scholarly journals Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo–electron microscopy

2019 ◽  
Vol 5 (8) ◽  
pp. eaax1803 ◽  
Author(s):  
Chai C. Gopalasingam ◽  
Rachel M. Johnson ◽  
George N. Chiduza ◽  
Takehiko Tosha ◽  
Masaki Yamamoto ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Electron Microscopy ◽  
Cytochrome C ◽  
Active Site ◽  
Proton Transport ◽  
Water Channel ◽  
Water Molecules ◽  
Cryo Electron Microscopy ◽  
Proton Source ◽  
Key Residues

Quinol-dependent nitric oxide reductases (qNORs) are membrane-integrated, iron-containing enzymes of the denitrification pathway, which catalyze the reduction of nitric oxide (NO) to the major ozone destroying gas nitrous oxide (N2O). Cryo–electron microscopy structures of active qNOR from Alcaligenes xylosoxidans and an activity-enhancing mutant have been determined to be at local resolutions of 3.7 and 3.2 Å, respectively. They unexpectedly reveal a dimeric conformation (also confirmed for qNOR from Neisseria meningitidis) and define the active-site configuration, with a clear water channel from the cytoplasm. Structure-based mutagenesis has identified key residues involved in proton transport and substrate delivery to the active site of qNORs. The proton supply direction differs from cytochrome c–dependent NOR (cNOR), where water molecules from the cytoplasm serve as a proton source similar to those from cytochrome c oxidase.

Membranes Assembled from Narrow Carbon Nanotubes Block Proton Transport and Can Form Effective Nano-Filtration Devices

2006 ◽  
Vol 3 (2) ◽  
pp. 237-242 ◽  
Author(s):  
Anton Burykin ◽  
Arieh Warshel
Keyword(s):  
Carbon Nanotubes ◽  
Proton Transport ◽  
Computational Study ◽  
Water Channel ◽  
Water Transfer ◽  
Water Molecules ◽  
Nano Technology ◽  
Nano Filtration ◽  
Double Wall ◽  
Aquaporin Water Channel

The use of carbon nanotubes in various filtration devices is a promising current direction in nano-technology. The direction of progress is, however, far from obvious when it involves devices that can allow water to be transferred while blocking proton transport. This problem is addressed in the present paper by exploiting the perspective that emerge from our recent studies of the mechanism of proton blockage in aquaporins. The paper focuses on a computational study of the free energy barriers for transfer of proton and water molecules through the membrane assembled from the double wall (5;5)@(10;10) armchair carbon nanotubes. It shows that such system can be used as a water nano filter that allows water transfer while blocking protons. Thus such carbon nanotube membrane will work as an artificial analog of aquaporin water channel. The general mechanisms of proton transfer/blockage in biological and artificial nanosystems are also discussed.

scholarly journals Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Benjamin G Horst ◽  
Adam L Yokom ◽  
Daniel J Rosenberg ◽  
Kyle L Morris ◽  
Michal Hammel ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Electron Microscopy ◽  
Guanylate Cyclase ◽  
Soluble Guanylate Cyclase ◽  
Coiled Coil ◽  
X Ray ◽  
Nitric Oxide Signaling ◽  
Catalytic Domains ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy

Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length Manduca sexta sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.

scholarly journals Cryo-electron microscopy structures of pyrene-labeled ADP-Pi- and ADP-actin filaments

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Steven Z. Chou ◽  
Thomas D. Pollard
Keyword(s):  
Electron Microscopy ◽  
Skeletal Muscle ◽  
Active Site ◽  
Actin Filaments ◽  
Actin Polymerization ◽  
Actin Binding ◽  
Muscle Actin ◽  
Hydrophobic Cavity ◽  
Cryo Electron Microscopy ◽  
Kinetics Of

AbstractSince the fluorescent reagent N-(1-pyrene)iodoacetamide was first used to label skeletal muscle actin in 1981, the pyrene-labeled actin has become the most widely employed tool to measure the kinetics of actin polymerization and the interaction between actin and actin-binding proteins. Here we report high-resolution cryo-electron microscopy structures of actin filaments with N-1-pyrene conjugated to cysteine 374 and either ADP (3.2 Å) or ADP-phosphate (3.0 Å) in the active site. Polymerization buries pyrene in a hydrophobic cavity between subunits along the long-pitch helix with only minor differences in conformation compared with native actin filaments. These structures explain how polymerization increases the fluorescence 20-fold, how myosin and cofilin binding to filaments reduces the fluorescence, and how profilin binding to actin monomers increases the fluorescence.

Nitric oxide-induced persistent inhibition and nitrosylation of active site cysteine residues of mitochondrial cytochrome-c oxidase in lung endothelial cells

2005 ◽  
Vol 288 (4) ◽  
pp. C840-C849 ◽  
Author(s):  
Jianliang Zhang ◽  
Bilian Jin ◽  
Liuzhe Li ◽  
Edward R. Block ◽  
Jawaharlal M. Patel
Keyword(s):  
Nitric Oxide ◽  
Endothelial Cells ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Active Site ◽  
Prolonged Exposure ◽  
Site Directed Mutagenesis ◽  
Cysteine Residues ◽  
Complex Iv ◽  
Lung Endothelial Cells

Persistent inhibition of cytochrome- c oxidase, a terminal enzyme of the mitochondrial electron transport chain, by excessive nitric oxide (NO) derived from inflammation, polluted air, and tobacco smoke contributes to enhanced oxidant production and programmed cell death or apoptosis of lung cells. We sought to determine whether the long-term exposure of pulmonary artery endothelial cells (PAEC) to pathophysiological concentrations of NO causes persistent inhibition of complex IV through redox modification of its key cysteine residues located in a putative NO-sensitive motif. Prolonged exposure of porcine PAEC to 1 mM 2,2′-(hydroxynitrosohydrazino)-bis-ethanamine (NOC-18; slow-releasing NO donor, equivalent to 1–5 μM NO) resulted in a gradual, persistent inhibition of complex IV concomitant with a reduction in ratios of mitochondrial GSH and GSSG. Overexpression of thioredoxin in mitochondria of PAEC attenuated NO-induced loss of complex IV activities, suggesting redox regulation of complex IV activity. Sequence analysis of complex IV subunits revealed a novel putative NO-sensitive motif in subunit II (S2). There are only two cysteine residues in porcine complex IV S2, located in the putative motif. Immunoprecipitation and Western blot analysis and “biotin switch” assay demonstrated that exposure of PAEC to 1 mM NOC-18 increased S-nitrosylation of complex IV S2 by 200%. Site-directed mutagenesis of these two cysteines of complex IV S2 attenuated NO-increased nitrosylation of complex IV S2. These results demonstrate for the first time that NO nitrosylates active site cysteines of complex IV, which is associated with persistent inhibition of complex IV. NO inhibition of complex IV via nitrosylation of NO-sensitive cysteine residues can be a novel upstream event in NO-complex IV signaling for NO toxicity in lung endothelial cells.

scholarly journals Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy

2019 ◽  
Author(s):  
Benjamin G. Horst ◽  
Adam L. Yokom ◽  
Daniel J. Rosenberg ◽  
Kyle L. Morris ◽  
Michal Hammel ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Electron Microscopy ◽  
Guanylate Cyclase ◽  
Soluble Guanylate Cyclase ◽  
Coiled Coil ◽  
X Ray ◽  
Nitric Oxide Signaling ◽  
Catalytic Domains ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy

AbstractSoluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-lengthManduca sextasGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.

scholarly journals High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

2020 ◽  
Author(s):  
Ricardo D. Righetto ◽  
Leonie Anton ◽  
Ricardo Adaixo ◽  
Roman P. Jakob ◽  
Jasenko Zivanov ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Carbon Dioxide ◽  
High Resolution ◽  
Yersinia Enterocolitica ◽  
Active Site ◽  
High Data ◽  
Cryo Electron Microscopy ◽  
Acidic Environments ◽  
The Impact ◽  
Better Than

AbstractUrease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at better than 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. Our data are of sufficient quality to support drug development efforts.

scholarly journals High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803

2021 ◽  
Vol 119 (1) ◽  
pp. e2116765118
Author(s):  
Christopher J. Gisriel ◽  
Jimin Wang ◽  
Jinchan Liu ◽  
David A. Flesher ◽  
Krystle M. Reiss ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Photosystem Ii ◽  
Water Oxidation ◽  
Genetic Manipulation ◽  
Water Channel ◽  
Global Scale ◽  
Cryo Electron Microscopy ◽  
C Terminus ◽  
Pcc 6803

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.

scholarly journals Cryo-electron microscopy structures of pyrene-labeled ADP-Pi- and ADP-actin filaments

2020 ◽  
Author(s):  
Steven Z. Chou ◽  
Thomas D. Pollard
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Active Site ◽  
Actin Filaments ◽  
Hydrophobic Cavity ◽  
Cryo Electron Microscopy

AbstractWe report high resolution cryo-electron microscopy structures of actin filaments with N-1-pyrene conjugated to cysteine 374 and either ADP (3.2 Å) or ADP-phosphate (3.0 Å) in the active site. Polymerization buries pyrene in a hydrophobic cavity between subunits along the long-pitch helix with only minor differences in conformation compared with native actin filaments. These structures explain how polymerization increases the fluorescence 20-fold, how myosin and cofilin binding to filaments reduces the fluorescence and how profilin binding to actin monomers increases the fluorescence.

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