相关论文: Flux cost functions and optimal metabolic states
Enzyme costs play a major role in the choice of metabolic routes, both in evolution and bioengineering. Given desired fluxes, necessary enzyme levels can be estimated based on known rate laws and on a principle of minimal enzyme cost. With…
Metabolic fluxes in cells are governed by physical, physiological, and economic principles. Here I assume an optimal allocation of enzyme resources and postulate a general principle for metabolism: each enzyme must convert less valuable…
Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
Constraint based methods, such as the Flux Balance Analysis, are widely used to model cellular growth processes without relying on extensive information on the regulatory features. The regulation is instead substituted by an optimization…
Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
Constraint-based metabolic modeling is the predominant framework for simulating cellular metabolism. The central assumption of these models is that metabolism operates at a steady state, meaning that the production and consumption rates of…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state. Of the many variants of…
New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained…
Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
An extensive rewiring of cell metabolism supports enhanced proliferation in cancer cells. We propose a systems level approach to describe this phenomenon based on Flux Balance Analysis (FBA). The approach does not explicit a cell biomass…
Elementary flux modes (EFMs) are pathways through a metabolic reaction network that connect external substrates to products. Using EFMs, a metabolic network can be transformed into its macroscopic counterpart, in which the internal…
The connection between optimal biological function and energy use, measured for example by the rate of metabolite consumption, is a current topic of interest in the systems biology literature which has been explored in several different…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
Microorganisms have developed complex regulatory features controlling their reaction and internal adaptation to changing environments. When modeling these organisms we usually do not have full understanding of the regulation and rely on…
Cells can use periodic enzyme activities to adapt to periodic environments or existing internal rhythms and to establish metabolic cycles that schedule biochemical processes in time. A periodically changing allocation of the protein budget…
Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…
Constraint-based metabolic models can be used to investigate the intracellular physiology of microorganisms. These models couple genes to reactions, and typically seek to predict metabolite fluxes that optimize some biologically important…