Wolfram Liebermeister wolfram.liebermeister@gmail.com INRAE - Unité MaIAGE Domaine de Vilvert 78352 Jouy-en-Josas, France

DFG-funded research project "Dynamics and function of enzyme regulation in large metabolic networks" (Ll 1676/2-1)

Kinetic models are essential to better understand the dynamics and function of enzyme regulation, and hence to predict the metabolic effects of differential enzyme expression and enzyme-inhibiting drugs. However, kinetic modelling is not yet applicable to large, genome-scale networks. Existing genome-scale modelling approaches, such as flux balance analysis, are based on stoichiometry only and therefore inherently limited in use. This project aims to fill the gap between genome-scale stoichiometric and small-scale kinetic models by the development of a novel kinetic modelling approach for large metabolic networks. The method combines metabolic control analysis with data integration and sampling techniques and accounts for thermodynamic constraints. The results will be probabilistic, reflecting the availability and quality of input data.

The applicability of the new method will be tested through its use to create large network models and to predict flux changes caused by enzyme regulation, to couple these models with detailed kinetic pathway models, to compute synergisms between enzyme-inhibiting drugs, to predict the dynamic effects of alternating enzyme levels, and to study the advantages of enzymatic regulation and alternating enzyme levels in fluctuating environments through a computational cost-benefit approach. Through external collaborations, model predictions will be validated with experimental omics data from bacterial and yeast cultures and from human hepatocytes. By extending dynamic modelling to large metabolic networks, the project will substantially improve the understanding of enzyme regulation, with potential future applications in cell simulation, prediction of drug interactions and side effects, and chronotherapies.

Methods for model construction

Overview

1. Parameter balancing
2. Structural thermokinetic modelling
3. Model embedding
4. Enzyme cost minimization
5. Flux cost minimization

Optimal resource allocation in cells

1. Economic principles in cell metabolism
2. Economics of periodic enzyme activities

Cell simulations

1. Metabolic oscillations in yeast

Tools for data handling

1. Proteomaps
2. SBtab data format

Models, data, and software tools

1. Models and data resources
2. Software code