Rapid photodynamics of vitamin B6 coenzyme pyridoxal 5'-phosphate and its Schiff bases in solution

Threonine Aldolase-Catalyzed Enantioselective α-Alkylation of Amino Acids through Unconventional Photoinduced Radical Initiation

Visible light-driven pyridoxal radical biocatalysis has emerged as a promising strategy for the stereoselective synthesis of valuable noncanonical amino acids (ncAAs). Previously, the use of well-tailored photoredox catalysts represented the key to enable efficient pyridoxal phosphate (PLP) enzyme-catalyzed radical reactions. Here, we report a PLP-dependent threonine aldolase-catalyzed asymmetric α-C-H alkylation of abundant amino acids using Katritzky pyridinium salts as alkylating agents. The use of engineered threonine aldolases allowed for this redox-neutral radical alkylation to proceed efficiently, giving rise to challenging α-trisubstituted and -tetrasubstituted ncAA products in a protecting-group-free fashion with excellent enantiocontrol. Mechanistically, this enantioselective α-alkylation capitalizes on the unique reactivity of the persistent enzymatic quinonoid intermediate derived from the PLP cofactor and the amino acid substrate to allow for novel radical C-C coupling. Surprisingly, this photobiocatalytic process does not require the use of well-established photoredox catalysts and operates through an unconventional photoinduced radical generation involving a PLP-derived aldimine. The ability to develop photobiocatalytic reactions without relying on classic photocatalysts or photoenzymes opens up new avenues for advancing stereoselective intermolecular radical reactions that are not known in either organic chemistry or enzymology.

Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media

The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.

PLP-Dependent Enzyme Methionine γ-Lyase: Insights into the Michaelis Complex from Molecular Dynamics and Free Energy Simulations

Methionine γ-lyase (MGL) breaks down methionine, with the help of its cofactor pyridoxal-5'-phosphate (PLP), or vitamin B6. Methionine depletion is damaging for cancer cells but not normal cells, so MGL is of interest as a therapeutic protein. To increase our understanding and help engineer improved activity, we focused on the reactive, Michaelis complex M between MGL, covalently bound PLP, and substrate Met. M is not amenable to crystallography, as it proceeds to products. Experimental activity measurements helped exclude a mechanism that would bypass M . We then used molecular dynamics and alchemical free energy simulations to elucidate its structure and dynamics. We showed that the PLP phosphate has a pKa strongly downshifted by the protein, whether Met is present or not. Met binding affects the structure surrounding the reactive atoms. With Met, the Schiff base linkage between PLP and a nearby lysine shifts from a zwitterionic, keto form to a neutral, enol form that makes it easier for Met to approach its labile, target atom. The Met ligand also stabilizes the correct orientation of the Schiff base, more strongly than in simulations without Met, and in agreement with structures in the Protein Data Bank, where the Schiff base orientation correlates with the presence or absence of a co-bound anion or substrate analogue in the active site. Overall, the Met ligand helps organize the active site for the enzyme reaction by reducing fluctuations and shifting protonation states and conformational populations.

Photoinduced Reductive Dehalogenation of Phenacyl Bromides with Pyridoxal 5'-Phosphate

We describe the photoinduced reductive debromination of phenacyl bromides using pyridoxal 5'-phosphate (PLP). The reaction requires irradiation with cyan or blue light in an anaerobic atmosphere. Mechanistic analysis reveals the formation of the phenacyl radical as an intermediate in the reaction, implying a single electron transfer to phenacyl bromides from a PLP-derived species resulting from excitation by illumination.

Probing mechanistic questions in the PLP- and O2-dependent l-Arg oxidases

The pyridoxal-5'-phosphate-dependent l-Arg oxidases are unusual in that they are able to catalyze 4-electron oxidations of arginine using only the PLP cofactor. No metals or other accessory cosubstrates are involved; only arginine, dioxygen, and PLP. The catalytic cycles of these enzymes are replete with colored intermediates whose accumulation and decay can be monitored spectrophotometrically. This makes the l-Arg oxidases excellent subjects for detailed mechanistic investigations. They are worth studying, because they can teach us much about how PLP-dependent enzymes modulate the cofactor (structure-function-dynamics) and how new activities can arise from existing enzyme scaffolds. Herein we describe a series of experiments that can be used to probe the mechanisms of l-Arg oxidases. These methods by no means originated in our lab but were learned from talented researchers in other enzyme fields (flavoenzymes and Fe(II)-dependent oxygenases) and have been adapted to fit the requirements of our system. We present practical information for expressing and purifying the l-Arg oxidases, protocols for running stopped-flow experiments to examine the reactions with l-Arg and with dioxygen, and a tandem mass spectrometry-based quench-flow assay to follow the accumulation of the products of the hydroxylating l-Arg oxidases.

Two-Photon Excited Fluorescence of NADH-Alcohol Dehydrogenase Complex in a Mixture with Bacterial Enzymes

Thorough study of composition and fluorescence properties of a commercial reagent of active equine NAD-dependent alcohol dehydrogenase expressed and purified from E. coli has been carried out. Several experimental methods: spectral- and time-resolved two-photon excited fluorescence, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, fast protein liquid chromatography, and mass spectrometry were used for analysis. The reagent under study was found to contain also a number of natural fluorophores: free NAD(P)H, NADH-alcohol dehydrogenase, NADPH-isocitrate dehydrogenase, and pyridoxal 5-phosphate-serine hydroxymethyltransferase complexes. The results obtained demonstrated the potential and limitations of popular optical methods as FLIM for separation of fluorescence signals from free and protein-bound forms of NADH, NADPH, and FAD that are essential coenzymes in redox reactions in all living cells. In particular, NADH-alcohol dehydrogenase and NADPH-isocitrate dehydrogenase complexes could not be optically separated in our experimental conditions although fast protein liquid chromatography and mass spectrometry analysis undoubtedly indicated the presence of both enzymes in the molecular sample used. Also, the results of fluorescence, fast protein liquid chromatography, and mass spectrometry analysis revealed a significant contribution of the enzyme-bound coenzyme pyridoxal 5-phosphate to the fluorescence signal that could be separated from enzyme-bound NADH by using bandpass filters, but could effectively mask contribution from enzyme-bound FAD because the fluorescence spectra of the species practically overlapped. It was shown that enzyme-bound pyridoxal 5-phosphate fluorescence can be separated from enzyme-bound NAD(P)H and FAD through analysis of short fluorescence decay times of about tens of picoseconds. However, this analysis was found to be effective only at relatively high number of peak photon counts in recorded fluorescence signals. The results obtained in this study can be used for interpretation of fluorescence signals from a mixture of enzyme-bound fluorophores and should be taken into consideration when determining the intracellular NADH/FAD ratio using FLIM.

Enantioselective Dynamic Exchange Reactions of Imines

Although dynamic reactions of imines have been extensively studied, the dynamic behaviors manipulated by chirality remain nearly unexplored. In this work, enantioselective amine exchange reactions were demonstrated as a first example via the reaction of enantiomeric chiral amines such as natural amino acids with a series of innovative axially chiral 1,1'-binaphthyl-2,2'-diamine (BNDA)-based imines that were prepared from the condensation reactions between BNDA and salicylaldehyde (SA) or its derivatives. This enantioselective dynamic behavior can be directly indicated by the degree of the fluorescence response of the R-configuration of imines to the d-enantiomer of chiral amine, because the released BNDA can serve as the fluorescence signal output when the amine exchange reaction occurs, which is far higher than the response to its l-enantiomer under identical experimental conditions. For the S-configuration of chiral imines, the fluorescence response is the opposite. The enantioselective exchange reaction can be tuned by altering the electron-withdrawing or electron-donating capability of the substituent at position 4 or 5 of the SA part of chiral imines. Not only o-OH groups in SA-based imines but also protic solvents used as reaction media were found to be important to the dynamic behavior at high rates.

The Effect of Visible Light on the Catalytic Activity of PLP-Dependent Enzymes

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a versatile class of biocatalysts and feature a variety of industrial applications. However, PLP is light sensitive and can cause inactivation of enzymes in certain light conditions. As most of the PLP-dependent enzymes are usually not handled in dark conditions, we evaluated the effect of visible light on the activity of PLP-dependent enzymes during production as well as transformation. We tested four amine transaminases, from Chromobacterium violaceum, Bacillus megaterium, Vibrio fluvialis and a variant from Arthrobacter species as well as two lysine decarboxylases, from Selenomonas ruminantium and the LDCc from Escherichia coli. It appeared that five of these six enzymes suffered from a significant decrease in activity by up to 90 % when handled in laboratory light conditions. Surprisingly, only the amine transaminase variant from Arthrobacter species appeared to be unaffected by light exposure and even showed an activation to 150 % relative activity over the course of 6 h regardless of the light conditions.

Non-enzymatic hydrogen sulfide production from cysteine in blood is catalyzed by iron and vitamin B6

Hydrogen sulfide (H2S) plays important roles in metabolism and health. Its enzymatic generation from sulfur-containing amino acids (SAAs) is well characterized. However, the existence of non-enzymatic H2S production from SAAs, the chemical mechanism, and its biological implications remain unclear. Here we present non-enzymatic H2S production in vitro and in blood via a reaction specific for the SAA cysteine serving as substrate and requires coordinated catalysis by Vitamin B6, pyridoxal(phosphate), and iron under physiological conditions. An initial cysteine-aldimine is formed by nucleophilic attack of the cysteine amino group to the pyridoxal(phosphate) aldehyde group. Free or heme-bound iron drives the formation of a cysteine-quinonoid, thiol group elimination, and hydrolysis of the desulfurated aldimine back to pyridoxal(phosphate). The reaction ultimately produces pyruvate, NH3, and H2S. This work highlights enzymatic production is inducible and robust in select tissues, whereas iron-catalyzed production contributes underappreciated basal H2S systemically with pathophysiological implications in hemolytic, iron overload, and hemorrhagic disorders.

Biomimetic Chirality Sensing with Pyridoxal-5'-phosphate

Pyridoxal-5'-phosphate (PLP) is introduced to a biomimetic indicator displacement assay for simultaneous determination of the absolute configuration, enantiomeric composition and concentration of unprotected amino acids, amino alcohols and amines. The chiroptical assay is based on fast imine metathesis with a PLP aryl imine probe to capture the target compound for circular dichroism and fluorescence sensing analysis. The substrate binding yields characteristic Cotton effects that provide information about the target compound ee and the synchronous release of the indicator results in a nonenantioselective off-on fluorescence response that is independent of the enantiomeric sample composition and readily correlated to the total analyte concentration.

Pyridoxal conjugated gold nanoparticles for distinct colorimetric detection of chromium(iii) and iodide ions in biological and environmental fluids

We developed pyridoxal conjugated gold nanoparticles (CAPy-AuNPs) for the selective colorimetric detection of Cr³⁺ and iodide ions in an aqueous medium.

Aspartate aminotransferase: an old dog teaches new tricks

Aspartate aminotransferase (AAT) is a prototypical pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyzes the reversible interconversion of l-aspartate and α-ketoglutarate with oxalacetate and l-glutamate via a ping-pong catalytic cycle in which the pyridoxamine 5'-phosphate enzyme form is an intermediate. There is a bountiful literature on AAT that spans approximately 60years, and much fundamental mechanistic information on PLP dependent reactions has been gained from its study. Here, we review our recent work on AAT, where we again used it as a test bed for fundamental concepts in PLP chemistry. First, we discuss the role that coenzyme protonation state plays in controlling reaction specificity, then ground state destabilization via hyperconjugation in the external aldimine intermediate is examined. The third topic is light enhancement of catalysis of Cα-H deprotonation by PLP in solution and in AAT, which occurs through a triplet state of the external aldimine intermediate. Lastly, we consider recent advances in our analyses of enzyme multiple sequence alignments for the purpose of predicting mutations that are required to interconvert structurally similar but catalytically distinct enzymes, and the application of our program JANUS to the conversion of AAT into tyrosine aminotransferase.

Computational and spectroscopic studies of a new Schiff base 3-hydroxy-4-methoxybenzylidene(2-hydroxyphenyl)amine and molecular structure of its corresponding zwitterionic form

Computational and spectroscopic properties of a novel Schiff base compound, 3-hydroxy-4-methoxybenzylidene(2-hydroxyphenyl)amine were studied. The crystal structures of the title compound and its corresponding zwitterionic form were analyzed by X-ray diffraction. The presence of N-H, C-O and C=N stretching vibrations in IR spectrum strongly suggest that the title compound has zwitterionic form in the solid state. Molecular geometry of the title compound in the ground state has been calculated using the density functional method (DFT) at B3LYP 6-31++G(d,p) basis set and was compared with the experimental data. The calculated results of the title compound show that the optimized geometry can well reproduce the crystal structure. The molecule shows absorption bands at 345 and 363 nm in EtOH. The shoulder-shaped bands at 415 nm can be assigned to n→π(*) transitions. The absorption band is observed at 285 nm in EtOH corresponds to the π→π(*) transitions.

Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases

DOPA decarboxylase, the dimeric enzyme responsible for the synthesis of neurotransmitters dopamine and serotonin, is involved in severe neurological diseases such as Parkinson disease, schizophrenia, and depression. Binding of the pyridoxal-5'-phosphate (PLP) cofactor to the apoenzyme is thought to represent a central mechanism for the regulation of its activity. We solved the structure of the human apoenzyme and found it exists in an unexpected open conformation: compared to the pig kidney holoenzyme, the dimer subunits move 20 Å apart and the two active sites become solvent exposed. Moreover, by tuning the PLP concentration in the crystals, we obtained two more structures with different conformations of the active site. Analysis of three-dimensional data coupled to a kinetic study allows to identify the structural determinants of the open/close conformational change occurring upon PLP binding and thereby propose a model for the preferential degradation of the apoenzymes of Group II decarboxylases.

The role of nonenzymatic glycation and carbonyls in collagen cross-linking for the treatment of keratoconus

PURPOSE

Corneal cross-linking (CXL) is a treatment for keratoconus that eliminates the need for keratoplasty in most patients. However, its molecular mechanisms remain under study. Advanced glycation end products (AGEs) have been suggested by many studies as the causative strengthening agent during CXL, though no studies to date have directly tested this hypothesis.

METHODS

Corneas of young rabbits and sharks were pretreated with pyridoxal hydrochloride and copper ions before CXL. Two known inhibitors of AGE formation, aminoguanidine and rifampicin, were applied during CXL in the treatment solution. Tensile strength tests were conducted after these experiments to detect diminished or accentuated corneal stiffening after CXL. SDS-PAGE was performed on type I collagen cross-linked in the absence and presence of AGE inhibitors.

RESULTS

Pretreatment with pyridoxal hydrochloride resulted in significantly higher corneal stiffening after CXL. AGE inhibitors significantly diminished cross-linking as detected by both tensile strength measurements using whole corneas and gel electrophoresis of in vitro cross-linking of type I collagen in solution, in the presence and absence of the inhibitors. Rifampicin inhibited CXL more significantly than aminoguanidine in gel electrophoresis and tensile strength tests, confirming recent findings on its efficacy as an AGE inhibitor.

CONCLUSIONS

Data presented here suggest that CXL is carbonyl dependent and involves the formation of AGE cross-links. Six possible cross-linking mechanisms are discussed.

Light-enhanced catalysis by pyridoxal phosphate-dependent aspartate aminotransferase

The mechanisms of pyridoxal 5'-phosphate (PLP)-dependent enzymes require substrates to form covalent "external aldimine" intermediates, which absorb light strongly between 410 and 430 nm. Aspartate aminotransferase (AAT) is a prototypical PLP-dependent enzyme that catalyzes the reversible interconversion of aspartate and α-ketoglutarate with oxalacetate and glutamate. From kinetic isotope effects studies, it is known that deprotonation of the aspartate external aldimine C(α)-H bond to give a carbanionic quinonoid intermediate is partially rate limiting in the thermal AAT reaction. We show that excitation of the 430-nm external aldimine absorption band increases the steady-state catalytic activity of AAT, which is attributed to the photoenhancement of C(α)-H deprotonation on the basis of studies with Schiff bases in solution. Blue light (250 mW) illumination gives an observed 2.3-fold rate enhancement for WT AAT activity, a 530-fold enhancement for the inactive K258A mutant, and a 58600-fold enhancement for the PLP-Asp Schiff base in water. These different levels of enhancement correlate with the intrinsic reactivities of the C(α)-H bond in the different environments, with the less reactive Schiff bases exhibiting greater enhancement. Time-resolved spectroscopy, ranging from femtoseconds to minutes, was used to investigate the nature of the photoactivation of C(α)-H bond cleavage in PLP-amino acid Schiff bases both in water and bound to AAT. Unlike the thermal pathway, the photoactivation pathway involves a triplet state with a C(α)-H pK(a) that is estimated to be between 11 and 19 units lower than the ground state for the PLP-Val Schiff base in water.

Internal proton transfer in the external pyridoxal 5'-phosphate Schiff base in dopa decarboxylase

Combined quantum mechanical and molecular mechanical (QM/MM) simulations of dopa decarboxylase have been carried out to elucidate the factors that contribute to the tautomeric equilibrium of the intramolecular proton transfer in the external PLP-L-dopa Schiff base. The presence of a carboxylate anion on the alpha-carbon of the Schiff base stabilizes the zwitterions and shifts the equilibrium in favor of the oxoenamine tautomer (protonated Schiff base). Moreover, protonation of the PLP pyridine nitrogen further drives the equilibrium toward the oxoenamine direction. On the other hand, solvent effects favor the hydroxyimine configuration, although the equilibrium favors the oxoenamine isomer with a methyl group as the substituent on the imino nitrogen. In dopa decarboxylase, the hydroxyimine form of the PLP(H+)-L-dopa Schiff base is predicted to be the major isomer with a relative free energy of -1.3 kcal/mol over that of the oxoenamine isomer. Both Asp271 and Lys303 stabilize the hydroxyimine configuration through hydrogen-bonding interactions with the pyridine nitrogen of the PLP and the imino nitrogen of the Schiff base, respectively. Interestingly, Thr246 plays a double role in the intramolecular proton transfer process, in which it initially donates a hydrogen bond to the phenolate oxygen in the oxoenamine configuration and then switches to a hydrogen bond acceptor from the phenolic hydroxyl group in the hydroxyimine tautomer.

Photophysics and photochemical studies of the vitamin B6 group and related derivatives

The photophysics and photochemical properties of vitamin B6 constituents and analogs were studied as function of pH and solvent. The pK of the phenolic oxygen and the pyridine ring nitrogen depends on the electron donor-acceptor ability of the 4-substituent, and agrees with the calculated proton affinity. For all studied compounds, the fluorescence properties showed that the phenolic oxygen is 8 units more acidic in the lowest singlet excited state than in the ground state. The pyridine N-atom is slightly more basic in the excited state. At pH of biological significance, pH 6-8, pyridoxamine and 4-pyridoxic acid are the more efficient chromophores with higher fluorescence yield and longer lifetime. Spectroscopic studies showed that the tautomeric equilibrium depends on the nature of the 4-substituent. The quenching of the singlet excited state of pyridoxamine and 4-pyridoxic acid by amino acids, free or in a peptide, and DNA bases at pH 7 was studied by time-resolved fluorescence techniques. The quenching rate constants are well correlated with the redox properties of the pyridoxinic compound and amino acids, and are related to the free energy change in the electron transfer process. Guanosine and pyrimidine bases also are efficient quenchers, involving an electron transfer reaction.

A single source femtosecond-millisecond broadband spectrometer

Time-resolved measurement of population dynamics extending over femtosecond to millisecond time scales typically requires a combination of transient absorption techniques involving different laser systems and detection schemes. The spectrometer design presented here facilitates transient absorption measurements over 12 decades with a single ultrafast laser system by picking pump and probe pulses independently from the laser oscillator pulse train. Unamplified pulses seed a photonic crystal fiber to a supercontinuum probe source for spectrally resolved measurements. The utility of the system is demonstrated by measuring triplet state dynamics following photoexcitation of vitamin B(6) in aqueous solution.