The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
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.
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“This equation was first derived in Hofmeyr et al. (2013) for the case where the enzyme is more abundant than its template polymer.”
From Fundamental behaviors emerge from simulations of a living minimal cell (2022) · cites this paper as Hofmeyr et al., 2013
Citations
Cites
The Original Michaelis Constant: Translation of the 1913 Michaelis-Menten Paper
Johnson, K., & Goody, R. (2011) · Biochemistry · doi:10.1021/bi201284u · Cited by 1,377
Die Kinetik der Invertinwirkung
Michaelis, L., & Menten, M. L. (2007) · Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) · Cited by 1,240
Kinetics of biopolymerization on nucleic acid templates
MacDonald, C. T., Gibbs, J. H., & PIPKIN, A. C. (1968) · Biopolymers · doi:10.1002/bip.1968.360060102 · Cited by 843
Model for the regulation of mRNA translation applied to haemoglobin synthesis
Lodish, H. F. (1974) · Nature · doi:10.1038/251385a0 · Cited by 423
Concerning the kinetics of polypeptide synthesis on polyribosomes
MacDonald, C. T., & Gibbs, J. H. (1969) · Biopolymers · doi:10.1002/bip.1969.360070508 · Cited by 294
Regulating the cellular economy of supply and demand
Hofmeyr, J. S., & Cornish-Bowden, A. J. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)01668-9 · Cited by 225
Modelling cellular systems with PySCeS
Olivier, B. G., Rohwer, J. M., & Hofmeyr, J. S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti046 · Cited by 180
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Liebermeister, W., Uhlendorf, J., & Klipp, E. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq141 · Cited by 146
A kinetic model of protein synthesis. Application to hemoglobin synthesis and translational control.
Bergmann, J. E., & Lodish, H. F. (1979) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)86406-2 · Cited by 140
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis
Fluitt, A. M., Pienaar, E., & Viljoen, H. J. (2007) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2007.07.003 · Cited by 134
Research works printed but not linked: 1
- Rohwer J.M., 2007, Experimental Standard Conditions of Enzyme Characterizations. Proceedings of the 2nd International Beilstein Workshop, 175
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Sorted by citations
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
Noor, Ε., Flamholz, A. I., Bar‐Even, A., Davidi, D., Milo, R., & Liebermeister, W. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005167 · Cited by 193
“This convexity holds for a variety of rate laws, including rate laws describing polymerization reactions [37], and even for the more complicated problem of preemptive enzyme expression, i.”
BackgroundFundamental behaviors emerge from simulations of a living minimal cell
Thornburg, Z. R., Bianchi, D. M., Brier, T. A., Gilbert, B. R., Earnest, E. E., Melo, M. C. R., Safronova, N., Sáenz, J. P., Cook, A. T., Wise, K. S., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.025 · Cited by 165
“…uthor M anuscript A uthor M anuscript νpolymerizationCME − ODE = kcat 1 + K0[Enzyme] KD1KD2 Monomer1 Monomer2 + ∑i niKDi Monomeri + Lpolymer − 1 NTemplate (Equation 5) This equation was first derived in Hofmeyr et al. (2013) for the case where the enzyme is more abundant than its template polymer.”
Zhang, Z., Zheng, H., Huang, F., Li, X., He, S., & Zhao, C. J. (2016) · Industrial & Engineering Chemistry Research · doi:10.1021/acs.iecr.6b01894 · Cited by 50
Bringing the genetically minimal cell to life on a computer in 4D
Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44
Kinetic modeling of the genetic information processes in a minimal cell
Thornburg, Z. R., Melo, M. C. R., Bianchi, D., Brier, T. A., Crotty, C., Breuer, M., Smith, H. O., Hutchison, C. A., Glass, J. I., & Luthey-Schulten, Z. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00130 · Cited by 22
Metadata
- Authors
- Hofmeyr, J.-H. S., Gqwaka, O. P. C., & Rohwer, J. M.
- Affiliations
- Stellenbosch University (ZA)
- Venue
- FEBS Letters
- Publisher
- Wiley
- Published
- 2013-07-11
- Volume
- 587
- Issue
- 17
- Pages
- 2868-2875
- ISSN
- 0014-5793 (ISSN-L)
- 1873-3468
- OpenAlex
- W2140066782
- Cited by
- 11
- References
- 25
- Citations by year
- 2026: 1 · 2025: 1 · 2023: 1 · 2022: 1 · 2020: 3 · 2019: 1 · 2017: 1 · 2016: 2
- FWCI
- 0.30
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- FEBS Letters (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- rate equations, Michaelis-Menten mechanism, template binding, chain extension, chain length, steady-state kinetics, monomer composition
- MeSH terms
- Algorithms, DNA Replication, Enzymes, Kinetics, Protein Binding, Transcription, Genetic, Protein Biosynthesis, Biocatalysis, Polymerization
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- Hofmeyr, J.-H. S., Gqwaka, O. P. C., & Rohwer, J. M. (2013). A generic rate equation for catalysed, template-directed polymerisation. FEBS Letters. https://doi.org/10.1016/j.febslet.2013.07.011
