Capturing fleeting intermediates in a catalytic C-H amination reaction cycle.
Ontology highlight
ABSTRACT:
SUBMITTER: Perry RH
PROVIDER: S-EPMC3494934 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme's catalytic cycle may have to be turned by 180 degrees.
| S-EPMC8617209 | biostudies-literature
Project description:Metal carbenes are often proposed as reactive intermediates in the late transition metal-catalysed transformations of alkynes. Owing to their high reactivity, however, isolation and structural characterization of metal carbene intermediates in these transformations has remained unknown. Herein, we report the isolation of two acyclic gold and copper carbene intermediates in either Au(I)- or Cu(I)-catalysed cyclization of N-alkynyl formamidines through five-exo-dig cyclization. X-ray diffraction, 13C NMR spectra data and computational analyses provide evidence for the formation of a gold carbene intermediate with a carbocation-like electronic character. Using the intrinsic bond orbital (IBO) approach, we also evaluate the π-stabilizing effects of organic substituents at the carbene carbon atom in the gold carbene intermediate. Another rare six-membered copper carbene complex is also obtained through 6-endo-dig cyclization. These metal carbenes have proven reactive toward oxidation. The metal-promoted cyclization of N-alkynyl formamidine provides a facile approach to synthesize metal carbene species.
| S-EPMC5343500 | biostudies-literature
Project description:Site-specific recombination plays key roles in microbe biology and is exploited extensively to manipulate the genomes of higher organisms. Cre is a well studied site-specific recombinase, responsible for establishment and maintenance of the P1 bacteriophage genome in bacteria. During recombination, Cre forms a synaptic complex between two 34-bp DNA sequences called loxP after which a pair of strand exchanges forms a Holliday junction (HJ) intermediate; HJ isomerization then allows a second pair of strand exchanges and thus formation of the final recombinant product. Despite extensive work on the Cre-loxP system, many of its mechanisms have remained unclear, mainly due to the transient nature of complexes formed and the ensemble averaging inherent to most biochemical work. Here, we address these limitations by introducing tethered fluorophore motion (TFM), a method that monitors large-scale DNA motions through reports of the diffusional freedom of a single fluorophore. We combine TFM with Förster resonance energy transfer (FRET) and simultaneously observe both large- and small-scale conformational changes within single DNA molecules. Using TFM-FRET, we observed individual recombination reactions in real time and analyzed their kinetics. Recombination was initiated predominantly by exchange of the "bottom-strands" of the DNA substrate. In productive complexes we used FRET distributions to infer rapid isomerization of the HJ intermediates and that a rate-limiting step occurs after this isomerization. We also observed two nonproductive synaptic complexes, one of which was structurally distinct from conformations in crystals. After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination.
| S-EPMC3529024 | biostudies-literature
Project description:Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
| S-EPMC8461649 | biostudies-literature
Project description:Towards the goal of on-line monitoring of transient neutral intermediates during electrochemical reactions, an electrochemistry-neutral reionization-mass spectrometry (EC-NR-MS) technique was developed in this work. The EC-NR setup consisted of a customized EC flow cell, a sonic spray ionization source, a heating tube, an ion deflector and an electrospray ionization source, which were respectively used for the precise control of the electrochemical reaction, solution nebulization, droplet desolvation, ion deflection and neutral intermediate ionization. Based on the EC-NR-MS approach, some long-sought neutral radicals including TPrA˙, DBAE˙ and TEOA˙, which belong to important reductive intermediates in electrochemiluminescence (ECL) reactions, were successfully identified which helps to clarify the previously unproven ECL reaction mechanism. These findings were also supported by spin-trapping experiments and the tandem MS technique. Accordingly, the EC-NR-MS method provides a direct solution for studying complicated electrochemical reactions, especially for detecting short-lived neutral radicals as well as ionic intermediates.
| S-EPMC8278903 | biostudies-literature
Project description:The enantioselective allylic amination of unactivated terminal olefins represents a direct and attractive strategy for the synthesis of enantioenriched amines. We have developed the first use of a nitrogen-containing reagent and a chiral palladium catalyst to convert unfunctionalized olefins into enantioenriched allylic amines via an ene reaction/[2,3]-rearrangement.
| S-EPMC3511869 | biostudies-literature
Project description:While plastics-to-plastics recycling via melting and re-extrusion is often the preferred option due to a relatively low CO2 footprint, this technique requires a highly sorted waste stream and plastic properties can often not be maintained. Obtaining aromatics, such as benzene, toluene, and xylene (BTX), via catalytic pyrolysis of polyolefins, such as polypropylene and polyethylene, offers another attractive recycling technology. In this process, a discarded crude oil refinery catalyst (ECAT) was previously shown to lower the unwanted formation of deactivating coke species compared to a fresh crude oil refinery catalyst (FCC-cat), while yielding 20 wt% aromatics from polypropylene. In this work, we study the underlying reaction mechanism for this chemical recycling process over the fresh and used refinery catalyst as well as a model system, not containing any zeolite material, using a combination of microscopy and spectroscopy. More specifically, by using in situ fluorescence microscopy, in situ infrared spectroscopy, in situ ultraviolet-visible spectroscopy as well as ex situ solid-state nuclear magnetic resonance, we observe highly fluorescent methylated aromatic intermediates that differ for the three catalyst materials under study both in their fluorescence, IR, UV-vis, and NMR spectroscopy features. This detailed micro-spectroscopic comparison informs which potential reaction intermediates lead to increased coke formation. Our results suggests that a next generation of catalyst materials for this process would profit from a higher accessibility and a milder acidity compared to an FCC-cat and shows the great potential of using ECAT to reduce coking and obtain a BTX stream, which could be become the chemical building blocks for the manufacturing of e.g., plastics and coating materials.
| S-EPMC10876043 | biostudies-literature
Project description:Escherichia coli dihydrofolate reductase (DHFR) provides a paradigm for the integrated study of the role of protein dynamics in enzyme function. Previous studies of backbone and side chain dynamics have yielded unprecedented insights into the mechanism by which DHFR progresses through the structural changes that occur during its catalytic cycle. Here we report a comprehensive study of the χ1 rotamer populations of the aromatic and γ-methyl containing residues for complexes of the catalytic cycle, based on NMR measurement of (3)JCγCO and (3)JCγN coupling constants. We report conformational and dynamic information for eight distinct complexes, where transitions between rotamer wells may occur on a broad picosecond to millisecond time scale. This large volume of (3)J data has allowed us to fit new Karplus parameterizations for aromatic side chains and to select the best available of previously determined parameters for Ile, Thr, and Val. The (3)JCγCO and (3)JCγN coupling constants are found to be extremely sensitive measures of side chain χ1 rotamers and to give important insights into the extent of conformational averaging. For a subset of residues in DHFR, the extent of rotamer averaging is invariant to the nature of the bound ligand, while for other residues the rotamer averaging differs in one or more complexes of the enzymatic cycle. These variable-averaging residues are generally located near the active site, but the phenomenon extends into the adenosine binding domain. For several residues, the rotamer populations in different DHFR complexes appear to depend on whether the complex is in the closed or occluded state, and some residues are exquisitely sensitive to small changes in the nature of the bound ligand.
| S-EPMC3796204 | biostudies-literature
Project description:5-Aminolevulinate (ALA), an essential metabolite in all heme-synthesizing organisms, results from the pyridoxal 5'-phosphate (PLP)-dependent enzymatic condensation of glycine with succinyl-CoA in non-plant eukaryotes and ?-proteobacteria. The predicted chemical mechanism of this ALA synthase (ALAS)-catalyzed reaction includes a short-lived glycine quinonoid intermediate and an unstable 2-amino-3-ketoadipate intermediate. Using liquid chromatography coupled with tandem mass spectrometry to analyze the products from the reaction of murine erythroid ALAS (mALAS2) with O-methylglycine and succinyl-CoA, we directly identified the chemical nature of the inherently unstable 2-amino-3-ketoadipate intermediate, which predicates the glycine quinonoid species as its precursor. With stopped-flow absorption spectroscopy, we detected and confirmed the formation of the quinonoid intermediate upon reacting glycine with ALAS. Significantly, in the absence of the succinyl-CoA substrate, the external aldimine predominates over the glycine quinonoid intermediate. When instead of glycine, L-serine was reacted with ALAS, a lag phase was observed in the progress curve for the L-serine external aldimine formation, indicating a hysteretic behavior in ALAS. Hysteresis was not detected in the T148A-catalyzed L-serine external aldimine formation. These results with T148A, a mALAS2 variant, which, in contrast to wild-type mALAS2, is active with L-serine, suggest that active site Thr-148 modulates ALAS strict amino acid substrate specificity. The rate of ALA release is also controlled by a hysteretic kinetic mechanism (observed as a lag in the ALA external aldimine formation progress curve), consistent with conformational changes governing the dissociation of ALA from ALAS.
| S-EPMC4132793 | biostudies-literature
Project description:Pyruvate ferredoxin oxidoreductase (PFOR) is central to the anaerobic metabolism of many bacteria and amitochondriate eukaryotes. PFOR contains thiamine pyrophosphate (TPP) and three [4Fe-4S] clusters, which link pyruvate oxidation to reduction of ferredoxin. In the PFOR reaction, TPP reacts with pyruvate to form lactyl-TPP, which undergoes decarboxylation to form a hydroxyethyl-TPP (HE-TPP) intermediate. One electron is then transferred from HE-TPP to one of the three [4Fe-4S] clusters to form an HE-TPP radical and a [4Fe-4S]1+ intermediate. Pulsed EPR methods have been used to measure the distance between the HE-TPP radical and the [4Fe-4S]1+ cluster to which it is coupled. Computational analysis including the PFOR crystal structure and the spin distribution in the HE-TPP radical and in the reduced [4Fe-4S] cluster demonstrates that the distance between the HE-TPP radical and the medial cluster B matches the experimentally determined dipolar interaction, while one of the other two clusters is too close and the other is too far away. These results clearly demonstrate that it is the medial cluster (cluster B) that is reduced. Thus, rapid electron transfer occurs through the electron-transfer chain, which leaves an oxidized proximal cluster poised to accept an electron from the HE-TPP radical in the subsequent reaction step.
| S-EPMC3119504 | biostudies-literature