21 results on '"Barry D. Howes"'
Search Results
2. Nanohybrid Assemblies of Porphyrin and Au10 Cluster Nanoparticles
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Mariachiara Trapani, Maria Angela Castriciano, Andrea Romeo, Giovanna De Luca, Nelson Machado, Barry D. Howes, Giulietta Smulevich, and Luigi Monsù Scolaro
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gold clusters ,plating ,porphyrin ,chirality ,SERS ,Chemistry ,QD1-999 - Abstract
The interaction between gold sub-nanometer clusters composed of ten atoms (Au10) and tetrakis(4-sulfonatophenyl)porphyrin (TPPS) was investigated through various spectroscopic techniques. Under mild acidic conditions, the formation, in aqueous solutions, of nanohybrid assemblies of porphyrin J-aggregates and Au10 cluster nanoparticles was observed. This supramolecular system tends to spontaneously cover glass substrates with a co-deposit of gold nanoclusters and porphyrin nanoaggregates, which exhibit circular dichroism (CD) spectra reflecting the enantiomorphism of histidine used as capping and reducing agent. The morphology of nanohybrid assemblies onto a glass surface was revealed by atomic force microscopy (AFM), and showed the concomitant presence of gold nanoparticles with an average size of 130 nm and porphyrin J-aggregates with lengths spanning from 100 to 1000 nm. Surface-enhanced Raman scattering (SERS) was observed for the nanohybrid assemblies.
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- 2019
- Full Text
- View/download PDF
3. Study of manganese binding to the ferroxidase centre of human H-type ferritin
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M. Lantieri, Emilia Chiancone, Silvia Sottini, Maria Fittipaldi, Annarita Fiorillo, Barry D. Howes, Gabriele Spina, Elisabetta Falvo, Donella Rovai, Simonetta Stefanini, Andrea Ilari, Dante Gatteschi, and Matteo Ardini
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0301 basic medicine ,Human H ferritin ,Kinetics ,Ferroxidase activity ,Biochemistry ,Cofactor ,law.invention ,Inorganic Chemistry ,03 medical and health sciences ,law ,Mössbauer spectroscopy ,Heterodimetal manganese-iron centre ,Humans ,Electron paramagnetic resonance ,Manganese ,biology ,Chemistry ,Electron Spin Resonance Spectroscopy ,Ceruloplasmin ,Ferroxidase centre ,EPR ,Mössbauer ,Apoferritins ,Protein Binding ,Ferritin ,Crystallography ,030104 developmental biology ,biology.protein ,Titration - Abstract
Ferritins are ubiquitous and conserved proteins endowed with enzymatic ferroxidase activity, that oxidize Fe(II) ions at the dimetal ferroxidase centre to form a mineralized Fe(III) oxide core deposited within the apo-protein shell. Herein, the in vitro formation of a heterodimetal cofactor constituted by Fe and Mn ions has been investigated in human H ferritin (hHFt). Namely, Mn and Fe binding at the hHFt ferroxidase centre and its effects on Fe(II) oxidation have been investigated by UV–Vis ferroxidation kinetics, fluorimetric titrations, multifrequency EPR, and preliminary Mossbauer spectroscopy. Our results show that in hHFt, both Fe(II) and Mn(II) bind the ferroxidase centre forming a Fe-Mn cofactor. Moreover, molecular oxygen seems to favour Mn(II) binding and increases the ferroxidation activity of the Mn-loaded protein. The data suggest that Mn influences the Fe binding and the efficiency of the ferroxidation reaction. The higher efficiency of the Mn-Fe heterometallic centre may have a physiological relevance in specific cell types (i.e. glia cells), where the concentration of Mn is the same order of magnitude as iron.
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- 2018
4. Probing the non-native states of Cytochrome c with resonance Raman spectroscopy: A tool for investigating the structure-function relationship
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Barry D. Howes, Giulietta Smulevich, Lorenzo Tognaccini, and Lisa Milazzo
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0301 basic medicine ,030102 biochemistry & molecular biology ,biology ,Chemistry ,Cytochrome c ,Structure function ,Resonance Raman spectroscopy ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,03 medical and health sciences ,symbols.namesake ,Nuclear magnetic resonance ,symbols ,biology.protein ,General Materials Science ,Raman spectroscopy ,Spectroscopy - Published
- 2018
5. Unravelling the Non-Native Low-Spin State of the Cytochrome c–Cardiolipin Complex: Evidence of the Formation of a His-Ligated Species Only
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Rebecca Pogni, Roberto Santucci, Maria Cristina Piro, Federica Sinibaldi, Barry D. Howes, Lisa Milazzo, Maria Camilla Baratto, Maria Fittipaldi, Lorenzo Tognaccini, and Giulietta Smulevich
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0301 basic medicine ,Protein Folding ,Protein Structure ,Secondary ,Cardiolipins ,Stereochemistry ,Mutant ,Gene Expression ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Protein Structure, Secondary ,Dissociation (chemistry) ,law.invention ,03 medical and health sciences ,chemistry.chemical_compound ,Methionine ,law ,Genes, Synthetic ,Escherichia coli ,Cardiolipin ,Animals ,Histidine ,Horses ,Cloning, Molecular ,Settore BIO/10 ,Electron paramagnetic resonance ,Conformational isomerism ,Protein Unfolding ,Carbon Monoxide ,biology ,Hydrogen bond ,Chemistry ,Myocardium ,Cytochrome c ,Synthetic ,Temperature ,Molecular ,Cytochromes c ,Hydrogen Bonding ,Recombinant Proteins ,0104 chemical sciences ,030104 developmental biology ,Genes ,Protein Binding ,biology.protein ,Cloning ,Peroxidase - Abstract
The interaction between cytochrome c (Cyt c) and cardiolipin (CL) plays a vital role in the early stages of apoptosis. The binding of CL to Cyt c induces a considerable increase in its peroxidase activity that has been attributed to the partial unfolding of the protein, dissociation of the Met80 axial ligand, and formation of non-native conformers. Although the interaction between Cyt c and CL has been extensively studied, there is still no consensus regarding the conformational rearrangements of Cyt c that follow the protein-lipid interaction. To rationalize the different results and gain better insight into the Cyt c-CL interaction, we have studied the formation of the CL complex of the horse heart wild-type protein and selected mutants in which residues considered to play a key role in the interaction with CL (His26, His33, Lys72, Lys73, and Lys79) have been mutated. The analysis was conducted at both room temperature and low temperatures via ultraviolet-visible absorption, resonance Raman, and electron paramagnetic resonance spectroscopies. The trigger and the sequence of CL-induced structural variations are discussed in terms of disruption of the His26-Pro44 hydrogen bond. We unequivocally identify the sixth ligand in the partially unfolded, non-native low-spin state that Cyt c can adopt following the protein-lipid interaction, as a His ligation, ruling out the previously proposed involvement of a Lys residue or an OH- ion.
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- 2017
6. Nanohybrid Assemblies of Porphyrin and Au10 Cluster Nanoparticles
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Luigi Monsù Scolaro, Giulietta Smulevich, Andrea Romeo, Nelson Machado, Maria Angela Castriciano, Mariachiara Trapani, Barry D. Howes, and Giovanna De Luca
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Circular dichroism ,Materials science ,Aqueous solution ,Reducing agent ,SERS ,General Chemical Engineering ,gold clusters ,plating ,porphyrin ,chirality ,Supramolecular chemistry ,Nanoparticle ,Photochemistry ,Porphyrin ,Nanoclusters ,lcsh:Chemistry ,chemistry.chemical_compound ,lcsh:QD1-999 ,chemistry ,Colloidal gold ,General Materials Science - Abstract
The interaction between gold sub-nanometer clusters composed of ten atoms (Au10) and tetrakis(4-sulfonatophenyl)porphyrin (TPPS) was investigated through various spectroscopic techniques. Under mild acidic conditions, the formation, in aqueous solutions, of nanohybrid assemblies of porphyrin J-aggregates and Au10 cluster nanoparticles was observed. This supramolecular system tends to spontaneously cover glass substrates with a co-deposit of gold nanoclusters and porphyrin nanoaggregates, which exhibit circular dichroism (CD) spectra reflecting the enantiomorphism of histidine used as capping and reducing agent. The morphology of nanohybrid assemblies onto a glass surface was revealed by atomic force microscopy (AFM), and showed the concomitant presence of gold nanoparticles with an average size of 130 nm and porphyrin J-aggregates with lengths spanning from 100 to 1000 nm. Surface-enhanced Raman scattering (SERS) was observed for the nanohybrid assemblies.
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- 2019
- Full Text
- View/download PDF
7. Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes
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Lisa, Milazzo, Stefan, Hofbauer, Barry D, Howes, Thomas, Gabler, Paul G, Furtmüller, Christian, Obinger, and Giulietta, Smulevich
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Structure-Activity Relationship ,Amino Acid Substitution ,Bacterial Proteins ,Carboxy-Lyases ,Catalytic Domain ,Mutation, Missense ,Listeria monocytogenes ,Article - Abstract
Coproheme decarboxylases (ChdC) catalyze the hydrogen peroxide-mediated conversion of coproheme to heme b. This work compares the structure and function of wild-type (WT) coproheme decarboxylase from Listeria monocytogenes and its M149A, Q187A, and M149A/Q187A mutants. The UV–vis, resonance Raman, and electron paramagnetic resonance spectroscopies clearly show that the ferric form of the WT protein is a pentacoordinate quantum mechanically mixed-spin state, which is very unusual in biological systems. Exchange of the Met149 residue to Ala dramatically alters the heme coordination, which becomes a 6-coordinate low spin species with the amide nitrogen atom of the Q187 residue bound to the heme iron. The interaction between M149 and propionyl 2 is found to play an important role in keeping the Q187 residue correctly positioned for closure of the distal cavity. This is confirmed by the observation that in the M149A variant two CO conformers are present corresponding to open (A0) and closed (A1) conformations. The CO of the latter species, the only conformer observed in the WT protein, is H-bonded to Q187. In the absence of the Q187 residue or in the adducts of all the heme b forms of ChdC investigated herein (containing vinyls in positions 2 and 4), only the A0 conformer has been found. Moreover, M149 is shown to be involved in the formation of a covalent bond with a vinyl substituent of heme b at excess of hydrogen peroxide.
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- 2018
8. Structural determinants of ligand binding in truncated hemoglobins: Resonance Raman spectroscopy of the native states and their carbon monoxide and hydroxide complexes
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Barry D. Howes, Lisa Milazzo, Daniela Coppola, Alessandro Feis, and Giulietta Smulevich
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0301 basic medicine ,Stereochemistry ,Resonance Raman spectroscopy ,Biophysics ,Heme ,Ligands ,Spectrum Analysis, Raman ,Biochemistry ,Pseudoalteromonas haloplanktis ,Biomaterials ,03 medical and health sciences ,chemistry.chemical_compound ,Residue (chemistry) ,Hydroxides ,Amino Acid Sequence ,Carbon Monoxide ,030102 biochemistry & molecular biology ,biology ,Chemistry ,Hydrogen bond ,Organic Chemistry ,Truncated Hemoglobins ,General Medicine ,Ligand (biochemistry) ,biology.organism_classification ,030104 developmental biology ,Hydroxide ,Carbon monoxide - Abstract
The ligand binding characteristics of heme-containing proteins are determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. In this regard, the heme pockets of truncated hemoglobins (TrHbs) constitute an interesting case study as they share many common features, including a number of polar cavity residues. In this review, we will focus on three proteins of group II TrHbs, from Thermobifida fusca (Tf-HbO) and Pseudoalteromonas haloplanktis TAC125 (Ph-HbO). Although the residues in positions G8 (Trp) and B10 (Tyr) are conserved in all three proteins, the CD1 residue is a Tyr in T. fusca and a His in P. haloplanktis. Comparison of the ligand binding characteristics of these proteins, in particular the hydroxo and CO ligands by means of resonance Raman spectroscopy, reveals that this single difference in the key heme cavity residues markedly affects their ligand binding capability and conformation. Furthermore, although the two Ph-HbOs (Ph-HbO-2217 and Ph-HbO-0030) have identical key cavity residues, they display distinct ligand binding properties.
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- 2017
9. Coexistence of multiple globin genes conferring protection against nitrosative stress to the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125
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Cinzia Verde, Giulietta Smulevich, Barry D. Howes, Paolo Ascenzi, Daniela Giordano, Daniela Coppola, Lisa Milazzo, Guido di Prisco, Robert K. Poole, Coppola, D, Giordano, D, Milazzo, L, Howes, Bd, Ascenzi, P, di Prisco, G, Smulevich, G, Poole, Rk, and Verde, C.
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0301 basic medicine ,Cancer Research ,Nitrosative/oxidative stress ,Physiology ,030106 microbiology ,Clinical Biochemistry ,Mutant ,Antarctic Regions ,Heme ,medicine.disease_cause ,Nitric Oxide ,Biochemistry ,Antarctic cold-adapted bacterium ,Pseudoalteromonas haloplanktis ,03 medical and health sciences ,chemistry.chemical_compound ,Pseudoalteromonas ,Bacterial Proteins ,Isomerism ,Peroxynitrous Acid ,Resonance Raman spectroscopy ,medicine ,Escherichia coli ,Globin ,Cloning, Molecular ,Gene ,Reactive nitrogen species ,Mutation ,biology ,biology.organism_classification ,Globins ,Complementation ,Truncated globin ,030104 developmental biology ,chemistry ,Nitrosative Stress ,Inactivation, Metabolic ,S-Nitrosoglutathione ,Genome, Bacterial - Abstract
Despite the large number of globins recently discovered in bacteria, our knowledge of their physiological functions is restricted to only a few examples. In the microbial world, globins appear to perform multiple roles in addition to the reversible binding of oxygen; all these functions are attributable to the heme pocket that dominates functional properties. Resistance to nitrosative stress and involvement in oxygen chemistry seem to be the most prevalent functions for bacterial globins, although the number of globins for which functional roles have been studied via mutation and genetic complementation is very limited. The acquisition of structural information has considerably outpaced the physiological and molecular characterisation of these proteins. The genome of the Antarctic cold-adapted bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) contains genes encoding three distinct single-chain 2/2 globins, supporting the hypothesis of their crucial involvement in a number of functions, including protection against oxidative and nitrosative stress in the cold and O2-rich environment. In the genome of PhTAC125, the genes encoding 2/2 globins are constitutively transcribed, thus suggesting that these globins are not functionally redundant in their physiological function in PhTAC125. In the present study, the physiological role of one of the 2/2 globins, Ph-2/2HbO-2217, was investigated by integrating in vivo and in vitro results. This role includes the involvement in the detoxification of reactive nitrogen and O2 species including NO by developing two in vivo and in vitro models to highlight the protective role of Ph-2/2HbO-2217 against reactive nitrogen species. The PSHAa2217 gene was cloned and over-expressed in the flavohemoglobin-deficient mutant of Escherichia coli and the growth properties and O2 uptake in the presence of NO of the mutant carrying the PSHAa2217 gene were analysed. The ferric form of Ph-2/2HbO-2217 is able to catalyse peroxynitrite isomerisation in vitro, indicating its potential role in the scavenging of reactive nitrogen species. Here we present in vitro evidence for the detoxification of NO by Ph-2/2HbO-2217.
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- 2017
10. Addition of sodium ascorbate to extend the shelf-life of tuna meat fish: A risk or a benefit for consumers?
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Barry D. Howes, Mila Nocentini, Giulietta Smulevich, Lisa Milazzo, and Enrica Droghetti
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Sodium ascorbate ,Yellowfin tuna ,Antioxidant ,medicine.medical_treatment ,Ascorbic Acid ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Inorganic Chemistry ,chemistry.chemical_compound ,Food Preservation ,Fish Products ,Sodium citrate ,medicine ,Animals ,Humans ,Food science ,biology ,Tuna ,010405 organic chemistry ,Chemistry ,food and beverages ,Ascorbic acid ,biology.organism_classification ,0104 chemical sciences ,Myoglobin ,Food Preservatives ,Food Analysis ,Carbon monoxide - Abstract
We investigate the effects of antimicrobial (sodium citrate tribasic, E331) and antioxidant (ascorbic acid, E300 and sodium ascorbate, E301) additives on the meat drip from defrosted yellowfin tuna fish loins obtained from the local market and horse heart myoglobin. The effects have been followed by electronic absorption, its second derivative spectra, and resonance Raman spectroscopies. Upon addition of the additives, a final form is reached after about 24 h. It is characterized by a 4 nm red-shifted Soret band compared to that typical of the oxy species (418 nm) but with similar Q bands. Resonance Raman experiments carried out in 16O2 and 18O2 allowed us to identify the presence of the native oxy form coexisting with a second oxygen bound species, characterized by a ν(Fe O2) stretching frequency upshifted 7 cm−1 compared to the native oxy form and with a greater (33 cm−1) isotopic shift in 18O2. These data suggest the presence of a highly bent ligand conformation. The new species induced by the addition of the additives imparts a red colour to the tuna fish meat, a characteristic that is of some concern. In fact, the presence of the new red form can mask the aging of the product that, consequently, might contain histamine. Furthermore, the electronic absorption spectrum is very similar to that of the tuna fish myoglobin carbon monoxide complex, which has important regulatory consequences. Carbon monoxide treatment of tuna is banned in the EU for masking the effects of aging on the appearance of meats.
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- 2019
11. The key role played by charge in the interaction of cytochrome c with cardiolipin
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Lisa Milazzo, Paolo Ascenzi, Massimo Coletta, Giulietta Smulevich, Laura Fiorucci, Federica Sinibaldi, Fabio Polticelli, Roberto Santucci, Maria Cristina Piro, Barry D. Howes, Sinibaldi, Federica, Milazzo, Lisa, Howes, Barry D., Piro, Maria Cristina, Fiorucci, Laura, Polticelli, Fabio, Ascenzi, Paolo, Coletta, Massimo, Smulevich, Giulietta, and Santucci, Roberto
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0301 basic medicine ,Models, Molecular ,Circular dichroism ,Resonance Raman ,Stereochemistry ,Cardiolipins ,Protein Conformation ,Mutant ,Apoptosis ,Plasma protein binding ,Biochemistry ,Inorganic Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Enzyme Stability ,Cardiolipin ,Animals ,Horses ,Settore BIO/10 ,Inner mitochondrial membrane ,Cardiolipin-cytochrome c complex ,Peroxidase ,030102 biochemistry & molecular biology ,biology ,Chemistry ,Cytochrome c ,Apoptosi ,Cytochromes c ,Hydrogen-Ion Concentration ,030104 developmental biology ,Liposomes ,Mutation ,biology.protein ,Protein Binding - Abstract
Cytochrome c undergoes structural variations upon binding of cardiolipin, one of the phospholipids constituting the mitochondrial membrane. Although several mechanisms governing cytochrome c/cardiolipin (cyt c/CL) recognition have been proposed, the interpretation of the process remains, at least in part, unknown. To better define the steps characterizing the cyt c–CL interaction, the role of Lys72 and Lys73, two residues thought to be important in the protein/lipid binding interaction, were recently investigated by mutagenesis. The substitution of the two (positively charged) Lys residues with Asn revealed that such mutations cancel the CL-dependent peroxidase activity of cyt c; furthermore, CL does not interact with the Lys72Asn mutant. In the present paper, we extend our study to the Lys→Arg mutants to investigate the influence exerted by the charge possessed by the residues located at positions 72 and 73 on the cyt c/CL interaction. On the basis of the present work a number of overall conclusions can be drawn: (i) position 72 must be occupied by a positively charged residue to assure cyt c/CL recognition; (ii) the Arg residues located at positions 72 and 73 permit cyt c to react with CL; (iii) the replacement of Lys72 with Arg weakens the second (low-affinity) binding transition; (iv) the Lys73Arg mutation strongly increases the peroxidase activity of the CL-bound protein. Graphical abstract: [Figure not available: see fulltext.]
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- 2016
12. From chlorite dismutase towards HemQ - the role of the proximal H-bonding network in haeme binding
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Stefan, Hofbauer, Barry D, Howes, Nicola, Flego, Katharina F, Pirker, Irene, Schaffner, Georg, Mlynek, Kristina, Djinović-Carugo, Paul G, Furtmüller, Giulietta, Smulevich, and Christian, Obinger
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H-bonding network ,Original Paper ,Bacteria ,Mutation, Missense ,electron paramagnetic resonance spectroscopy ,Hydrogen Bonding ,chlorite dismutase ,Heme ,Original Papers ,Amino Acid Substitution ,Bacterial Proteins ,Models, Chemical ,resonance Raman spectroscopy ,haeme binding ,Oxidoreductases ,HemQ - Abstract
Structurally and phylogenetically closely related chlorite dismutase (Cld) and HemQ differ fundamentally in their enzymatic properties. Reconstruction of the proximal H-bonding network renders Cld HemQ-like, the latter being proposed to bind coprohaeme and release protohaeme., Chlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from ‘Candidatus Nitrospira defluvii’ (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV–vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure–function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.
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- 2016
13. Structure-function relationships in human cytochrome c: The role of tyrosine 67
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Lorenzo Tognaccini, Paolo Mariottini, Massimo Coletta, Laura Fiorucci, Manuela Cervelli, Barry D. Howes, Chiara Ciaccio, Giulietta Smulevich, Valentina D'Oria, Tognaccini, Lorenzo, Ciaccio, Chiara, D'Oria, Valentina, Cervelli, Manuela, Howes, Barry D, Coletta, Massimo, Mariottini, Paolo, Smulevich, Giulietta, and Fiorucci, Laura
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0301 basic medicine ,Models, Molecular ,Resonance Raman ,Cytochrome ,Stereochemistry ,Peroxidase activity ,Mutant ,Apoptosis ,Ligand binding kinetics ,Circular dichroism ,Spectrum Analysis, Raman ,Ligands ,Biochemistry ,Inorganic Chemistry ,03 medical and health sciences ,Residue (chemistry) ,chemistry.chemical_compound ,Structure-Activity Relationship ,Site directed mutagenesis ,Circular Dichroism ,Cytochromes c ,Humans ,Kinetics ,Protein Binding ,Tyrosine ,Models ,medicine ,Structure–activity relationship ,Settore BIO/10 ,Ligand binding kinetic ,Heme ,Raman ,030102 biochemistry & molecular biology ,biology ,Cytochrome c ,Spectrum Analysis ,Molecular ,Apoptosi ,030104 developmental biology ,chemistry ,biology.protein ,Ferric ,Peroxidase ,medicine.drug - Abstract
Spectroscopic and functional properties of human cytochrome c and its Tyr67 residue mutants (i.e., Tyr67His and Tyr67Arg) have been investigated. In the case of the Tyr67His mutant, we have observed only a very limited structural alteration of the heme pocket and of the Ω-loop involving, among others, the residue Met80 and its bond with the heme iron. Conversely, in the Tyr67Arg mutant the Fe-Met80 bond is cleaved; consequently, a much more extensive structural alteration of the Ω-loop can be envisaged. The structural, and thus the functional modifications, of the Tyr67Arg mutant are present in both the ferric [Fe(III)] and the ferrous [Fe(II)] forms, indicating that the structural changes are independent of the heme iron oxidation state, depending instead on the type of substituting residue. Furthermore, a significant peroxidase activity is evident for the Tyr67Arg mutant, highlighting the role of Arg as a basic, positively charged residue at pH7.0, located in the heme distal pocket, which may act as an acid to cleave the O-O bond in H2O2. As a whole, our results indicate that a delicate equilibrium is associated with the spatial arrangement of the Ω-loop. Clearly, Arg, but not His, is able to stabilize and polarize the negative charge on the Fe(III)-OOH complex during the formation of Compound I, with important consequences on cytochrome peroxidation activity and its role in the apoptotic process, which is somewhat different in yeast and mammals.
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- 2016
14. Pichia pastoris Fep1 is a [2Fe-2S] protein with a Zn finger that displays an unusual oxygen-dependent role in cluster binding
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Rossella Miele, Maria Carmela Bonaccorsi di Patti, Alessandra Giorgi, Adriana E. Miele, Antimo Cutone, Andrea Battistoni, Giovanni Musci, Giulietta Smulevich, Barry D. Howes, Department of Biochemical Sciences 'Rossi Fanelli', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Assemblages Supramoléculaires Péricellulaires et Extracellulaires (ASPE), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Dipartimento de Biologia, Università degli Studi di Roma Tor Vergata [Roma], Dipartimento di Chimica ‘Ugo Schiff', Università degli Studi di Firenze, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Dipartimento di Bioscienze e Territorio, and Università degli Studi del Molise
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0301 basic medicine ,Zinc finger ,Multidisciplinary ,biology ,[CHIM.ORGA]Chemical Sciences/Organic chemistry ,Mutant ,Wild type ,biology.organism_classification ,Article ,Yeast ,In vitro ,Pichia pastoris ,Serine ,03 medical and health sciences ,030104 developmental biology ,Biochemistry ,Biophysical chemistryIron ,Settore BIO/10 ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Cysteine - Abstract
Fep1, the iron-responsive GATA factor from the methylotrophic yeast Pichia pastoris, has been characterised both in vivo and in vitro. This protein has two Cys2-Cys2 type zinc fingers and a set of four conserved cysteines arranged in a Cys-X5-Cys-X8-Cys-X2-Cys motif located between the two zinc fingers. Electronic absorption and resonance Raman spectroscopic analyses in anaerobic and aerobic conditions indicate that Fep1 binds iron in the form of a [2Fe-2S] cluster. Site-directed mutagenesis shows that replacement of the four cysteines with serine inactivates this transcriptional repressor. Unexpectedly, the inactive mutant is still able to bind a [2Fe-2S] cluster, employing two cysteine residues belonging to the first zinc finger. These two cysteine residues can act as alternative cluster ligands selectively in aerobically purified Fep1 wild type, suggesting that oxygen could play a role in Fep1 function by causing differential localization of the [Fe-S] cluster.
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- 2016
15. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO
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Barry D, Howes, Leonardo, Boechi, Alberto, Boffi, Dario E, Estrin, and Giulietta, Smulevich
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Actinobacteria ,Hemoglobins ,Bacterial Proteins ,Catalytic Domain ,Protein Binding - Abstract
In this chapter, we will discuss the paradigmatic case of Thermobifida fusca (Tf-trHb) HbO in its ferrous and ferric states and its behaviour towards a battery of possible ligands. This choice was dictated by the fact that it has been one of the most extensively studied truncated haemoglobins, both in terms of spectroscopic and molecular dynamics studies. Tf-trHb typifies the structural properties of group II trHbs, as the active site is characterized by a highly polar distal environment in which TrpG8, TyrCD1, and TyrB10 provide three potential H-bond donors in the distal cavity capable of stabilizing the incoming ligands. The role of these residues in key topological positions, and their interplay with the iron-bound ligands, has been addressed in studies carried out on the CO, F(-), OH(-), CN(-), and HS(-) adducts formed with the wild-type protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. In this context, such a complete analysis provides an excellent benchmark for the investigation of the relationship between protein structure and function, allowing one to translate physicochemical properties of the active site into the observed functional behaviour. Tf-trHb will be compared with other members of the group II trHbs and, more generally, with members of the other trHb subgroups.
- Published
- 2015
16. Structural and Functional Properties of Heme-containing Peroxidases: a Resonance Raman Perspective for the Superfamily of Plant, Fungal and Bacterial Peroxidases
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Giulietta Smulevich, Barry D. Howes, and Enrica Droghetti
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chemistry.chemical_compound ,Hemeprotein ,biology ,chemistry ,Biochemistry ,Cytochrome c peroxidase ,Resonance Raman spectroscopy ,Mutagenesis ,biology.protein ,Active site ,Heme ,Function (biology) ,Peroxidase - Abstract
The heme-containing peroxidases of the plant peroxidase superfamily have been the subject of extensive studies to gain a complete understanding of their structure and function properties. Spectroscopic techniques have been fundamental to the comprehension of peroxidase function under physiological conditions. Resonance Raman spectroscopy has assumed a particularly important role due to its extreme sensitivity to alterations in the surroundings of the heme, which makes it an ideal tool for studying molecular interactions at the peroxidase active sites. In combination with site-directed mutagenesis and X-ray structural data, it has given insight into the influence exerted on protein architecture in the vicinity of the active site by key amino acids and furnished critical information on subtle structural features important for protein flexibility, functionality and stability. The mutation of key catalytic residues on both the distal and proximal sides of the heme cavity not only revealed their roles in the reaction mechanism of peroxidases, but also demonstrated that in peroxidases there are common structural mechanisms which facilitate communication between the two sides of the heme cavity and highlighted the importance of long range interactions in maintaining the functional properties of the heme. The overwhelming success of this approach using the combination of site-directed mutagenesis together with spectroscopic techniques and X-ray structural data to unveil detailed aspects of the structure–function relationships of heme peroxidases, firstly in the pioneering studies on yeast cytochrome c peroxidase then for other peroxidases, has led to its subsequent widespread general application in the characterization of heme proteins.
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- 2015
17. Nitrite dismutase reaction mechanism: kinetic and spectroscopic investigation of the interaction between nitrophorin and nitrite
- Author
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Chunmao He, Giulietta Smulevich, Sigrun Rumpel, Nicholas Cox, Edward J. Reijerse, Barry D. Howes, Wolfgang Lubitz, and Markus Knipp
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Hemeproteins ,Models, Molecular ,Reaction mechanism ,Resonance Raman spectroscopy ,Inorganic chemistry ,Disproportionation ,Photochemistry ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Nitrophorin ,medicine ,Animals ,Nitrite ,Salivary Proteins and Peptides ,Nitrites ,Chemistry ,Electron Spin Resonance Spectroscopy ,Isothermal titration calorimetry ,General Chemistry ,Heme B ,Kinetics ,Rhodnius ,Ferric ,Insect Proteins ,Nitrogen Oxides ,Iron Compounds ,medicine.drug - Abstract
Nitrite is an important metabolite in the physiological pathways of NO and other nitrogen oxides in both enzymatic and nonenzymatic reactions. The ferric heme b protein nitrophorin 4 (NP4) is capable of catalyzing nitrite disproportionation at neutral pH, producing NO. Here we attempt to resolve its disproportionation mechanism. Isothermal titration calorimetry of a gallium(III) derivative of NP4 demonstrates that the heme iron coordinates the first substrate nitrite. Contrary to previous low-temperature EPR measurements, which assigned the NP4-nitrite complex electronic configuration solely to a low-spin (S = 1/2) species, electronic absorption and resonance Raman spectroscopy presented here demonstrate that the NP4-NO2(-) cofactor exists in a high-spin/low-spin equilibrium of 7:3 which is in fast exchange in solution. Spin-state interchange is taken as evidence for dynamic NO2(-) coordination, with the high-spin configuration (S = 5/2) representing the reactive species. Subsequent kinetic measurements reveal that the dismutation reaction proceeds in two discrete steps and identify an {FeNO}(7) intermediate species. The first reaction step, generating the {FeNO}(7) intermediate, represents an oxygen atom transfer from the iron bound nitrite to a second nitrite molecule in the protein pocket. In the second step this intermediate reduces a third nitrite substrate yielding two NO molecules. A nearby aspartic acid residue side-chain transiently stores protons required for the reaction, which is crucial for NPs' function as nitrite dismutase.
- Published
- 2015
18. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125
- Author
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Daniela Giordano, Darío A. Estrin, Martino Bolognesi, Juan Pablo Bustamante, Guido di Prisco, Alessia Riccio, Leonardo Boechi, Barry D. Howes, Giulietta Smulevich, Marco Nardini, Cinzia Verde, Alessandra Pesce, and Elena Caldelli
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Hemeprotein ,hemeprotein ,Protein Conformation ,Stereochemistry ,Molecular Sequence Data ,Antarctic Regions ,Marine Biology ,Heme ,adaptation ,Biology ,Crystallography, X-Ray ,Biochemistry ,Pseudoalteromonas haloplanktis ,resonance Raman ,Hemoglobins ,chemistry.chemical_compound ,Oxidoreductase ,extreme environment ,Amino Acid Sequence ,Globin ,Molecular Biology ,chemistry.chemical_classification ,Sequence Homology, Amino Acid ,Otras Ciencias Químicas ,Ciencias Químicas ,Cell Biology ,computer.file_format ,Protein superfamily ,biology.organism_classification ,Protein Data Bank ,molecular dynamics ,Pseudoalteromonas ,chemistry ,bacterial hemoglobin ,haloplanktis ,X-ray structure ,computer ,Alpha helix ,CIENCIAS NATURALES Y EXACTAS - Abstract
Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two‐on‐two α‐helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group‐II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph‐2/2HbO), a cold‐adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph‐2/2HbO aquo‐met crystal structure (at 2.21 Å resolution) shows typical features of group‐II truncated hemoglobins, namely the two‐on‐two α‐helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal‐site hydrogen‐bonded network that includes water molecules and several distal‐site residues, including His(58)CD1. Analysis of Ph‐2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph‐2/2HbO can access diverse heme ligation states. Among these, detection of a low‐spin heme hexa‐coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme‐Fe ligand. Altogether, the results show that Ph‐2/2HbO maintains the general structural features of group‐II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment. Fil: Giordano, Daniela. Consiglio Nazionale delle Ricerche; Italia Fil: Pesce, Alessandra. Università degli Studi di Genova; Italia Fil: Boechi, Leonardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Bustamante, Juan Pablo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Caldelli, Elena. Universita Degli Studi Di Firenze; Italia Fil: Howes, Barry D.. Universita Degli Studi Di Firenze; Italia Fil: Riccio, Alessia. Consiglio Nazionale delle Ricerche; Italia Fil: di Prisco, Guido. Consiglio Nazionale delle Ricerche; Italia Fil: Nardini, Marco. Università degli Studi di Milano; Italia Fil: Estrin, Dario Ariel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Smulevich, Giulietta. Universita Degli Studi Di Firenze; Italia Fil: Bolognesi, Martino. Università degli Studi di Milano; Italia Fil: Verde, Cinzia. Consiglio Nazionale delle Ricerche; Italia. Universita Di Roma; Italia
- Published
- 2015
19. Anatomy of an iron-sulfur cluster scaffold protein: Understanding the determinants of [2Fe-2S] cluster stability on IscU
- Author
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Annalisa Pastore, Clara Iannuzzi, Miquel Adrover, Giulietta Smulevich, Barry D. Howes, Adrover, M, Howes, Bd, Iannuzzi, Clara, Smulevich, G, Pastore, A., Adrover, Miquel, Howes Barry, D., Smulevich, Giulietta, and Pastore, Annalisa
- Subjects
Iron-Sulfur Proteins ,Models, Molecular ,Scaffold protein ,Iron–sulfur cluster ,Mutant ,Sequence Homology ,Spectrum Analysis, Raman ,01 natural sciences ,chemistry.chemical_compound ,Iron-Sulfur Protein ,Mutant Protein ,Escherichia coli Protein ,Isc operon ,Raman ,Spectrum Analysi ,0303 health sciences ,biology ,Protein Stability ,Escherichia coli Proteins ,Circular Dichroism ,Medicine (all) ,Amino Acid ,Biochemistry ,QM/MM methods ,Hydrophobic and Hydrophilic Interactions ,Protein Binding ,Protein Structure ,Molecular Sequence Data ,Mutation, Missense ,Computational biology ,010402 general chemistry ,03 medical and health sciences ,Hydrophobic and Hydrophilic Interaction ,Cluster (physics) ,Amino Acid Sequence ,Molecular Biology ,QM/MM method ,030304 developmental biology ,Sequence Homology, Amino Acid ,Molecular ,Cell Biology ,Protein Structure, Tertiary ,0104 chemical sciences ,Metabolic pathway ,chemistry ,Mutation ,biology.protein ,Mutant Proteins ,ISCU ,Missense ,Iron-sulfur cluster ,Function (biology) ,Biogenesis ,Tertiary ,Model - Abstract
Protein-bound iron sulfur clusters are prosthetic groups involved in several metabolic pathways. Understanding how they interact with the host protein and which factors influence their stability is therefore an important goal in biology. Here, we have addressed this question by studying the determinants of the 2Fe–2S cluster stability in the IscU/Isu protein scaffold. Through a detailed computational study based on a mixed quantum and classical mechanics approach, we predict that the simultaneous presence of two conserved residues, D39 and H105, has a conflicting role in cluster coordination which results in destabilizing cluster-loaded IscU/Isu according to a ‘tug-of-war’ mechanism. The effect is absent in the D39A mutant already known to host the cluster more stably. Our theoretical conclusions are directly supported by experimental data, also obtained from the H105A mutant, which has properties intermediate between the wild-type and the D39A mutant. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
- Published
- 2015
20. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins
- Author
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Dario E. Estrin, Alberto Boffi, Barry D. Howes, Leonardo Boechi, and Giulietta Smulevich
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Molecular dynamics ,Residue (chemistry) ,biology ,Stereochemistry ,Chemistry ,Hydrogen bond ,Mutant ,biology.protein ,Active site ,Context (language use) ,Plasma protein binding ,Adduct - Abstract
In this chapter, we will discuss the paradigmatic case of Thermobifida fusca (Tf-trHb) HbO in its ferrous and ferric states and its behaviour towards a battery of possible ligands. This choice was dictated by the fact that it has been one of the most extensively studied truncated haemoglobins, both in terms of spectroscopic and molecular dynamics studies. Tf-trHb typifies the structural properties of group II trHbs, as the active site is characterized by a highly polar distal environment in which TrpG8, TyrCD1, and TyrB10 provide three potential H-bond donors in the distal cavity capable of stabilizing the incoming ligands. The role of these residues in key topological positions, and their interplay with the iron-bound ligands, has been addressed in studies carried out on the CO, F(-), OH(-), CN(-), and HS(-) adducts formed with the wild-type protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. In this context, such a complete analysis provides an excellent benchmark for the investigation of the relationship between protein structure and function, allowing one to translate physicochemical properties of the active site into the observed functional behaviour. Tf-trHb will be compared with other members of the group II trHbs and, more generally, with members of the other trHb subgroups.
- Published
- 2015
21. Interplay of the H-bond donor-acceptor role of the distal residues in hydroxyl ligand stabilization of Thermobifida fusca truncated hemoglobin
- Author
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Francesco P. Nicoletti, Giulietta Smulevich, Maria Fittipaldi, Alberto Boffi, Enrica Droghetti, Juan Pablo Bustamante, Alessandra Bonamore, Darío A. Estrin, Paola Baiocco, Barry D. Howes, Alessandro Feis, Department of Chemistry 'Ugo Schiff', Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Biochemical Sciences 'Rossi Fanelli', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Département de mathématiques [Sherbrooke] (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), Departamento de Química Inorgánica, Analítica y Química Física (DQIAQF), Facultad de Ciencias Exactas y Naturales [Buenos Aires] (FCEyN), and Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA)
- Subjects
SPIN-STATE EQUILIBRIA ,Models, Molecular ,Hemeprotein ,Heme binding ,Stereochemistry ,Metal Binding Site ,Heme ,Molecular Dynamics Simulation ,Ligands ,Spectrum Analysis, Raman ,Biochemistry ,chemistry.chemical_compound ,Bacterial Proteins ,Actinomycetales ,SPECTRA ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Globin ,HYDROXYL LIGAND STABILIZATION ,HEME-PROTEINS ,METALLOPROTEINS ,TRUNCATED HEMOGLOBIN ,Binding Sites ,biology ,Hydrogen bond ,Chemistry ,Ligand ,ACTIVE-SITE ,RESONANCE RAMAN ,Protein Stability ,Otras Ciencias Químicas ,Ciencias Químicas ,Electron Spin Resonance Spectroscopy ,Active site ,MOLECULAR DYNAMIC SIMULATIONS ,Truncated Hemoglobins ,HORSERADISH-PEROXIDASE ,METMYOGLOBIN ,Hydrogen Bonding ,Hydrogen-Ion Concentration ,ELECTRON-PARAMAGNETIC RESONANCE, SPIN-STATE EQUILIBRIA, HEME-PROTEINS, HORSERADISH-PEROXIDASE, ACTIVE-SITE, SPECTRA, COMPLEXES, METALLOPROTEINS, METHEMOGLOBIN, METMYOGLOBIN ,Recombinant Proteins ,ELECTRON-PARAMAGNETIC RESONANCE ,biology.protein ,Mutagenesis, Site-Directed ,COMPLEXES ,CIENCIAS NATURALES Y EXACTAS ,METHEMOGLOBIN - Abstract
The unique architecture of the active site of Thermobifida fusca truncated hemoglobin (Tf-trHb) and other globins belonging to the same family has stimulated extensive studies aimed at understanding the interplay between iron-bound ligands and distal amino acids. The behavior of the heme-bound hydroxyl, in particular, has generated much interest in view of the relationships between the spin-state equilibrium of the ferric iron atom and hydrogen-bonding capabilities (as either acceptor or donor) of the OH− group itself. The present investigation offers a detailed molecular dynamics and spectroscopic picture of the hydroxyl complexes of the WT protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. Each mutant is characterized by a complex interplay of interactions in which the hydroxyl ligand may act both as a H-bond donor or acceptor. The resonance Raman stretching frequencies of the Fe−OH moiety, together with electron paramagnetic resonance spectra and MD simulations on each mutant, have enabled the identification of specific contributions to the unique ligand-inclusive H-bond network typical of this globin family. Fil: Nicoletti, Francesco P.. Universita Degli Studi Di Firenze; Italia Fil: Bustamante, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina Fil: Droghetti, Enrica. Universita Degli Studi Di Firenze; Italia Fil: Howes, Barry D.. Universita Degli Studi Di Firenze; Italia Fil: Fittipaldi, Maria. Universita Degli Studi Di Firenze; Italia Fil: Bonamore, Alessandra. Universita Di Roma; Italia Fil: Baiocco, Paola. Italian Institute of Technology; Italia Fil: Feis, Alessandro. Universita Degli Studi Di Firenze; Italia Fil: Boffi, Alberto. Universita Di Roma; Italia Fil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina Fil: Smulevich, Giulietta. Universita Degli Studi Di Firenze; Italia
- Published
- 2014
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