Role of Dps (DNA-binding proteins from starved cells) aggregation on DNA.

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

Ligand binding to the dimeric hemoglobin from Scapharca inaequivalvis, a hemoglobin with a novel mechanism for cooperativity.

Abstract The homodimeric hemoglobin from Scapharca inaequivalvis has an unusual spatial arrangement of the subunits (Royer, W.E., Jr., Love, W.E., and Fenderson, F.F. (1985) Nature 316, 277-280). The time course of oxygen and nitric oxide rebinding to this protein following flash photolysis has been measured on a nanosecond time scale. A large amplitude is observed with a half-time of 20 ns (NO). With oxygen the half-time decreases from 70 ns at low fractional photolysis to 30 ns at large breakdown. The second order rate of NO binding is 1.6 x 10(7)/MS, and is the same as that for oxygen. Analysis of the geminate data suggests that oxygen and nitric oxide react more rapidly with the heme than in myoglobin, but also escape much more rapidly from its vicinity

Studies on the Relations between Molecular and Functional Properties of Hemoglobin: VII. KINETIC EFFECTS OF THE REVERSIBLE DISSOCIATION OF HEMOGLOBIN INTO SINGLE CHAIN MOLECULES

Abstract The kinetics of the reactions of human hemoglobin with carbon monoxide and oxygen has been studied in photochemical and rapid mixing experiments over a large range of hemoglobin concentration. When the reaction is initiated by rapid removal of the ligand from ligand-bound hemoglobin, the kinetics of the combination of hemoglobin with CO shows a marked concentration dependence in both the photochemical and the rapid mixing experiments. In dilute hemoglobin solutions (below 10-5 m in heme), dissociation of the ligand from oxyhemoglobin or carbonmonoxyhemoglobin is followed by slow changes (half-time of the order of seconds) in the properties of the system. These results lead to the following picture, which is also consistent with other as yet unexplained aspects of hemoglobin kinetics. (a) Ligand-bound hemoglobin dissociates reversibly into single chain molecules at concentrations below 10-5 m. (b) Deoxygenated hemoglobin has a much lower tendency to dissociate into single chain molecules, and there is no appreciable dissociation even at concentrations of the order of 10-6 to 10-7 m. (c) The association of deoxygenated α and β chains is a relatively slow process. Therefore, after sudden dissociation of the ligand from dilute hemoglobin solutions, the properties of the system, for a brief time, are those of a mixture of deoxygenated hemoglobin and deoxygenated α and β chains. (d) The properties of the single chain molecules obtained by dilution of ligand-bound hemoglobin are the same as those of isolated α and β hemoglobin chains as obtained by preparative procedures

The neutrophil-activating Dps protein of Helicobacter pylori, HP-NAP, adopts a mechanism different from Escherichia coli Dps to bind and condense DNA

The Helicobacter pylori neutrophil-activating protein (HP-NAP), a member of the Dps family, is a fundamental virulence factor involved in H.pylori-associated disease. Dps proteins protect bacterial DNA from oxidizing radicals generated by the Fenton reaction and also from various other damaging agents. DNA protection has a chemical component based on the highly conserved ferroxidase activity of Dps proteins, and a physical one based on the capacity of those Dps proteins that contain a positively charged N-terminus to bind and condense DNA. HP-NAP does not possess a positively charged N-terminus but, unlike the other members of the family, is characterized by a positively charged protein surface. To establish whether this distinctive property could be exploited to bind DNA, gel shift, fluorescence quenching and atomic force microscopy (AFM) experiments were performed over the pH range 6.5–8.5. HP-NAP does not self-aggregate in contrast to Escherichia coli Dps, but is able to bind and even condense DNA at slightly acid pH values. The DNA condensation capacity acts in concert with the ferritin-like activity and could be used to advantage by H.pylori to survive during host-infection and other stress challenges. A model for DNA binding/condensation is proposed that accounts for all the experimental observations

The 2.4-A crystal structure of Scapharca dimeric hemoglobin. Cooperativity based on directly communicating hemes at a novel subunit interface.

The crystal structure of the cooperative dimeric hemoglobin from the arcid clam, Scapharca inaequivalvis, has been determined in the carbonmonoxy state. The phase problem was solved for reflections with Bragg spacings greater than 3 A using anomalous scattering from the porphyrin iron atoms measured at a single wavelength in combination with molecular averaging. The model built into this electron density map has been refined at 2.4 A resolution by means of stereochemically restrained least squares minimization to a conventional R-value of 0.156. The root mean square deviation from ideal bond lengths and angles are 0.013 A and 1.7 °, respectively. In addition to the 2336 hemoglobin atoms, 214 water molecules have been incorporated into the model. This structure reveals the details of an assemblage of two identical myoglobin-like subunits that is radically different from vertebrate hemoglobins. The subunit interface is formed by direct apposition of the E and F helices, whereas these surfaces are external in vertebrate hemoglobins. The interface has both hydrophobic and hydrophilic character. Two symmetrically related hydrophobic regions are formed between subunits. Six residues are involved in each of these regions that pack tightly enough to exclude water but have only a few atoms in close van der Waals contact. A number of ordered water molecules line the interface and form bridging hydrogen bonds between subunits. Four intersubunit ionic interactions are formed, two of which involve negatively charged propionate groups of the porphyrin. In contrast to cooperative vertebrate hemoglobins, a hydrogen bond network provides a direct route for communication between the two heme groups

The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: x-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties.

Agrobacterium tumefaciens Dps (DNA-binding proteins from starved cells), encoded by the dps gene located on the circular chromosome of this plant pathogen, was cloned, and its structural and functional properties were determined in vitro. In Escherichia coli Dps, the family prototype, the DNA binding properties are thought to be associated with the presence of the lysine-containing N-terminal tail that extends from the protein surface into the solvent. The x-ray crystal structure of A. tumefaciens Dps shows that the positively charged N-terminal tail, which is 11 amino acids shorter than in the E. coli protein, is blocked onto the protein surface. This feature accounts for the lack of interaction with DNA. The intersubunit ferroxidase center characteristic of Dps proteins is conserved and confers to the A. tumefaciens protein a ferritin-like activity that manifests itself in the capacity to oxidize and incorporate iron in the internal cavity and to release it after reduction. In turn, sequestration of Fe(II) correlates with the capacity of A. tumefaciens Dps to reduce the production of hydroxyl radicals from H2O2 through Fenton chemistry. These data demonstrate conclusively that DNA protection from oxidative damage in vitro does not require formation of a Dps-DNA complex. In vivo, the hydroxyl radical scavenging activity of A. tumefaciens Dps may be envisaged to act in concert with catalase A to counteract the toxic effect of H2O2, the major component of the plant defense system when challenged by the bacterium

Hydroxide Rather Than Histidine Is Coordinated to the Heme in Five-coordinate Ferric Scapharca inaequivalvisHemoglobin

The ferric form of the homodimeric Scapharca hemoglobin undergoes a pH-dependent spin transition of the heme iron. The transition can also be modulated by the presence of salt. From our earlier studies it was shown that three distinct species are populated in the pH range 6-9. At acidic pH, a low-spin six-coordinate structure predominates. At neutral and at alkaline pHs, in addition to a small population of a hexacoordinate high-spin species, a pentacoordinate species is significantly populated. Isotope difference spectra clearly show that the heme group in the latter species has a hydroxide ligand and thereby is not coordinated by the proximal histidine. The stretching frequency of the Fe-OH moiety is 578 cm-1 and shifts to 553 cm-1 in H218O, as would be expected for a Fe-OH unit. On the other hand, the ferrous form of the protein shows substantial stability over a wide pH range. These observations suggest that Scapharca hemoglobin has a unique heme structure that undergoes substantial redox-dependent rearrangements that stabilize the Fe-proximal histidine bond in the functional deoxy form of the protein but not in the ferric form

Oxidized dimeric Scapharca inaequivalvis. Co-driven perturbation of the redox equilibrium.

The dimeric hemoglobin isolated from Scapharca inaequivalvis, HbI, is notable for its highly cooperative oxygen binding and for the unusual proximity of its heme groups. We now report that the oxidized protein, an equilibrium mixture of a dimeric high spin aquomet form and a monomeric low spin hemichrome, binds ferrocyanide tightly which allows for internal electron transfer with the heme iron. Surprisingly, when ferricyanide-oxidized HbI is exposed to CO, its spectrum shifts to that of the ferrous CO derivative. Gasometric removal of CO leads to the oxidized species rather than to ferrous deoxy-HbI. At equilibrium, CO binds with an apparent affinity (p50) of about 10-25 mm of Hg and no cooperativity (20 degrees C, 10-50 mM buffers at pH 6.1). The kinetics of CO binding under pseudo-first order conditions are biphasic (t1/2 of 15-50 s at pH 6.1). The rates depend on protein, but not on CO concentration. The nitrite-oxidized protein is not reduced readily in the presence of CO unless one equivalent of ferrocyanide, but not of ferricyanide, is added. We infer that ferrocyanide, produced in the oxidation reaction, is tightly bound to the protein forming a redox couple with the heme iron. CO shifts the redox equilibrium by acting as a trap for the reduced heme. The equilibrium and kinetic aspects of the process have been accounted for in a reaction scheme where the internal electron transfer reaction is the rate-limiting step

Reassessment of protein stability, DNA binding, and protection of Mycobacterium smegmatis Dps.

Abstract The structure and function of Mycobacterium smegmatis Dps (DNA-binding proteins from starved cells) and of the protein studied by Gupta and Chatterji (Gupta, S., and Chatterji, D. (2003) J. Biol. Chem. 278, 5235-5241), in which the C terminus that is used for binding DNA contains a histidine tag, have been characterized in parallel. The native dodecamer dissociated reversibly into dimers above pH 7.5 and below pH 6.0, with apparent pKa values of ∼7.65 and 4.75; at pH ∼4.0, dimers formed monomers. Based on structural analysis, the two dissociation steps have been attributed to breakage of the salt bridges between Glu157 and Arg99 located at the 3-fold symmetry axes and to protonation of Asp66 hydrogen-bonded to Lys36 across the dimer interface, respectively. The C-terminal tag did not affect subunit dissociation, but altered DNA binding dramatically. At neutral pH, protonation of the histidine tag promoted DNA condensation, whereas in the native C terminus, compensation of negative and positive charges led to DNA binding without condensation. This different mode of interaction with DNA has important functional consequences as indicated by the failure of the native protein to protect DNA from DNase-mediated cleavage and by the efficiency of the tagged protein in doing so as a result of DNA sequestration in the condensates. Chemical protection of DNA from oxidative damage is realized by Dps proteins in a multistep iron oxidation/uptake/mineralization process. Dimers have a decreased protection efficiency due to disruption of the dodecamer internal cavity, where iron is deposited and mineralized after oxidation at the ferroxidase center

Iron Incorporation into Escherichia coli Dps Gives Rise to a Ferritin-like Microcrystalline Core

Abstract Escherichia coli Dps belongs to a family of bacterial stress-induced proteins to protect DNA from oxidative damage. It shares with Listeria innocua ferritin several structural features, such as the quaternary assemblage and the presence of an unusual ferroxidase center. Indeed, it was recently recognized to be able to oxidize and incorporate iron. Since ferritins are endowed with the unique capacity to direct iron deposition toward formation of a microcrystalline core, the structure of iron deposited in the E. coli Dps cavity was studied. Polarized single crystal absorption microspectrophotometry of iron-loaded Dps shows that iron ions are oriented. The spectral properties in the high spin 3d5 configuration point to a crystal form with tetrahedral symmetry where the tetrahedron center is occupied by iron ions and the vertices by oxygen. Crystals of iron-loaded Dps also show that, as in mammalian ferritins, iron does not remain bound to the site after oxidation has taken place. The kinetics of the iron reduction/release process induced by dithionite were measured in the crystal and in solution. The reaction appears to have two phases, witht of a few seconds and several minutes at neutral pH values, as in canonical ferritins. This behavior is attributed to a similar composition of the iron core