title: A generic rate equation for catalysed, template-directed polymerisation.
abstract: Biosynthetic networks link to growth and reproduction processes through template-directed synthesis of macromolecules such as polynucleotides and polypeptides. No rate equation exists that captures this link in a way that it can effectively be incorporated into a single computational model of the overall process. This paper describes the derivation of such a generic steady-state rate equation for catalysed, template-directed polymerisation reactions with varying monomer stoichiometry and varying chain length. The derivation is based on a classical Michaelis-Menten mechanism with template binding and an arbitrary number of chain elongation steps that produce a polymer composed of an arbitrary number of monomer types. The rate equation only requires the identity of the first dimer in the polymer sequence; for the remainder only the monomer composition needs be known. Further simplification of a term in the denominator yielded an equation requiring no positional information at all, only the monomer composition of the polymer; this equation still gave an excellent estimate of the reaction rate provided that either the monomer concentrations are at least half-saturating, or the polymer is very long.
authors.affiliation: Dept. of Biochemistry, University of Stellenbosch, Private Bag X1, 7602 Stellenbosch, South Africa. jhsh@sun.ac.za
authors.forename: Jan-Hendrik S
authors.initials: JH
authors.lastname: Hofmeyr
authors.forename: Olona P C
authors.initials: OP
authors.lastname: Gqwaka
authors.forename: Johann M
authors.initials: JM
authors.lastname: Rohwer
mesh_terms: D000465:Algorithms; D055162:Biocatalysis; D004261:DNA Replication; D004798:Enzymes / Q000737:chemistry*; D007700:Kinetics; D058105:Polymerization; D011485:Protein Binding; D014176:Protein Biosynthesis; D014158:Transcription, Genetic
chemical_list: D004798:Enzymes
keywords: Generic rate equation; Template-directed polymerisation