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William E Royer - One of the best experts on this subject based on the ideXlab platform.
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insight into the allosteric mechanism of Scapharca dimeric hemoglobin
Biochemistry, 2014Co-Authors: Jennifer M Laine, William E Royer, Miguel Amat, Brittany R Morgan, Francesca MassiAbstract:Allosteric regulation is an essential function of many proteins that control a variety of different processes such as catalysis, signal transduction, and gene regulation. Structural rearrangements have historically been considered the main means of communication between different parts of a protein. Recent studies have highlighted the importance, however, of changes in protein flexibility as an effective way to mediate allosteric communication across a protein. Scapharca dimeric hemoglobin (HbI) is the simplest possible allosteric system, with cooperative ligand binding between two identical subunits. Thermodynamic equilibrium studies of the binding of oxygen to HbI have shown that cooperativity is an entropically driven effect. The change in entropy of the system observed upon ligand binding may arise from changes in the protein, the ligand, or the water of the system. The goal of this study is to determine the contribution of the change in entropy of the protein backbone to HbI cooperative binding. Mole...
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tertiary and quaternary allostery in tetrameric hemoglobin from Scapharca inaequivalvis
Biochemistry, 2013Co-Authors: Luca Ronda, William E Royer, Stefano Bettati, Eric R Henry, Tara Kashav, Jeffrey M Sanders, Andrea MozzarelliAbstract:The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that me...
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ligand migration and cavities within Scapharca dimeric hbi studies by time resolved crystallo graphy xe binding and computational analysis
Structure, 2009Co-Authors: J E Knapp, R Pahl, Jordi Cohen, Jeffry C Nichols, Klaus Schulten, Quentin H Gibson, V Srajer, William E RoyerAbstract:Summary As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.
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ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis
Biochemistry, 2007Co-Authors: Karin Nienhaus, William E Royer, J E Knapp, P Palladino, Ulrich G NienhausAbstract:Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a...
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ligand linked assembly of Scapharca dimeric hemoglobin
Journal of Biological Chemistry, 1997Co-Authors: William E Royer, Francine R Smith, Emory H BraswellAbstract:Abstract The assembly of Scapharca dimeric hemoglobin as a function of ligation has been explored by analytical gel chromatography, sedimentation equilibrium, and oxygen binding experiments to test the proposal that its cooperativity is based on quaternary enhancement. This hypothesis predicts that the liganded form would be assembled more tightly into a dimer than the unliganded form and that dissociation would lead to lower oxygen affinity. Our experiments demonstrate that although the dimeric interface is quite tight in this hemoglobin, dissociation can be clearly detected in the liganded states with monomer to dimer association constants in the range of 108 M−1 for the CO-liganded state and lower association constants measured in the oxygenated state. In contrast, the deoxy dimer shows no detectable dissociation by analytical ultracentrifugation. Thus, the more highly hydrated deoxy interface of this dimer is also the more tightly assembled. Equilibrium oxygen binding experiments reveal an increase in oxygen affinity and decrease in cooperativity as the concentration is lowered (in the μM range). These experiments unambiguously refute the hypothesis of quaternary enhancement and indicate that, as in the case of human hemoglobin and other allosteric proteins, quaternary constraint underlies cooperativity in Scapharca dimeric hemoglobin.
Emilia Chiancone - One of the best experts on this subject based on the ideXlab platform.
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cooperativity and ligand linked polymerisation in Scapharca tetrameric haemoglobin
2008Co-Authors: Gianni Colotti, Alberto Boffi, Emilia ChianconeAbstract:The assembly of two heterodimers into the A2B2 tetrameric haemoglobin from Scapharca inaequivalvis (HbII) confers to the molecule additional properties relative to the dimeric component (HbI), namely the capacity to undergo an oxygen- and anion-linked polymerisation process. This manifests itself functionally in an increase in cooperativity and a decrease in oxygen affinity at high protein concentrations. The functional parameters of the HbII tetramer as distinct from the effect of ligand-linked polymerisation, i.e. from the so-called polysteric effect, were evaluated in the present work. In conditions where polymerisation is abolished, the A2B2 tetramer is characterised by a significantly higher Hill coefficient than the HbI dimer (n=1.8 vs. 1.5), indicating that in Scapharca HbII heme-heme communication takes place also over long-range pathways that differ with respect to the direct pathway operative in HbI and by inference in the AB dimer of HbII. At high HbII concentration, where polymerisation of deoxygenated HbII is at a maximum, an additional increase in cooperativity is observed due to the association of the A2B2 tetramer into the (A2B2)4 and (A2B2)8 species. Thus, the consequent increase in Hill coefficient from 1.8 to 3.0 can be attributed to polysteric linkage.
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the interplay between heme iron and protein sulfhydryls in the reaction of dimeric Scapharca inaequivalvis hemoglobin with nitric oxide
Biophysical Chemistry, 2002Co-Authors: Alberto Boffi, Paolo Sarti, Gino Amiconi, Emilia ChianconeAbstract:Abstract The homodimeric hemoglobin from the mollusk Scapharca inaequivalvis possesses a single reactive cysteine residue per monomer, Cys92, which is located in the subunit interface in the vicinity of the heme group. The interplay between the heme iron and Cys92 towards the reaction with NO has been investigated by the combined use of electrospray mass spectrometry, FTIR and UV-Visible spectroscopy. When the ferrous liganded or unliganded protein reacts with free NO in solution Cys92 is not modified, but undergoes nitrosation when the hemoglobin is exposed to the nitric oxide releaser S -nitrosocysteine. When the ferric protein reacts with free NO under anaerobic conditions the heme iron is reduced and Cys92 is nitrosated. At variance with other hemeproteins investigated to date, in Scapharca HbI the heme-iron NO driven reduction is not accompanied by the formation of a ferric iron nitrosyl intermediate in detectable amounts. The results are consistent with the hypothesis that the nitrosating agent is the NO + species, which is generated during the NO driven reduction of the ferric heme iron. The possible reaction mechanism is discussed in comparison with recent findings on human hemoglobin and myoglobin.
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LIGAND-LINKED CHANGES AT THE SUBUNIT INTERFACES IN Scapharca HEMOGLOBINS PROBED THROUGH THE SULFHYDRYL INFRARED ABSORPTION
Biochemistry, 1999Co-Authors: Laura Guarrera, Emilia Chiancone, Gianni Colotti, Alberto BoffiAbstract:: FTIR spectra of native Scapharca homodimeric hemoglobin (HbI) and of the Phe97-->Ile mutant have been measured in the region 2400-2700 cm(-1) where the absorption of the sulfhydryl groups can be observed. In native HbI, the two Cys92 residues give rise to a relatively intense band centered at 2559 cm(-1) that is shifted to 2568 cm(-1) and strongly quenched upon ligand binding. In the Phe97-->Leu mutant, such ligand-linked changes are not observed and the strong peak at around 2560 cm(-1) persists in the liganded derivatives. In native HbI, the observed changes have been attributed to the decrease in polarity of the interface due to the ligand-induced extrusion of the Phe97 phenyl ring from the heme pocket to the interface and the subsequent release of several water molecules that are clustered in the vicinity of Cys92. In contrast, in the Phe97-->Leu mutant, the Leu residue does not leave the heme pocket upon ligand binding and the interface is unaltered. The Cys92/S-H infrared band, therefore, represents a sensitive probe of the structural rearrangements that take place in the intersubunit interface upon ligand binding to HbI. The heterotetrameric Scapharca hemoglobin HbII contains, in addition to the Cys92 residues in the interfaces, two extra sulfhydryl groups per tetramer (Cys9 in the B chain) that are exposed to solvent in the A helix. The frequency of the Cys9/S-H stretching vibration occurs at 2582 cm(-1) in the unliganded and at 2586 cm(-1) in the liganded derivative, pointing to the involvement of the A helix in the ligand-linked polymerization characteristic of HbII.
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Dynamics of cyanide binding to ferrous Scapharca inaequivalvis homodimeric hemoglobin.
Biochemistry, 1997Co-Authors: Alberto Boffi, Emilia Chiancone, Eric S. Peterson, Jiaqian Wang, Denis L. Rousseau, Joel M. FriedmanAbstract:Flash photolysis experiments have been carried out for the first time on a hemoglobin ferrous cyanide adduct with an 8 ns laser pulse. A 95% nonexponential rebinding process occurs within 2 μs after full photolysis in ferrous cyanide dimeric Scapharca inaequivalvis hemoglobin (HbI), indicating that once photolyzed the cyanide anion is not able to escape from the protein matrix and rebinds to the heme iron. The resonance Raman spectrum of the 10 ns photoproduct is identical to that of the fully relaxed deoxy derivative, indicating that in the ferrous cyanide HbI adduct protein relaxation occurs within 10 ns after photolysis. This behavior is at variance with that of the carbonmonoxy HbI derivative in which very little geminate rebinding is observed and the photoproduct relaxes with a lifetime of 1 μs. The fast relaxation of the cyanide HbI photoproduct can be accounted for by the small perturbation of the heme structure induced by cyanide binding to ferrous HbI. This is consistent with a deoxy-like conform...
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cooperative oxygen binding to Scapharca inaequivalvis hemoglobin in the crystal
Journal of Biological Chemistry, 1996Co-Authors: Andrea Mozzarelli, Gianni Colotti, Stefano Bettati, Claudio Rivetti, Gian Luigi Rossi, Emilia ChianconeAbstract:Abstract Oxygen binding to homodimeric Scapharca inaequivalvis hemoglobin (HbI) crystals has been investigated by single-crystal polarized absorption microspectrophotometry. The saturation curve, characterized by a Hill coefficient n = 1.45 and an oxygen pressure at half saturation p = 4.8 torr, at 15°C, shows that HbI in the crystalline state retains positive cooperativity in ligand binding. This finding will permit the correlation of the oxygen-linked conformational changes in the crystal with the expression of cooperativity. Polarized absorption spectra of deoxy-HbI, oxy-HbI, and oxidized HbI crystals indicate that oxygenation does not induce heme reorientation, whereas oxidation does. Lattice interactions prevent the dissociation of oxidized dimers that occurs in solution and stabilize an equilibrium distribution of pentacoordinate and hexacoordinate high spin species.
Baoshan Xing - One of the best experts on this subject based on the ideXlab platform.
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bioaccumulation and biotransformation of polybrominated diphenyl ethers in the marine bivalve Scapharca subcrenata influence of titanium dioxide nanoparticles
Marine Pollution Bulletin, 2015Co-Authors: Shengyan Tian, Yaodan Zhang, Chunzheng Song, Baoshan XingAbstract:Abstract Titanium dioxide nanoparticles (nTiO2) have the potential to adsorb co-existing contaminants in aqueous environment to form nanoparticle-contaminant complexes. Adsorption by nTiO2 might impact the fate of contaminants in water. Bioaccumulation experiments were conducted to compare the accumulation of polybrominated diphenyl ethers (PBDEs) in marine bivalve (Scapharca subcrenata) exposed to PBDEs in the presence and absence of nTiO2. PBDEs can be taken up by S. subcrenata through aqueous exposure. nTiO2 acts as a carrier and can enhance the ingestion of PBDEs, but the bioaccumulation of PBDEs was not facilitated significantly in the presence of nTiO2. Similar accumulation kinetics pattern was found after exposing to PBDEs in the presence and absence of nTiO2. Further analysis showed that no significant difference between the congener profiles of PBDEs in the presence and absence of nTiO2, suggesting that nTiO2 would not influence the biotransformation of PBDEs in clams.
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titanium dioxide nanoparticles as carrier facilitate bioaccumulation of phenanthrene in marine bivalve ark shell Scapharca subcrenata
Environmental Pollution, 2014Co-Authors: Shengyan Tian, Yaodan Zhang, Chunzheng Song, Baoshan XingAbstract:To evaluate the impact of titanium dioxide nanoparticles (nTiO2) on the uptake of hydrophobic organic chemicals by marine bivalves, we conducted a comparative bioaccumulation study by exposing clam, Scapharca subcrenata, to phenanthrene (Phe) in the presence and absence of nTiO2. The large surface area of nTiO2 resulted in adsorption of co-existing Phe in aqueous solution to form nTiO2-Phe complexes. Accumulation of nTiO2 was not observed in clams at exposed concentration (500 mg/L) in this study. However, enhanced uptake of Phe by clams was observed in the presence of nTiO2, with ku and BAFs values being 2 and 1.7 times higher than that of Phe alone, respectively. The enhanced uptake can be explained by ingestion of nTiO2-Phe complexes into the gut and subsequent desorption of Phe there. Therefore, nTiO2 as a carrier facilitated the uptake of Phe by marine bivalves.
Junghoon Yoon - One of the best experts on this subject based on the ideXlab platform.
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roseovarius Scapharcae sp nov isolated from ark shell Scapharca broughtonii
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Sooyeon Park, Jimin Park, Junghoon YoonAbstract:A Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated MA4-5T, was isolated from ark shell (Scapharca broughtonii) collected from the South Sea, South Korea. The novel strain grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences showed that strain MA4-5T forms a coherent cluster with the type strains of Roseovarius albus, Roseovarius aestuarii and Roseovarius nubinhibens, sharing 97.0–99.2 % sequence similarity. It exhibited 16S rRNA gene sequence similarity of 93.1–96.1 % to the type strains of other Roseovarius species. Strain MA4-5T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain MA4-5T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA4-5T was 53.8 mol% and its mean DNA–DNA relatedness values with the type strains of R. albus, R. aestuarii and R. nubinhibens were 11–26 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, indicated that strain MA4-5T is separate from recognized species of the genus Roseovarius. On the basis of the data presented, strain MA4-5T is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius Scapharcae sp. nov. is proposed. The type strain is MA4-5T ( = KCTC 42703T = NBRC 111226T).
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Aliisedimentitalea Scapharcae gen. nov., sp. nov., isolated from ark shell Scapharca broughtonii
Journal of Microbiology, 2015Co-Authors: Sooyeon Park, Jimin Park, Junghoon YoonAbstract:A Gram-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, designated MA2-16^T, was isolated from ark shell ( Scapharca broughtonii ) collected from the South Sea, South Korea. Strain MA2-16^T was found to grow optimally at 30°C, at pH 7.0–8.0 and in the presence of 2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain MA2-16^T clustered with the type strain of Sedimentitalea nanhaiensis . The novel strain exhibited a 16S rRNA gene sequence similarity value of 97.1% to the type strain of S. nanhaiensis . In the neighbour-joining phylogenetic tree based on gyrB sequences, strain MA2-16^T formed an evolutionary lineage independent of those of other taxa. Strain MA2-16^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c and 11-methyl C_18:1 ω7c as the major fatty acids. The major polar lipids of strain MA2-16^T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA2-16^T was 57.7 mol% and its DNA-DNA relatedness values with the type strains of S. nanhaiensis and some phylogenetically related species of the genera Leisingera and Phaeobacter were 13–24%. On the basis of the data presented, strain MA2-16^T is considered to represent a novel genus and novel species within the family Rhodobacteraceae , for which the name Aliisedimentitalea Scapharcae gen. nov., sp. nov. is proposed. The type strain is MA2-16^T (=KCTC 42119^T =CECT 8598^T).
Shengyan Tian - One of the best experts on this subject based on the ideXlab platform.
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bioaccumulation and biotransformation of polybrominated diphenyl ethers in the marine bivalve Scapharca subcrenata influence of titanium dioxide nanoparticles
Marine Pollution Bulletin, 2015Co-Authors: Shengyan Tian, Yaodan Zhang, Chunzheng Song, Baoshan XingAbstract:Abstract Titanium dioxide nanoparticles (nTiO2) have the potential to adsorb co-existing contaminants in aqueous environment to form nanoparticle-contaminant complexes. Adsorption by nTiO2 might impact the fate of contaminants in water. Bioaccumulation experiments were conducted to compare the accumulation of polybrominated diphenyl ethers (PBDEs) in marine bivalve (Scapharca subcrenata) exposed to PBDEs in the presence and absence of nTiO2. PBDEs can be taken up by S. subcrenata through aqueous exposure. nTiO2 acts as a carrier and can enhance the ingestion of PBDEs, but the bioaccumulation of PBDEs was not facilitated significantly in the presence of nTiO2. Similar accumulation kinetics pattern was found after exposing to PBDEs in the presence and absence of nTiO2. Further analysis showed that no significant difference between the congener profiles of PBDEs in the presence and absence of nTiO2, suggesting that nTiO2 would not influence the biotransformation of PBDEs in clams.
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titanium dioxide nanoparticles as carrier facilitate bioaccumulation of phenanthrene in marine bivalve ark shell Scapharca subcrenata
Environmental Pollution, 2014Co-Authors: Shengyan Tian, Yaodan Zhang, Chunzheng Song, Baoshan XingAbstract:To evaluate the impact of titanium dioxide nanoparticles (nTiO2) on the uptake of hydrophobic organic chemicals by marine bivalves, we conducted a comparative bioaccumulation study by exposing clam, Scapharca subcrenata, to phenanthrene (Phe) in the presence and absence of nTiO2. The large surface area of nTiO2 resulted in adsorption of co-existing Phe in aqueous solution to form nTiO2-Phe complexes. Accumulation of nTiO2 was not observed in clams at exposed concentration (500 mg/L) in this study. However, enhanced uptake of Phe by clams was observed in the presence of nTiO2, with ku and BAFs values being 2 and 1.7 times higher than that of Phe alone, respectively. The enhanced uptake can be explained by ingestion of nTiO2-Phe complexes into the gut and subsequent desorption of Phe there. Therefore, nTiO2 as a carrier facilitated the uptake of Phe by marine bivalves.
