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1.
J Inorg Biochem ; 182: 103-112, 2018 05.
Article in English | MEDLINE | ID: mdl-29454149

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 Mössbauer 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.


Subject(s)
Apoferritins/chemistry , Apoferritins/metabolism , Ceruloplasmin/chemistry , Ceruloplasmin/metabolism , Manganese/chemistry , Manganese/metabolism , Electron Spin Resonance Spectroscopy , Humans , Protein Binding
2.
Future Med Chem ; 9(9): 899-910, 2017 06.
Article in English | MEDLINE | ID: mdl-28636417

ABSTRACT

In this review we discuss evidences suggesting that bacterial zinc homeostasis represents a promising target for new antimicrobial strategies. The ability of the gut pathogen Salmonella enterica sv Typhimurium to withstand the host responses aimed at controlling growth of the pathogen critically depends on the zinc importer ZnuABC. Strains lacking a functional ZnuABC or its soluble component ZnuA display a dramatic loss of pathogenicity, due to a reduced ability to express virulence factors; withstand the inflammatory response; and compete with other gut microbes. Based on this data, ZnuA was chosen as a candidate for the rational design of novel antibiotics. Through a combination of structural and functional investigations, we have provided a proof of concept of the potential of this approach.


Subject(s)
Anti-Bacterial Agents/pharmacology , Salmonella enterica/drug effects , Salmonella typhimurium/drug effects , Zinc/pharmacology , Anti-Bacterial Agents/chemistry , Microbial Sensitivity Tests , Models, Molecular , Molecular Structure , Zinc/chemistry
3.
Biochim Biophys Acta ; 1860(3): 534-41, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26691136

ABSTRACT

BACKGROUND: Under conditions of Zn(II) deficiency, the most relevant high affinity Zn(II) transport system synthesized by many Gram-negative bacteria is the ZnuABC transporter. ZnuABC is absent in eukaryotes and plays an important role in bacterial virulence. Consequently, ZnuA, the periplasmic component of the transporter, appeared as a good target candidate to find new compounds able to contrast bacterial growth by interfering with Zn(II) uptake. METHODS: Antibacterial activity assays on selected compounds from and in-house library against Salmonella enterica serovar Typhimurium ATCC14028 were performed. The X-ray structure of the complex formed by SeZnuA with an active compound was solved at 2.15Å resolution. RESULTS: Two di-aryl pyrrole hydroxamic acids differing in the position of a chloride ion, RDS50 ([1-[(4-chlorophenyl)methyl]-4-phenyl-1H-pyrrol-3-hydroxamic acid]) and RDS51 (1-[(2-chlorophenyl)methyl]-4-phenyl-1H-pyrrol-3-hydroxamic acid) were able to inhibit Salmonella growth and its invasion ability of Caco-2 cells. The X-ray structure of SeZnuA containing RDS51 revealed its presence at the metal binding site concomitantly with Zn(II) which is coordinated by protein residues and the hydroxamate moiety of the compound. CONCLUSIONS: Two molecules interfering with ZnuA-mediated Zn(II) transport in Salmonella have been identified for the first time. The resolution of the SeZnuA-RDS51 X-ray structure revealed that RDS51 is tightly bound both to the protein and to Zn(II) thereby inhibiting its release. These features pave the way to the rational design of new Zn(II)-binding drugs against Salmonella. GENERAL SIGNIFICANCE: The data reported show that targeting the bacterial ZnuABC transporter can represent a good strategy to find new antibiotics against Gram-negative bacteria.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bacterial Proteins/metabolism , Hydroxamic Acids/pharmacology , Pyrroles/pharmacology , Salmonella typhimurium/drug effects , Zinc/metabolism , Caco-2 Cells , Cation Transport Proteins/metabolism , Humans , Hydroxamic Acids/chemistry , Pyrroles/chemistry , Salmonella typhimurium/growth & development , Salmonella typhimurium/metabolism , Zinc/pharmacology
4.
Biochim Biophys Acta ; 1848(11 Pt B): 3032-46, 2015 Nov.
Article in English | MEDLINE | ID: mdl-25838125

ABSTRACT

Lysozymes play an important role in host defense by degrading peptidoglycan in the cell envelopes of pathogenic bacteria. Several Gram-negative bacteria can evade this mechanism by producing periplasmic proteins that inhibit the enzymatic activity of lysozyme. The Escherichia coli inhibitor of vertebrate lysozyme, Ivyc and its Pseudomonas aeruginosa homolog, Ivyp1 have been shown to be potent inhibitors of hen egg white lysozyme (HEWL). Since human lysozyme (HL) plays an important role in the innate immune response, we have examined the binding of HL to Ivyc and Ivyp1. Our results show that Ivyp1 is a weaker inhibitor of HL than Ivyc even though they inhibit HEWL with similar potency. Calorimetry experiments confirm that Ivyp1 interacts more weakly with HL than HEWL. Analytical ultracentrifugation studies revealed that Ivyp1 in solution is a monomer and forms a 30kDa heterodimer with both HL and HEWL, while Ivyc is a homodimer that forms a tetramer with both enzymes. The interaction of Ivyp1 with HL was further characterized by NMR chemical shift perturbation experiments. In addition to the characteristic His-containing Ivy inhibitory loop that binds into the active site of lysozyme, an extended loop (P2) between the final two beta-strands also participates in forming protein-protein interactions. The P2 loop is not conserved in Ivyc and it constitutes a flexible region in Ivyp1 that becomes more rigid in the complex with HL. We conclude that differences in the electrostatic interactions at the binding interface between Ivy inhibitors and distinct lysozymes determine the strength of this interaction. This article is part of a Special Issue entitled: Bacterial Resistance to Antimicrobial Peptides.


Subject(s)
Carrier Proteins/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Muramidase/metabolism , Pseudomonas aeruginosa/metabolism , Binding Sites , Calorimetry, Differential Scanning , Carrier Proteins/chemistry , Carrier Proteins/immunology , Escherichia coli/immunology , Escherichia coli/pathogenicity , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/immunology , Host-Pathogen Interactions , Humans , Immunity, Innate , Models, Molecular , Muramidase/antagonists & inhibitors , Muramidase/chemistry , Muramidase/immunology , Nuclear Magnetic Resonance, Biomolecular , Protein Binding , Protein Conformation , Pseudomonas aeruginosa/immunology , Pseudomonas aeruginosa/pathogenicity , Static Electricity , Ultracentrifugation
5.
Biochim Biophys Acta ; 1840(1): 535-44, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24128931

ABSTRACT

BACKGROUND: In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the metal-binding protein ZinT was suggested to operate as an accessory component of ZnuABC in periplasmic zinc recruitment. Since ZinT is known to form a ZinT-ZnuA complex in the presence of Zn(II) it was proposed to transfer Zn(II) to ZnuA. The present work was undertaken to test this claim. METHODS: ZinT and its structural relationship with ZnuA have been characterized by multiple biophysical techniques (X-ray crystallography, SAXS, analytical ultracentrifugation, fluorescence spectroscopy). RESULTS: The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with Zn(II) yield a KD value of 22±2nM for ZinT, while those with ZnuA point to one high affinity (KD<20nM) and one low affinity Zn(II) binding site (KD in the micromolar range). Sedimentation velocity experiments established that Zn(II)-bound ZinT interacts with ZnuA, whereas apo-ZinT does not. The model of the ZinT-ZnuA complex derived from small angle X-ray scattering experiments points to a disposition that favors metal transfer as the metal binding cavities of the two proteins face each other. CONCLUSIONS: ZinT acts as a Zn(II)-buffering protein that delivers Zn(II) to ZnuA. GENERAL SIGNIFICANCE: Knowledge of the ZinT-ZnuA relationship is crucial for understanding bacterial Zn(II) uptake.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Periplasm/metabolism , Salmonella enterica/metabolism , Zinc/metabolism , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , Protein Conformation , Scattering, Small Angle , Sequence Homology, Amino Acid , Ultracentrifugation , X-Ray Diffraction
6.
Biochim Biophys Acta ; 1830(6): 3745-55, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23396000

ABSTRACT

BACKGROUND: The ferroxidase center of DNA-binding protein from starved cells (Dps) is a major player in the iron oxidation/detoxification process that leads to a decreased reactive oxygen species production. The possible Mn(II) participation in this process has been studied in Dps from Kineococcus radiotolerans, a radiation-resistant bacterium with a high cytosolic Mn/Fe ratio and a high capacity to survive ionizing and stress conditions. METHODS: The X-ray structure of recombinant K. radiotolerans Dps loaded with Mn(II) has been solved at 2.0Å resolution. Mn(II) binding to K. radiotolerans Dps and its effect on Fe(II) oxidation have been characterized in spectroscopic measurements. RESULTS: In K. radiotolerans Dps, the Fe-Fe ferroxidase center can have a Mn-Fe composition. Mn(II) binds only at the high affinity, so-called A site, whereas Fe(II) binds also at the low affinity, so-called B site. The Mn-Fe and Fe-Fe centers behave distinctly upon iron oxidation by O2. A site-bound Mn(II) or Fe(II) plays a catalytic role, while B site-bound Fe(II) behaves like a substrate and can be replaced by another Fe(II) after oxidation. When H2O2 is the Fe(II) oxidant, single electrons are transferred to aromatic residues near the ferroxidase center and give rise to intra-protein radicals thereby limiting OH release in solution. The presence of the Mn-Fe center results in significant differences in the development of such intra-protein radicals. CONCLUSIONS: Mn(II) bound at the Dps ferroxidase center A site undergoes redox cycling provided the B site contains Fe. GENERAL SIGNIFICANCE: The results provide a likely molecular mechanism for the protective role of Mn(II) under oxidative stress conditions as it participates in redox cycling in the hetero-binuclear ferroxidase center.


Subject(s)
Actinomycetales/enzymology , Bacterial Proteins/chemistry , Ceruloplasmin/chemistry , DNA-Binding Proteins/chemistry , Oxidative Stress/physiology , Actinomycetales/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , Ceruloplasmin/genetics , Ceruloplasmin/metabolism , Crystallography, X-Ray , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Hydroxyl Radical/chemistry , Hydroxyl Radical/metabolism , Iron/chemistry , Iron/metabolism , Manganese/chemistry , Manganese/metabolism , Protein Structure, Quaternary
7.
J Mol Biol ; 409(4): 630-41, 2011 Jun 17.
Article in English | MEDLINE | ID: mdl-21530543

ABSTRACT

ZnuA is the soluble component of the high-affinity ZnuABC zinc transporter belonging to the cluster 9 group of ATP-binding cassette-type periplasmic Zn- and Mn-binding proteins. In Gram-negative bacteria, the ZnuABC system is essential for zinc uptake and homeostasis and is an important determinant of bacterial resistance to the host defense mechanisms. The cluster 9 members share a two (α/ß)(4) domain architecture with a long α-helix connecting the two domains. In the Zn-specific proteins, the so-called α3c and the α4 helices are separated by an insert of variable length, rich in histidine and negatively charged residues. This distinctive His-rich loop is proposed to play a role in the management of zinc also due to its location at the entrance of the metal binding site located at the domain interface. The known Synechocystis 6803 and Escherichia coli ZnuA structures show the same metal coordination involving three conserved histidines and a glutamic acid or a water molecule as fourth ligand. The structures of Salmonella enterica ZnuA, with a partially or fully occupied zinc binding site, and of a deletion mutant missing a large part of the His-rich loop revealed unexpected differences in the metal-coordinating ligands, as histidine 140 from the mobile (at the C-terminal) part of the loop substitutes the conserved histidine 60. This unforeseen coordination is rendered possible by the "open conformation" of the two domains. The possible structural determinants of these peculiarities and their functional relevance are discussed.


Subject(s)
Bacterial Proteins/chemistry , Cation Transport Proteins/chemistry , Histidine/chemistry , Protein Structure, Tertiary , Salmonella enterica/chemistry , Zinc/chemistry , Amino Acid Sequence , Bacterial Proteins/genetics , Binding Sites , Cation Transport Proteins/genetics , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , Salmonella enterica/metabolism , Sequence Alignment
8.
J Biol Inorg Chem ; 16(6): 869-80, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21547575

ABSTRACT

DNA-binding proteins from starved cells (Dps) differ in the number and position of charged residues along the "ferritin-like" pores that are used by iron to reach the ferroxidase center and the protein cavity. These differences are shown to affect significantly the electrostatic potential at the pores, which determines the extent of cooperativity in the iron uptake kinetics and thereby the mass distribution of the ferric hydroxide micelles inside the protein cavity. These conclusions are of biotechnological value in the preparation of protein-enclosed nanomaterials and are expected to apply also to ferritins. They were reached after characterization of the Dps from Listeria innocua, Helicobacter pylori, Thermosynechococcus elongatus, Escherichia coli, and Mycobacterium smegmatis. The characterization comprised the calculation of the electrostatic potential at the pores, determination of the iron uptake kinetics in the presence of molecular oxygen or hydrogen peroxide, and analysis of the proteins by means of the sedimentation velocity after iron incorporation.


Subject(s)
Bacterial Proteins/chemistry , DNA-Binding Proteins/chemistry , Ferritins/chemistry , Iron/chemistry , Hydrogen Peroxide/chemistry , Models, Molecular , Molecular Sequence Data , Oxidants/chemistry , Oxidation-Reduction , Oxygen/chemistry , Protein Conformation , Static Electricity
9.
Extremophiles ; 15(3): 431-9, 2011 May.
Article in English | MEDLINE | ID: mdl-21487935

ABSTRACT

Ferritin from the hyperthermophilic anaerobe Thermotoga maritima, a bacterium of ancient phylogenetic origin, is structurally similar to known bacterial and eukaryotic ferritins: 24 identical subunits assemble into a shell having octahedral symmetry and a Mr of about 460 kDa. T. maritima ferritin (TmFtn), purified to homogeneity as a recombinant protein, contains approximately 2-3 iron atoms and can incorporate efficiently up to 3,500 atoms in the form of a ferric oxy-hydroxide mineral at 80°C, the optimal growth temperature of the bacterium. The 24-mer unexpectedly dissociates reversibly into dimers at low ionic strengths. In turn, dimers re-associate into the native 24-mer assembly at high protein concentrations and upon incorporation of iron micelles containing at least 500 Fe(III). TmFtn uses O(2) as efficient iron oxidant. The reaction stoichiometry is 3-4 O(2):Fe(II) as in all bacterial ferritins. Accordingly no H(2)O(2) is released into solution, a feature reflected in the in vitro ability of TmFtn to reduce significantly iron-mediated oxidative damage to DNA at 80°C. A similar TmFtn-mediated ROS detoxifying role likely occurs in the bacterium which lacks the SOD/catalase defense systems of the aerobic world.


Subject(s)
Bacterial Proteins/metabolism , DNA Damage , DNA, Bacterial/metabolism , Ferritins/metabolism , Iron/metabolism , Oxidative Stress , Thermotoga maritima/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Cloning, Molecular , Crystallography, X-Ray , Ferritins/chemistry , Ferritins/genetics , Hot Temperature , Models, Molecular , Molecular Sequence Data , Osmolar Concentration , Oxidation-Reduction , Protein Stability , Protein Structure, Quaternary , Protein Subunits , Reactive Oxygen Species/metabolism , Recombinant Proteins/metabolism , Thermotoga maritima/genetics
10.
J Mol Cell Cardiol ; 49(1): 132-41, 2010 Jul.
Article in English | MEDLINE | ID: mdl-20298697

ABSTRACT

Sorcin is a penta-EF-hand protein that interacts with intracellular target proteins after Ca(2+) binding. The sarcolemmal Na(+)/Ca(2+) exchanger (NCX1) may be an important sorcin target in cardiac muscle. In this study, RNAi knockdown of sorcin, purified sorcin or sorcin variants was employed in parallel measurements of: (i) NCX activity in isolated rabbit cardiomyocytes using electrophysiological techniques and (ii) sorcin binding to the NCX1 calcium binding domains (CBD1 and (iii) using surface plasmon resonance and gel overlay techniques. Sorcin is activated by Ca(2+) binding to the EF3 and EF2 regions, which are connected by the D helix. To investigate the importance of this region in the interaction with NCX1, three variants were examined: W105G and W99G, mutated respectively near EF3 and EF2, and E124A that does not bind Ca(2+) due to a mutation at EF3. Downregulation of sorcin decreased and supplementation with wt sorcin (3muM) increased NCX activity in isolated cardiomyocytes. The relative stimulatory effects of the sorcin variants were: W105G>wt sorcin>Sorcin Calcium Binding Domain (SCBD)>W99G>E124A. Sorcin binding to both CBD1 and 2 was observed. In the presence of 50microM Ca(2+), the interaction with CBD1 followed the order W105G>SCBD>wt sorcin>W99G>E124A. In sorcin, the interacting surface can be mapped on the C-terminal Ca(2+)-binding domain in the D helix region comprising W99. The fast association/dissociation rates that characterize the interaction of sorcin with CBD1 and 2 may permit complex formation/dissociation during an excitation/contraction cycle.


Subject(s)
Calcium/metabolism , Animals , EF Hand Motifs , Male , Myocardium/metabolism , Myocytes, Cardiac/cytology , Myocytes, Cardiac/metabolism , Protein Structure, Secondary , Rabbits , Sarcolemma/metabolism , Sodium-Calcium Exchanger/genetics , Sodium-Calcium Exchanger/metabolism
11.
Biochim Biophys Acta ; 1800(8): 798-805, 2010 Aug.
Article in English | MEDLINE | ID: mdl-20138126

ABSTRACT

BACKGROUND: The widely expressed Dps proteins, so named after the DNA-binding properties of the first characterized member of the family in Escherichia coli, are considered major players in the bacterial response to stress. SCOPE OF REVIEW: The review describes the distinctive features of the "ferritin-like" ferroxidation reaction, which uses hydrogen peroxide as physiological iron oxidant and therefore permits the concomitant removal of the two reactants that give rise to hydroxyl radicals via Fenton chemistry. It also illustrates the structural elements identified to date that render the interaction of some Dps proteins with DNA possible and outlines briefly the significance of Dps-DNA complex formation and of the Dps interaction with other DNA-binding proteins in relation to the organization of the nucleoid and microbial survival. GENERAL SIGNIFICANCE: Understanding in molecular terms the distinctive role of Dps proteins in bacterial resistance to general and specific stress conditions. MAJOR CONCLUSIONS: The state of the art is that the response to oxidative and peroxide-mediated stress is mediated directly by Dps proteins via their ferritin-like activity. In contrast, the response to other stress conditions derives from the concerted interplay of diverse interactions that Dps proteins may establish with DNA and with other DNA-binding proteins.


Subject(s)
Bacterial Proteins/physiology , DNA, Bacterial/metabolism , DNA-Binding Proteins/physiology , Hydrogen Peroxide/pharmacokinetics , Iron/pharmacokinetics , Stress, Physiological/physiology , Adaptation, Biological/genetics , Adaptation, Biological/physiology , Amino Acid Sequence , Animals , Bacterial Proteins/genetics , DNA-Binding Proteins/genetics , Humans , Hydrogen Peroxide/metabolism , Inactivation, Metabolic/genetics , Inactivation, Metabolic/physiology , Iron/metabolism , Models, Molecular , Molecular Sequence Data , Protein Binding , Sequence Homology, Amino Acid , Stress, Physiological/genetics
12.
FEBS J ; 277(4): 903-17, 2010 Feb.
Article in English | MEDLINE | ID: mdl-20088882

ABSTRACT

The cyanobacterium Thermosynechococcus elongatus is one the few bacteria to possess two Dps proteins, DpsA-Te and Dps-Te. The present characterization of DpsA-Te reveals unusual structural and functional features that differentiate it from Dps-Te and the other known Dps proteins. Notably, two Zn(II) are bound at the ferroxidase center, owing to the unique substitution of a metal ligand at the A-site (His78 in place of the canonical aspartate) and to the presence of a histidine (His164) in place of a hydrophobic residue at a metal-coordinating distance in the B-site. Only the latter Zn(II) is displaced by incoming iron, such that Zn(II)-Fe(III) complexes are formed upon oxidation, as indicated by absorbance and atomic emission spectroscopy data. In contrast to the typical behavior of Dps proteins, where Fe(II) oxidation by H(2)O(2) is about 100-fold faster than by O(2), in DpsA-Te the ferroxidation efficiency of O(2) is very high and resembles that of H(2)O(2). Oxygraphic experiments show that two Fe(II) are required to reduce O(2), and that H(2)O(2) is not released into solution at the end of the reaction. On this basis, a reaction mechanism is proposed that also takes into account the formation of Zn(II)-Fe(III) complexes. The physiological significance of the DpsA-Te behavior is discussed in the framework of a possible localization of the protein at the thylakoid membranes, where photosynthesis takes place, with the consequent increased formation of reactive oxygen species.


Subject(s)
Bacterial Proteins/metabolism , Ceruloplasmin/metabolism , Cyanobacteria/enzymology , DNA-Binding Proteins/metabolism , Histidine/metabolism , Iron/metabolism , Oxygen/chemistry , Zinc/metabolism , Amino Acid Sequence , Amino Acid Substitution , Bacterial Proteins/genetics , Crystallography, X-Ray , DNA-Binding Proteins/genetics , Histidine/chemistry , Iron/chemistry , Models, Molecular , Molecular Sequence Data , Oxidation-Reduction , Protein Structure, Tertiary , Sequence Alignment , Zinc/chemistry
13.
Free Radic Biol Med ; 48(2): 292-7, 2010 Jan 15.
Article in English | MEDLINE | ID: mdl-19892013

ABSTRACT

Dps (DNA-binding proteins from starved cells) proteins belong to a widespread bacterial family of proteins expressed under nutritional and oxidative stress conditions. In particular, Dps proteins protect DNA against Fenton-mediated oxidative stress, as they catalyze iron oxidation by hydrogen peroxide at highly conserved ferroxidase centers and thus reduce significantly hydroxyl radical production. This work investigates the possible generation of intraprotein radicals during the ferroxidation reaction by Escherichia coli and Listeria innocua Dps, two representative members of the family. Stopped-flow analyses show that the conserved tryptophan and tyrosine residues located near the metal binding/oxidation center are in a radical form after iron oxidation by hydrogen peroxide. DNA protection assays indicate that the presence of both residues is necessary to limit release of hydroxyl radicals in solution and the consequent oxidative damage to DNA. In general terms, the demonstration that conserved protein residues act as a trap that dissipates free electrons generated during the oxidative process brings out a novel role for the Dps protein cage.


Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Escherichia coli/genetics , Listeria/genetics , Listeria/physiology , Mutant Proteins/metabolism , Apoptosis/genetics , Bacterial Proteins/genetics , Catalytic Domain/genetics , Ceruloplasmin/metabolism , DNA-Binding Proteins/genetics , Escherichia coli/physiology , Free Radical Scavengers/metabolism , Hydrogen Peroxide/metabolism , Hydroxyl Radical/metabolism , Iron/metabolism , Mutagenesis, Site-Directed , Mutant Proteins/genetics , Oxidation-Reduction , Oxidative Stress/genetics , Protein Binding
14.
Chemistry ; 16(2): 709-17, 2010 Jan 11.
Article in English | MEDLINE | ID: mdl-19859920

ABSTRACT

A comparative analysis of the magnetic properties of iron oxide nanoparticles grown in the cavity of the DNA-binding protein from starved cells of the bacterium Listeria innocua, LiDps, and of its triple-mutant lacking the catalytic ferroxidase centre, LiDps-tm, is presented. TEM images and static and dynamic magnetic and electron magnetic resonance (EMR) measurements reveal that, under the applied preparation conditions, namely alkaline pH, high temperature (65 degrees C), exclusion of oxygen, and the presence of hydrogen peroxide, maghemite and/or magnetite nanoparticles with an average diameter of about 3 nm are mineralised inside the cavities of both LiDps and LiDps-tm. The magnetic nanoparticles (MNPs) thus formed show similar magnetic properties, with superparamagnetic behaviour above 4.5 K and a large magnetic anisotropy. Interestingly, in the EMR spectra an absorption at half-field is observed, which can be considered as a manifestation of the quantum behaviour of the MNPs. These results indicate that Dps proteins can be advantageously used for the production of nanomagnets at the interface between molecular clusters and traditional MNPs and that the presence of the ferroxidase centre, though increasing the efficiency of nanoparticle formation, does not affect the nature and fine structure of the MNPs. Importantly, the self-organisation of MNP-containing Dps on HRTEM grids suggests that Dps-enclosed MNPs can be deposited on surfaces in an ordered fashion.


Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Ferric Compounds/chemical synthesis , Listeria/metabolism , Nanoparticles , Bacterial Proteins/ultrastructure , Catalysis , Ceruloplasmin/metabolism , DNA-Binding Proteins/ultrastructure , Ferric Compounds/metabolism , Listeria/genetics
15.
Front Biosci (Landmark Ed) ; 15(1): 122-31, 2010 01 01.
Article in English | MEDLINE | ID: mdl-20036810

ABSTRACT

The review outlines the experimental studies that have led to the current understanding at a molecular level of the protective role exerted by Dps proteins under stress conditions. After a brief description of the structural signatures and of the ferroxidase activity, which confers to all Dps proteins the capacity to decrease the hydroxyl radical induced DNA damage, the interaction of some family members with DNA is analysed. Special emphasis is given to the Dps structural elements that render the interaction with DNA possible and to the consequences that complex formation has on nucleoid organization and microbial survival.


Subject(s)
Bacterial Proteins/metabolism , DNA, Bacterial/metabolism , DNA-Binding Proteins/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Models, Biological , Models, Molecular , Molecular Sequence Data , Protein Binding , Protein Multimerization , Protein Structure, Quaternary , Sequence Homology, Amino Acid
16.
J Biol Chem ; 284(28): 19101-9, 2009 Jul 10.
Article in English | MEDLINE | ID: mdl-19457858

ABSTRACT

Elucidating pore function at the 3-fold channels of 12-subunit, microbial Dps proteins is important in understanding their role in the management of iron/hydrogen peroxide. The Dps pores are called "ferritin-like" because of the structural resemblance to the 3-fold channels of 24-subunit ferritins used for iron entry and exit to and from the protein cage. In ferritins, negatively charged residues lining the pores generate a negative electrostatic gradient that guides iron ions toward the ferroxidase centers for catalysis with oxidant and destined for the mineralization cavity. To establish whether the set of three aspartate residues that line the pores in Listeria innocua Dps act in a similar fashion, D121N, D126N, D130N, and D121N/D126N/D130N proteins were produced; kinetics of iron uptake/release and the size distribution of the iron mineral in the protein cavity were compared. The results, discussed in the framework of crystal growth in a confined space, indicate that iron uses the hydrophilic 3-fold pores to traverse the protein shell. For the first time, the strength of the electrostatic potential is observed to modulate kinetic cooperativity in the iron uptake/release processes and accordingly the size distribution of the microcrystalline iron minerals in the Dps protein population.


Subject(s)
Bacterial Proteins/physiology , DNA-Binding Proteins/physiology , Ferritins/chemistry , Listeria/metabolism , Amino Acid Sequence , Bacterial Proteins/metabolism , Catalysis , Crystallization , DNA-Binding Proteins/metabolism , Iron/chemistry , Kinetics , Models, Molecular , Molecular Conformation , Molecular Sequence Data , Oxidants/chemistry , Proteins/chemistry , Sequence Homology, Amino Acid , Static Electricity
17.
Archaea ; 2(4): 221-31, 2009 Feb 17.
Article in English | MEDLINE | ID: mdl-19478917

ABSTRACT

Recombinant amidase from Sulfolobus solfataricus occurred as a dimer of 110 kDa comprising identical subunits. Only dimers were present at pHs above 7.0, but with decreasing pH, dimers associated into octamers, with complete oligomerization occurring at pH 3.0. Oligomerization showed reversible temperature-dependence, with octamer formation increasing with temperature from 36 degrees C to between 70 and 80 degrees C. Increasing salt concentrations, favored dissociation of the octamers. Among the three investigated factors affecting the dimer-octamer equilibrium, the most important was pH. Among four mutants obtained by site-specific mutagenesis and selection for pH and temperature sensitivity, the T319I and D487N mutant amidases, like that of the native Sulfolobus solfataricus, responded to changes in pH and temperature with a conformational change affecting the dimer-octamer equilibrium. The Y41C and L34P mutant amidases were unaffected by pH and temperature, remaining always in the dimeric state. The differences among mutants in protein conformation must be related to the position of the introduced mutation. Although the L34P and Y41C mutations are located in the helical region 33-48 (LLKLQLESYERLDSLP), which is close to the amino-terminal segment of the protein, the T319I mutation is located in a strand on the surface of the protein, which is far from, and opposite to, the amino-terminal segment. The D487N mutation is located in the center of the protein, far distant from the 33-48 segment. These observations suggest that the segment of the protein closest to the amino-terminus plays a key role in the association of dimers into octamers.


Subject(s)
Amidohydrolases/chemistry , Amidohydrolases/metabolism , Mutagenesis, Site-Directed , Sulfolobus solfataricus/enzymology , Amidohydrolases/genetics , Cyclodextrins/metabolism , Dimerization , Enzyme Stability , Hydrogen-Ion Concentration , Ions/metabolism , Protein Folding , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sulfolobus solfataricus/genetics , Temperature , Thermodynamics
18.
Pflugers Arch ; 457(5): 1049-60, 2009 Mar.
Article in English | MEDLINE | ID: mdl-18830620

ABSTRACT

Modulation of the L-type Ca(2+) channel (LTCC) by sorcin was investigated by measuring the L-type Ca(2+) current (I (Ca,L)) in isolated rabbit ventricular myocytes using ruptured patch, single electrode voltage clamp in the absence of extracellular Na(+). Fifty millimolars EGTA (170 nM Ca(2+)) in the pipette solution buffered bulk cytoplasmic [Ca(2+)], but retained rapid Ca(2+)-dependant inactivation of I (Ca,L,). Recombinant sorcin (3 microM) in the pipette significantly slowed time-dependant inactivation (tau (fast): 8.8 +/- 0.9 vs. 15.1 +/- 1.7 ms). Sorcin had no significant effect on I (Ca,L,) after inhibition of the sarcoplasmic reticulum (SR). Using 10 mM 1,2-bis(o-N,N,N',N'-tetraacetic acid (170 nM Ca(2+)), I (Ca,L) inactivation was then determined by a Ca(2+) -independent, voltage-dependant process. Under these conditions, 3 microM sorcin speeded up inactivation. A similar effect was observed by substitution of Ca(2+) with Ba(2+). Down-regulation of endogenous sorcin to 27 +/- 7% using an RNAi adenoviral vector slowed inactivation of I (Ca,L) by approximately 42%. The effects of sorcin on voltage-dependant inactivation were mimicked by a truncated form of the protein containing only the Ca(2+)-binding domain. This data is consistent with two independent actions of sorcin on the LTCC: (1) slowing Ca(2+)-dependant inactivation and (2) stimulating voltage-dependant inactivation. The net effect of sorcin on the time-dependent inactivation of I (Ca,L) was a balance between these two effects. Under normal conditions, sorcin slows I (Ca,L) inactivation because the effects of Ca(2+)-dependant inactivation out-weigh the effects on voltage-dependant inactivation.


Subject(s)
Calcium Channels, L-Type/metabolism , Calcium-Binding Proteins/pharmacology , Myocytes, Cardiac/metabolism , Animals , Calcium Channels, L-Type/drug effects , Calcium Signaling/drug effects , Calcium-Calmodulin-Dependent Protein Kinase Type 2/physiology , Cyclic AMP-Dependent Protein Kinases/physiology , Egtazic Acid/analogs & derivatives , Egtazic Acid/pharmacology , Protein Kinase Inhibitors/pharmacology , RNA Interference , Rabbits
19.
Exp Physiol ; 93(12): 1233-8, 2008 Dec.
Article in English | MEDLINE | ID: mdl-18603601

ABSTRACT

We examined the modulation of the cardiac L-type Ca(2+) channel (LTCC) by the regulatory protein sorcin and tested the hypothesis that modulation occurred by direct interaction. Whole-cell patch-clamp recordings were made on native rabbit ventricular myocytes and HEK 293 cells expressing cardiac alpha(1C) subunits. In ventricular cells, sorcin increased peak current when using either Ca(2+) or Ba(2+) as charge carriers. In HEK 293 cells, sorcin increased peak current density when using Ba(2+) as a charge carrier but not when using Ca(2+). In ventricular myocytes, current inactivation (tau(fast), in ms) was slowed by sorcin with Ca(2+) as the charge carrier, whilst in the presence of Ba(2+) it was enhanced. In HEK 293 cells, sorcin significantly enhanced tau(fast), but no significant change was observed with Ba(2+). This trend was mimicked by the truncated peptide, sorcin Ca(2+)-binding domain, which lacks the N-terminal domain. These data suggest that sorcin interacts with LTCC via its C-terminal domain, which alters current magnitude and tau(fast). These effects appear to be influenced by the prevailing experimental conditions.


Subject(s)
Calcium Channels, L-Type/metabolism , Calcium Signaling , Calcium-Binding Proteins/metabolism , Animals , Barium/metabolism , Binding Sites , CHO Cells , Calcium/metabolism , Calcium Channels, L-Type/genetics , Calcium-Binding Proteins/genetics , Cricetinae , Cricetulus , Humans , Kinetics , Membrane Potentials , Protein Binding , Protein Structure, Tertiary , Rabbits , Recombinant Proteins/metabolism , Transfection
20.
Arch Biochem Biophys ; 478(1): 69-74, 2008 Oct 01.
Article in English | MEDLINE | ID: mdl-18625196

ABSTRACT

Ferritins from the liver and spleen of the cold-adapted Antarctic teleosts Trematomus bernacchii and Trematomus newnesi have been isolated and characterized. Interestingly, only H- and M-chains are expressed and no L-chains. The H-chains contain the conserved ferroxidase center residues while M-chains harbor both the ferroxidase center and the micelle nucleation site ligands. Ferritins have an organ-specific subunit composition, they are: M homopolymers in spleen and H/M heteropolymers in liver. The M-chain homopolymer mineralizes iron at higher rate with respect to the H/M heteropolymer, which however is endowed with a lower activation energy for the iron incorporation process, indicative of a higher local flexibility. These findings and available literature data on ferritin expression in fish point to the role of tissue-specific expression of different chains in modulating the iron oxidation/mineralization process.


Subject(s)
Ferritins/chemistry , Ferritins/isolation & purification , Animals , Ferritins/metabolism , Iron/chemistry , Ligands , Liver/metabolism , Peptides/chemistry , Perciformes , Polymers/chemistry , Protein Binding , Protein Conformation , Species Specificity , Spleen/metabolism , Temperature
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