A new method to discriminate between enzyme-kinetic models

Buckwitz, D; Holzhütter, Hermann Georg

doi:10.1016/0898-1221(90)90321-a

Cited by 12 publications

(5 citation statements)

References 48 publications

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“…Comparison of the results obtained by Equation 1 and 2 by the F-test on chi-square indicated that the additional term added to the Equation 1 significantly improved the fits [Cook and Weisberg, 1990; Buckwitz and HolzHütter, 1990] except for three mutants (p.Thr553Asn, p.Ala557, and p.Ser572Trp) discussed below.…”

Section: Patients Materials and Methodsmentioning

confidence: 99%

Functional consequences and structural interpretation of mutations of human choline acetyltransferase

et al. 2011

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Choline acetyltransferase (ChAT; EC 2.3.1.6) catalyzes synthesis of acetylcholine from acetyl-CoA and choline in cholinergic neurons. Mutations in CHAT (MIM # 118490) cause potentially lethal congenital myasthenic syndromes associated with episodic apnea (ChAT-CMS) (MIM # 254210). Here we analyze the functional consequences of 12 missense and 1 nonsense mutations of CHAT in 11 patients. Nine of the mutations are novel. We examine expression of the recombinant missense mutants in Bosc 23 cells, determine their kinetic properties and thermal stability, and interpret the functional effects of 11 mutations in the context of the atomic structural model of human ChAT. Five mutations (p.Trp421Ser, p.Ser498Pro, p.Thr553Asn, p.Ala557Thr, p.Ser572Trp) reduce enzyme expression to <50% of wild-type. Mutations with severe kinetic effects are located in the active-site tunnel (p.Met202Arg, p.Thr553Asn and p.Ala557Thr) or adjacent to the substrate binding site (p.Ser572Trp), or exert their effect allosterically (p.Trp421Ser and p.Ile689Ser). Two mutations with milder kinetic effects (p.Val136Met, p.Ala235Thr) are also predicted to act allosterically. One mutation (p.Thr608Asn) below the nucleotide binding site of CoA enhances dissociation of AcCoA from the enzyme-substrate complex. Two mutations introducing a proline residue into an α-helix (p.Ser498Pro and p.Ser704Pro) impair the thermal stability of ChAT.

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Section: Patients Materials and Methodsmentioning

confidence: 99%

Functional consequences and structural interpretation of mutations of human choline acetyltransferase

et al. 2011

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“…However, we wanted to determine which of the considered models is actually preferable. To that end, we applied three different types of information criteria for model selection, known as the Akaike (AIC), Bayesian (BIC), and Hannan-Quinn (HQIC) criteria (46)(47)(48). These criteria take into account the number of parameters as well as the obtained c 2 o .…”

Section: Model Validation By Least-squares Fittingmentioning

confidence: 99%

“…In addition, we used Zwanzig's model-selection criterion (47,49). This criterion provides a quantitative comparison of fits by two models and determines which of the two models is preferable, or that there is no statistically significant difference in fits by the two models.…”

Section: Model Validation By Least-squares Fittingmentioning

confidence: 99%

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Validation of Fractal-Like Kinetic Models by Time-Resolved Binding Kinetics of Dansylamide and Carbonic Anhydrase in Crowded Media

Neff

Offord

Caride

et al. 2011

Biophysical Journal

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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.

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“…The best model is expected to have the largest MSC and lowest BIC and HQIC values. On the basis of the MSC, BIC, and HQIC values for the different models reported in Table 3A, the best model would have to be model K. We note, however, that the values for model K are not very far from those of the other models, except models A and B, prompting us to include Zwanzig's statistical selection criterion (38,39) (see the Supporting Information for details) in our model search. Zwanzig's statistical selection criterion allows direct comparison of two models, u and V. Accordingly, if T uv > 1.96, model V is more appropriate than model u (with a significance level R ) 0.05), and if |T uv | e 1.96, both models are equally appropriate.…”

Section: Biphasicmentioning

confidence: 99%

Kinetic Analysis of Interaction of BRCA1 Tandem Breast Cancer C-Terminal Domains with Phosphorylated Peptides Reveals Two Binding Conformations

et al. 2008

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Tandem breast cancer C-terminal (BRCT) domains, present in many DNA repair and cell cycle checkpoint signaling proteins, are phosphoprotein binding modules. The best-characterized tandem BRCT domains to date are from the protein BRCA1 (BRCA1-BRCT), an E3 ubiquitin ligase that has been linked to breast and ovarian cancer. While X-ray crystallography and NMR spectroscopy studies have uncovered the structural determinants of specificity of BRCA1-BRCT for phosphorylated peptides, a detailed kinetic and thermodynamic characterization of the interaction is also required to understand how structure and dynamics are connected and therefore better probe the mechanism of phosphopeptide recognition by BRCT domains. Through a global analysis of binding kinetics data obtained from surface plasmon resonance (SPR) and stopped-flow fluorescence spectroscopy, we show that the recognition mechanism is complex and best modeled by two equilibrium conformations of BRCA1-BRCT in the free state that both interact with a phosphopeptide, with dissociation constants (Kd) in the micromolar range. We show that the apparent global dissociation constant derived from this kinetic analysis is similar to the Kd values measured using steady-state SPR, isothermal titration calorimetry, and fluorescence anisotropy. The dynamic nature of BRCA1-BRCT may facilitate the binding of BRCA1 to different phosphorylated protein targets.

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A new method to discriminate between enzyme-kinetic models

Cited by 12 publications

References 48 publications

Functional consequences and structural interpretation of mutations of human choline acetyltransferase

Functional consequences and structural interpretation of mutations of human choline acetyltransferase

Validation of Fractal-Like Kinetic Models by Time-Resolved Binding Kinetics of Dansylamide and Carbonic Anhydrase in Crowded Media

Kinetic Analysis of Interaction of BRCA1 Tandem Breast Cancer C-Terminal Domains with Phosphorylated Peptides Reveals Two Binding Conformations

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