The importance of helical structures to the overall activity and structural stability of a lipase from Pseudomonas aeruginosa PAO1 in n-hexane.

Bacterial lipases are versatile extracellular enzymes with a catalytic triad at the active site and a flexible 'lid' that modulates catalytic accessibility. We combined computational modeling with preliminary in vitro testing to assess the structural stability and activity of the Pseudomonas aeruginosa PAO1 lipase (PAL). We evaluated several systems consisting of the native and mutant forms of the lipase in n-hexane using molecular dynamics simulations.

Phosphoproteomic analysis reveals distinctive responses in Mangrovibacter phragmatis under high-salinity condition.

We conducted a thorough genome-wide investigation of protein phosphorylation in the halotolerant bacterium Mangrovibacter phragmitis (MPH) ASIOC01, using the Fe-IMAC enrichment method combined with tandem mass spectrometry under low- and high-salinity conditions. The phosphoproteome comprises 86 unique phosphorylated proteins, crucially involving pathways such as glycolysis/gluconeogenesis, the citrate cycle, chaperones, ribosomal proteins, and cell division. This study represents the first and most extensive investigation to-date comparing the bacterial phosphoproteome under different osmotic conditions using a gel-free approach.

Isolation, molecular identification, and genomic analysis of strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity.

The physiological and genotypic characteristics of (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source.

Voltage-Gated Electrocatalysis of Efficient and Selective Methane Oxidation by Tricopper Clusters under Ambient Conditions.

Selective methane oxidation is difficult chemistry. Here we describe a strategy for the electrocatalysis of selective methane oxidation by immobilizing tricopper catalysts on the cathodic surface. In the presence of dioxygen and methane, the activation of these catalysts above a threshold cathodic potential can initiate the dioxygen chemistry for O atom transfer to methane.

Catalytic machinery of methane oxidation in particulate methane monooxygenase (pMMO).

In this focused review, we portray the recently reported 2.5 Å cyro-EM structure of the particulate methane monooxygenase (pMMO) from M. capsulatus (Bath).

Resolving Entangled -Coupling Patterns for Steroidal Structure Determinations by NMR Spectroscopy.

For decades, high-resolution H NMR spectroscopy has been routinely utilized to analyze both naturally occurring steroid hormones and synthetic steroids, which play important roles in regulating physiological functions in humans. Because the H signals are inevitably superimposed and entangled with various splitting patterns, such that the individual H chemical shift and associated coupling identities are hardly resolved. Given this, applications of thess information for elucidating steroidal molecular structures and steroid/ligand interactions at the atomic level were largely restricted.

Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry from Spectroscopic and High-Resolution X-ray Structural Studies of the Methanol Dehydrogenase from (Bath).

The active site of methanol dehydrogenase (MDH) contains a rare disulfide bridge between adjacent cysteine residues. As a vicinal disulfide, the structure is highly strained, suggesting it might work together with the pyrroloquinoline quinone (PQQ) prosthetic group and the Ca ion in the catalytic turnover during methanol (CHOH) oxidation. We purify MDH from (Bath) with the disulfide bridge broken into two thiols.

The PmoB subunit of particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath): The Cu sponge and its function.

In this study, we describe efforts to clarify the role of the copper cofactors associated with subunit B (PmoB) of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) (M. capsulatus). This subunit exhibits strong affinity toward Cu ions.

A Carbon Electrode Functionalized by a Tricopper Cluster Complex: Overcoming Overpotential and Production of Hydrogen Peroxide in the Oxygen Reduction Reaction.

A study of the oxygen reduction reaction (ORR) on a screen printed carbon electrode surface mediated by the tricopper cluster complex Cu (7-N-Etppz(CH OH)) dispersed on electrochemically reduced carbon black, where 7-N-Etppz(CH OH) is the ligand 3,3'-(6-(hydroxymethyl)-1,4-diazepane-1,4-diyl)bis(1-(4-ethyl piperazin-1-yl)propan-2-ol), is described. Onset oxygen reduction potentials of about 0.92 V and about 0.

Electrochemical Hydroxylation of C-C n-Alkanes by Recombinant Alkane Hydroxylase (AlkB) and Rubredoxin-2 (AlkG) from Pseudomonas putida GPo1.

An unprecedented method for the efficient conversion of C-C linear alkanes to their corresponding primary alcohols mediated by the membrane-bound alkane hydroxylase (AlkB) from Pseudomonas putida GPo1 is demonstrated. The X-ray absorption spectroscopy (XAS) studies support that electrons can be transferred from the reduced AlkG (rubredoxin-2, the redox partner of AlkB) to AlkB in a two-phase manner. Based on this observation, an approach for the electrocatalytic conversion from alkanes to alcohols mediated by AlkB using an AlkG immobilized screen-printed carbon electrode (SPCE) is developed.

Alkane Oxidation: Methane Monooxygenases, Related Enzymes, and Their Biomimetics.

Methane monooxygenases (MMOs) mediate the facile conversion of methane into methanol in methanotrophic bacteria with high efficiency under ambient conditions. Because the selective oxidation of methane is extremely challenging, there is considerable interest in understanding how these enzymes carry out this difficult chemistry. The impetus of these efforts is to learn from the microbes to develop a biomimetic catalyst to accomplish the same chemical transformation.

Mechanistic Study of the Stereoselective Hydroxylation of [2- H ,3- H ]Butanes Catalyzed by Cytochrome P450 BM3 Variants.

Engineered bacterial cytochrome P450s are noted for their ability in the oxidation of inert small alkanes. Cytochrome P450 BM3 L188P A328F (BM3 PF) and A74E L188P A328F (BM3 EPF) variants are able to efficiently oxidize n-butane to 2-butanol. Esterification of the 2-butanol derived from this reaction mediated by the aforementioned two mutants gives diastereomeric excesses (de) of -56±1 and -52±1 %, respectively, with the preference for the oxidation occurring at the C-H bond.

Inactivation of the particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath) by acetylene.

Acetylene (HCCH) has a long history as a mechanism-based enzyme inhibitor and is considered an active-site probe of the particulate methane monooxygenase (pMMO). Here, we report how HCCH inactivates pMMO in Methylococcus capsulatus (Bath) by using high-resolution mass spectrometry and computational simulation. High-resolution MALDI-TOF MS of intact pMMO complexes has allowed us to confirm that the enzyme oxidizes HCCH to the ketene (C2H2O) intermediate, which then forms an acetylation adduct with the transmembrane PmoC subunit.

The bacteriohemerythrin from Methylococcus capsulatus (Bath): Crystal structures reveal that Leu114 regulates a water tunnel.

The bacteriohemerythrin (McHr) from Methylococcus capsulatus (Bath) is an oxygen carrier that serves as a transporter to deliver O2 from the cytosol of the bacterial cell body to the particulate methane monooxygenase residing in the intracytoplasmic membranes for methane oxidation. Here we report X-ray protein crystal structures of the recombinant wild type (WT) McHr and its L114A, L114Y and L114F mutants. The structure of the WT reveals a possible water tunnel in the McHr that might be linked to its faster autoxidation relative to hemerythrin in marine invertebrates.

Controlled oxidation of aliphatic CH bonds in metallo-monooxygenases: mechanistic insights derived from studies on deuterated and fluorinated hydrocarbons.

The control over the regio- and/or stereo-selective aliphatic CH oxidation by metalloenzymes is of great interest to scientists. Typically, these enzymes invoke host-guest chemistry to sequester the substrates within the protein pockets, exploiting sizes, shapes and specific interactions such as hydrogen-bonding, electrostatic forces and/or van der Waals interactions to control the substrate specificity, regio-specificity and stereo-selectivity. Over the years, we have developed a series of deuterated and fluorinated variants of these hydrocarbon substrates as probes to gain insights into the controlled CH oxidations of hydrocarbons facilitated by these enzymes.

Vaccinia viral protein A27 is anchored to the viral membrane via a cooperative interaction with viral membrane protein A17.

The vaccinia viral protein A27 in mature viruses specifically interacts with heparan sulfate for cell surface attachment. In addition, A27 associates with the viral membrane protein A17 to anchor to the viral membrane; however, the specific interaction between A27 and A17 remains largely unclear. To uncover the active binding sites and the underlying binding mechanism, we expressed and purified the N-terminal (18-50 residues) and C-terminal (162-203 residues) fragments of A17, which are denoted A17-N and A17-C.

Identification of the proteins required for fatty acid desaturation in zebrafish (Danio rerio).

Zebrafish Δ-5/Δ-6 fatty acid desaturase (Z-FADS) catalyzes the cascade synthesis of long-chain polyunsaturated fatty acids (PUFAs), thereby playing a pivotal role in several biological processes. In the current study, we report that the Z-FADS protein exists in close proximity to certain cytochrome b5 reductases (CYB5R2 and 3) and elongases (ELOVL2, 4, 5 and 7) on the endoplasmic reticulum, as determined using fluorescence microscopy and fluorescence resonance energy transfer. HeLa cells co-transfected with zebrafish fads and elovl2, 4, and 5 produced docosahexaenoic acid (DHA), as detected by gas chromatography.

Regioselective hydroxylation of C(12)-C(15) fatty acids with fluorinated substituents by cytochrome P450 BM3.

We demonstrate herein that wild-type cytochrome P450 BM3 can recognize non-natural substrates, such as fluorinated C12 -C15 chain-length fatty acids, and show better catalysis for their efficient conversion. Although the binding affinities for fluorinated substrates in the P450 BM3 pocket are marginally lower than those for non-fluorinated substrates, spin-shift measurements suggest that fluoro substituents at the ω-position can facilitate rearrangement of the dynamic structure of the bulk-water network within the hydrophobic pocket through a micro desolvation process to expel the water ligand of the heme iron that is present in the resting state. A lowering of the Michaelis-Menten constant (Km ), however, indicates that fluorinated fatty acids are indeed better substrates compared with their non-fluorinated counterparts.

Improved mass spectrometric analysis of membrane proteins based on rapid and versatile sample preparation on nanodiamond particles.

We have developed a novel streamlined sample preparation procedure for mass spectrometric (MS) analysis of membrane proteins using surface-oxidized nanodiamond particles. The platform consists of solid-phase extraction and elution of the membrane proteins on nanodiamonds, concentrating the membrane proteins on the nanodiamonds and separating out detergents, chaotropic agents, and salts, and other impurities that are often present at high concentrations in solubilized membrane preparations. In this manner, membrane-protein extracts are transformed into MS-ready samples in minutes.

Dioxygen activation of a trinuclear Cu(I)Cu(I)Cu(I) cluster capable of mediating facile oxidation of organic substrates: competition between O-atom transfer and abortive intercomplex reduction.

The dioxygen activation of a series of Cu(I)Cu(I)Cu(I) complexes based on the ligands (L) 3,3'-(1,4-diazepane- 1,4-diyl)bis(1-{[2-(dimethylamino)ethyl](methyl)amino}propan-2-ol)(7-Me) or 3,3'-(1,4-diazepane-1,4-diyl)bis(1-{[2-(diethylamino)ethyl](ethyl)amino}propan-2-ol)(7-Et) forms an intermediate capable of mediating facile O-atom transfer to simple organic substrates at room temperature. To elucidate the dioxygen chemistry, we have examined the reactions of 7-Me, 7-Et, and 3,3'-(1,4-diazepane-1,4-diyl)bis[1-(4-methylpiperazin-1-yl)propan-2-ol] (7-N-Meppz) with dioxygen at -80, -55, and -35 °C in propionitrile (EtCN) by UV-visible, 77 K EPR, and X-ray absorption spectroscopy, and 7-N-Meppz and 7-Me with dioxygen at room temperature in acetonitrile (MeCN) by diode array spectrophotometry. At both -80 and -55 °C, the mixing of the starting [Cu(I)Cu(I)Cu(I)(L)](1+) complex (1) with O(2)-saturated propionitrile (EtCN) led to a bright green solution consisting of two paramagnetic species: the green dioxygen adduct [Cu(II)Cu(II)(μ-η(2):η(2)-peroxo)Cu(II)(L)](2+) (2) and the blue [Cu(II)Cu(II)(μ-O)Cu(II)(L)](2+) species (3).

The metal core structures in the recombinant Escherichia coli transcriptional factor SoxR.

X-ray absorption, circular dichroism, and EPR spectroscopy were employed to investigate the metal-core structures in the Escherichia coli transcriptional factor SoxR under reduced, oxidized, and nitrosylated conditions. The spectroscopic data revealed that the coordination environments of the metal active centers varied only very slightly between the reduced and oxidized states, similar to most other proteins containing iron-sulfur clusters. Upon nitrosylation of oxidized SoxR, however, we observed a low-temperature EPR spectrum characteristic of a protein dinitrosyl iron complex (DNIC), with an intensity corresponding to about two DNICs per iron sulfur cluster in the protein, according to spin quantification relative to a low-molecular-weight DNIC standard.

Overexpression and purification of the particulate methane monooxygenase from Methylococcus capsulatus (Bath).

The particulate methane monooxygenase (pMMO) is a multi-copper enzyme that mediates the facile conversion of methane to methanol in methanotrophic bacteria. As a membrane-bound multi-subunit metalloprotein, the highly active protein has been difficult to isolate and purify to homogeneity for biochemical and biophysical studies. In this chapter, we describe a method to overexpress pMMO with good specific activity in high yields in the intracytoplasmic membranes of the host organism, together with two protocols to isolate and purify the enzyme from pMMO-enriched membranes without loss of the copper cofactors and enzymatic activity.

Tuning the regio- and stereoselectivity of C-H activation in n-octanes by cytochrome P450 BM-3 with fluorine substituents: evidence for interactions between a C-F bond and aromatic π systems.

We employed the water-soluble cytochrome P450 BM-3 to study the activity and regiospecificity of oxidation of fluorinated n-octanes. Three mutations, A74G, F87V, and L188Q, were introduced into P450 BM-3 to allow the system to undergo n-octane oxidation. In addition, the alanine at residue 328 was replaced with a phenylalanine to introduce an aromatic residue into the hydrophobic pocket to examine whether or not van der Waals interactions between a C-F substituent in the substrate and the polarizable π system of the phenylalanine may be used to steer the positioning of the substrate within the active-site pocket of the enzyme and control the regioselectivity and stereoselectivity of hydroxylation.