Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions.

ABSTRACT: Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations.

SUBMITTER: Kelly PP

PROVIDER: S-EPMC4660908 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions.

Kelly Paul P PP Eichler Anja A Herter Susanne S Kranz David C DC Turner Nicholas J NJ Flitsch Sabine L SL

Beilstein journal of organic chemistry 20150922

Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints o ...[more]

PMID: 26664590

Similar Datasets

Spring-loading the active site of cytochrome P450cam.

Project description:A hydrogen bond network has been identified that adjusts protein-substrate contacts in cytochrome P450(cam) (CYP101A1). Replacing the native substrate camphor with adamantanone or norcamphor causes perturbations in NMR-detected NH correlations assigned to the network, which includes portions of a ? sheet and an adjacent helix that is remote from the active site. A mutation in this helix reduces enzyme efficiency and perturbs the extent of substrate-induced spin state changes at the haem iron that accompany substrate binding. In turn, the magnitude of the spin state changes induced by alternate substrate binding parallel the NMR-detected perturbations observed near the haem in the enzyme active site.

| S-EPMC3071453 | biostudies-literature

Active Site Hydrogen Bonding Induced in Cytochrome P450cam by Effector Putidaredoxin.

Project description:Cytochrome P450s are diverse and powerful catalysts that can activate molecular oxygen to oxidize a wide variety of substrates. Catalysis relies on effective uptake of two electrons and two protons. For cytochrome P450cam, an archetypal member of the superfamily, the second electron must be supplied by the redox partner putidaredoxin (Pdx). Pdx also plays an effector role beyond electron transfer, but after decades the mechanism remains under investigation. We applied infrared spectroscopy to heme-ligated CN- to examine the influence of Pdx binding. The results indicate that Pdx induces the population of a conformation wherein the CN- ligand forms a strong hydrogen bond to a solvent water molecule, experimentally corroborating the formation of a proposed proton delivery network. Further, characterization of T252A P450cam implicates the side chain of Thr252 in regulating the population equilibrium of hydrogen-bonded states within the P450cam/Pdx complex, which could underlie its role in directing activated oxygen toward product formation and preventing reaction uncoupling through peroxide release.

| S-EPMC8750573 | biostudies-literature

Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process.

Project description:Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

| S-EPMC3177059 | biostudies-literature

Enantioselective Halolactonization Reactions using BINOL-Derived Bifunctional Catalysts: Methodology, Diversification, and Applications.

Project description:A general protocol is described for inducing enantioselective halolactonizations of unsaturated carboxylic acids using novel bifunctional organic catalysts derived from a chiral binaphthalene scaffold. Bromo- and iodolactonization reactions of diversely substituted, unsaturated carboxylic acids proceed with high degrees of enantioselectivity, regioselectivity, and diastereoselectivity. Notably, these BINOL-derived catalysts are the first to induce the bromo- and iodolactonizations of 5-alkyl-4( Z)-olefinic acids via 5- exo mode cyclizations to give lactones in which new carbon-halogen bonds are created at a stereogenic center with high diastereo- and enantioselectivities. Iodolactonizations of 6-substituted-5( Z)-olefinic acids also occur via 6- exo cyclizations to provide ?-lactones with excellent enantioselectivities. Several notable applications of this halolactonization methodology were developed for desymmetrization, kinetic resolution, and epoxidation of Z-alkenes. The utility of these reactions is demonstrated by their application to a synthesis of precursors of the F-ring subunit of kibdelone C and to the shortest catalytic, enantioselective synthesis of (+)-disparlure reported to date.

| S-EPMC5984189 | biostudies-literature

Porphyrin-Based Metal-Organic Frameworks as Heterogeneous Catalysts in Oxidation Reactions.

Project description:Porphyrin-based Metal-Organic Frameworks (Por-MOFs) constitute a special branch of the wide MOF family that has proven its own value and high potential in different applications. In this mini-review the application of these materials as catalysts in oxidation reactions is highlighted.

| S-EPMC6273352 | biostudies-literature

Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin.

Project description:Combined QM/MM calculations of the active-site of cytochrome P450cam have been performed before and after the binding of P450cam to putidaredoxin. The calculations were carried out for both a 5-coordinated and a 6-coordinated active-site of cytochrome P450cam, with either a water molecule or a carbon monoxide molecule as a 6th distal ligand. An experimentally observed increase in the Fe-S stretching frequency that occurs after cytochrome P450cam binds to putidaredoxin, has been reproduced in our study. Experimentally observed changes in the Fe-C and C-O vibration frequencies that occur after binding of both proteins, have also been reproduced in our study. The computed increase of the Fe-S and Fe-C stretching frequencies is correlated with a corresponding decrease of the Fe-S and Fe-C interatomic distances. According to our calculations, for the active-site with carbon monoxide in the triplet electronic state, the binding process increases the spin densities on the iron and sulfur atoms, which changes the Fe-C and C-O stretching frequencies in opposite directions, in agreement with experimental data.

| S-EPMC2292843 | biostudies-literature

The Origin of Catalytic Benzylic C-H Oxidation over a Redox-Active Metal-Organic Framework.

Project description:Selective oxidation of benzylic C-H compounds to ketones is important for the production of a wide range of fine chemicals, and is often achieved using toxic or precious metal catalysts. Herein, we report the efficient oxidation of benzylic C-H groups in a broad range of substrates under mild conditions over a robust metal-organic framework material, MFM-170, incorporating redox-active [Cu2 II (O2 CR)4 ] paddlewheel nodes. A comprehensive investigation employing electron paramagnetic resonance (EPR) spectroscopy and synchrotron X-ray diffraction has identified the critical role of the paddlewheel moiety in activating the oxidant t BuOOH (tert-butyl hydroperoxide) via partial reduction to [CuII CuI (O2 CR)4 ] species.

| S-EPMC8361671 | biostudies-literature

Surface oxygenation of multicomponent nanoparticles toward active and stable oxidation catalysts.

Project description:The need for active and stable oxidation catalysts is driven by the demands in production of valuable chemicals, remediation of hydrocarbon pollutants and energy sustainability. Traditional approaches focus on oxygen-activating oxides as support which provides the oxygen activation at the catalyst-support peripheral interface. Here we report a new approach to oxidation catalysts for total oxidation of hydrocarbons (e.g., propane) by surface oxygenation of platinum (Pt)-alloyed multicomponent nanoparticles (e.g., platinum-nickel cobalt (Pt-NiCo)). The in-situ/operando time-resolved studies, including high-energy synchrotron X-ray diffraction and diffuse reflectance infrared Fourier transform spectroscopy, demonstrate the formation of oxygenated Pt-NiOCoO surface layer and disordered ternary alloy core. The results reveal largely-irregular oscillatory kinetics associated with the dynamic lattice expansion/shrinking, ordering/disordering, and formation of surface-oxygenated sites and intermediates. The catalytic synergy is responsible for reduction of the oxidation temperature by ~100 °C and the high stability under 800 °C hydrothermal aging in comparison with Pt, and may represent a paradigm shift in the design of self-supported catalysts.

| S-EPMC7443134 | biostudies-literature

Constructing multiple active sites in iron oxide catalysts for improving carbonylation reactions.

Project description:Surface engineering is a promising strategy to improve the catalytic activities of heterogeneous catalysts. Nevertheless, few studies have been devoted to investigate the catalytic behavior differences of the multiple metal active sites triggered by the surface imperfections on catalysis. Herein, oxygen vacancies induced Fe2O3 catalyst are demonstrated with different Fe sites around one oxygen vacancy and exhibited significant catalytic performance for the carbonylation of various aryl halides and amines/alcohols with CO. The developed catalytic system displays excellent activity, selectivity, and reusability for the synthesis of carbonylated chemicals, including drugs and chiral molecules, via aminocarbonylation and alkoxycarbonylation. Combined characterizations disclose the formation of oxygen vacancies. Control experiments and density functional theory calculations demonstrate the selective combination of the three Fe sites is vital to improve the catalytic performance by catalyzing the elemental steps of PhI activation, CO insertion and C-N/C-O coupling respectively, endowing combinatorial sites catalyst for multistep reactions.

| S-EPMC10435489 | biostudies-literature

An approach to the site-selective diversification of apoptolidin A with peptide-based catalysts.

Project description:We report the application of peptide-based catalysts to the site-selective modification of apoptolidin A (1), an agent that displays remarkable selectivity for inducing apoptosis in E1A-transformed cell lines. Key to the approach was the development of an assay suitable for the screening of dozens of catalysts in parallel reactions that could be conducted using only microgram quantities of the starting material. Employing this assay, catalysts (e.g., 11 and ent-11) were identified that afforded unique product distributions, distinct from the product mixtures produced when a simple catalyst (N,N-dimethyl-4-aminopyridine (10)) was employed. Preparative reactions were then carried out with the preferred catalysts so that unique, homogeneous apoptolidin analogues could be isolated and characterized. From these studies, three new apoptolidin analogues were obtained (12-14), each differing from the other in either the location of acyl group substituents or the number of acetate groups appended to the natural product scaffold. Biological evaluation of the new apoptolidin analogues was then conducted using growth inhibition assays based on the H292 human lung carcinoma cell line. The new analogues exhibited activities comparable to apoptolidin A.

| S-EPMC2857549 | 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