Signatures of Arithmetic Simplicity in Metabolic Network Architecture 英文参考文献.docVIP

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Signatures of Arithmetic Simplicity in Metabolic Network Architecture 英文参考文献.doc

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Signatures of Arithmetic Simplicity in Metabolic Network Architecture 英文参考文献

SignaturesofArithmeticSimplicityinMetabolicNetwork Architecture WilliamJ.Riehl1,PaulL.Krapivsky2,SidneyRedner2,DanielSegre`1,3,4* 1PrograminBioinformaticsandSystemsBiology,BostonUniversity,Boston,Massachusetts,UnitedStatesofAmerica,2DepartmentofPhysics,BostonUniversity,Boston, Massachusetts, United States of America, 3Department of Biology, Boston University, Boston, Massachusetts, United States of America, 4Department of Biomedical Engineering,BostonUniversity,Boston,Massachusetts,UnitedStatesofAmerica Abstract Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life’s origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictableaccumulationofmultiplehistoricalaccidents?Herewesearchforsuchprinciplesbyapplyingtoanartificial chemicaluniversesomeofthemethodologiesdevelopedforthestudyofgenomescalemodelsofcellularmetabolism.In particular,weusemetabolicfluxconstraint-basedmodelstoexhaustivelysearchforartificialchemistrypathwaysthatcan optimallyperformanarrayofelementarymetabolicfunctions.Despitethesimplicityofthemodelemployed,wefindthat the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbonatomreactionbackbone,wefindthatpropertiessimilartothosepredictedfortheartificialchemistryholdalsofor realmetabolicn