Binding isotope effects: boon and bane

Schramm, Vern L.

doi:10.1016/j.cbpa.2007.07.013

Cited by 72 publications

(58 citation statements)

References 37 publications

(53 reference statements)

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“…Interestingly, the following isomerization step (k 2 in Schemes 2 and 3) shows an inverse isotope effect (k 2H /k 2D of ∼0.60). This indicates that upon isomerization to the active P2O-glucose complex, the C2-H bond is stiffer and more constrained compared with that in the free D-glucose (53,54). However, since the accuracy of k 2H /k 2D measured experimentally is limited due to limitation of the measurement, at this point, we refrain from making any mechanistic interpretation of the inverse isotope effect observed.…”

Section: Discussionmentioning

confidence: 99%

Kinetic Mechanism of Pyranose 2-Oxidase from Trametes multicolor

et al. 2009

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Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoprotein oxidase that catalyzes the oxidation of aldopyranoses by molecular oxygen to yield the corresponding 2-keto-aldoses and hydrogen peroxide. P2O is the first enzyme in the class of flavoprotein oxidases, for which a C4a-hydroperoxy-flavin adenine dinucleotide (FAD) intermediate has been detected during the oxidative half-reaction. In this study, the reduction kinetics of P2O by D-glucose and 2-d-D-glucose at pH 7.0 was investigated using stopped-flow techniques. The results indicate that D-glucose binds to the enzyme with a two-step binding process; the first step is the initial complex formation, while the second step is the isomerization to form an active Michaelis complex (E-Fl ox :G). Interestingly, the complex (E-Fl ox : G) showed greater absorbance at 395 nm than the oxidized enzyme, and the isomerization process showed a significant inverse isotope effect, implying that the C2-H bond of D-glucose is more rigid in the E-Fl ox :G complex than in the free form. A large normal primary isotope effect (k H /k D = 8.84) was detected in the flavin reduction step. Steady-state kinetics at pH 7.0 shows a series of parallel lines. Kinetics of formation and decay of C-4a-hydroperoxy-FAD is the same in absence and presence of 2-keto-D-glucose, implying that the sugar does not bind to P2O during the oxidative half-reaction. This suggests that the kinetic mechanism of P2O is likely to be the ping-pong-type where the sugar product leaves prior to the oxygen reaction. The movement of the active site loop when oxygen is present is proposed to facilitate the release of the sugar product. Correlation between data from presteady-state and steady-state kinetics has shown that the overall turnover of the reaction is limited by the steps of flavin reduction and decay of C4a-hydroperoxy-FAD.Pyranose 2-oxidase (P2O; 1 pyranose:oxygen 2-oxidoreductase; EC 1.13.10) is a flavoprotein oxidase catalyzing the oxidation of several aldopyranoses by molecular oxygen at the C2 position to yield the corresponding 2-keto-aldoses and hydrogen peroxide (Scheme 1) (1). The enzyme was identified and isolated from several species of fungi (2) and is thought to be involved in lignin degradation by providing H 2 O 2 for lignin peroxidase (3). H 2 O 2 production by P2O can also be important for maintaining an oxidative stress level that helps control the growth of other competing organisms (4). The regiospecific oxidation at the pyranose C2 position catalyzed by P2O is a very useful reaction for carbohydrate syntheses since it can be applied in the syntheses of D-tagatose (5), cortalcerone (6), and other valuable sugar synthons (2, 4).P2O from Trametes multicolor is a homotetrameric enzyme with a native molecular mass of 270 kDa (subunit molecular mass of 68 kDa) (1). Each subunit contains one flavin adenine dinucleotide (FAD) covalently attached to the N3 of His167 (7). The enzyme sequence and structure indicate that P2O belongs to the glucose-methanol-choline (GMC) oxidored...

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Section: Discussionmentioning

confidence: 99%

Kinetic Mechanism of Pyranose 2-Oxidase from Trametes multicolor

et al. 2009

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“…BIEs are suited for studying tautomerism because, like vibrational spectroscopy, they are also influenced by alterations in vibrational frequencies between the bound and the unbound states of a ligand (Schramm 2007). This approach has been used for characterizing the tautomeric forms of OxyTPP bound to the TPP riboswitch ( Fig.…”

Section: Methods For Studying Tautomerism In Nucleic Acidsmentioning

confidence: 99%

Role of tautomerism in RNA biochemistry

Singh

Fedeles

Essigmann

2014

RNA

121

117

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Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solventexchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.

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“…Ligand-receptor interactions can be both attractive and repulsive, involving hydrogen bonding, van der Waals, cation-π, π-π, ion-ion, dipoledipole, steric, and hydrophobic interactions with the receptor, with water channels and bridging water molecules mediating hydrogen bonds, as well as metal-ion coordination, as we have recently demonstrated in the latter case (15,16). Therefore, molecular shape can be considered a "straw-man" alternative to the vibration theory when describing the differing affinities of ligands bound to GPCRs (17,18), including isotopomers (19,20). Some of these attractive and repulsive interactions were identified in 1940 by Pauling and Delbrück (21), who note that interacting biomolecules "must have complementary surfaces, like die and coin, and also a complementary distribution of active groups."…”

Section: Significancementioning

confidence: 99%

Implausibility of the vibrational theory of olfaction

Block

Jang

Matsunami

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

115

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The vibrational theory of olfaction assumes that electron transfer occurs across odorants at the active sites of odorant receptors (ORs), serving as a sensitive measure of odorant vibrational frequencies, ultimately leading to olfactory perception. A previous study reported that human subjects differentiated hydrogen/ deuterium isotopomers (isomers with isotopic atoms) of the musk compound cyclopentadecanone as evidence supporting the theory. Here, we find no evidence for such differentiation at the molecular level. In fact, we find that the human musk-recognizing receptor, OR5AN1, identified using a heterologous OR expression system and robustly responding to cyclopentadecanone and muscone, fails to distinguish isotopomers of these compounds in vitro. Furthermore, the mouse (methylthio)methanethiol-recognizing receptor, MOR244-3, as well as other selected human and mouse ORs, responded similarly to normal, deuterated, and 13 C isotopomers of their respective ligands, paralleling our results with the musk receptor OR5AN1. These findings suggest that the proposed vibration theory does not apply to the human musk receptor OR5AN1, mouse thiol receptor MOR244-3, or other ORs examined. Also, contrary to the vibration theory predictions, muscone-d 30 lacks the 1,380-to 1,550-cm −1 IR bands claimed to be essential for musk odor. Furthermore, our theoretical analysis shows that the proposed electron transfer mechanism of the vibrational frequencies of odorants could be easily suppressed by quantum effects of nonodorant molecular vibrational modes. These and other concerns about electron transfer at ORs, together with our extensive experimental data, argue against the plausibility of the vibration theory.olfaction | isotopomers | cyclopentadecanone | muscone | electron transfer I n 1870, the British physician William Ogle wrote: "As in the eye and the ear the sensory impression is known to result not from the contact of material particles given off by the object seen or heard, but from waves or undulations of the ether or the air, one cannot but suspect that the same may be true in the remaining sense, and that the undulatory theory of smell. . . [may be] the true one" (1, 2). Of the 29 different "theories of odour" listed in the 1967 edition of The Chemical Senses (3), nine associate odor with vibrations, particularly those theories championed by Dyson (4, 5) and Wright (6-8). However, the premise that olfaction involves detection of vibrational frequencies of odorants remains highly speculative because neither the structures of the odorant receptors (ORs) nor the binding sites or the activation mechanisms triggered upon odorant binding to ORs have been established. In 1996-1997, Turin (9-12) elaborated on the undulatory theory of smell, as considered in more detail below, and suggested that a mechanism analogous to inelastic electron tunneling spectroscopy (13) may be involved, where tunneling electrons in the receptor probe the vibrational frequencies of odorants. In 2013, Gane et al. (14) In judging the plausibility...

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Binding isotope effects: boon and bane

Cited by 72 publications

References 37 publications

Kinetic Mechanism of Pyranose 2-Oxidase from Trametes multicolor

Kinetic Mechanism of Pyranose 2-Oxidase from Trametes multicolor

Role of tautomerism in RNA biochemistry

Implausibility of the vibrational theory of olfaction

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