Document Detail


Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems.
MedLine Citation:
PMID:  11146883     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The structural design of ATP and NADH producing systems, such as glycolysis and the citric acid cycle (TCA), is analysed using optimization principles. It is assumed that these pathways combined with oxidative phosphorylation have reached, during their evolution, a high efficiency with respect to ATP production rates. On the basis of kinetic and thermodynamic principles, conclusions are derived concerning the optimal stoichiometry of such pathways. Extending previous investigations, both the concentrations of adenine nucleotides as well as nicotinamide adenine dinucleotides are considered variable quantities. This implies the consideration of the interaction of an ATP and NADH producing system, an ATP consuming system, a system coupling NADH consumption with ATP production and a system consuming NADH decoupled from ATP production. It is examined in what respect real metabolic pathways can be considered optimal by studying a large number of alternative pathways. The kinetics of the individual reactions are described by linear or bilinear functions of reactant concentrations. In this manner, the steady-state ATP production rate can be calculated for any possible ATP and NADH producing pathway. It is shown that most of the possible pathways result in a very low ATP production rate and that the very efficient pathways share common structural properties. Optimization with respect to the ATP production rate is performed by an evolutionary algorithm. The following results of our analysis are in close correspondence to the real design of glycolysis and the TCA cycle. (1) In all efficient pathways the ATP consuming reactions are located near the beginning. (2) In all efficient pathways NADH producing reactions as well as ATP producing reactions are located near the end. (3) The number of NADH molecules produced by the consumption of one energy-rich molecule (glucose) amounts to four in all efficient pathways. A distance measure and a measure for the internal ordering of reactions are introduced to study differences and similarities in the stoichiometries of metabolic pathways.
Authors:
O Ebenhöh; R Heinrich
Related Documents :
7559583 - Kinetic mechanism of aminoglycoside phosphotransferase type iiia. evidence for a theore...
8914933 - Characterization of the import pathway of the f(a)d subunit of mitochondrial atp syntha...
18397883 - Transglutaminase induces protofibril-like amyloid beta-protein assemblies that are prot...
Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Bulletin of mathematical biology     Volume:  63     ISSN:  0092-8240     ISO Abbreviation:  Bull. Math. Biol.     Publication Date:  2001 Jan 
Date Detail:
Created Date:  2001-01-05     Completed Date:  2001-02-15     Revised Date:  2004-11-17    
Medline Journal Info:
Nlm Unique ID:  0401404     Medline TA:  Bull Math Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  21-55     Citation Subset:  IM    
Affiliation:
Humboldt-Universität zu Berlin, Institut für Biologie/Theoretische Biophysik, Invalidenstrasse 42, D-10115 Berlin, Germany. oliver.ebenhoeh@rz.hu-berlin.de
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Adenosine Triphosphate / biosynthesis*,  metabolism
Algorithms
Citric Acid Cycle / genetics
Computer Simulation*
Evolution, Molecular*
Glucose / metabolism
Glycolysis / genetics
Humans
Kinetics
Models, Biological*
NAD / biosynthesis*,  metabolism
Oxidative Phosphorylation
Chemical
Reg. No./Substance:
50-99-7/Glucose; 53-84-9/NAD; 56-65-5/Adenosine Triphosphate

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  A physical force may expose Hox genes to express in a morphogenetic density gradient.
Next Document:  Replication and mutation on neutral networks.