Analysis of Kinetic Data

Swinbourne, E. S.

doi:10.1007/978-1-4684-7685-9

Cited by 88 publications

(33 citation statements)

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“…To our knowledge, this behavior has not been reported previously for rhodopsin. Concave Arrhenius plots can be attributed to several factors, although the most common interpretation is that at least two different rate-limiting steps are involved (73). With this interpretation in mind, we fit our WT rhodopsin data assuming two different activation energies may be present, and we find E a values of ϳ16 kcal/mol for the lower temperature range (37-47.5°C) and ϳ103 kcal/ mol for the higher temperature range (47.5-55°C).…”

Section: Arrhenius Analysis Indicates the Thermal Decay In Rhodopsin mentioning

confidence: 99%

“…Alternatively, the lower E a observed at the lower temperatures suggests that at these temperatures another process also contributes to Schiff base hydrolysis, one that occurs more efficiently at lower temperatures (such as proton tunneling) than the process that dominates at higher temperatures. Another possibility is that the pre-exponential factor in the Arrhenius analysis has changed; the pre-exponential factor is related to steric factors and/or the efficiency with which the collisions lead to a productive reaction (73).…”

Section: Arrhenius Analysis Indicates the Thermal Decay In Rhodopsin mentioning

confidence: 99%

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Stability of Dark State Rhodopsin Is Mediated by a Conserved Ion Pair in Intradiscal Loop E-2

Janz

Fay

Farrens

2003

Journal of Biological Chemistry

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The rhodopsin crystal structure reveals that intradiscal loop E-2 covers the 11-cis-retinal, creating a "retinal plug." Recently, we noticed the ends of loop E-2 are linked by an ion pair between residues Arg-177 and Asp-190, near the highly conserved disulfide bond. This ion pair appears biologically significant; it is conserved in almost all vertebrate opsins and may occur in other G-protein-coupled receptors. We report here that the Arg-177/Asp-190 ion pair is critical for the folding and stability of dark state rhodopsin. We find ion pair mutants that regenerate with retinal are functionally and spectrally wild-type-like yet thermally unstable in their dark state because of rapid hydrolysis of the retinal Schiff base linkage. Surprisingly, Arrhenius analysis indicates that the activation energies for the hydrolysis process are similar between the ion pair mutants and wild-type rhodopsin. Furthermore, the ion pair mutants do not show increased reactivity toward hydroxylamine, suggesting that their instability is not caused by an increased exposure to bulk solvent. Our results indicate that the loop E-2 ion pair is important for rhodopsin stability and thus suggest that retinitis pigmentosa observed in patients with Asp-190 mutations may in part be the result of thermally unstable rhodopsin proteins.

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Section: Arrhenius Analysis Indicates the Thermal Decay In Rhodopsin mentioning

confidence: 99%

Section: Arrhenius Analysis Indicates the Thermal Decay In Rhodopsin mentioning

confidence: 99%

Stability of Dark State Rhodopsin Is Mediated by a Conserved Ion Pair in Intradiscal Loop E-2

Janz

Fay

Farrens

2003

Journal of Biological Chemistry

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“…Absorbance readings were taken for 10 half-lives, and whenever possible those covering 3-4 half-lives were analyzed for first-order behaviour, in the normal way (7). In cases where the infinity readings were not stable (vide supra), values were estimated by the Kezdy-Swinbourne method (24).…”

Section: Methodsmentioning

confidence: 99%

Catalysis of the deprotonation of β-keto esters by cyclodextrins

Tee¹,

Iyengar²,

Takasaki³

1993

Can. J. Chem.

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. Can. J. Chem. 71, 2139 (1993). The rates of deprotonation of several P-keto esters in basic aqueous solution are elevated by a -and P-cyclodextrin (a-and P-CD). In most cases saturation kinetics are observed that indicate fairly strong binding of the esters to the CDs (K, = 0.22-1 1 mM); catalytic ratios (k,/k,) are in the range 1.9-17. For esters of the form RCO-CH,COOEt with both a-and P-CD the values of Kd and k,/k, show little sensitivity to the acyl group, RCO (R = Me, Et, Pr, i-Pr), and for 2-carboethoxycyclopentanone, a cyclic analogue, these parameters are similar. In contrast, for R-COCH,CO-OR' (R = Me or Et; R' = Me, Et, allyl) there is a marked dependence of the parameters on the alkoxyl group, OR'. These results suggest that the P-keto esters studied bind to the CDs with their alkoxyl groups in the CD cavity and that the catalysis ensues from the complexes thus formed. Variations in two other kinetic parameters, k, = k,/K, (substrate selectivity) and KT, = k,/k, (apparent constant for dissociation of CD from the transition state) support this interpretation. Apparent second-order rate constants for the reaction of the esters with neutral CD (k, = k,/K,) are 1900-360 000 M-' s-I (at pH ; = lo), whereas for hydroxide ion attack on ethyl acetoacetate koH = 5500 M-' s-I. Assuming the pK,s of the CDs are 12.2 and 12.3, deprotonation of the esters by the CD anions has rate constants of lo5 to 5 x lo7 M-' s-'. Thus, binding of the P-keto esters in the CD cavities, adjacent to a basic oxyanion site, enhances the reactivity of the CD anions towards these weak carbon acids by at least 2-4 orders of magnitude.OSWALD S. TEE, N. RANI IYENGAR et BRYAN K. TAKASAKI. Can. J. Chem. 71, 2 139 (1993). U s vitesses de dkprotonation de plusieurs p-cktoesters en solutions aqueuses basiques sont augmentkes par la prksence d'a-ou de P-cyclodextrine (a-et P-CD). Dans la plupart des cas, on observe des cinktiques de saturation qui indiquent la prksence d'une forte liaison des esters sur les CD (K, = 0,022-1 1 mM); les rapports catalytiques (k,/k,) sont de l'ordre de 1,9 2 1 17. Pour des esters de la forme RCO-CH,COOEt avec des CD tant a que P, les valeurs de Kd et de k,/k, ne prksentent qu'une faible sensibilitk i la nature du groupe acyle, RCO (R = Me, Et, Pr, i-Pr); pour le 2-carbokthoxycyclopentanone, un analogue cyclique, ces paramktres sont semblables. Par ailleurs, pour les esters du type R-COCH,CO-OR' (R = Me ou Et; R' = Me, Et ou allyle), il existe une dkpendance marquke des paramktres sur la nature du groupe alcoxyle, OR'. Ces rksultats suggkrent que les p-cktoesters se lient par leurs groupes alcoxyles ?I la cavitk des CD et que la catalyse dkcoule de la formation de ces complexes. Les variations dans deux autres paramktres cinktiques, k, = k,/K, (sklectivitk du substrat) et KT, = k,/k, (constante apparente de la dissociation de la CD de l'ktat de transition) sont en accord avec cette interpretation. Les constantes apparentes de vitesse du deuxikme ordre pour la rkaction des esters avec de la CD neutre (k, = kc/Kd)...

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“…4͑a͔͒ of the graph to a least squares regression following the method of initial rates. 50 Rate constants and reaction orders with respect to both QH 2 and the reactive surface sites can be found using Eq. ͑3͒ ͑adapted from the method used by Stack et al 40 …”

Section: B Kineticsmentioning

confidence: 99%

Reduction of crystalline iron(III) oxyhydroxides using hydroquinone: Influence of phase and particle size

Anschutz

2005

Geochem. Trans.

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Iron oxides and oxyhydroxides are common and important materials in the environment, and they strongly impact the biogeochemical cycle of iron and other species at the Earth's surface. These materials commonly occur as nanoparticles in the 3 -10 nm size range. This paper presents quantitative results demonstrating that iron oxide reactivity is particle size dependent. The rate and extent of the reductive dissolution of iron oxyhydroxide nanoparticles by hydroquinone in batch experiments were measured as a function of particle identity, particle loading, and hydroquinone concentration. Rates were normalized to surface areas determined by both transmission electron microscopy and Braunauer-Emmett-Teller surface. Results show that surface-area-normalized rates of reductive dissolution are fastest ͑by as much as 100 times͒ in experiments using six-line ferrihydrite versus goethite. Furthermore, the surface-area-normalized rates for 4 nm ferrihydrite nanoparticles are up to 20 times faster than the rates for 6 nm ferrihydrite nanoparticles, and the surface-area-normalized rates for 5 ϫ 64 nm goethite nanoparticles are up to two times faster than the rates for 22ϫ 367 nm goethite nanoparticles.

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Analysis of Kinetic Data

Cited by 88 publications

References 0 publications

Stability of Dark State Rhodopsin Is Mediated by a Conserved Ion Pair in Intradiscal Loop E-2

Stability of Dark State Rhodopsin Is Mediated by a Conserved Ion Pair in Intradiscal Loop E-2

Catalysis of the deprotonation of β-keto esters by cyclodextrins

Reduction of crystalline iron(III) oxyhydroxides using hydroquinone: Influence of phase and particle size

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