title: Validation of fractal-like kinetic models by time-resolved binding kinetics of dansylamide and carbonic anhydrase in crowded media.
abstract: Kinetic studies of biochemical reactions are typically carried out in a dilute solution that rarely contains anything more than reactants, products, and buffers. In such studies, mass-action-based kinetic models are used to analyze the progress curves. However, intracellular compartments are crowded by macromolecules. Therefore, we investigated the adequacy of the proposed generalizations of the mass-action model, which are meant to describe reactions in crowded media. To validate these models, we measured time-resolved kinetics for dansylamide binding to carbonic anhydrase in solutions crowded with polyethylene glycol and Ficoll. The measured progress curves clearly show the effects of crowding. The fractal-like model proposed by Savageau was used to fit these curves. In this model, the association rate coefficient k(a) allometrically depends on concentrations of reactants. We also considered the fractal kinetic model proposed by Schnell and Turner, in which k(a) depends on time according to a Zipf-Mandelbrot distribution, and some generalizations of these models. We found that the generalization of the mass-action model, in which association and dissociation rate coefficients are concentration-dependent, represents the preferred model. Other models based on time-dependent rate coefficients were inadequate or not preferred by model selection criteria.
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Neff
authors.forename: Chetan P
authors.initials: CP
authors.lastname: Offord
authors.forename: Ariel J
authors.initials: AJ
authors.lastname: Caride
authors.forename: Emanuel E
authors.initials: EE
authors.lastname: Strehler
authors.forename: Franklyn G
authors.initials: FG
authors.lastname: Prendergast
authors.forename: Zeljko
authors.initials: Z
authors.lastname: Bajzer
mesh_terms: D000818:Animals; D002256:Carbonic Anhydrases / Q000737:chemistry / Q000378:metabolism*; D002417:Cattle; D003619:Dansyl Compounds / Q000737:chemistry / Q000378:metabolism*; D005362:Ficoll / Q000737:chemistry; D017709:Fractals; D007700:Kinetics; D016018:Least-Squares Analysis; D046911:Macromolecular Substances / Q000737:chemistry*; D008956:Models, Chemical; D008970:Molecular Weight; D011092:Polyethylene Glycols / Q000737:chemistry; D011485:Protein Binding; D015203:Reproducibility of Results; D013997:Time Factors
chemical_list: D003619:Dansyl Compounds; D046911:Macromolecular Substances; C001026:5-dimethylaminonaphthalene-1-sulfonamide; D005362:Ficoll; D011092:Polyethylene Glycols; D002256:Carbonic Anhydrases