Shapes of curves of pH-dependence of reactions

Dixon, H. B. F.

doi:10.1042/bj1310149

Cited by 60 publications

(57 citation statements)

References 4 publications

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“…2). The macroscopic pK a values derived from curve-fitting are probably a poor reflection of the true pK a values owing to (i) the narrowness of the bell in the plot (30) and (ii) the relatively low number of points defining the bell. For this reason the plot is of qualitative value in indicating the presence of kinetically influential ionizations, but we do not place too much promi- (Fig.…”

Section: Resultsmentioning

confidence: 99%

Optimizing the Michaelis Complex of Trimethylamine Dehydrogenase

Basran

Sutcliffe

Scrutton

2001

Journal of Biological Chemistry

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Recent evidence from isotope studies supports the view that catalysis by trimethylamine dehydrogenase (TMADH) proceeds from a Michaelis complex involving trimethylamine base and not, as thought previously, trimethylammonium cation. In native TMADH reduction of the flavin by substrate (perdeuterated trimethylamine) is influenced by two ionizations in the Michaelis complex with pK a values of 6.5 and 8.4; maximal activity is realized in the alkaline region. The latter ionization has been attributed to residue His-172 and, more recently, the former to the ionization of substrate itself. In the Michaelis complex, the ionization of substrate (pK a ϳ 6.5 for perdeuterated substrate) is perturbed by ϳ؊3.3 to ؊3.6 pH units compared with that of free trimethylamine (pK a ‫؍‬ 9.8) and free perdeuterated trimethylamine (pK a ‫؍‬ 10.1), respectively, thus stabilizing trimethylamine base by ϳ2 kJ mol ؊1. We show, by targeted mutagenesis and stoppedflow studies that this reduction of the pK a is a consequence of electronic interaction with residues Tyr-60 and His-172, thus these two residues are key for optimizing catalysis in the physiological pH range. We also show that residue Tyr-174, the remaining ionizable group in the active site that we have not targeted previously by mutagenesis, is not implicated in the pH dependence of flavin reduction. Formation of a Michaelis complex with trimethylamine base is consistent with a mechanism of amine oxidation that we advanced in our previous computational and kinetic studies which involves nucleophilic attack by the substrate nitrogen atom on the electrophilic C4a atom of the flavin isoalloxazine ring. Stabilization of trimethylamine base in the Michaelis complex over that in free solution is key to optimizing catalysis at physiological pH in TMADH, and may be of general importance in the mechanism of other amine dehydrogenases that require the unprotonated form of the substrate for catalysis.The oxidation of amines is widespread in biology and a number of enzymes have evolved to catalyze these reactions. The oxidoreductases responsible for these reactions can be grouped broadly into the flavoprotein and quinoprotein families. The mechanism of amine oxidation catalyzed by the quinoprotein amine oxidases is understood reasonably well and occurs through the formation of enzyme-substrate covalent adducts with topaquinone or tryptophan tryptophylquinone redox centers (1, 2). In some cases C-H bond cleavage by these enzymes has been shown to involve quantum tunneling mechanisms for transfer of the H nucleus to a base in the enzyme active site (3-5). By contrast, the mechanism of amine oxidation by flavoproteins is understood less well. Although H-transfer has been shown to occur by vibrationally assisted tunneling in two flavoprotein amine dehydrogenases (6, 7), the chemical mechanism of oxidation remains to be established. The cleavage of the reactive C-H bond in amine substrates by flavoproteins has been reviewed (8, 9) and discussed in terms of (i) a proton abstraction mechanism invo...

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Section: Resultsmentioning

confidence: 99%

Optimizing the Michaelis Complex of Trimethylamine Dehydrogenase

Basran

Sutcliffe

Scrutton

2001

Journal of Biological Chemistry

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“…The polarization vectors for a massless spin 1 particle with momentum k utilize an arbitrary gauge-fixing "reference"momentum r for each gauge boson [31], which can be chosen to be any light-like momentum except k. They can be written as:…”

Section: A Massless Spin 1/2 and 1 Wave Functionsmentioning

confidence: 99%

Direct production of lightest Regge resonances

et al. 2011

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We discuss direct production of Regge excitations in the collisions of massless four-dimensional superstring states, focusing on the first excited level of open strings ending on D-branes extending into higher dimensions. We construct covariant vertex operators and identify "universal" Regge states with the internal parts either trivial or determined by the world-sheet SCFT describing superstrings propagating on an arbitrary Calabi-Yau manifold. We evaluate the amplitudes involving one such massive state and up to three massless ones and express them in the helicity basis. The most important phenomenological applications of our results are in the context of low-mass string (and large extra dimensions) scenarios in which excited string states are expected to be produced at the LHC as soon as the string mass threshold is reached in the center-of-mass energies of the colliding partons. In order to facilitate the use of partonic cross sections, we evaluate them and tabulate for all production processes: gluon fusion, quark absorbing a gluon, quark-antiquark annihilation and quark-quark scattering.

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“…We first list our conventions (for reviews of spinor helicity methods see e.g. [80,81]). With spinor helicity methods we can express scattering amplitudes in terms of massless Weyl spinors of helicity ± 1 2 ,…”

Section: Calculation Of the Amplitudesmentioning

confidence: 99%

Fully differential single-top-quark cross section in next-to-leading order QCD

et al. 2002

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We present a new next-to-leading order calculation for fully differential single-topquark final states. The calculation is performed using phase space slicing and dipole subtraction methods. The results of the methods are found to be in agreement. The dipole subtraction method calculation retains the full spin dependence of the final state particles. We show a few numerical results to illustrate the utility and consistency of the resulting computer implementations.

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Shapes of curves of pH-dependence of reactions

Cited by 60 publications

References 4 publications

Optimizing the Michaelis Complex of Trimethylamine Dehydrogenase

Optimizing the Michaelis Complex of Trimethylamine Dehydrogenase

Direct production of lightest Regge resonances

Fully differential single-top-quark cross section in next-to-leading order QCD

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