Kinetic Solvent Viscosity Effects as Probes for Studying the Mechanisms of Enzyme Action

The study of enzyme reaction mechanisms is fundamentally important to our understanding of biochemistry, cellular metabolism, and drug development. This Perspective focuses on the use of kinetic solvent viscosity effects (KSVEs) to study enzyme reactions. This technique is easily implemented and uses steady-state kinetic analyses to probe whether substrate binding is diffusion-controlled and whether product release is the rate-limiting step in the catalytic cycle. In addition, KSVEs can identify isomerization steps that are important for catalysis. The use of KSVEs in combination with other techniques, such as kinetic isotope effects, pH effects, and site-directed mutagenesis, can provide a detailed view of the mechanism of enzyme action. We present the basic theory, important experimental considerations, and potential outcomes and briefly discuss some examples from the literature. The derivation of the equations that are important for data analysis is also presented

C4a-Hydroperoxyflavin Formation in <i>N</i>‑Hydroxylating Flavin Monooxygenases Is Mediated by the 2′-OH of the Nicotinamide Ribose of NADP⁺

Flavin-dependent monooxygenases must stabilize a C4a-hydroperoxyflavin intermediate to hydroxylate their respective substrates. Formation and decay of the C4a-hydroperoxyflavin were monitored under rapid reaction kinetic conditions in SidA, an <i>N</i>-hydroxylating monooxygenase involved in siderophore biosynthesis. Solvent kinetic isotope effect studies of flavin oxidation indicate that both hydrogen peroxide elimination and water elimination occur via abstraction of hydrogen from the N5 of the flavin. Kinetic isotope effect and density functional theory results are consistent with the transfer of a proton from the 2′-OH of the nicotinamide ribose of nicotinamide adenine dinucleotide phosphate (NADP⁺) to the C4a-peroxyflavin to form the C4a-hydroperoxyflavin. This represents a novel role for NADP⁺ in the reaction of flavin-dependent enzymes

Mechanism of <i>N</i>‑Hydroxylation Catalyzed by Flavin-Dependent Monooxygenases

Aspergillus fumigatus siderophore (SidA), a member of class B flavin-dependent monooxygenases, was selected as a model system to investigate the hydroxylation mechanism of heteroatom-containing molecules by this group of enzymes. SidA selectively hydroxylates ornithine to produce <i>N</i>⁵-hydroxyornithine. However, SidA is also able to hydroxylate lysine with lower efficiency. In this study, the hydroxylation mechanism and substrate selectivity of SidA were systematically studied using DFT calculations. The data show that the hydroxylation reaction is initiated by homolytic cleavage of the O–O bond in the <i>C</i>^4a-hydroperoxyflavin intermediate, resulting in the formation of an internal hydrogen-bonded hydroxyl radical (HO^•). As the HO^• moves to the ornithine N⁵ atom, it rotates and donates a hydrogen atom to form the <i>C</i>^4a-hydroxyflavin. Oxygen atom transfer yields an aminoxide, which is subsequently converted to hydroxylamine via water-mediated proton shuttling, with the water molecule originating from dehydration of the <i>C</i>^4a-hydroxyflavin. The selectivity of SidA for ornithine is predicted to be the result of the lower energy barrier for oxidation of ornithine relative to that of lysine (16 vs 24 kcal/mol, respectively), which is due to the weaker stabilizing hydrogen bond between the incipient HO^• and O3′ of the ribose ring of NADP⁺ in the transition state for lysine

TcUGM activity with UDP-Gal<i>f</i>.

<p>TcUGM was reduced with either 20 mM dithionite (▪), 0.5 mM NADPH(•), or 2.5 mM NADH(▴). Reactions were performed with 200 nM TcUGM incubated with varying concentrations of substrate for 1 min at 37°C. The data were fit to the Michaelis-Menten equation. Summary of data is presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032918#pone-0032918-t003" target="_blank">Table 3</a>.</p

Fluorescence anisotropy assay to measure the affinity of UDP-Gal<i>p</i> to TcUGM.

<p>A) UDP-rhodamine chromophore used in the fluorescence anisotropy experiments. B) Fluorescence polarization binding assay. The binding of UDP-Gal<i>p</i> to chemically reduced TcUGM was monitored by measuring the changes in anisotropy as it displaces UDP-rhodamine from the active site. The K<i>_d</i> values were obtained using equation 3.</p

Anaerobic reduction of TcUGM with NAD(P)H.

<p>Reduction was monitored using the stopped flow spectrophotometer at 15°C. The data was collected from 2 ms to 100 s on a logarithmic timescale. A) Changes in the spectra of oxidized TcUGM after mixing with 0.5 mM NADPH over 23 s. B) Traces of the flavin reduction at various concentrations of NADPH. The data were fit to a single exponential decay equation. C) The k<i>_obs</i> values were plotted as a function NADPH (•) and NADH (▴) concentrations and fitted using the equation 2.</p

Chemical mechanism of TcUGM.

<p>The reaction requires the oxidized flavin cofactor (<b>a</b>) to be reduced for activity. First, NADPH binds to the oxidized enzyme (<b>b</b>), and only after the flavin is reduced (<b>c</b>) will UDP-Gal<i>p</i> bind (<b>d</b>). The flavin then acts as a nucleophile attacking the C1 of galactose and forming a flavin sugar adduct (<b>e</b>), which occurs rapidly (<b>f</b>). This is followed by ring opening and recyclization (<b>g</b>). The rate limiting step in the reaction corresponds to either galactose isomerization or reattachment of the UDP (<b>f</b> to <b>g</b>). We postulate that the rate limiting step is the isomerization step. The final step is release of UDP-Gal<i>f</i>, which occurs rapidly. The enzyme can proceed to the next reaction cycle or be slowly oxidized by molecular oxygen (<b>h</b> to <b>a</b>).</p

Trapping of a covalent flavin intermediate.

<p>A) HPLC traces of the flavin sugar adduct from free FAD. The peak eluding at 22.5 min is the adduct, while the second peak at 23.6 min is FAD. B) Spectrum of the C4a- hydroxyflavin-galactose adduct. C) High resolution mass spectrometry results of the peak containing the flavin adduct. The inset shows the structure of the adduct with a hydroxyl group at the flavin C4a-position.</p

TcUGM Reduction by NAD(P)H^a.

a<p>Reactions were measured under anaerobic conditions at 15°C in 50 mM phosphate buffer pH 7.0.</p

Viscosity effect on k_cat.

<p>The effect of viscosity was determined by measuring the activity of TcUGM as a function of increasing concentrations of glycerol. The data was fit to a linear equation; the dashed line depicts the results of a diffusion controlled reaction. This line has a slope of 1.</p