Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Direct observation of an enamine intermediate in amine catalysis.

ABSTRACT: An enamine intermediate is believed to be the central feature of biological catalysts, such as aldolases and small molecule amine organocatalysts. Despite decades of investigation of naturally occurring aldolase enzymes and recent studies on designed aldolase antibodies and organocatalysts, direct structural observation of an enamine intermediate has proven to be rare. Herein, we report the observation of a stable enamine intermediate in the crystal structure of an aldolase antibody 33F12 in complex with a 1,3-diketone derivative. This enamine complex structure provides strong evidence that fewer residues are essential for amine catalysis within the hydrophobic environments of this catalytic antibody than speculated for natural aldolase enzymes and should serve to guide future studies aimed at the rational design of these types of catalysts, as well as organocatalysts. Indeed, enamine catalysis in proteins might be more simplistic than previously imagined.

SUBMITTER: Zhu X

PROVIDER: S-EPMC3227542 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Direct observation of an enamine intermediate in amine catalysis.

Zhu Xueyong X Tanaka Fujie F Lerner Richard A RA Barbas Carlos F CF Wilson Ian A IA

Journal of the American Chemical Society 20091201 51

An enamine intermediate is believed to be the central feature of biological catalysts, such as aldolases and small molecule amine organocatalysts. Despite decades of investigation of naturally occurring aldolase enzymes and recent studies on designed aldolase antibodies and organocatalysts, direct structural observation of an enamine intermediate has proven to be rare. Herein, we report the observation of a stable enamine intermediate in the crystal structure of an aldolase antibody 33F12 in com ...[more]

PMID: 19968282

Similar Datasets

Dynamic Covalent Chemistry of Aldehyde Enamines: BiIII - and ScIII -Catalysis of Amine-Enamine Exchange.

Project description:The dynamic exchange of enamines from secondary amines and enolizable aldehydes has been demonstrated in organic solvents. The enamine exchange with amines was efficiently catalyzed by Bi(OTf)3 and Sc(OTf)3 (2?mol?%) and the equilibria (60?mm) could be attained within hours at room temperature. The formed dynamic covalent systems displayed high stabilities in basic environment with <2?% by-product formation within one week after complete equilibration. This study expands the scope of dynamic C-N bonds from imine chemistry to enamines, enabling further dynamic methodologies in exploration of this important class of structures in systems chemistry.

| S-EPMC5656824 | biostudies-other

Direct observation of intermediate states in model membrane fusion.

Project description:We introduce a novel assay for membrane fusion of solid supported membranes on silica beads and on coverslips. Fusion of the lipid bilayers is induced by bringing an optically trapped bead in contact with the coverslip surface while observing the bead's thermal motion with microsecond temporal and nanometer spatial resolution using a three-dimensional position detector. The probability of fusion is controlled by the membrane tension on the particle. We show that the progression of fusion can be monitored by changes in the three-dimensional position histograms of the bead and in its rate of diffusion. We were able to observe all fusion intermediates including transient fusion, formation of a stalk, hemifusion and the completion of a fusion pore. Fusion intermediates are characterized by axial but not lateral confinement of the motion of the bead and independently by the change of its rate of diffusion due to the additional drag from the stalk-like connection between the two membranes. The detailed information provided by this assay makes it ideally suited for studies of early events in pure lipid bilayer fusion or fusion assisted by fusogenic molecules.

| S-EPMC4814778 | biostudies-literature

Direct observation of the intermediate in an ultrafast isomerization.

Project description:Using a combination of two-dimensional infrared (2D IR) and variable temperature Fourier transform infrared (FTIR) spectroscopies the rapid structural isomerization of a five-coordinate ruthenium complex is investigated. In methylene chloride, three exchanging isomers were observed: (1) square pyramidal equatorial, (1); (2) trigonal bipyramidal, (0); and (3) square pyramidal apical, (2). Exchange between 1 and 0 was found to be an endergonic process (ΔH = 0.84 (0.08) kcal mol-1, ΔS = 0.6 (0.4) eu) with an isomerization time constant of 4.3 (1.5) picoseconds (ps, 10-12 s). Exchange between 0 and 2 however was found to be exergonic (ΔH = -2.18 (0.06) kcal mol-1, ΔS = -5.3 (0.3) eu) and rate limiting with an isomerization time constant of 6.3 (1.6) ps. The trigonal bipyramidal complex was found to be an intermediate, with an activation barrier of 2.2 (0.2) kcal mol-1 and 2.4 (0.2) kcal mol-1 relative to the equatorial and apical square pyramidal isomers respectively. This study provides direct validation of the mechanism of Berry pseudorotation - the pairwise exchange of ligands in a five-coordinate complex - a process that was first described over fifty years ago. This study also clearly demonstrates that the rate of pseudorotation approaches the frequency of molecular vibrations.

| S-EPMC6333165 | biostudies-literature

Direct observation of subunit exchange along mature vimentin intermediate filaments.

Project description:Actin filaments, microtubules, and intermediate filaments (IFs) are central elements of the metazoan cytoskeleton. At the molecular level, the assembly mechanism for actin filaments and microtubules is fundamentally different from that of IFs. The former two types of filaments assemble from globular proteins. By contrast, IFs assemble from tetrameric complexes of extended, half-staggered, and antiparallel oriented coiled-coils. These tetramers laterally associate into unit-length filaments; subsequent longitudinal annealing of unit-length filaments yields mature IFs. In vitro, IFs form open structures without a fixed number of tetramers per cross-section along the filament. Therefore, a central question for the structural biology of IFs is whether individual subunits can dissociate from assembled filaments and rebind at other sites. Using the fluorescently labeled IF-protein vimentin for assembly, we directly observe and quantitatively determine subunit exchange events between filaments as well as with soluble vimentin pools. Thereby we demonstrate that the cross-sectional polymorphism of donor and acceptor filaments plays an important role. We propose that in segments of donor filaments with more than the standard 32 molecules per cross-section, subunits are not as tightly bound and are predisposed to be released from the filament.

| S-EPMC4269786 | biostudies-literature

Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase.

Project description:Methylation of the five position of cytosine in DNA plays important roles in epigenetic regulation in diverse organisms including humans. The transfer of methyl groups from the cofactor S-adenosyl-L-methionine is carried out by methyltransferase enzymes. Using the paradigm bacterial methyltransferase M.HhaI we demonstrate, in a chemically unperturbed system, the first direct real-time analysis of the key mechanistic events-the flipping of the target cytosine base and its covalent activation; these changes were followed by monitoring the hyperchromicity in the DNA and the loss of the cytosine chromophore in the target nucleotide, respectively. Combined with studies of M.HhaI variants containing redesigned tryptophan fluorophores, we find that the target base flipping and the closure of the mobile catalytic loop occur simultaneously, and the rate of this concerted motion inversely correlates with the stability of the target base pair. Subsequently, the covalent activation of the target cytosine is closely followed by but is not coincident with the methyl group transfer from the bound cofactor. These findings provide new insights into the temporal mechanism of this physiologically important reaction and pave the way to in-depth studies of other base-flipping systems.

| S-EPMC3089467 | biostudies-literature

Effect of the enamine pyramidalization direction on the reactivity of secondary amine organocatalysts.

Project description:Chiral secondary amines are valuable catalysts for reactions that proceed through an enamine intermediate. Here, we explored the importance of the pyramidalization direction of the enamine-N on the reactivity of chiral enamines with a combination of computational, NMR spectroscopic, and kinetic experiments. Studies with peptidic catalysts that bear cyclic amines with different ring sizes revealed that endo-pyramidalized enamines are significantly more reactive compared to exo-pyramidalized analogs. The results show that the pyramidalization direction can have a greater effect than n→π* orbital overlap on the reactivity of chiral enamines. The data enabled the development of a catalyst with higher reactivity compared to the parent catalyst.

| S-EPMC8148379 | biostudies-literature

Counterion-Enhanced Pd/Enamine Catalysis: Direct Asymmetric α-Allylation of Aldehydes with Allylic Alcohols by Chiral Amines and Achiral or Racemic Phosphoric Acids.

Project description:We report a straightforward and efficient Pd/enamine catalytic procedure for the direct asymmetric α-allylation of branched aldehydes. The use of simple chiral amines and easily prepared achiral or racemic phosphoric acids, together with a suitable Pd-source resulted in a highly active and enantioselective catalyst system for the allylation of various α-branched aldehydes with different allylic alcohols. The reported procedure could provide an easy access to both product antipodes. Furthermore, two possible orthogonal derivatizations of the enantioenriched aldehydes were performed without any decrease in enantioselectivity.

| S-EPMC7783732 | biostudies-literature

Enamine/Carbene Cascade Catalysis in the Diastereo- and Enantioselective Synthesis of Functionalized Cyclopentanones.

Project description:Herein we report an enantioselective synthesis of complex cyclopentanones using aliphatic aldehydes and activated enones. With the combination of a chiral secondary amine and a chiral triazolium catalyst, high diastereoselectivity and excellent enantioselectivity can be achieved. We present evidence of a clear cooperative effect when these two catalysts are present simultaneously in the system.

| S-EPMC3173771 | biostudies-literature

Bronsted acid catalysis of achiral enamine for regio- and enantioselective nitroso aldol synthesis.

Project description:Two types of chiral Brønsted acid catalysts have been shown to catalyze regio- and enantioselective nitroso aldol synthesis between nitrosobenzene and achiral enamine. The combination of Brønsted acidity and amine moiety of enamine realizes complete regioselectivity with high enantioselectivity. After a survey of Brønsted acid catalysts, 1-naphthyl glycolic acid is found to be optimal in the O-nitroso aldol pathway, while 1-naphthyl TADDOL is the best catalyst for the N-nitroso aldol pathway. This is based on our finding on the control of regioselectivity by changing the amine moiety of enamine and the choice of Brønsted acidity.

| S-EPMC1460970 | biostudies-literature

Synergistic palladium/enamine catalysis for asymmetric hydrocarbon functionalization of unactivated alkenes with ketones.

Project description:Synergistic palladium and enamine catalysis was explored to promote ketone addition to unactivated olefins. A secondary amine-based organocatalyst was identified as the optimal co-catalyst for the directed Pd-catalyzed alkene activation. Furthermore, asymmetric hydrocarbon functionalization of unactivated alkenes was also achieved with good to excellent yield (up to 96% yields) and stereoselectivity (up to 96% ee). This strategy presented an efficient approach to prepare ?-branched ketone derivatives under mild conditions.

| S-EPMC6677245 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data