Alternative modes of O2 activation in P450 and NOS enzymes are clarified by DFT modeling and resonance Raman spectroscopy

Heme pocket modulates protein conformation and diguanylate cyclase activity of a tetrameric globin coupled sensor

Bacteria use the second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) to control biofilm formation and other key phenotypes in response to environmental signals. Changes in oxygen levels can alter c-di-GMP signaling through a family of proteins termed globin coupled sensors (GCS) that contain diguanylate cyclase domains. Previous studies have found that GCS diguanylate cyclase activity is controlled by ligand binding to the heme within the globin domain, with oxygen binding resulting in the greatest increase in catalytic activity. Herein, we present evidence that heme-edge residues control O2-dependent signaling in PccGCS, a GCS protein from Pectobacterium carotovorum, by modulating heme distortion. Using enzyme kinetics, resonance Raman spectroscopy, small angle X-ray scattering, and multi-wavelength analytical ultracentrifugation, we have developed an integrated model of the full-length PccGCS tetramer and have identified conformational changes associated with ligand binding, heme conformation, and cyclase activity. Taken together, these studies provide new insights into the mechanism by which O2 binding modulates activity of diguanylate cyclase-containing GCS proteins.

Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy

The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.

Resonance Raman Characterization of O2-Binding Heme Proteins

A vast array of critical in vivo processes and pathways are dependent on a multitude of O₂-binding heme proteins which contain a diverse range of functions. Resonance Raman (rR) spectroscopy is an ideal technique for structural investigation of these proteins, providing information about the geometry of the Fe-O-O fragment and its electrostatic interactions with the distal active site. Characterization of these oxy adducts is an endeavor that is complicated by their instability for many heme proteins in solution, an obstacle which can be overcome by applying the rR technique to cryogenically frozen samples. We describe here how to measure rR spectra of heme proteins with stable oxy forms, as well as the technical adaptations required to measure unstable samples at 77 K.

Pretreatment of sludge with sodium iron chlorophyllin-H2O2 for enhanced biogas production during anaerobic digestion

This study investigated a novel sodium iron chlorophyllin-H₂O₂ (SIC-H₂O₂) sludge pretreatment strategy before anaerobic digestion to enhance methane production. The efficiencies and mechanism of the proposed strategy to enhance sludge biodegradability were explored. The SIC-H₂O₂ pretreatment could enhance the oxidation performance for sludge floc disintegration to dissociate TB-EPS into S-EPS increased SCOD to 521.38 mg/L. The increase of solubilization and release of EPS with the pretreatment facilitate the biogas production at 702 L kg^-1 VS, which was 3-folds of the control and significantly higher than other pretreatments. The result of excitation-emission matrix and parallel factor (EEM-PARAFAC) analysis showed that the SIC-H₂O₂ pretreatment enhanced the dissociation of TB-EPS fractions, especially the protein-like and soluble microbial by-product-like substances. Electron paramagnetic resonance (EPR) results provided evidence for homolytic catalysis H₂O₂ for the generation OH and the production of high-valent (Por)Fe^IV(O) intermediates. Synergistic effects of reactive oxygen species (OH, H₂O₂ and /HO₂) and (Por)Fe^IV(O) enhanced the EPS disintegration during SIC-H₂O₂ pretreatment. The mixed-acid type fermentation provided continuous VFAs supply under the enrichment of Chloroflexi and Actinobacteria and multiplication Methanosaeta also promoted methane production. This research provides a feasible pretreatment strategy increase sludge biodegradability and enhance biogas production in the anaerobic digestion process.