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Biosystems. 2014 Aug;122:38-54. doi: 10.1016/j.biosystems.2014.06.011. Epub 2014 Jun 24.

Transient and sustained elementary flux mode networks on a catalytic string-based chemical evolution model.

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ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313 Porto, Portugal; REQUIMTE/CEQUP - Centro de Química da Universidade do Porto, R. D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal. Electronic address:


Theoretical models designed to test the metabolism-first hypothesis for prebiotic evolution have yield strong indications about the hypothesis validity but could sometimes use a more extensive identification between model objects and real objects towards a more meaningful interpretation of results. In an attempt to go in that direction, the string-based model SSE ("steady state evolution") was developed, where abstract molecules (strings) and catalytic interaction rules are based on some of the most important features of carbon compounds in biological chemistry. The system is open with a random inflow and outflow of strings but also with a permanent string food source. Although specific catalysis is a key aspect of the model, used to define reaction rules, the focus is on energetics rather than kinetics. Standard energy change tables were constructed and used with standard formation reactions to track energy flows through the interpretation of equilibrium constant values. Detection of metabolic networks on the reaction system was done with elementary flux mode (EFM) analysis. The combination of these model design and analysis options enabled obtaining metabolic and catalytic networks showing several central features of biological metabolism, some more clearly than in previous models: metabolic networks with stepwise synthesis, energy coupling, catalysts regulation, SN2 coupling, redox coupling, intermediate cycling, coupled inverse pathways (metabolic cycling), autocatalytic cycles and catalytic cascades. The results strongly suggest that the main biological metabolism features, including the genotype-phenotype interpretation, are caused by the principles of catalytic systems and are prior to modern genetic systems principles. It also gives further theoretical support to the thesis that the basic features of biologic metabolism are a consequence of the time evolution of a random catalyst search working on an open system with a permanent food source. The importance of the food source characteristics and evolutionary possibilities are discussed.


Artificial chemistry; Catalytic network model; Chemical evolution model; Elementary flux modes; Metabolism-first; Pattern-matching catalysis

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