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1.
Chemistry ; : e202401193, 2024 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-38652483

RESUMO

Here we report the efficient synthetic access to 13C/15N-labelled pseudouridine phosphoramidites, which were incorporated into a binary H/ACA box guide RNA/product complex comprising 77 nucleotides (nts) in total and into a 75 nt E. coli tRNAGly. The stable isotope (SI) labelled pseudouridines were produced via a highly efficient chemo-enzymatic synthesis. 13C/15N labelled uracils were produced via chemical synthesis and enzymatically converted to 5'-monophosphate pseudouridine (ΨMP) by using YeiN, a Ψ-5'-monophosphate C-glycosidase. Removal of the 5'-phosphate group yielded the desired pseudouridine nucleoside (Ψ), which was transformed into a phosphoramidite building suitable for RNA solid phase synthesis. A Ψ -building block carrying both a 13C and a 15N label was incorporated into a product RNA and the complex formation with a 63 nt H/ACA box RNA could be observed via NMR. Furthermore, the SI labelled pseudouridine building block was used to determine imino proton bulk water exchange rates of a 75 nt E. coli tRNAGly CCmnm5U, identifying the TΨC-loop 5-methyluridine as a modifier of the exchange rates. The efficient synthetic access to SI labelled Ψ building blocks will allow the solution and solid-state NMR spectroscopic studies of Ψ containing RNAs and will facilitate the mass spectrometric analysis of Ψ-modified nucleic acids.

2.
Magn Reson Chem ; 62(4): 259-268, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-37438985

RESUMO

The application of compact NMR instruments to hot flowing samples or exothermically reacting mixtures is limited by the temperature sensitivity of permanent magnets. Typically, such temperature effects directly influence the achievable magnetic field homogeneity and hence measurement quality. The internal-temperature control loop of the magnet and instruments is not designed for such temperature compensation. Passive insulation is restricted by the small dimensions within the magnet borehole. Here, we present a design approach for active heat shielding with the aim of variable temperature control of NMR samples for benchtop NMR instruments using a compressed airstream which is variable in flow and temperature. Based on the system identification and surface temperature measurements through thermography, a model predictive control was set up to minimise any disturbance effect on the permanent magnet from the probe or sample temperature. This methodology will facilitate the application of variable-temperature shielding and, therefore, extend the application of compact NMR instruments to flowing sample temperatures that differ from the magnet temperature.

3.
Nat Commun ; 14(1): 7123, 2023 11 06.
Artigo em Inglês | MEDLINE | ID: mdl-37932298

RESUMO

Biological degradation of natural product glycosides involves, alongside hydrolysis, ß-elimination for glycosidic bond cleavage. Here, we discover an O-glycoside ß-eliminase (OGE) from Agrobacterium tumefaciens that converts the C3-oxidized O-ß-D-glucoside of phloretin (a plant-derived flavonoid) into the aglycone and the 2-hydroxy-3-keto-glycal elimination product. While unrelated in sequence, OGE is structurally homologous to, and shows effectively the same Mn2+ active site as, the C-glycoside deglycosylating enzyme (CGE) from a human intestinal bacterium implicated in ß-elimination of 3-keto C-ß-D-glucosides. We show that CGE catalyzes ß-elimination of 3-keto O- and C-ß-D-glucosides while OGE is specific for the O-glycoside substrate. Substrate comparisons and mutagenesis for CGE uncover positioning of aglycone for protonic assistance by the enzyme as critically important for C-glycoside cleavage. Collectively, our study suggests convergent evolution of active site for ß-elimination of 3-keto O-ß-D-glucosides. C-Glycoside cleavage is a specialized feature of this active site which is elicited by substrate through finely tuned enzyme-aglycone interactions.


Assuntos
Glicosídeos Cardíacos , Glicosídeos , Humanos , Glicosídeos/química , Flavonoides/metabolismo , Glucosídeos/metabolismo , Intestinos/microbiologia , Especificidade por Substrato
4.
Environ Monit Assess ; 195(12): 1500, 2023 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-37985477

RESUMO

Mongolia is a country with a quickly growing economy mainly based on mining of gold, copper, coal, and other minerals. Mining, urbanization, and agriculture impact the water quality in the upper Selenga River Basin in northern Mongolia, which is the center of the Mongolian economy. Previous measurements of pollution loads were alarming, but restricted to chemical measurements. Here, for the first time, we combine freshwater biomonitoring and laboratory water quality data across a broad gradient of water quality and land use intensity. We track the effects of different types of pollution on aquatic invertebrates and test their use as bioindicators. We collected water samples, environmental parameters, and macroinvertebrates at 36 sampling sites at the rivers of Tuul, Kharaa, and Orkhon and their tributaries Sugnugur, Boroo, Sharyn Gol, Gatsuurt, and Yeröö. PCA of catchment water quality distinguished three groups of pollutants prevalent at the sites: (1) nutrients, (2) saline components (Cl-, Na +, Mg2+, SO42-, Ca2+) and mining by-products (B, Sr, U, Mo), and (3) (heavy) metals, which often exceeded regulatory standards. We recorded a total of 59 macroinvertebrate taxa belonging to 32 families in seven insect orders plus Amphipoda and Gastropoda. Species diversity declined with higher impact. Five environmental factors structured macroinvertebrate community composition in RDA: elevation of sample location, site total nitrogen, dissolved oxygen, electrical conductivity, and water chemistry. We conclude that macroinvertebrate communities are an appropriate and inexpensive tool for monitoring water quality in Mongolia and suggest government action to establish a long-term monitoring program.


Assuntos
Metais Pesados , Poluentes Químicos da Água , Humanos , Animais , Qualidade da Água , Rios/química , Monitoramento Ambiental , Mongólia , Urbanização , Água Doce , Metais Pesados/análise , Invertebrados , Poluentes Químicos da Água/análise
5.
Molecules ; 28(18)2023 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-37764440

RESUMO

Phytochemical investigation of the two Tabernaemontana species (Apocynaceae) T. peduncularis Wall. and T. divaricata (L.) R.Br. ex Roem. & Schult. indicated closely related biosynthetic pathways leading to lipophilic and hydrophilic alkaloids. In total, 18 specialized metabolites comprising indole-derived alkaloid aglycones, three oxindole-derived alkaloid glycosides, and two iridoid glucosides could be identified in the studied species. Among the alkaloids, the two Iboga-type alkaloids 3,7-coronaridine isoindolenine, coronaridine 3,4-iminium and a javaniside derivative bearing a glucuronic acid, named javanuronic acid, could be described by spectroscopic and spectrometric methods for the first time. A docking experiment using alpha-fold was performed to generate a protein model of the enzyme 7-deoxyloganetic acid glucosyl transferase. Performed bioassays exhibited a growth reduction of neonate Spodoptera littoralis larvae and reduced cell viability of HepG2 cells of the extracts containing Iboga alkaloids, whilst the javaniside derivatives containing hydrophilic fraction did not show any effects. These findings indicate a high flexibility in the formation of bioactive indole alkaloid aglycones by Tabernaemontana species and also evidence similar accumulation trends in both species as well as indicate that biosynthetic routes leading to oxindole alkaloids like javanisides are more widespread than reported. Furthermore, the incorporation of the three novel compounds into potential biosynthetic pathways is discussed.


Assuntos
Tabernaemontana , Humanos , Recém-Nascido , Oxindóis , Glucuronídeos , Vias Biossintéticas
6.
Phys Rev Lett ; 130(23): 236403, 2023 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-37354414

RESUMO

The density of states (DOS) is fundamentally important for understanding physical processes in organic disordered semiconductors, yet hard to determine experimentally. We evaluated the DOS by considering recombination via tail states and using the temperature and open-circuit voltage (V_{oc}) dependence of the ideality factor. By performing Suns-V_{oc} measurements, we find that the energetic disorder increases deeper into the band gap, which is not expected for a Gaussian or exponential DOS. The linear dependence of the disorder on energy reveals the power-law DOS in organic solar cells.


Assuntos
Distribuição Normal , Temperatura
7.
Nat Commun ; 14(1): 2261, 2023 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-37081027

RESUMO

As a crucial factor of their therapeutic efficacy, the currently marketed mRNA vaccines feature uniform substitution of uridine (U) by the corresponding C-nucleoside, pseudouridine (Ψ), in 1-N-methylated form. Synthetic supply of the mRNA building block (1-N-Me-Ψ-5'-triphosphate) involves expedient access to Ψ as the principal challenge. Here, we show selective and atom-economic 1N-5C rearrangement of ß-D-ribosyl on uracil to obtain Ψ from unprotected U in quantitative yield. One-pot cascade transformation of U in four enzyme-catalyzed steps, via D-ribose (Rib)-1-phosphate, Rib-5-phosphate (Rib5P) and Ψ-5'-phosphate (ΨMP), gives Ψ. Coordinated function of the coupled enzymes in the overall rearrangement necessitates specific release of phosphate from the ΨMP, but not from the intermediary ribose phosphates. Discovery of Yjjg as ΨMP-specific phosphatase enables internally controlled regeneration of phosphate as catalytic reagent. With driving force provided from the net N-C rearrangement, the optimized U reaction yields a supersaturated product solution (∼250 g/L) from which the pure Ψ crystallizes (90% recovery). Scale up to 25 g isolated product at enzyme turnovers of ∼105 mol/mol demonstrates a robust process technology, promising for Ψ production. Our study identifies a multistep rearrangement reaction, realized by cascade biocatalysis, for C-nucleoside synthesis in high efficiency.


Assuntos
Nucleosídeos , Pseudouridina , Uridina/metabolismo , Pseudouridina/metabolismo , Biocatálise , Uracila
8.
Curr Opin Biotechnol ; 79: 102873, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36630750

RESUMO

Nucleosides and their analogs, including those that feature substitution of the canonical N-glycosidic by a C-glycosidic linkage, provide access to potent antiviral, antibacterial, and antitumor drugs. Furthermore, they are key building blocks of m-RNA vaccines and play a crucial role for vaccine therapeutic effectiveness. As the medicinal applications of nucleosides increase in number and importance, there is a growing need for efficiency-enhanced routes of nucleoside synthesis. Cascade biocatalysis, that is, the application of natural or evolved enzymes promoting complex transformations in multiple steps in one pot and without the need of intermediate purification, emerges as a powerful tool to obtain nucleosides from readily available starting materials. Recent efforts in enzyme discovery and protein engineering expand the toolbox of catalysts active toward nucleosides or nucleotides. In this review, we highlight recent applications, and discuss challenges, of cascade biocatalysis for nucleoside synthesis. We focus on C-nucleosides and important analogs of the canonical N-nucleosides.


Assuntos
Antineoplásicos , Nucleosídeos , Nucleosídeos/metabolismo , Biocatálise , Nucleotídeos/metabolismo , Catálise
9.
ACS Catal ; 12(6): 3357-3370, 2022 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-35356705

RESUMO

The cooperative interplay between the functional devices of a preorganized active site is fundamental to enzyme catalysis. An in-depth understanding of this phenomenon is central to elucidating the remarkable efficiency of natural enzymes and provides an essential benchmark for enzyme design and engineering. Here, we study the functional interconnectedness of the catalytic nucleophile (His18) in an acid phosphatase by analyzing the consequences of its replacement with aspartate. We present crystallographic, biochemical, and computational evidence for a conserved mechanistic pathway via a phospho-enzyme intermediate on Asp18. Linear free-energy relationships for phosphoryl transfer from phosphomonoester substrates to His18/Asp18 provide evidence for the cooperative interplay between the nucleophilic and general-acid catalytic groups in the wild-type enzyme, and its substantial loss in the H18D variant. As an isolated factor of phosphatase efficiency, the advantage of a histidine compared to an aspartate nucleophile is ∼104-fold. Cooperativity with the catalytic acid adds ≥102-fold to that advantage. Empirical valence bond simulations of phosphoryl transfer from glucose 1-phosphate to His and Asp in the enzyme explain the loss of activity of the Asp18 enzyme through a combination of impaired substrate positioning in the Michaelis complex, as well as a shift from early to late protonation of the leaving group in the H18D variant. The evidence presented furthermore suggests that the cooperative nature of catalysis distinguishes the enzymatic reaction from the corresponding reaction in solution and is enabled by the electrostatic preorganization of the active site. Our results reveal sophisticated discrimination in multifunctional catalysis of a highly proficient phosphatase active site.

10.
Angew Chem Int Ed Engl ; 60(43): 23202-23206, 2021 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-34278673

RESUMO

A big problem with the chemistry literature is that it is not standardized with respect to precise operational parameters, and real time corrections are hard to make without expert knowledge. This lack of context means difficult reproducibility because many steps are ambiguous, and hence depend on tacit knowledge. Here we present the integration of online NMR into an automated chemical synthesis machine (CSM aka. "Chemputer" which is capable of small-molecule synthesis using a universal programming language) to allow automated analysis and adjustment of reactions on the fly. The system was validated and benchmarked by using Grignard reactions which were chosen due to their importance in synthesis. The system was monitored in real time using online-NMR, and spectra were measured continuously during the reactions. This shows that the synthesis being done in the Chemputer can be dynamically controlled in response to feedback optimizing the reaction conditions according to the user requirements.

11.
Sci Rep ; 11(1): 15018, 2021 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-34294812

RESUMO

Little is known about the diversity and distribution patterns of moths along latitudinal gradients. We studied macro-moths in Mongolia along an 860 km latitudinal climatic gradient to gain knowledge on community composition, alpha, beta, and gamma diversity as well as underlying factors, which can be used as baseline information for further studies related to climate change. We identified 236 species of moths of ten families. Our study shows that the diversity of moths increased with the latitude, i.e., low species richness in the south and higher richness in the north. Moth community composition changed along the gradient, and we revealed a breakpoint of beta diversity that divided grassland and desert communities. In the desert, beta diversity was driven by species loss (i.e., nestedness), and few tolerant species existed with high abundance. In contrast, in the grassland, beta diversity was driven by species replacement with more unique species, (i.e., species which occurred only in one site). We found the lowest species diversity in the transitional zones dominated by few generalist species such as Agrotis ripae and Anarta trifolii. Low precipitation and an increasing number of grazing goats are drivers of species loss. We suggest different conservation strategies regarding the contrasting patterns of beta diversity in desert and grassland.

12.
Appl Microbiol Biotechnol ; 105(13): 5383-5394, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34189615

RESUMO

Advanced biotransformation processes typically involve the upstream processing part performed continuously and interlinked tightly with the product isolation. Key in their development is a catalyst that is highly active, operationally robust, conveniently produced, and recyclable. A promising strategy to obtain such catalyst is to encapsulate enzymes as permeabilized whole cells in porous polymer materials. Here, we show immobilization of the sucrose phosphorylase from Bifidobacterium adolescentis (P134Q-variant) by encapsulating the corresponding E. coli cells into polyacrylamide. Applying the solid catalyst, we demonstrate continuous production of the commercial extremolyte 2-α-D-glucosyl-glycerol (2-GG) from sucrose and glycerol. The solid catalyst exhibited similar activity (≥70%) as the cell-free extract (~800 U g-1 cell wet weight) and showed excellent in-operando stability (40 °C) over 6 weeks in a packed-bed reactor. Systematic study of immobilization parameters related to catalyst activity led to the identification of cell loading and catalyst particle size as important factors of process optimization. Using glycerol in excess (1.8 M), we analyzed sucrose conversion dependent on space velocity (0.075-0.750 h-1) and revealed conditions for full conversion of up to 900 mM sucrose. The maximum 2-GG space-time yield reached was 45 g L-1 h-1 for a product concentration of 120 g L-1. Collectively, our study establishes a step-economic route towards a practical whole cell-derived solid catalyst of sucrose phosphorylase, enabling continuous production of glucosides from sucrose. This strengthens the current biomanufacturing of 2-GG, but also has significant replication potential for other sucrose-derived glucosides, promoting their industrial scale production using sucrose phosphorylase. KEY POINTS: • Cells of sucrose phosphorylase fixed in polyacrylamide were highly active and stable. • Solid catalyst was integrated with continuous flow to reach high process efficiency. • Generic process technology to efficiently produce glucosides from sucrose is shown.


Assuntos
Glucosídeos , Sacarose , Escherichia coli , Glucosiltransferases , Tecnologia
13.
Nat Commun ; 12(1): 427, 2021 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-33462200

RESUMO

Spectral domain optical coherence tomography (OCT) is a widely employed, minimally invasive bio-medical imaging technique, which requires a broadband light source, typically implemented by super-luminescent diodes. Recent advances in soliton based photonic integrated frequency combs (soliton microcombs) have enabled the development of low-noise, broadband chipscale frequency comb sources, whose potential for OCT imaging has not yet been unexplored. Here, we explore the use of dissipative Kerr soliton microcombs in spectral domain OCT and show that, by using photonic chipscale Si3N4 resonators in conjunction with 1300 nm pump lasers, spectral bandwidths exceeding those of commercial OCT sources are possible. We characterized the exceptional noise properties of our source (in comparison to conventional OCT sources) and demonstrate that the soliton states in microresonators exhibit a residual intensity noise floor at high offset frequencies that is ca. 3 dB lower than a traditional OCT source at identical power, and can exhibit significantly lower noise performance for powers at the milli-Watt level. Moreover, we demonstrate that classical amplitude noise of all soliton comb teeth are correlated, i.e., common mode, in contrast to superluminescent diodes or incoherent microcomb states, which opens a new avenue to improve imaging speed and performance beyond the thermal noise limit.


Assuntos
Desenho de Equipamento , Tomografia de Coerência Óptica/instrumentação , Animais , Artefatos , Encéfalo/diagnóstico por imagem , Estudos de Viabilidade , Camundongos
14.
Curr Opin Chem Biol ; 61: 43-52, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33166830

RESUMO

Sugar nucleotide-modifying enzymes of the short-chain dehydrogenase/reductase type use transient oxidation-reduction by a tightly bound nicotinamide cofactor as a common strategy of catalysis to promote a diverse set of reactions, including decarboxylation, single- or double-site epimerization, and dehydration. Although the basic mechanistic principles have been worked out decades ago, the finely tuned control of reactivity and selectivity in several of these enzymes remains enigmatic. Recent evidence on uridine 5'-diphosphate (UDP)-glucuronic acid decarboxylases (UDP-xylose synthase, UDP-apiose/UDP-xylose synthase) and UDP-glucuronic acid-4-epimerase suggests that stereo-electronic constraints established at the enzyme's active site control the selectivity, and the timing of the catalytic reaction steps, in the conversion of the common substrate toward different products. The mechanistic idea of stereo-electronic control is extended to epimerases and dehydratases that deprotonate the Cα of the transient keto-hexose intermediate. The human guanosine 5'-diphosphate (GDP)-mannose 4,6-dehydratase was recently shown to use a minimal catalytic machinery, exactly as predicted earlier from theoretical considerations, for the ß-elimination of water from the keto-hexose species.


Assuntos
Redutases-Desidrogenases de Cadeia Curta/química , Sequência de Aminoácidos , Animais , Ácidos Carboxílicos/química , Catálise , Humanos , Água/química
15.
Nat Commun ; 11(1): 6270, 2020 12 08.
Artigo em Inglês | MEDLINE | ID: mdl-33293530

RESUMO

C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, we identify pseudouridine monophosphate C-glycosidase for selective 5-ß-C-glycosylation of uracil and derivatives thereof from pentose 5-phosphate (D-ribose, 2-deoxy-D-ribose, D-arabinose, D-xylose) substrates. Substrate requirements of the enzymatic reaction are consistent with a Mannich-like addition between the pyrimidine nucleobase and the iminium intermediate of enzyme (Lys166) and open-chain pentose 5-phosphate. ß-Elimination of the lysine and stereoselective ring closure give the product. We demonstrate phosphorylation-glycosylation cascade reactions for efficient, one-pot synthesis of C-nucleoside phosphates (yield: 33 - 94%) from unprotected sugar and nucleobase. We show incorporation of the enzymatically synthesized C-nucleotide triphosphates into nucleic acids by RNA polymerase. Collectively, these findings implement biocatalytic methodology for C-nucleotide synthesis which can facilitate XNA engineering for synthetic biology applications.


Assuntos
Glicosídeo Hidrolases/metabolismo , Ácidos Nucleicos/metabolismo , Biologia Sintética/métodos , Biocatálise , Glicosilação , Simulação de Acoplamento Molecular , Ácidos Nucleicos/química , Pentoses/química , Pentoses/metabolismo , Fosforilação , Pseudouridina/metabolismo , Uracila/química , Uracila/metabolismo , Xenobióticos/metabolismo
16.
Anal Bioanal Chem ; 412(18): 4447-4459, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32388578

RESUMO

Industry 4.0 is all about interconnectivity, sensor-enhanced process control, and data-driven systems. Process analytical technology (PAT) such as online nuclear magnetic resonance (NMR) spectroscopy is gaining in importance, as it increasingly contributes to automation and digitalization in production. In many cases up to now, however, a classical evaluation of process data and their transformation into knowledge is not possible or not economical due to the insufficiently large datasets available. When developing an automated method applicable in process control, sometimes only the basic data of a limited number of batch tests from typical product and process development campaigns are available. However, these datasets are not large enough for training machine-supported procedures. In this work, to overcome this limitation, a new procedure was developed, which allows physically motivated multiplication of the available reference data in order to obtain a sufficiently large dataset for training machine learning algorithms. The underlying example chemical synthesis was measured and analyzed with both application-relevant low-field NMR and high-field NMR spectroscopy as reference method. Artificial neural networks (ANNs) have the potential to infer valuable process information already from relatively limited input data. However, in order to predict the concentration at complex conditions (many reactants and wide concentration ranges), larger ANNs and, therefore, a larger training dataset are required. We demonstrate that a moderately complex problem with four reactants can be addressed using ANNs in combination with the presented PAT method (low-field NMR) and with the proposed approach to generate meaningful training data. Graphical abstract.

17.
Opt Lett ; 45(7): 1794-1797, 2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-32236001

RESUMO

We experimentally demonstrate Kramers-Kronig detection of four 20 Gbaud 16-quadrature-amplitude-modulated (QAM) channels after 50 km fiber transmission using two soliton Kerr combs as signal sources and local oscillators. The estimated carrier phase at the receiver for each of the channels is relatively similar due to the coherence between the frequency comb lines. The standard deviation of the estimated carrier phase difference of the channels is less than 0.08 rad after 50 km single-mode fiber (SMF) transmission. This enables the carrier phase recovery derived from one channel to be shared among multiple channels. In the back-to-back scenario, the bit error rate (BER) performance for shared carrier phase recovery shows an optical signal-to-noise ratio penalty of ${\sim}{0.5}\;{\rm dB}$∼0.5dB compared to the BER performance for carrier phase recovery when derived for each channel independently. BERs below the forward error correction threshold are achieved after 50 km SMF transmission with both independent and shared carrier phase recovery for four 20-Gbaud 16-QAM signals.

18.
ACS Photonics ; 7(1): 147-153, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-32030349

RESUMO

Silicon nitride has emerged as a prominent platform for building photonics integrated circuits. While its nonlinear properties based on third-order effects have been successfully exploited, an efficient second harmonic generation in standard stoichiometric silicon nitride (Si3N4) waveguides can also be achieved after all-optical poling, as was recently shown. The root of such a phenomenon has been attributed to the inscription of a self-organized periodic space-charge grating along the waveguide, allowing an effective χ(2) and automatic quasi-phase-matching of pump and second harmonic. However, the different parameters and their role in increasing the efficiency of the process are still not fully comprehended. In this work, we use optical means to identify the general conditions of mode matching occurring during all-optical poling. The overlap integral between pump and second harmonic optical modes is shown to be the governing parameter in determining the features of the χ(2) gratings. Two-photon microscopy measurements of the χ(2) gratings reveal the presence of a secondary periodicity in some of the waveguides used in the study. According to overlap integral simulations, such an effect can occur due to mode mixing in the waveguide bends. From a study of poling dynamics, we observe that poling efficiency and rate increase as a function of optical pump power and waveguide length. However, in order to initiate poling, a critical pump intensity, which is lower for longer waveguides, must be coupled into a waveguide. Temporal and thermal stability tests reveal the nature of charge traps responsible for grating inscription. After applying thermally activated hopping as a conductivity mechanism in our samples, we show that only shallow traps seem to be activated during the all-optical poling process.

19.
Nat Catal ; 2(12): 1115-1123, 2019 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-31844840

RESUMO

D-Apiose is a C-branched pentose sugar important for plant cell wall development. Its biosynthesis as UDP-D-apiose involves decarboxylation of the UDP-D-glucuronic acid precursor coupled to pyranosyl-to-furanosyl sugar ring contraction. This unusual multistep reaction is catalyzed within a single active site by UDP-D-apiose/UDP-D-xylose synthase (UAXS). Here, we decipher the UAXS catalytic mechanism based on crystal structures of the enzyme from Arabidopsis thaliana, molecular dynamics simulations expanded by QM/MM calculations, and mutational-mechanistic analyses. Our studies show how UAXS uniquely integrates a classical catalytic cycle of oxidation and reduction by a tightly bound nicotinamide coenzyme with retro-aldol/aldol chemistry for the sugar ring contraction. They further demonstrate that decarboxylation occurs only after the sugar ring opening and identify the thiol group of Cys100 in steering the sugar skeleton rearrangement by proton transfer to and from the C3'. The mechanistic features of UAXS highlight the evolutionary expansion of the basic catalytic apparatus of short-chain dehydrogenases/reductases for functional versatility in sugar biosynthesis.

20.
ACS Catal ; 9(4): 2962-2968, 2019 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-30984471

RESUMO

Biosynthesis of 6-deoxy sugars, including l-fucose, involves a mechanistically complex, enzymatic 4,6-dehydration of hexose nucleotide precursors as the first committed step. Here, we determined pre- and postcatalytic complex structures of the human GDP-mannose 4,6-dehydratase at atomic resolution. These structures together with results of molecular dynamics simulation and biochemical characterization of wildtype and mutant enzymes reveal elusive mechanistic details of water elimination from GDP-mannose C5″ and C6″, coupled to NADP-mediated hydride transfer from C4″ to C6″. We show that concerted acid-base catalysis from only two active-site groups, Tyr179 and Glu157, promotes a syn 1,4-elimination from an enol (not an enolate) intermediate. We also show that the overall multistep catalytic reaction involves the fewest position changes of enzyme and substrate groups and that it proceeds under conserved exploitation of the basic (minimal) catalytic machinery of short-chain dehydrogenase/reductases.

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