Abstract
Evolution of the kinetic potential of enzyme reactions is discussed. Quantitative assessment of the evolution of enzyme action has usually focused on optimization of the parametric ratio kcat./Km, which is the apparent second-order rate constant for the reaction of free substrate with free enzyme to give product. We propose that the general form kcat.[E]T/Km (where [E]T is total enzyme concentration), which is designated the 'kinetic power', is the real measure of kinetic/catalytic potential in situ. The standard paradigm of 'perfection' dictates the evolutionary maximum of 'kinetic power' to be k+s[E]T/2, where k+s is the diffusion-controlled rate constant for formation of the ES complex (and, hence, for the overall enzyme reaction). We discuss the role of protein conformational mobility in determining this state of 'perfection', via gating of substrate binding and determination of the catalytic configuration. Going beyond the level of the individual enzyme, we indicate the manner by which the organizational features of enzyme action in vivo may enhance the 'kinetic power'. Through evolutionary 'perfection' of the microenvironment, one finds that the 'kinetic power' of enzymes can be affected by alteration of [E]T as well as the unitary rate constants. At this level of complexity, we begin to realize that the 'kinetic' description of cell metabolism must be supplemented with thermodynamic concepts.
Full text
PDF




Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Brocklehurst K., Cornish-Bowden A. The pre-eminence of k(cat) in the manifestation of optimal enzymic activity delineated by using the Briggs-Haldane two-step irreversible kinetic model. Biochem J. 1976 Oct 1;159(1):165–166. doi: 10.1042/bj1590165. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brocklehurst K. Evolution of enzyme catalytic power. Characteristics of optimal catalysis evaluated for the simplest plausible kinetic model. Biochem J. 1977 Apr 1;163(1):111–116. doi: 10.1042/bj1630111. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Careri G., Fasella P., Gratton E. Statistical time events in enzymes: a physical assessment. CRC Crit Rev Biochem. 1975 Aug;3(2):141–164. doi: 10.3109/10409237509102555. [DOI] [PubMed] [Google Scholar]
- Clegg J. S. Properties and metabolism of the aqueous cytoplasm and its boundaries. Am J Physiol. 1984 Feb;246(2 Pt 2):R133–R151. doi: 10.1152/ajpregu.1984.246.2.R133. [DOI] [PubMed] [Google Scholar]
- Cleland W. W. Determining the chemical mechanisms of enzyme-catalyzed reactions by kinetic studies. Adv Enzymol Relat Areas Mol Biol. 1977;45:273–387. doi: 10.1002/9780470122907.ch4. [DOI] [PubMed] [Google Scholar]
- Cornish-Bowden A. The effect of natural selection on enzymic catalysis. J Mol Biol. 1976 Feb 15;101(1):1–9. doi: 10.1016/0022-2836(76)90062-0. [DOI] [PubMed] [Google Scholar]
- Friedrich P. Dynamic compartmentation in soluble enzyme systems. Acta Biochim Biophys Acad Sci Hung. 1974;9(3):159–173. [PubMed] [Google Scholar]
- Karplus M., McCammon J. A. Dynamics of proteins: elements and function. Annu Rev Biochem. 1983;52:263–300. doi: 10.1146/annurev.bi.52.070183.001403. [DOI] [PubMed] [Google Scholar]
- Keleti T. Effect of steric changes in the protein on the kinetics of enzymic reactions. II. Steady-state treatment of reactions with one substrate. Acta Biochim Biophys Acad Sci Hung. 1968;3(3):247–258. [PubMed] [Google Scholar]
- Knowles J. R. Whither enzyme mechanisms? FEBS Lett. 1976 Feb 4;62(Suppl):E53–E61. doi: 10.1016/0014-5793(76)80854-x. [DOI] [PubMed] [Google Scholar]
- Koshland D. E., Jr Role of flexibility in the specificity, control and evolutiion of enzymes. FEBS Lett. 1976 Feb 4;62(Suppl):E47–E52. doi: 10.1016/0014-5793(76)80853-8. [DOI] [PubMed] [Google Scholar]
- Masters C. J. Interactions between soluble enzymes and subcellular structure. CRC Crit Rev Biochem. 1981;11(2):105–143. doi: 10.3109/10409238109108700. [DOI] [PubMed] [Google Scholar]
- McConkey E. H. Molecular evolution, intracellular organization, and the quinary structure of proteins. Proc Natl Acad Sci U S A. 1982 May;79(10):3236–3240. doi: 10.1073/pnas.79.10.3236. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ricard J. Generalized microscopic reversibility, kinetic co-operativity of enzymes and evolution. Biochem J. 1978 Dec 1;175(3):779–791. doi: 10.1042/bj1750779. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Somogyi B., Damjanovich S. A theoretical model for calculation of the rate constant of enzyme-substrate complex formation. I. Calculation of rate constant in the case of motionless enzyme molecule without nonspecific intermolecular forces. Acta Biochim Biophys Acad Sci Hung. 1973;8(3):153–160. [PubMed] [Google Scholar]
- Welch G. R., Keleti T. On the "cytosociology" of enzyme action in vivo: a novel thermodynamic correlate of biological evolution. J Theor Biol. 1981 Dec 21;93(4):701–735. doi: 10.1016/0022-5193(81)90336-2. [DOI] [PubMed] [Google Scholar]
- Welch G. R. On the free energy "cost of transition" in intermediary metabolic processes and the evolution of cellular infrastructure. J Theor Biol. 1977 Sep 21;68(2):267–291. doi: 10.1016/0022-5193(77)90165-5. [DOI] [PubMed] [Google Scholar]
- Welch G. R. On the role of organized multienzyme systems in cellular metabolism: a general synthesis. Prog Biophys Mol Biol. 1977;32(2):103–191. [PubMed] [Google Scholar]
- Welch G. R., Somogyi B., Damjanovich S. The role of protein fluctuations in enzyme action: a review. Prog Biophys Mol Biol. 1982;39(2):109–146. doi: 10.1016/0079-6107(83)90015-9. [DOI] [PubMed] [Google Scholar]
- Wombacher H. Molecular compartmentation by enzyme cluster formation. A view over current investigations. Mol Cell Biochem. 1983;56(2):155–164. doi: 10.1007/BF00227216. [DOI] [PubMed] [Google Scholar]