Messinian‐Zanclean vegetation and climate in North‐Central Italy

A palynological study was carried out on four Italian Miocene‐Pliocene sections ranging in age from uppermost Tortonian to Zanclean located on the Adriatic side of the North‐Central Apennines. The study documents the Mediterranean isolation, the salinity crisis (s.s), the “lago‐mare”; event and the re‐establishment of open‐marine conditions in the Mediterranean at the beginning of the Pliocene. From a climatic point of view, a transition from subtropical/warm‐temperate conditions during the Messinian to warm‐temperate/temperate conditions during the Zanclean is recorded. The presence of a lower thermic level, with respect to the Messinian, the re‐establishment of open‐marine conditions and the uplift of the Apennines were major factors controlling paleoenvironmental variations during the Zanclean. The latter is also characterized by cyclic temperature oscillations. Correlations with coeval sections in the Mediterranean area confirm the existence of latitudinal climatic gradients within the studied area.     

The different intermolecular interactions of the soluble copper-binding domains of the menkes protein, ATP7A

ATP7A is a P-type ATPase involved in copper(I) homeostasis in humans. It possesses a long N-terminal cytosolic tail containing six domains that are individually folded and capable of binding one copper(I) ion each. We investigated the entire N-terminal tail (MNK1-6) in solution by NMR spectroscopy and addressed its interaction with copper(I) and with copper(I)-HAH1, the physiological partner of ATP7A. At copper(I)-HAH1:MNK1-6 ratios of up to 3:1, thus encompassing the range of protein ratios in vivo, both the first and fourth domain of the tail formed a metal-mediated adduct with HAH1 whereas the sixth domain was simultaneously able to partly remove copper(I) from HAH1. These processes are not dependent on one another. In particular, formation of the adducts is not necessary for copper(I) transfer from HAH1 to the sixth domain. The present data, together with available in vivo studies, suggest that the localization of ATP7A between the trans-Golgi network and the plasma membrane may be regulated by the accumulation of the adducts with HAH1, whereas the main role of domains 5 and 6 is to assist copper(I) translocation.     

The functions of Sco proteins from genome-based analysis

Sco proteins are widespread proteins found in eukaryotic as well as in many prokaryotic organisms. The 3D structure of representatives from human, yeast, and Bacillus subtilis has been determined, showing a thioredoxin-like fold. Sco proteins have been implicated mainly as copper transporters involved in the assembly of the CuA cofactor in cytochrome c oxidase. Some mutations have been identified in humans that lead to defective cytochrome c oxidase formation and thus to fatal illnesses. However, it appears that the physiological function of Sco proteins goes beyond assembly of the CuA cofactor. Extensive analysis of completely sequenced prokaryotic genomes reveals that 18% of them contain either Sco proteins but not CuA-containing proteins or vice versa. In addition, in several cases, multiple Sco-encoding genes occur even if only a single potential Sco target is encoded in the genome. Genomic context analysis indeed points to a more general role for Sco proteins in copper transport, also to copper enzymes lacking a CuA cofactor. To obtain further insight into the possible role of Sco in the assembly of other cofactors, a search for Cox11 proteins, which are important for CuB biosynthesis, was also performed. A general framework for the action of Sco proteins is proposed, based on the hypothesis that they can couple metal transport and thiol/disulfide-based oxidoreductase activity, as well as select between either of these two cellular functions. This model reconciles the variety of experimental observations made on these proteins over the years, and can constitute a basis for further studies.     

Effects of age, gender and time on receptor expression and anti-Aspergillus functions of human phagocytes

Phagocytes play a central role in immune defense. Their dysfunction predisposes to infections. This study determined the expression level of nine receptors involved in Aspergillus immune response as well as the values of phagocytosis and production of radical oxygen species after Aspergillus stimulation, in a healthy adult population.The expression values of the CD11b, CD11c, CD14, CD18, CD35, CD181, CD182, CD282 and CD284 receptors on peripheral human monocytes and granulocytes was established. A heterogenous expression of the CD282 on granulocytes was observed as CD181, CD182 and CD284 on monocytes. Similarly, we observed considerable variation in the expression of these receptors over time. Only CD282 on granulocytes varied with sex. No variation with age was observed. Adherence of Aspergillus conidia to phagocytes was dependent of individual, sex, age and time. A better characterization of these innate immunity parameters is necessary to develop in the future an immunologic surveillance strategy for transplant recipients.     

Copper exposure effects on yeast mitochondrial proteome

Mitochondria play an important role on the entire cellular copper homeostatic mechanisms. Alteration of cellular copper levels may thus influence mitochondrial proteome and its investigation represents an important contribution to the general understanding of copper-related cellular effects. In these study we have performed an organelle targeted proteomic investigation focusing our attention on the effect of non-lethal 1mM copper concentration on Saccharomyces cerevisiae mitochondrial proteome. Functional copper effects on yeast mitochondrial proteome were evaluated by using both 2D electrophoresis (2-DE) and liquid chromatography coupled with tandem mass spectrometry. Proteomic data have been then analyzed by different unsupervised meta-analysis approaches that highlight the impairment of mitochondrial functions and the activation of oxidative stress response. Interestingly, our data have shown that stress response generated by 1mM copper treatment determines the activation of S. cerevisiae survival pathway. To investigate these findings we have treated yeast cells responsiveness to copper with hydrogen peroxide and observed a protective role of this metal. These results are suggestive of a copper role in the protection from oxidative stress possibly due to the activation of mechanisms involved in cellular survival and growth.     

A hint to search for metalloproteins in gene banks

MOTIVATION: With the advent of genome sequencing, a huge database of protein primary sequences has been accumulating. In parallel, a number of tools to investigate and expand upon this information, e.g. reconstructing and building relationships between protein families and superfamilies, have been developed. Metalloproteins are proteins capable of binding one or more metal ions, which are required for their biological function or for regulation of their activities or for structural purposes. Sometimes, metal binding can be observed in vitro but not be physiologically relevant. At present, there is a lack of specific tools to address the matter of the identification of metalloproteins in databases of gene sequences. RESULTS: In the present work, an approach exploiting metal-binding patterns (MBPs) of metalloproteins present in the Protein Data Bank to search gene banks for new metalloproteins is presented and applied to copper proteins. Nearly 100 different MBPs have been identified and then used for subsequent applications. The ensemble of sequences of the whole PDB is used to assess the potentiality and limits of the method and to identify levels of confidence for the predictions output by the search. It appears that copper-binding capabilities are identified with a confidence >90% when the percentage of identical amino acids aligned around the MBP by PHI-BLAST is at least 20% with respect to the entire protein domain length. If this percentage is between 10% and 20%, the level of confidence is approximately 50%. Application of the methodology to the entire genome sequences of Pyrococcus furiosus, Escherichia coli, Drosophila melanogaster and Homo sapiens suggests some differentiation between prokaryotes and eukaryotes. SUPPLEMENTARY INFORMATION: A table reporting statistics on the MBP identified; a list of all hits retrieved for the four organisms considered; a figure showing the number of hits for the four organisms as a function of I(d)(Global).     

Solution structure of a monoheme ferrocytochrome c from Shewanella putrefaciens and structural analysis of sequence-similar proteins: functional implications

Within the frame of the characterization of the structure and function of cytochromes c, an 81-amino acid cytochrome c was identified in the genome of Shewanella putrefaciens. Because of the scarce information about bacterial cytochromes of this type and the large variability in sequences and possibly function, we decided to proceed to its structural characterization. This protein was expressed in Escherichia coli and purified. The oxidized species is largely high spin, with a detached methionine, whereas the reduced species has the classical His/Met axial ligation to iron. The NMR solution structure of the reduced form was determined on a (15)N-labeled sample, for which 99% of all non-proline backbone (1)H and (15)N resonances have been assigned. One thousand three hundred two meaningful NOEs, out of 1775 NOEs, together with 66 dihedral angles provide a structure with rmsd values from the mean of 0.50 and 0.96 A for backbone and all heavy atoms, respectively. A search of gene banks allowed us to locate 10 different cytochromes c, the sequences of which are more than 30% identical to that of the S. putrefacienscytochrome. For two of them, the structures are known. The structures of the others have been modeled by using the available templates and internally validated. Structural similarities in terms of surface properties account for their biophysical features and provide hints about the function.     

Stable analogues of geranylgeranyl diphosphate possessing improved geranylgeranyl versus farnesyl protein transferase inhibitory selectivity

Phosphonoacetamido(oxy) groups have proven to be good mimics of the diphosphate portion in geranylgeranyl protein transferase I (GGTase I) inhibitors. The introduction of small alkyl groups (Me, Et) into the diphosphate mimic moiety caused a further decrease in collateral farnesyl protein transferase (FTase) inhibitory activity, thereby improving GGTase I over FTase selectivity.     

Backbone dynamics of human Cu,Zn superoxide dismutase and of its monomeric F50E/G51E/E133Q mutant: the influence of dimerization on mobility and function

The backbone assignment of reduced human dimeric Cu,Zn superoxide dismutase (SOD) was performed on a sample 100% enriched in (15)N, (13)C and 70% enriched in (2)H. (15)N T(1), T(2), and T(1)(rho) and (15)N-(1)H NOE assignment was performed at 600 MHz proton frequency on both wild-type SOD and the monomeric F50E/G51E/E133Q mutant. This allowed a comparison of the mobility in the subnanosecond and in the millisecond to microsecond time scales of the two systems. Both proteins are rather rigid, although some breathing of the beta sheets is detected in the wild type dimer. The monomer displays large mobility in the loops in the first part of the sequence, in loop IVa where point mutations have been introduced and at the C-terminus. The dimeric wild type is rigidified at loop IVa and at the C-terminus. Only loop VII shows a higher mobility in the dimer (besides some individual NH moieties). Conformational equilibria are displayed in the monomeric form around cysteines 57 and 146, thus explaining the disorder of arginine 143 which is the most important residue in guiding O(2)(-) toward the copper ion. The larger mobility in the wild type form with respect to the monomer in the picosecond to nanosecond time scale of helix alpha1 and loop VIIb, which provides the correct electrostatic driving force for O(2)(-) in the active channel, has been discussed in terms of favoring the activity of SOD.