model Gram+ bacterium called Bacillus subtilis. B. subtilis has been particularly well studied and thus acts as a highly amenable model organism for studies of bacterial physiology. In our consortium, which brings together biologists from complementary disciplines and mathematicians, we will focus on the way in which carbon is assimilated by this organism and the interplay between carbon and nitrogen metabolism. In recent years it has become clear that many key aspects of physiology are regulated not by discrete enzymes, but by multi-component complexes. Central to this research proposal is the way in which many of the key enzymes in carbon/nitrogen assimilation may function as complexes. We seek to identify and validate these complexes in metabolism. These macromolecular complexes are likely to confer special properties to the enzymatic reactions that are catalysed by these essential proteins. For instance, maintaining two enzymes that catalyse consecutive steps in the biochemical pathway of carbon/nitrogen metabolism in a tightly-associated complex may increase the rate at which substrate A is converted to product C via intermediate B through the process of substrate channeling. Although it may seem intuitive that this ought to be the case, it has not been demonstrated unequivocally. Moreover, these essential protein:protein complexes may change composition depending on the energy status of the cell, a possibility that has yet to be explored. Consequently, by a series of experiments designed to identify key complexes, we will assess the impact on the life cycle of the organism by targeted disruption by mutagenesis of interface regions. By feeding strands of data from a variety of sources into a computer model that aims to describe the metabolic pathway on a mathematical basis, we can use the model to form a hypothesis about the likely effect of changes to the system, and then go back to the laboratory to test these predictions. Central to our aims is the description of key biochemical parameters that define the interactions between proteins for the completion of the computer model in the most robust form, and also to determine the 3-dimensional structures of key complexes so that we can place a cellular phenomenon on an atomic scale.