Mapping intersubunit interactions of the regulatory subunit (RIalpha) in the type I holoenzyme of protein kinase A by amide hydrogen/deuterium exchange mass spectrometry (DXMS)

Protein kinase A (PKA), a central locus for cAMP signaling in the cell, is composed of regulatory (R) and catalytic (C) subunits. The C-subunits are maintained in an inactive state by binding to the R-subunit dimer in a tetrameric holoenzyme complex (R(2)C(2)). PKA is activated by cAMP binding to the R-subunits which induces a conformational change leading to release of the active C-subunit. Enzymatic activity of the C-subunit is thus regulated by cAMP via the R-subunit, which toggles between cAMP and C-subunit bound states. The R-subunit is composed of a dimerization/docking (D/D) domain connected to two cAMP-binding domains (cAMP:A and cAMP:B). While crystal structures of the free C-subunit and cAMP-bound states of a deletion mutant of the R-subunit are known, there is no structure of the holoenzyme complex or of the cAMP-free state of the R-subunit. An important step in understanding the cAMP-dependent activation of PKA is to map the R-C interface and characterize the mutually exclusive interactions of the R-subunit with cAMP and C-subunit. Amide hydrogen/deuterium exchange mass spectrometry is a suitable method that has provided insights into the different states of the R-subunit in solution, thereby allowing mapping of the effects of cAMP and C-subunit on different regions of the R-subunit. Our study has localized interactions with the C-subunit to a small contiguous surface on the cAMP:A domain and the linker region. In addition, C-subunit binding causes increased amide hydrogen exchange within both cAMP-domains, suggesting that these regions become more flexible in the holoenzyme and are primed to bind cAMP. Furthermore, the difference in the protection patterns between RIalpha and the previously studied RIIbeta upon cAMP-binding suggests isoform-specific differences in cAMP-dependent regulation of PKA activity.     

Structural analysis of the stalk subunit Vma5p of the yeast V-ATPase in solution

Vma5p (subunit C) of the yeast V-ATPase was produced in Escherichia coli and purified to homogeneity. Analysis of secondary structure by circular dichroism spectroscopy showed that Vma5p comprises 64% -helix and 17% β-sheet content. The molecular mass of this subunit, determined by gel filtration analysis and small angle X-ray scattering (SAXS), was approximately 51 ± 4 kDa, indicating a high hydration level of the protein in solution. The radius of gyration and the maximum size of Vma5p were determined to be 3.74 ± 0.03 and 12.5 ± 0.1 nm, respectively. Using two independent ab initio approaches, the first low-resolution shape of the protein was determined. Vma5p is an elongated boot-shaped particle consisting of two distinct domains. Co-reconstitution of Vma5p to V₁ without C from Manduca sexta resulted in a V₁–Vma5p hybrid complex and a 20% increase in ATPase hydrolysis activity.     

Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides

Hexitol nucleic acids (HNAs) are nuclease resistant and provide strong hybridization to RNA. However, there is relatively little information on the biological properties of HNA antisense oligonucleotides. In this study, we compared the antisense effects of a chimeric HNA ‘gapmer’ oligonucleotide comprising a phosphorothioate central sequence flanked by 5′ and 3′ HNA sequences to conventional phosphorothioate oligonucleotides and to a 2′-O-methoxyethyl (2′-O-ME) phosphorothioate ‘gapmer’. The antisense oligomers each targeted a sequence bracketing the start codon of the message of MDR1, a gene involved in multi-drug resistance in cancer cells. Antisense and control oligonucleotides were delivered to MDR1-expressing cells using transfection with the cationic lipid Lipofectamine 2000. The anti-MDR1 HNA gapmer was substantially more potent than a phosphorothioate oligonucleotide of the same sequence in reducing expression of P-glycoprotein, the MDR1 gene product. HNA and 2′-O-ME gapmers displayed similar potency, but a pure HNA antisense oligonucleotide (lacking the phosphorothioate ‘gap’) was ineffective, indicating that RNase H activity was likely required. Treatment with anti-MDR1 HNA gapmer resulted in increased cellular accumulation of the drug surrogate Rhodamine 123 that correlated well with the reduced cell surface expression of P-glycoprotein. Thus, HNA gapmers may provide a valuable additional tool for antisense-based investigations and therapeutic approaches.     

Enzymic Degradation of Starch Granules in the Cotyledons of Germinating Peas

Starch, total alpha- and beta-amylase, and phosphorylase levels and the zymogram patterns of these 3 starch-degrading enzymes were determined in the cotyledons of smooth pea (Pisum sativum L.) during the first 15 days of germination. Starch is degraded slowly in the first 6 days; during this time, alpha-amylase is very low, beta-amylase is present at a constant level while phosphorylase gradually increases and reaches a peak on the fifth day. Beginning on the sixth day there is a more rapid degradation of starch which coincides with alpha-amylase production. One phosphorylase band and 2 beta-amylase bands are present in the zymogram of the imbibed cotyledon. An additional phosphorylase band and 1 alpha-amylase band appear during germination. Seeds imbibed in benzyladenine, chloramphenicol, and in cycloheximide show retarded growth and slower starch degradation and enzyme production than the controls. We conclude that alpha-amylase is the major enzyme involved in the initial degradation of starch into more soluble forms while phosphorylase and beta-amylase assist in the further conversion to free sugars.     

In vitro, ex vivo and in vivo models: A comparative analysis of Paracoccidioides spp. proteomic studies

Members of the Paracoccidioides complex are human pathogens that infect different anatomic sites in the host. The ability of Paracoccidioides spp. to infect host niches is putatively supported by a wide range of virulence factors, as well as fitness attributes that may comprise the transition from mycelia/conidia to yeast cells, response to deprivation of micronutrients in the host, expression of adhesins on the cell surface, response to oxidative and nitrosative stresses, as well as the secretion of hydrolytic enzymes in the host tissue. Our understanding of how those molecules can contribute to the infection establishment has been increasing significantly, through the utilization of several models, including in vitro, ex vivo and in vivo infection in animal models. In this review we present an update of our understanding on the strategies used by the pathogen to establish infection. Our results were obtained through a comparative proteomic analysis of Paracoccidioides spp. in models of infection.     

Comparison of the specificity, stability and individual rate constants with respective activation parameters for the peptidase activity of cruzipain and its recombinant form, cruzain, from Trypanosoma cruzi.

The Trypanosoma cruzi cysteine protease cruzipain contains a 130-amino-acid C-terminal extension, in addition to the catalytic domain. Natural cruzipain is a complex of isoforms, because of the simultaneous expression of several genes, and the presence of either high mannose-type, hybrid monoantennary-type or complex biantenary-type oligosacharide chains at Asn255 of the C-terminal extension. Cruzipain and its recombinant form without this extension (cruzain) were studied comparatively in this work. S2 to S2' subsite specificities of these enzymes were examined using four series of substrates derived from the internally quenched fluorescent peptide Abz-KLRFSKQ-EDDnp (Abz, ortho-aminobenzoic acid; EDDnp, N-(2,4-dinitrophenyl)-ethylenediamine). Large differences in the kinetic parameters were not observed between the enzymes; however, Km values were consistently lower for the hydrolysis of most of the substrates by cruzain. No difference in the pH-activity profile between the two enzymes was found, but in 1 m NaCl cruzipain presented a kcat value significantly higher than that of cruzain. The activation energy of denaturation for the enzymes did not differ significantly; however, a negative entropy value was observed for cruzipain denaturation whereas the value for cruzain was positive. We determined the individual rate constants (k1, substrate diffusion; k-1, substrate dissociation; k2, acylation; k3, deacylation) and the respective activation energies and entropies for hydrolysis of Abz-KLRFSKQ-EDDnp determining the temperature dependence of the Michaelis-Menten parameters kcat/Km and kcat as previously described [Ayala, Y.M. & Di Cera, E. (2000) Protein Sci. 9, 1589-1593]. Differences between the two enzymes were clearly detected in the activation energies E1 and E-1, which are significantly higher for cruzipain. The corresponding DeltaS1 and DeltaS-1 were positive and significantly higher for cruzipain than for cruzain. These results indicate the presence of a larger energy barrier for cruzipain relating to substrate diffusion and dissociation, which could be related to the C-terminal extension and/or glycosylation state of cruzipain.     

Ortho-aminobenzoic acid as a fluorescent probe for the interaction between peptides and micelles

Ortho-aminobenzoic acid (o-Abz) has been used as a fluorescent probe in internally quenched fluorescent peptides for continuous protease assays. We investigated the fluorescent properties of the probe in order to verify if it can be used to monitor the interaction of peptides with micelles. Abz-aminoacyl-monomethyl amides (Abz-Xaa-NHCH(3), where Xaa=Arg, Phe, Leu and Glu) were synthesized. Quantum yield, spectral position, anisotropy and lifetime decay were analyzed in the presence and absence of sodium dodecyl sulfate (SDS) micelles. Significant changes in the fluorescence parameters were observed for Abz-Arg-NHCH(3) in comparison to Abz-Glu-NHCH(3), indicating a strong electrostatic component in the compound's interaction with the negative charged micelles. The change in fluorescence parameters, observed when the probe is bound to hydrophobic amino acids Abz-Phe-NHCH(3) and Abz-Leu-NHCH(3), is probably due to insertion of those compounds into micelles. Abz-NHCH(3) fluorescence is less affected by the presence of micelles, indicating that the occurrence of interaction is dependent on the properties of the amino acid to which the fluorophore is attached. The quenching data with acrylamide confirmed these results. Titration curves allowed the estimation of association constants between Abz compounds and SDS, according to a single partition model. Although the results cannot be strictly applied to the titration with charged compounds, it was verified that the association constant for the isolated Abz-NHCH(3) is significantly lower than those for Abz-Phe-NHCH(3) and Abz-Leu-NHCH(3). It is concluded that the Abz group is a sensitive and convenient fluorescent probe to monitor peptide binding to amphiphilic aggregates. That conclusion is supported by measurements with the peptide Abz-Leu-Arg-Phe-NH(2).     

N-acetylcysteine effects on a murine model of chronic critical limb ischemia

During chronic limb ischemia, oxidative damage and inflammation are described. Besides oxidative damage, the decrease of tissue oxygen levels is followed by several adaptive responses. The purpose of this study was to determine whether supplementation with N-acetylcysteine (NAC) is effective in an animal model of chronic limb ischemia. Chronic limb ischemia was induced and animals were treated once a day for 30 consecutive days with NAC (30 mg/kg). After this time clinical scores were recorded and soleus muscle was isolated and lactate levels, oxidative damage and inflammatory parameters were determined. In addition, several mechanisms associated with hypoxia adaptation were measured (vascular endothelial growth factor - VEGF and hypoxia inducible factor - HIF levels, ex vivo oxygen consumption, markers of autophagy/mitophagy, and mitochondrial biogenesis). The adaptation to chronic ischemia in this model included an increase in muscle VEGF and HIF levels, and NAC was able to decrease VEGF, but not HIF levels. In addition, ex vivo oxygen consumption under hypoxia was increased in muscle from ischemic animals, and NAC was able to decrease this parameter. This effect was not mediated by a direct effect of NAC on oxygen consumption. Ischemia was followed by a significant increase in muscle myeloperoxidase activity, as well as interleukin-6 and thiobarbituric acid reactive substances species levels. Supplementation with NAC was able to attenuate inflammatory and oxidative damage parameters, and improve clinical scores. In conclusion, NAC treatment decreases oxidative damage and inflammation, and modulates oxygen consumption under hypoxic conditions in a model of chronic limb ischemia.     

An immunofluorescent study of the microtubule organization in Trichomonas vaginalis using antitubulin antibodies

The flagellated protozoon Trichomonas vaginalis, parasite of the human urogenital tract, possesses a well developed microtubule system organized in highly differentiated structures. We have shown by immunoblotting that monospecific anti-sheep brain tubulin antibodies are able to react with the microtubular tubulin of T. vaginalis. These antibodies were used to study the microtubular system of T. vaginalis both in interphase and mitosis by indirect immunofluorescence. The interphase microtubular pattern, characterized by an axostyle, a pelta, four anterior flagella, and a recurrent flagellum, displayed remarkable changes at the onset of mitosis: the axostyle disappeared, and two pole bodies connected by a short spindle became evident; chromosomal fibers arose while pole-to-pole fibers elongated. The last phases of mitosis were marked by the disappearance of chromosomal fibers, the appearance of two small axostyles, and the depolymerization of the pole-to-pole bundle. At the end of mitosis, the normal interphase microtubule pattern was observed.     

Interactions of liposomes with serum proteins

The interactions of serum proteins are diverse, complex and can lead to dramatic effects on liposome stability and in vivo behavior; conversely lipids can modify the biological activities of serum proteins. Serum lipoproteins can potentially destabilize bilayer membranes leading to vesicle disruption and loss of contents; irregularities in the lipid bilayer, such as those which exist at phase boundaries, promote the destabilizing effects of lipoproteins. Other serum components such as fibronectin, immunoglobulins and C reactive protein can modify the biological properties of liposomes by promoting interactions with reticuloendothelial cells and/or activation of the complement system. Liposomes can avidly bind certain serum clotting factors, a process which can lead to dramatic effects on the clotting cascade. Thus the interactions of liposomes with serum proteins can reciprocally effect both components involved.