tailieunhanh - Báo cáo khoa học: Stoichiometric network theory for nonequilibrium biochemical systems

We introduce the basic concepts and develop a theory for nonequilibrium steady-state biochemical systems applicable to analyzing large-scale complex isothermal reaction networks. In terms of the stoichiometric matrix, we dem-onstrate both Kirchhoff’s flux lawR‘J‘ ¼0 over a bio-chemical species, and potential law R‘l‘ ¼0overa reaction loop. They reflect mass and energy conservation, respectively. | Eur. J. Biochem. 270 415-421 2003 FEBS 2003 doi Stoichiometric network theory for nonequilibrium biochemical systems Hong Qian1 2 Daniel A. Beard2 and Shou-dan Liang3 Departments of 1 Applied Mathematics and 2Bioengineering University of Washington Seattle USA 3NASA Ames Research Center Moffett Field CA USA We introduce the basic concepts and develop a theory for nonequilibrium steady-state biochemical systems applicable to analyzing large-scale complex isothermal reaction networks. In terms of the stoichiometric matrix we demonstrate both Kirchhoff s flux law R J 0 over a biochemical species and potential law R 1 0 over a reaction loop. They reflect mass and energy conservation respectively. For each reaction its steady-state flux J can be decomposed into forward and backward one-way fluxes J J - J_ with chemical potential difference All RT ln J_ J . The product JA1 gives the isothermal heat dissipation rate which is necessarily non-negative accord ing to the second law of thermodynamics. The stoichiometric network theory SNT embodies all of the relevant fundamental physics. Knowing J and Al of a biochemical reaction a conductance can be computed which directly reflects the level of gene expression for the particular enzyme. For sufficiently small flux a linear relationship between J and Al can be established as the linear fluxforce relation in irreversible thermodynamics analogous to Ohm s law in electrical circuits. Keywords biochemical network chemical potential flux nonequilibrium thermodynamics steady-state. With the completion of the Human Genome Project understanding of complex biochemical systems is entering a new era that emphasizes engineering approaches and quantitative analysis 1 . In order to develop a comprehensive theory for biochemical networks Palsson and colleagues have utilized flux balance analysis FBA which is based on the fundamental law of mass conservation 2-4 . In terms of general network theory flux .