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Biomedical subjects

Lucia Banci

Publications and source records attributed to Lucia Banci.

At least 73 records · Page 4Linked to original sources
PubMed2002

Solution structure and characterization of the heme chaperone CcmE.

The covalent attachment of the heme cofactor in c-type cytochromes is a surprisingly complex process, which in bacteria involves a number of different proteins. Among the latter, the ccmE gene product is known to perform a key role in the heme delivery pathway in Gram-negative bacteria. The solution structure of the soluble domain of apo-CcmE from Shewanella putrefaciens was determined through NMR spectroscopy on a 13C,15N-labeled sample. The structure is characterized by a compact core with large regions of beta structure, while the N-terminal and C-terminal regions are essentially unstructured. The overall folding is similar to that of the so-called oligo-binding proteins (OB fold). Solvent-exposed aromatic residues, conserved in all CcmE homologues, have been found in the proximity of His131, the putative heme-binding residue, that could have a role in the interaction with heme. No interaction between CcmE and heme, as well as between CcmE and holocytochrome c, could be detected in vitro by electronic spectroscopy or by NMR. The data available suggest that the heme transfer process is likely to involve a heterooligomeric protein complex and occur under a tight enzymatic control.

Aspartate-tRNA Ligase↗
PubMed2002

A new zinc-protein coordination site in intracellular metal trafficking: solution structure of the Apo and Zn(II) forms of ZntA(46-118).

Zinc, a metal ion that functions in a wide variety of catalytic and structural sites in metalloproteins, is shown here to adopt a novel coordination environment in the Escherichia coli transport protein ZntA. The ZntA protein is a P-type ATPase that pumps zinc out of the cytoplasm and into the periplasm. It is physiologically selective for Zn(II) and functions with metalloregulatory proteins in the cell to keep the zinc quota within strict limits. Yet, the N-terminal cytoplasmic domain contains a region that is highly homologous to the yeast Cu(I) metallochaperone Atx1. To investigate how the structure of this region may influence its function, this fragment, containing residues 46-118, has been cloned out of the gene and overexpressed. We report here the solution structure of this fragment as determined by NMR. Both the apo and Zn(II)-ZntA(46-118) structures have been determined. It contains a previously unknown protein coordination site for zinc that includes two cysteine residues, Cys59 and Cys62, and a carboxylate residue, Asp58. The solvent accessibility of this site is also remarkably high, a feature that increasingly appears to be a characteristic of domains of heavy metal ion transport proteins. The participation of Asp58 in this ZntA metal ion binding site may play an important role in modulating the relative affinities and metal exchange rates for Zn(II)/Pb(II)/Cd(II) as compared with other P-type ATPases, which are selective for Cu(I) or Ag(I).

Adenosine Triphosphatases↗
PubMed2002

Isolation and characterization of a microperoxidase-8 with a modified histidine axial ligand.

Microperoxidase-8, Fe(III)MP-8, the heme octapeptide obtained by horse heart cytochrome c digestion, was studied in the presence of H(2)O(2). A modified form of the catalyst was isolated by HPLC and showed a UV/visible spectrum similar to that of Fe(III)MP-8. ESI-MS measurements revealed a 16 Da increase in molecular mass for the modified catalyst when compared to Fe(III)MP-8, suggesting the insertion of an oxygen atom. ESI-MS(2) fragmentation measurements point at oxygen incorporation on the His18 residue of the octapeptide of the modified catalyst. Comparison of the (1)H NMR chemical shifts of the methyl protons of the porphyrin ring of Fe(III)MP-8 and the modified catalyst shows a large shift for especially the 3-methyl and 5-methyl resonances, whereas the other (1)H NMR chemical shifts are almost unaffected. These observations can best be ascribed to a reorientation of the histidine axial ligand. The latter is suggested to be the consequence of an oxygen insertion, possibly on the imidazole ring of His18, thereby corroborating the data obtained by ESI-MS(2). (1)H NMR NOE difference measurements on Fe(III)MP-8 and on the modified catalyst supported the assignment of the H(delta)2 and H(epsilon)1 protons of the His18 imidazole ring. The ring amine proton H(delta)1 could not be detected in both forms of the catalyst. For Fe(III)MP-8 this absence of the H(delta)1 resonance can be ascribed to fast H/D exchange. For the modified catalyst the NMR data are not contradictory, with an oxygen insertion on position delta1 of the His18 imidazole ring with a fast H/D exchanging hydroxyl proton. Together these data converge in suggesting the H(2)O(2) modified catalyst bears a hydroxylated His18 axial ligand. The mechanism that could underlie Fe(III)MP-8 axial histidine hydroxylation is further discussed.

Animals↗
PubMed2002

NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.

The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the available crystal structure. The solution structure is obtained from 1609 meaningful NOE data (22.7 per residue), 76 dihedral angles, and 59 pseudocontact shifts. The root mean square deviations from the average structure are 0.25+/-0.07 and 0.59+/-0.13 A for the backbone and all heavy atoms, respectively, and the quality assessment of the structure is satisfactory. The solution structure closely reproduces the fold observed in the crystal structure. The backbone mobility was then investigated through amide (15)N relaxation rate and (15)N-(1)H NOE measurements. The protein is rigid in both the sub-nanosecond and millisecond time scales, probably due to the relatively large heme:number of amino acids ratio. Modeling of eight c-type cytochromes from other Gram-positive bacteria with a high sequence identity (>30 %) to the present cytochrome c(553) was performed. Analysis of consensus features accounts for the relatively low reduction potential as being due to extensive heme hydration and indicates residues 34-35, 44-46, 69-72, and 75 as a conserved hydrophobic patch for the interaction with a protein partner. At variance with mitochondrial c-type cytochrome, this protein does not experience pH-dependent coordination equilibria. The reasons for this difference are analyzed.

Amino Acid Sequence↗
PubMed2002

Solution structure of the N-terminal domain of a potential copper-translocating P-type ATPase from Bacillus subtilis in the apo and Cu(I) loaded states.

A putative partner of the already characterized CopZ from Bacillus subtilis was found, both proteins being encoded by genes located in the same operon. This new protein is highly homologous to eukaryotic and prokaryotic P-type ATPases such as CopA, Ccc2 and Menkes proteins. The N-terminal region of this protein contains two soluble domains constituted by amino acid residues 1 to 72 and 73 to 147, respectively, which were expressed both separately and together. In both cases only the 73-147 domain is folded and is stable both in the copper(I)-free and in the copper(I)-bound forms. The folded and unfolded state is monitored through the chemical shift dispersion of 15N-HSQC spectra. In the absence of any structural characterization of CopA-type proteins, we determined the structure of the 73-147 domain in the 1-151 construct in the apo state through 1H, 15N and 13C NMR spectroscopies. The structure of the Cu(I)-loaded 73-147 domain has been also determined in the construct 73-151. About 1300 meaningful NOEs and 90 dihedral angles were used to obtain structures at high resolution both for the Cu(I)-bound and the Cu(I)-free states (backbone RMSD to the mean 0.35(+/-0.06) A and 0.39(+/-0.07) A, respectively). The structural assessment shows that the structures are accurate. The protein has the typical betaalpha(betabeta)alphabeta folding with a cysteine in the C-terminal part of helix alpha1 and the other cysteine in loop 1. The structures are similar to other proteins involved in copper homeostasis. Particularly, between BsCopA and BsCopZ, only the charges located around loop 1 are reversed for BsCopA and BsCopZ, thus suggesting that the two proteins could interact one with the other. The variability in conformation displayed by the N-terminal cysteine of the CXXC motif in a number of structures of copper transporting proteins suggests that this may be the cysteine which binds first to the copper(I) carried by the partner protein.

Adenosine Triphosphatases↗
PubMed2002

Direct detection of hydrogen bonds in monomeric superoxide dismutase: biological implications.

Hydrogen bonds were directly determined via NMR with different experimental approaches at 600 and 800 MHz for reduced monomeric superoxide dismutase (Q133M2SOD, 16 kDa). This protein contains a copper and a zinc ion and shows the classical superoxide dismutase (SOD) eight-stranded beta-barrel fold. The best results for this intermediate molecular mass protein were obtained using a TROSY version of the long-range HNCO experiment at high magnetic field (800 MHz) or with a cryoprobe at 600 MHz. The backbone hydrogen bond network that defines the secondary structure of the protein was detected. Thirty-five backbone hydrogen bonds were identified. The lower limit for their detection, their relation to the TROSY R(2) rates, and the correlation between hydrogen bond detectability and signal line width are discussed. Experiments were also optimized to detect hydrogen bonds involving key side chains, which lead to the observation of five hydrogen bonds. In particular, the hydrogen bonds involving the side chain of Asp 124 were observed, which show significant differences with respect to the bonds expected on the basis of the crystal structure. The relevance of this finding relies also on the fact that Asp 124 is a key residue in determining the affinity of the protein for zinc. It has now been determined that the gain of the toxic function of peroxynitrite formation in SOD mutants related to amyotrophic lateral sclerosis (ALS) is due to SOD species lacking the zinc ion, as a consequence of a reduced affinity for zinc. Therefore, this study provides structural hints for understanding the origin of the enzymatic behavior of the Zn-deficient SOD.

Catalysis↗
PubMed2002

Characterization and peroxidase activity of a myoglobin mutant containing a distal arginine.

The spectroscopic, conformational, and reactivity characteristics of the T67R variant of sperm whale myoglobin have been studied to assess the effects of introducing an arginine residue into the distal side of this protein, as occurs in the active site of heme peroxidases. The overall circular dichroism (CD) and NMR spectroscopic properties of various derivatives of the protein are little affected by the mutation. The mutant contains a high-spin ferric ion with a water molecule as the sixth ligand, which exhibits slightly enhanced acidity (pK(a)=8.43+/-0.03) with respect to the corresponding derivative of wild-type myoglobin (pK(a)=8.60+/-0.04). The presence of the distal arginine increases the affinity of the Fe(III) center for azide (K=(6.0+/-0.5)x10(4) M(-1)) and decreases that for imidazole (K=12.0+/-0.2 M(-1)), with respect to the wild-type protein (K=(5.0+/-0.1)x10(4) and 24.7+/-0.7 M(-1), respectively). The peroxidase activity of T67R and wild-type myoglobins has been studied with a group of phenolic substrates related to tyrosine. The mutant exhibits an increased rate of reaction with hydrogen peroxide (k=1550+/-10 versus 760+/-10 M(-1) x s(-1)) and a generally increased peroxidase activity with respect to wild-type myoglobin. Relaxation measurements of proton nuclei of the phenolic substrates in the presence of either the T67R variant or the wild-type protein show that binding of these molecules occurs at distances of 8-10 A from the iron center, that is, close to the heme pocket, except for p-cresol, which can approach the heme more closely and, therefore, probably enter into the distal cavity.

Animals↗
PubMed2002

Molecular dynamics characterization of the C2 domain of protein kinase Cbeta.

Protein kinase C (PKC) isozymes comprise a family of related enzymes that play a central role in many intracellular eukaryotic signaling events. Isozyme specificity is mediated by association of each PKC isozyme with specific anchoring proteins, termed RACKs. The C2 domain of betaPKC contains at least part of the RACK-binding sites. Because the C2 domain contains also a RACK-like sequence (termed pseudo-RACK), it was proposed that this pseudo-RACK site mediates intramolecular interaction with one of the RACK-binding sites in the C2 domain itself, stabilizing the inactive conformation of betaPKC. BetaPKC depends on calcium for its activation, and the C2 domain contains the calcium-binding sites. The x-ray structure of the C2 domain of betaPKC shows that three Ca(2+) ions can be coordinated by two opposing loops at one end of the domain. Starting from this x-ray structure, we have performed molecular dynamics (MD) calculations on the C2 domain of betaPKC bound to three Ca(2+) ions, to two Ca(2+) ions, and in the Ca(2+)-free state, in order to analyze the effect of calcium on the RACK-binding sites and the pseudo-RACK sites, as well as on the loops that constitute the binding site for the Ca(2+) ions. The results show that calcium stabilizes the beta-sandwich structure of the C2 domain and thus affects two of the three RACK-binding sites within the C2 domain. Also, the interactions between the third RACK-binding site and the pseudo-RACK site are not notably modified by the removal of Ca(2+) ions. On that basis, we predict that the pseudo-RACK site within the C2 domain masks a RACK-binding site in another domain of betaPKC, possibly the V5 domain. Finally, the MD modeling shows that two Ca(2+) ions are able to interact with two molecules of O-phospho-l-serine. These data suggest that Ca(2+) ions may be directly involved in PKC binding to phosphatidylserine, an acidic lipid located exclusively on the cytoplasmic face of membranes, that is required for PKC activation.

Amino Acid Sequence↗
PubMed2002

Solution structure of CopC: a cupredoxin-like protein involved in copper homeostasis.

The structure of the metal-free form of CopC, a protein involved in copper homeostasis, has been obtained. The fold is a Greek key beta barrel similar to that of functionally unrelated blue copper proteins but with important structural variations. The protein binds one equivalent of copper (II) with relatively high affinity and contains a cluster of conserved residues (His1, Glu27, Asp89, and His91) which could form a water-accessible metal binding site. The structure also reveals a loop containing the M(X)(n)M motif which is present in a number of proteins also involved in copper homeostasis. The present structure represents a link between copper-trafficking proteins and cupredoxins. Within a structural and genomic analysis, the role of CopC in copper trafficking is discussed.

Amino Acid Sequence↗
PubMed2002

The solution structure of reduced dimeric copper zinc superoxide dismutase. The structural effects of dimerization.

The solution structure of homodimeric Cu2Zn2 superoxide dismutase (SOD) of 306 aminoacids was determined on a 13C, 15N and 70% 2H labeled sample. Two-thousand eight-hundred and five meaningful NOEs were used, of which 96 intersubunit, and 115 dihedral angles provided a family of 30 conformers with an rmsd from the average of 0.78 +/- 0.11 and 1.15 +/- 0.09 A for the backbone and heavy atoms, respectively. When the rmsd is calculated for each subunit, the values drop to 0.65 +/- 0.09 and 1.08 +/- 0.11 A for the backbone and heavy atoms, respectively. The two subunits are identical on the NMR time scale, at variance with the X-ray structures that show structural differences between the two subunits as well as between different molecules in the unit cell. The elements of secondary structure, i.e. eight beta sheets, are the same as in the X-ray structures and are well defined. The odd loops (I, III and V) are well resolved as well as loop II located at the subunit interface. On the contrary, loops IV and VI show some disorder. The residues of the active cavity are well defined whereas within the various subunits of the X-ray structure some are disordered or display different orientation in different X-ray structure determinations. The copper(I) ion and its ligands are well defined. This structure thus represents a well defined model in solution relevant for structure-function analysis of the protein. The comparison between the solution structure of monomeric mutants and the present structure shows that the subunit-subunit interactions increase the order in loop II. This has the consequences of inducing the structural and dynamic properties that are optimal for the enzymatic function of the wild-type enzyme. The regions 37-43 and 89-95, constituting loops III and V and the initial part of the beta barrel and showing several mutations in familial amyotrophis lateral sclerosis (FALS)-related proteins have a quite extensive network of H-bonds that may account for their low mobility. Finally, the conformation of the key Arg143 residue is compared to that in the other dimeric and monomeric structures as well as in the recently reported structure of the CCS-superoxide dismutase (SOD) complex.

Deuterium↗
PubMed2002

Metallochaperones and metal-transporting ATPases: a comparative analysis of sequences and structures.

A comparative structural genomic analysis of a new class of metal-trafficking proteins can provide insights into the intracellular chemistry of reactive cofactors such as copper and zinc. Starting from the sequences of the metallochaperone Atx1 and from the first soluble domain of the copper-transporting ATPase Ccc2, both from yeast, a search on the available genomes was performed using a homology criterion and a metal-binding motif x'-x"-C-x'''-x''''-C. By limiting ourselves to 20% identity with any of the proteins found, several soluble copper-transport proteins were identified, as well as soluble domains of membrane-bound ATPases. Structural models were calculated using high-resolution solution structures as templates, and the models were validated using statistical and energy criteria. Residue conservation and substitution have been interpreted and discussed in terms of structure-function relationship. The potential energy surfaces have been analyzed in terms of protein-protein interactions. We find that metallochaperones and their physiological partner ATPases from several phylogenetic kingdoms recognize one another, via an interplay of electrostatics, hydrogen bonding, and hydrophobic interactions, in a manner that precisely orients the metal-binding side chains for rapid metal transfer between otherwise tight binding sites. Finally, other putative metal-transport proteins are mentioned that have low homology and/or a different metal-binding consensus motif and that appear to use similar structures for recognition and transfer. This analysis highlights the wealth and the complexity of the field.

Adenosine Triphosphatases↗
PubMed2002

Structure and dynamics of copper-free SOD: The protein before binding copper.

The solution structure of the copper-free state of a monomeric form of superoxide dismutase (153 amino acids) was determined through (13)C and (15)N labeling. The protein contained two mutations at the native subunit-subunit interface (F50E and G51E) to obtain a soluble monomeric species and a mutation in the active site channel (E133Q). About 93% of carbon atoms, 95% of nitrogen atoms, and 96% of the protons were assigned. A total of 2467 meaningful NOEs and 170 dihedral angles provided a family of 35 conformers with RMSD values of 0.76 +/- 0.09 A for the backbone and 1.22 +/- 0.13 A for all heavy atoms. The secondary structure elements, connected by loops, produce the typical superoxide dismutase Greek key fold, formed by an eight-stranded beta-barrel. The comparison with the copper-bound monomeric and dimeric structures shows that the metal ligands have a conformation very close to that of the copper-bound forms. This feature indicates that the copper-binding site is preorganized and well ordered also in the absence of the copper ion. The active-site channel shows a sizable increase in width, achieving a suitable conformation to receive the copper ion. The histidines ring NH resonances that bind the copper ion and the region around the active-site channel experience, as found from (15)N relaxation studies, conformational exchange processes. The increased width of the channel and the higher mobility of the histidine rings of the copper site in the copper-free form with respect to the holoprotein is discussed in terms of the process of copper insertion.

Copper↗
PubMed2001

Chemical shift-based constraints for solution structure determination of paramagnetic low-spin heme proteins with bis-His and His-CN axial ligands: the cases of oxidized cytochrome b(5) and Met80Ala cyano-cytochrome c.

The chemical shifts of the methyl protons of protoporphyrin IX, which are readily assigned, are related to the structural features of the axial histidine ligands in heme proteins with bis-His or His-CN axial coordination (Bertini I, Luchinat C, Parigi G, Walker FA (1999) JBIC 4:515-519). In the present paper, a module is developed which transforms the chemical shifts into a pseudo-potential energy that is a function of the dihedral angles defining the orientation of the axial ligand planes. Minimization of this pseudo-potential energy, together with the energetic contributions provided by the other constraints, yields structures consistent with the heme methyl chemical shifts. Oxidized cytochrome b(5) from rat and the cyanide derivative of the M80A mutant of yeast cytochrome c are used for test calculations. In the case of scarcity of NOEs for the axial ligands, owing to the presence of the paramagnetic center, the above structural constraints are shown to be quite precious. The newly refined structures are deposited in the PDB.

Alanine↗
PubMed1996

Individual Reduction Potentials of the Iron Ions in Fe(2)S(2) and High-Potential Fe(4)S(4) Ferredoxins.

The DelPhi program package has been used to confirm that the span in reduction potentials among high-potential Fe(4)S(4) ferredoxins must be mainly ascribed to the net protein charges arising from acidic and basic residues. Subsequently, the order of the individual reduction potentials of the iron ions in Fe(2)S(2) ferredoxins as found from NMR spectroscopy was explained mainly on the basis of different solvation contributions to the electrostatic potential. The individual reduction potentials of the iron ions in high-potential Fe(4)S(4) ferredoxins, again available from NMR spectroscopy, are only qualitatively reproduced. It is proposed that the protein triggers a distortion in the cluster which would be a further contribution to the electrochemical inequivalence of the individual iron ions.

Journal Article↗
PubMed1996

New Type 2 Copper-Cysteinate Proteins. Copper Site Histidine-to-Cysteine Mutants of Yeast Copper-Zinc Superoxide Dismutase.

Preparation and characterization of two new site-directed mutant copper-zinc superoxide dismutase proteins from Saccharomyces cerevisiae, i.e., His46Cys (H46C) and His120Cys (H120C), in which individual histidyl ligands in the copper-binding site were replaced by cysteine, are reported here. These two mutant CuZnSOD proteins may be described as type 2 (or normal) rather than type 1 (or blue) copper-cysteinate proteins and are characterized by their yellow rather than blue color, resulting from intense copper-to-sulfur charge transfer bands around 400 nm, their type 2 EPR spectra, with large rather than small nuclear hyperfine interactions, and their characteristic type 2 d-d electronic absorption spectra. An interesting difference between these two copper site His-to-Cys mutations is that the imidazolate bridge between the two metal sites that is characteristic of the wild-type protein remains intact in the case of the H46C mutant but is not present in the case of the H120C mutant.

Journal Article↗
PubMedDate not supplied

Bioinformatic comparison of structures and homology-models of matrix metalloproteinases.

The entire family of human matrix metalloproteinases (MMPs) was investigated using phylogenetic trees and homology modeling. The phylogenetic analysis indicates that individual domains of each MMP have evolved in a correlated manner. Despite their high sequence similarity, the phylogenetic tree of the catalytic domains already allows functional (e.g., linked to regulation and substrate recognition) homologies between different MMPs to be identified. The same pattern of functional homologies is confirmed by the phylogenetic analysis of the mature proteins. Structural models were built for the catalytic domains of the entire MMP family, for twelve hemopexin domains and for twelve mature proteins. The surface properties around the active site cleft of the modeled and experimental structures are quite conserved, whereas the hemopexin domains are more differentiated, possibly indicating a role in determining substrate specificity. The analysis of mature MMPs showed that the area of the interface between the catalytic and hemopexin domains is essentially conserved, with both hydrophobic and hydrophilic amino acids at the interface. The absence of specific conserved interdomain contacts suggests that the interface is tolerant to amino acid replacements, and that there may be a certain degree of plasticity with respect to the reciprocal orientation of the two domains.

Binding Sites↗
PubMedDate not supplied

Ortholog search of proteins involved in copper delivery to cytochrome C oxidase and functional analysis of paralogs and gene neighbors by genomic context.

Cytochrome c oxidase (COX) is a multi-subunit enzyme of the mitochondrial respiratory chain. Delivery of metal cofactors to COX is essential for assembly, which represents a long-standing puzzle. The proteins Cox17, Sco1/2, and Cox11 are necessary for copper insertion into CuA and CuB redox centers of COX in eukaryotes. A genome-wide search in all prokaryotic genomes combined with genomic context reveals that only Sco and Cox11 have orthologs in prokaryotes. However, while Cox11 function is confined to COX assembly, Sco acts as a multifunctional linker connecting a variety of biological processes. Multifunctionality is achieved by gene duplication and paralogs. Neighbor genes of Sco paralogs often encode cuproenzymes and cytochrome c domains and, in some cases, Sco is fused to cytochrome c. This led us to suggest that cytochrome c might be relevant to Sco function and the two proteins might jointly be involved in COX assembly. Sco is also related, in terms of gene neighborhood and phylogenetic occurrence, to a newly detected protein involved in copper trafficking in bacteria and archaea, but with no sequence similarity to the mitochondrial copper chaperone Cox17. By linking the assembly system to the copper uptake system, Sco allows COX to face alternative copper trafficking pathways.

Animals↗