Probing protonation/deprotonation of tyrosine residues in cytochrome ba3 oxidase from Thermus thermophilus by time-resolved step-scan Fourier transform infrared spectroscopy

Elucidating the properties of the heme Fe-Cu(B) binuclear center and the dynamics of the protein response in cytochrome c oxidase is crucial to understanding not only the dioxygen activation and bond cleavage by the enzyme but also the events related to the release of the produced water molecules. The time-resolved step-scan FTIR difference spectra show the ν(7a)(CO) of the protonated form of Tyr residues at 1247 cm(-1) and that of the deprotonated form at 1301 cm(-1). By monitoring the intensity changes of the 1247 and 1301 cm(-1) modes as a function of pH, we measured a pK(a) of 7.8 for the observed tyrosine. The FTIR spectral changes associated with the tyrosine do not belong to Tyr-237 but are attributed to the highly conserved in heme-copper oxidases Tyr-136 and/or Tyr-133 residue (Koutsoupakis, K., Stavrakis, S., Pinakoulaki, E., Soulimane, T., and Varotsis, C. (2002) J. Biol. Chem. 277, 32860-32866). The oxygenation of CO by the mixed-valence form of the enzyme revealed the formation of the ～607 nm P (Fe(IV)=O) species in the pH 6-9 range and the return to the oxidized form without the formation of the 580 nm F form. The data indicate that Tyr-237 is not involved in the proton transfer pathway in the oxygenation of CO by the mixed-valence form of the enzyme. The implication of these results with respect to the role of Tyr-136 and Tyr-133 in proton transfer/gating along with heme a(3) ring D propionate-H(2)O-ring A propionate-Asp-372 site to the exit/output proton channel (H(2)O pool) is discussed.     

A peptide corresponding to the C-terminal region of pleiotrophin inhibits angiogenesis in vivo and in vitro

Pleiotrophin (PTN) is a heparin-binding growth factor that plays a significant role in tumor growth and angiogenesis. We have previously shown that in order for PTN to induce migration of endothelial cells, binding to both α(ν) β(3) integrin and its receptor protein tyrosine phosphatase beta/zeta (RPTPβ/ζ) is required. In the present study we show that a synthetic peptide corresponding to the last 25 amino acids of the C-terminal region of PTN (PTN(112-136) ) inhibited angiogenesis in the in vivo chicken embryo chorioallantoic membrane (CAM) assay and PTN-induced migration and tube formation of human endothelial cells in vitro. PTN(112-136) inhibited binding of PTN to α(ν) β(3) integrin, and as shown by surface plasmon resonance (SPR) measurements, specifically interacted with the specificity loop of the extracellular domain of β(3) . Moreover, it abolished PTN-induced FAK Y397 phosphorylation, similarly to the effect of a neutralizing α(ν) β(3) -selective antibody. PTN(112-136) did not affect binding of PTN to RPTPβ/ζ in endothelial cells and induced β(3) Y773 phosphorylation and ERK1/2 activation to a similar extent with PTN. This effect was inhibited by down-regulation of RPTPβ/ζ by siRNA or by c-src inhibition, suggesting that PTN(112-136) may interact with RPTPβ/ζ. NMR spectroscopy studies showed that PTN(112-136) was characterized by conformational flexibility and absence of any element of secondary structure at room temperature, although the biologically active peptide segment 123-132 may adopt a defined structure at lower temperature. Collectively, our data suggest that although PTN(112-136) induces some of the signaling pathways triggered by PTN, it inhibits PTN-induced angiogenic activities through inhibition of PTN binding to α(ν) β(3) integrin.     

High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway

Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6^T, together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis.     

Tr-Noe and MD studies of Leishmania gp63 SRYD-containing sequences bound to anti-SRYD monoclonal antibody

The I²⁵⁰ASRYDQL²⁵⁷ synthetic octapeptideof the Leishmania major surface glycoproteingp63, which efficiently inhibits parasite attachmentto the macrophage receptors and mimics antigenicallyand functionally the RGDS sequence of fibronectin, wasstudied by 2D TR-NOESY in the presence of an anti-SRYDmonoclonal antibody (mAbSRYD) that recognizes bothSRYD-containing peptides and the cognate protein onintact parasites. Molecular modeling was performedusing distance constraints obtained from TR-NOEs. Thebound structure was compared with that of the freepeptide in DMSO solution and with the crystalstructure of the RYD fragment of the OPG2 Fab, anantireceptor antibody that mimics an RGD cell adhesion site.     

The PPGMRPP repetitive epitope of the Sm autoantigen: Antigenic specificity induced by conformational changes. Application of the Sequential Oligopeptide Carriers (SOCs)

The PPGMRPP sequence, found in several copies in the Sm and U1RNPautoantigens, is the main target of anti-Sm and anti-U1RNP antibodies insystemic lupus erythematosus (SLE) and mixed connective tissue disease(MCTD) patient's sera. It is also recognized, to a lower extent, byanti-Ro/SSA and anti-La/SSB specificities. The PPGMRPP-NH₂peptide amide and the PPGMRPP peptide, which is bound to a pentamericsequential oligopeptide carrier (SOC₅), were examined by¹H-NMR spectroscopy and ELISA assays, using sera from patientswith autoimmune rheumatic diseases. Among the three main conformers foundfor the free PPGMRPP, the extended one was also identified for PPGMRPP-NH₂ and (PPGMRPP)₅-SOC₅.This can be attributed to the absence of ionic interactions between theArg-guanidinium and the carboxylate group in the amide andSOC₅-bound forms of the peptide. Immunoassays using sera fromvarious specificities showed an enhanced anti-Sm and anti-U1RNP recognitionof PPGMRPP-NH₂ and(PPGMRPP)₅-SOC₅, and lowering of the anti-Ro/SSAand anti-La/SSB reactivity. The presence of multiple conformers of freePPGMRPP may explain the unexpected cross-reactivity to the anti-Ro/Lapositive sera, while the prevalence of the extended conformation inPPGMRPP-NH₂ and (PPGMRPP)₅-SOC₅is mainly responsible for the enhanced recognition from the anti-Sm andanti-U1RNP autoantibodies. It is concluded that the antigenic specificity ofPPGMRPP-NH₂ and (PPGMRPP)₅-SOC₅ ismainly induced by conformational changes resulting from the conversion ofthe C-terminal carboxylate group to the amide form.     

PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments

We present PhyloMeasures, a new software package including both a C++ and R version, that provides very fast computation of popular phylogenetic diversity measures. PhyloMeasures introduces two major advances over existing methods. First, it uses efficient algorithms for calculating basic phylogenetic metrics (such as Faith's PD and the mean pairwise distance, MPD) and two‐sample measures (such as common branch length, CBL, and the unique fraction) that are designed to perform well even on very large trees. Second, it computes exact richness‐standardised versions of these measures (such as the widely used net relatedness index, NRI) by efficiently evaluating analytical expressions for the mean and variance of the basic measures, rather than by the slow and inexact randomization techniques that are the current standard. Together, these lead to massive improvements in performance compared to the current state of the art. For example, running on a standard laptop, PhyloMeasures functions can provide the NRI for 20 samples from a tree of 100 000 tips in about 1.5 s, compared to an estimated 37 d using standard resampling approaches. This will allow analyses on larger data sets than were previously possible.