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1.
Chem Phys Lipids ; 203: 87-93, 2017 03.
Article in English | MEDLINE | ID: mdl-28048967

ABSTRACT

The osmotic condition modulates the properties of liposomes, particularly those related to their stability and response to external agents such as membrane-active proteins or peptides. In a previous work, we have demonstrated that an osmotic shock can increase, per se, water influx/efflux and the exit of the fluorophore calcein entrapped in the aqueous pool of dipalmitoylphosphatidylcholine (DPPC) and DPPC:sphingomyelin (SM) large unilamellar vesicles (LUVs), suggesting a loss of integrity of the liposome bilayer. In the present work, we have extended our study in order to assess how an osmotic imbalance prior to or synchronous with the addition of a recombinant variant of the pore-forming toxin sticholysin I (rSt I) modifies its pore forming capacity in DPPC and DPPC:SM (1:1) LUVs. Our results conclusively show the capacity of hypotonic gradients to improve the pore forming capacity of rSt I molecules, even in pure DPPC liposomes, rendering pore-formation less dependent on the presence of sphyngomyelin. In fact, non-active toxins in DPPC liposomes become active by a hypotonic imbalance in a similar way to those containing SM as a second component.


Subject(s)
1,2-Dipalmitoylphosphatidylcholine/chemistry , Osmotic Pressure , Pore Forming Cytotoxic Proteins/chemistry , Organic Chemicals/chemistry
2.
Protein J ; 33(5): 493-501, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25218252

ABSTRACT

Sea anemones synthesize a variety of toxic peptides and proteins of biological interest. The Caribbean Sea anemone Stichodactyla helianthus, produces two pore-forming toxins, Sticholysin I (St I) and Stichloysin II (St II), with the ability to form oligomeric pores in cell and lipid bilayers characteristically lacking cysteine in their amino acid sequences. Recently, two mutants of a recombinant variant of Sticholysin I (rSt I) have been obtained with a Cys residue in functionally relevant regions for the pore-forming activity of the toxin: r St I F15C (in the amino terminal sequence) and r St I R52C (in the binding site). Aiming at characterizing the effects of oxidants in toxins devoid (r St I) or containing -SH moieties (r St I F15C and r St I R52C), we measured their hemolytic activity and pore forming capacity prior and after their incubation with peroxynitrite (ONOO(-)). At low ONOO(-)/Toxin ratios, nearly 0.8 Trp groups are modified by each added peroxynitrite molecule, and the toxin activity is reduced in ca. 20 %. On the other hand, in -SH bearing mutants only 0.5 Trp groups are modified by each peroxynitrite molecule and the toxin activity is only reduced in 10 %. The results indicated that Cys is the initial target of the oxidative damage and that Trp residues in Cys-containing toxins were less damaged than those in r St I. This relative protection of Trp groups correlates with a smaller loss of hemolytic activity and permeabilization ability in liposomes and emphasizes the relevance of Trp groups in the pore forming capacity of the toxins.


Subject(s)
Peroxynitrous Acid/chemistry , Adult , Cysteine/chemistry , Erythrocytes/drug effects , Hemolysis/drug effects , Humans , Liposomes , Organic Chemicals/chemistry , Organic Chemicals/pharmacology , Oxidation-Reduction/drug effects , Permeability , Spectrometry, Fluorescence , Sulfhydryl Compounds , Young Adult
3.
Toxicon ; 58(1): 8-17, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21510967

ABSTRACT

Experimental evidence shows that the mechanism of pore formation by actinoporins is a multistep process, involving binding of the water-soluble monomer to the membrane and subsequent oligomerization on the membrane surface, leading to the formation of a functional pore. However, as for other eukaryotic pore-forming toxins, the molecular details of the mechanism of membrane insertion and oligomerization are not clear. In order to obtain further insight with regard to the structure-function relationship in sticholysins, we designed and produced three cysteine mutants of recombinant sticholysin I (rStI) in relevant functional regions for membrane interaction: StI E2C and StI F15C (in the N-terminal region) and StI R52C (in the membrane binding site). The conformational characterization derived from fluorescence and CD spectroscopic studies of StI E2C, StI F15C and StI R52C suggests that replacement of these residues by Cys in rStI did not noticeably change the conformation of the protein. The substitution by Cys of Arg5² in the phosphocholine-binding site, provoked noticeable changes in rStI permeabilizing activity; however, the substitutions in the N-terminal region (Glu², Phe¹5) did not modify the toxin's permeabilizing ability. The presence of a dimerized population stabilized by a disulfide bond in the StI E2C mutant showed higher pore-forming activity than when the protein is in the monomeric state, suggesting that sticholysins pre-ensembled at the N-terminal region could facilitate pore formation.


Subject(s)
Pore Forming Cytotoxic Proteins/chemistry , Animals , Arginine/chemistry , Arginine/genetics , Binding Sites , Cell Membrane/chemistry , Cell Membrane/metabolism , Cloning, Molecular , Cysteine/chemistry , Cysteine/genetics , Mutagenesis, Site-Directed , Mutation , Organic Chemicals/chemistry , Organic Chemicals/toxicity , Pore Forming Cytotoxic Proteins/genetics , Pore Forming Cytotoxic Proteins/toxicity , Protein Structure, Tertiary , Sea Anemones/metabolism , Structure-Activity Relationship
4.
Case Rep Med ; 2009: 745713, 2009.
Article in English | MEDLINE | ID: mdl-19901997

ABSTRACT

We report the occurrence of a bilateral pneumothoraces after unilateral central venous catheterization of the right subclavian vein in a 70-year-old patient. The patient had no history of pulmonary or pleural disease and no history of cardiothoracic surgery. Two days earlier, she had a median laparotomy under general and epidural anaesthesia. Prior to the procedure, the patient was hemodynamically stable and her transcutaneous oxygen saturation was 97% in room air. We punctured the right pleural space before cannulation of the right subclavian vein. After the procedure, the patient slowly became hemodynamically instable with respiratory distress. A chest radiograph revealed a complete left-side pneumothorax and a mild right-side pneumothorax. The right-side pneumothorax became under tension after left chest tube insertion. The symptoms finally resolved after insertion of a right chest tube. After a diagnostic work-up, we suspect a congenital "Buffalo chests" explaining bilateral pneumothoraces and a secondary tension pneumothorax.

5.
J Biosci ; 34(6): 891-8, 2009 Dec.
Article in English | MEDLINE | ID: mdl-20093742

ABSTRACT

Sticholysins I and II (St I/II) are cytolysins purified from the sea anemone Stichodactyla helianthus. In this study, we show their pharmacological action on guinea-pig and snail models in native and pH-denatured conditions in order to correlate the pharmacological findings with the pore-forming activity of both isoforms. In guinea-pig erythrocytes (N=3), St II possessed higher haemolytic activity in comparison with St I and this activity was lost at an alkaline pH. In molluscan central neurons (N=30), they irreversibly decreased the amplitude of the cholinergic response; St I (EC (50) 0.6 micromolL (-1)) was more potent than St II (EC50 > 6.6 micromolL (-1)) and they both increased the duration of the action potential; these effects were absent at an alkaline pH. In guinea-pig isolated atrium (N=25), both increased the amplitude of the contraction force, but St II was more potent than St I (EC (50) 0.03 micromolL (-1) and 0.3 micromolL (-1), respectively) and this effect persisted at an alkaline pH. In summary, both cytolysins have neuroactive and cardioactive properties. The main mechanism in molluscan neurons seems to be associated with the cytolytic activity of these molecules, whereas inguinea-pig atrium, the existence of an additional pharmacological mechanism might be contributing to the observed effect.


Subject(s)
Cnidarian Venoms/pharmacology , Cytotoxins/pharmacology , Pore Forming Cytotoxic Proteins/pharmacology , Sea Anemones/chemistry , Action Potentials/drug effects , Animals , Cnidarian Venoms/isolation & purification , Cytotoxins/isolation & purification , Erythrocytes/drug effects , Guinea Pigs , Heart Atria/drug effects , Hemolysis/drug effects , Neurons/cytology , Neurons/drug effects , Neurons/physiology , Organic Chemicals/isolation & purification , Organic Chemicals/pharmacology , Pore Forming Cytotoxic Proteins/isolation & purification , Snails
6.
J Biosci ; 34(6)Dec. 2009.
Article in Spanish | CUMED | ID: cum-43861

ABSTRACT

Sticholysins I and II (St I/II) are cytolysins purified from the sea anemone Stichodactyla helianthus. In this study, we show their pharmacological action on guinea-pig and snail models in native and pH-denatured conditions in order to correlate the pharmacological findings with the pore-forming activity of both isoforms. In guinea-pig erythrocytes (N=3), St II possessed higher haemolytic activity in comparison with St I and this activity was lost at an alkaline pH. In molluscan central neurons (N=30), they irreversibly decreased the amplitude of the cholinergic response; St I (EC (50) 0,6 micromolL (-1)) was more potent than St II (EC50 > 6,6 micromolL (-1)) and they both increased the duration of the action potential; these effects were absent at an alkaline pH. In guinea-pig isolated atrium (N=25), both increased the amplitude of the contraction force, but St II was more potent than St I (EC (50) 0,03 micromolL (-1) and 0,3 micromolL (-1), respectively) and this effect persisted at an alkaline pH. In summary, both cytolysins have neuroactive and cardioactive properties. The main mechanism in molluscan neurons seems to be associated with the cytolytic activity of these molecules, whereas inguinea-pig atrium, the existence of an additional pharmacological mechanism might be contributing to the observed effect(AU)


Subject(s)
Humans , Cytotoxins/isolation & purification , Cytotoxins/pharmacology , Sea Anemones/chemistry
7.
Lett Appl Microbiol ; 46(5): 548-54, 2008 May.
Article in English | MEDLINE | ID: mdl-18363654

ABSTRACT

AIMS: In this work, fatty acid content and profiles were analysed in order to differentiate the species Tenacibaculum maritimum, Tenacibaculum gallaicum, Tenacibaculum discolor and Tenacibaculum ovolyticum that are pathogenic for cultured marine fish and to assess the potential of fatty acid profiles as a tool for epizootiological typing. METHODS AND RESULTS: The fatty acid methylesters (FAMEs) were extracted from cells grown on marine agar for 48 h at 25 degrees C and were prepared and analysed according to the standard protocol of the MIDI/Hewlett Packard Microbial Identification System. The cellular fatty acid profiles of Tenacibaculum strains tested were characterized by the presence of large amounts of branched (36.1-40.2%) and hydroxylated (29.6-31.7%) fatty acids. The FAME products from the four species significantly (P < 0.05) differed in the content of iso-C(15:0)3-OH, iso-C(16:0)3-OH, iso-C(15:1)G, summed feature 3 (a component that contains C(16:1)omega7c and/or iso-C(15:0) 2-OH), iso-C(16:0), C(17:1)omega6c, C(15:0)3-OH, iso-C(17:0)3-OH. CONCLUSIONS: Results of present study demonstrated the existence of differences in the fatty acids content between the T. maritimum isolates from different marine fish/geographical origin and between strains of T. maritimum, T. discolor, T. gallaicum and T. ovolyticum. SIGNIFICANCE AND IMPACT OF THE STUDY: Profiling of fatty acids may be a useful tool to distinguish T. maritimum from other Tenacibaculum species pathogenic for fish as well as for epizootiological differentiation of T. maritimum isolates.


Subject(s)
Fatty Acids/analysis , Fish Diseases/microbiology , Flavobacteriaceae Infections/veterinary , Flavobacteriaceae/chemistry , Flavobacteriaceae/classification , Animals , Bacterial Typing Techniques , Fishes , Flavobacteriaceae Infections/microbiology
8.
Toxicon ; 48(8): 1083-94, 2006 Dec 15.
Article in English | MEDLINE | ID: mdl-17067649

ABSTRACT

Sticholysins I and II (Sts I and II) are two potent cytolysins from the sea anemone Stichodactyla helianthus. These isoforms present 13 substitutions, with three non-conservative located at the N-terminus. St II is considerably more hemolytic than St I in human red blood cells, a result explained by the smaller number of negatively charged groups present at St II's N-terminus. In the present work, we have obtained a recombinant St I (rSt I), differing from the wild type in a single amino acid residue (E16Q). This pseudo-wild type is structurally similar to St I and shows a similar capacity to interact with and form pores in model membranes. This was assessed by the intrinsic fluorescence increase in the presence of liposomes, their adsorption to bilayers (measured by SPR), their concentration at the air-water interface, their interaction with lipid monolayers and their capacity to promote the release of carboxyfluorescein entrapped in liposomes. In spite of these similarities, rSt I presents a larger hemolytic activity in human red blood cells than St I, being intermediate in activity between Sts I and II. The results obtained in the present work emphasize that even the change of one single E by Q at the N-terminal segment may modify the toxin HA and show that this functional property is the most sensitive to subtle changes in the protein primary structure.


Subject(s)
Pore Forming Cytotoxic Proteins/chemistry , Sea Anemones/chemistry , Amino Acid Sequence , Animals , Base Sequence , Circular Dichroism , Erythrocytes/drug effects , Lipid Bilayers/metabolism , Liposomes/metabolism , Models, Molecular , Molecular Sequence Data , Organic Chemicals/chemistry , Organic Chemicals/isolation & purification , Organic Chemicals/metabolism , Permeability/drug effects , Pore Forming Cytotoxic Proteins/genetics , Pore Forming Cytotoxic Proteins/metabolism , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Analysis, Protein , Surface Plasmon Resonance , Surface Tension/drug effects
9.
J Fish Dis ; 28(3): 165-72, 2005 Mar.
Article in English | MEDLINE | ID: mdl-15752277

ABSTRACT

The commercial furunculosis vaccine Aquavac Furovac 5 and an autogenous vaccine, based on the challenge strain, induced immune protection in turbot, Scophthalmus maximus (L.), as shown in challenge tests 120 days post-immunization by injection (relative percentage of survival, RPS = 72-99%). This protective effect lasted for at least 6 months post-immunization at appreciable levels (RPS = 50-52%). Neither the autogenous vaccine nor the commercial vaccine was able to induce significant levels of protection against Aeromonas salmonicida in turbot when administered by immersion. Antibody levels were high or moderate in fish vaccinated by injection with the different vaccines and very low in fish vaccinated by immersion. The field results show that delivering an oral boost after the primary vaccination by injection did not enhance protection of turbot against furunculosis and that water-based (autogenous vaccine) and oil adjuvanted (Alpha Ject 1200) vaccines administered by injection conferred similar levels of protection (RPS > 80%) in turbot.


Subject(s)
Aeromonas salmonicida/immunology , Fish Diseases/microbiology , Fish Diseases/prevention & control , Flatfishes , Furunculosis/veterinary , Gram-Negative Bacterial Infections/veterinary , Vaccination/veterinary , Administration, Oral , Animals , Antibodies, Bacterial/blood , Aquaculture/methods , Bacterial Vaccines/administration & dosage , Enzyme-Linked Immunosorbent Assay , Furunculosis/prevention & control , Gram-Negative Bacterial Infections/prevention & control , Immersion , Injections , Time Factors
10.
Endocrinol. nutr. (Ed. impr.) ; 51(9): 506-511, nov. 2004.
Article in Es | IBECS | ID: ibc-35932

ABSTRACT

El síndrome del ovario poliquístico (SOP) es un trastorno muy prevalente, en mujeres jóvenes, que se presume como la causa más frecuente de infertilidad por anovulación. Un nuevo consenso en 2003 ha establecido como diagnóstico la presencia de 2 de los 3 criterios que caracterizan este síndrome: oligo/anovulación, hiperandrogenismo clínico y/o bioquímico, y ovario poliquístico. Pero este síndrome también está asociado con un aumento en el riesgo de presentar diabetes mellitus tipo 2 y, posiblemente, enfermedad cardiovascular. En un gran porcentaje de mujeres con SOP se identifican una serie de alteraciones metabólicas o síndrome metabólico en cuya base se encuentra la resistencia a insulina. Este síndrome metabólico asociado a SOP modifica profundamente nuestro enfoque clínico y terapéutico. En primer lugar, un cribado de síndrome metabólico (glucemia basal, perfil lipídico, presión arterial y obesidad abdominal) y prueba de tolerancia a la glucosa, se recomienda en todas las mujeres con SOP y obesidad, si bien la utilidad de estos estudios no está bien determinada en el normopeso. En segundo lugar, aparte del tratamiento del hirsutismo y de la alteración menstrual, los objetivos de tratamiento se deben centrar en la prevención de la diabetes mellitus tipo 2 y posiblemente la enfermedad cardiovascular. Finalmente, en el objetivo de la prevención de diabetes mellitus tipo 2, la modificación de hábitos dietéticos y ejercicio físico son el pilar del tratamiento, y actualmente los fármacos hipoglucemiantes que aumentan la sensibilidad a insulina tienen un papel adyuvante (AU)


Subject(s)
Female , Humans , Polycystic Ovary Syndrome/metabolism , Risk Factors , Cardiovascular Diseases/prevention & control , Obesity/complications , Insulin Resistance , Polycystic Ovary Syndrome/drug therapy , Diabetes Mellitus, Type 2/prevention & control
11.
J Endocrinol Invest ; 27(7): 670-5, 2004.
Article in English | MEDLINE | ID: mdl-15505992

ABSTRACT

IGF-I has been demonstrated to stimulate basal and GnRH-induced gonadotropin release. IGF-I also elicites alpha-subunit secretion in human pituitary tumor cells. The aims of this study were to evaluate both the effect of IGF-I on gonadotropin LH-beta and FSH-beta mRNA levels and glycoprotein alpha-subunit gene expression in cultured rat anterior pituitary cells. The exposure of pituitary cells to recombinant human IGF-I (rhlGF-I; 2 microg/ml) for 72 h markedly stimulated basal LH and FSH release whereas their mRNA levels remained unmodified. IGF-I elicited a-subunit release from pituitary cells (p < 0.01) and augmented its mRNA levels. Exposure to IGF-I consistently reduced GH release from pituitary cells. This study shows that the gonadotropin-releasing effects of IGF-I are not paralleled by changes in their mRNAs whereas IGF-I stimulates not only alpha-subunit release but also its mRNA levels. This study provides the first observation of alpha-subunit regulation by IGF-I in normal pituitary cells, where a differential regulation between release and synthesis for gonadotropin a-and 1-subunits is also shown.


Subject(s)
Follicle Stimulating Hormone, beta Subunit/biosynthesis , Glycoprotein Hormones, alpha Subunit/biosynthesis , Insulin-Like Growth Factor I/pharmacology , Luteinizing Hormone, beta Subunit/biosynthesis , Pituitary Gland/physiology , Animals , Cell Culture Techniques , Gene Expression Regulation/drug effects , Male , RNA, Messenger/analysis , Rats , Rats, Wistar
12.
Int Immunopharmacol ; 4(6): 731-44, 2004 Jun.
Article in English | MEDLINE | ID: mdl-15135315

ABSTRACT

Sticholysin I (StI), a potent cytolysin isolated from the sea anemone Stichodactyla helianthus, was linked to the monoclonal antibody (mAb) ior C5. StI acts by forming hydrophilic pores in the membrane of the attacked cells leading to osmotic lysis. ior C5 is a murine IgG1, which recognizes the tumor associated antigen (TAA) ior C2. The cytolysin and the mAb were coupled by using the heterobifunctional cross-linking reagent sulfosuccinimidyl 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (SMCC). Two hybrid molecules composed by one ior C5 and one or two StI molecules were obtained (named conjugated I and II, respectively). The purified conjugates were evaluated by a binding affinity assay against an ior C2-positive colon cancer cell line (SW948). Both molecules were able to recognize the antigen (Ag) in the same way that unconjugated ior C5 does. The activity of both conjugates against human erythrocytes and SW948 cells was assessed. They lost most of their hemolytic activity but their residual activity was very similar. Nevertheless, when their cytotoxicity was studied on the SW948 cell line, only conjugate II killed efficiently the cells, indicating a specific mAb-Ag interaction. In this chimeric molecule the ratio between the cytotoxic and the hemolytic activity was larger than that of the free cytolysin. This fact indicates an increase of the specificity of the toxic effect toward the SW948 cell line and consequently an increase of the difference between its hemolytic and cytotoxic doses. The results herein support the feasibility of directing StI to the surface of cancer cells expressing ior C2 Ag via the mAb ior C5.


Subject(s)
Adenocarcinoma/drug therapy , Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/pharmacology , Colonic Neoplasms/drug therapy , Hemolysin Proteins/chemistry , Hemolysin Proteins/pharmacology , Immunotoxins/pharmacology , Porins/chemistry , Porins/pharmacology , Adenocarcinoma/pathology , Animals , Antibodies, Monoclonal/isolation & purification , Blotting, Western , Cell Line, Tumor , Cell Survival/drug effects , Colonic Neoplasms/pathology , Electrophoresis, Polyacrylamide Gel , Enzyme-Linked Immunosorbent Assay , Flow Cytometry , Hemolysin Proteins/isolation & purification , Hemolysis/drug effects , Humans , Indicators and Reagents , Mice , Mice, Inbred BALB C , Organic Chemicals , Spleen/cytology , Spleen/drug effects
13.
Proteins ; 50(4): 600-8, 2003 Mar 01.
Article in English | MEDLINE | ID: mdl-12577266

ABSTRACT

Fold recognition techniques assist the exploration of protein structures, and web-based servers are part of the standard set of tools used in the analysis of biochemical problems. Despite their success, current methods are only able to predict the correct fold in a relatively small number of cases. We propose an approach that improves the selection of correct folds from among the results of two methods implemented as web servers (SAMT99 and 3DPSSM). Our approach is based on the training of a system of neural networks with models generated by the servers and a set of associated characteristics such as the quality of the sequence-structure alignment, distribution of sequence features (sequence-conserved positions and apolar residues), and compactness of the resulting models. Our results show that it is possible to detect adequate folds to model 80% of the sequences with a high level of confidence. The improvements achieved by taking into account sequence characteristics open the door to future improvements by directly including such factors in the step of model generation. This approach has been implemented as an automatic system LIBELLULA, available as a public web server at http://www.pdg.cnb.uam.es/servers/libellula.html.


Subject(s)
Neural Networks, Computer , Protein Conformation , Proteins/chemistry , Structural Homology, Protein , Internet , Protein Folding , Sensitivity and Specificity , Sequence Alignment
14.
Toxicon ; 41(1): 65-70, 2003 Jan.
Article in English | MEDLINE | ID: mdl-12467663

ABSTRACT

The effect of sodium dodecyl sulfate (SDS) upon the conformation and hemolytic activity of St I and St II strongly depends on its concentration. At relatively low surfactant concentrations (ca. 0.5-5mM range) the surfactant leads to the formation of aggregates, as suggested by the turbidity observed even at relatively low (micromolar range) protein concentrations. In this surfactant range, the proteins show an increase in intrinsic fluorescence intensity and reduced quenching by acrylamide, with an almost total loss of its hemolytic activity. At higher surfactant concentrations the protein adducts disaggregates. This produces a decrease in fluorescence intensity, increase in quenching efficiency by acrylamide, loss of the native tertiary conformation (as reported by the near UV-CD spectra), and increase in alpha-helix content (as evidenced by the far UV-CD spectra). However, and in spite of these substantial changes, the toxins partially recover their hemolytic activity. The reasons for this recovering of the activity at high surfactant concentrations is discussed.


Subject(s)
Cnidarian Venoms/pharmacology , Hemolysin Proteins/pharmacology , Hemolysis/drug effects , Sodium Dodecyl Sulfate/pharmacology , Surface-Active Agents/pharmacology , Animals , Circular Dichroism , Cnidarian Venoms/chemistry , Dose-Response Relationship, Drug , Erythrocytes/drug effects , Hemolysin Proteins/chemistry , Humans , Organic Chemicals , Protein Conformation/drug effects , Sea Anemones , Sodium Dodecyl Sulfate/administration & dosage , Spectrometry, Fluorescence , Surface-Active Agents/administration & dosage
15.
Bioinformatics ; 17(12): 1242-3, 2001 Dec.
Article in English | MEDLINE | ID: mdl-11751240

ABSTRACT

UNLABELLED: Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu


Subject(s)
Protein Conformation , Proteins/analysis , Software , Automation , Internet
16.
Proteins ; 45(4): 372-81, 2001 Dec 01.
Article in English | MEDLINE | ID: mdl-11746685

ABSTRACT

The manganese-stabilizing protein (PsbO) is an essential component of photosystem II (PSII) and is present in all oxyphotosynthetic organisms. PsbO allows correct water splitting and oxygen evolution by stabilizing the reactions driven by the manganese cluster. Despite its important role, its structure and detailed functional mechanism are still unknown. In this article we propose a structural model based on fold recognition and molecular modeling. This model has additional support from a study of the distribution of characteristics of the PsbO sequence family, such as the distribution of conserved, apolar, tree-determinants, and correlated positions. Our threading results consistently showed PsbO as an all-beta (beta) protein, with two homologous beta domains of approximately 120 amino acids linked by a flexible Proline-Glycine-Glycine (PGG) motif. These features are compatible with a general elongated and flexible architecture, in which the two domains form a sandwich-type structure with Greek key topology. The first domain is predicted to include 8 to 9 beta-strands, the second domain 6 to 7 beta-strands. An Ig-like beta-sandwich structure was selected as a template to build the 3-D model. The second domain has, between the strands, long-loops rich in Pro and Gly that are difficult to model. One of these long loops includes a highly conserved region (between P148 and P174) and a short alpha-helix (between E181 and N188)). These regions are characteristic parts of PsbO and show that the second domain is not so similar to the template. Overall, the model was able to account for much of the experimental data reported by several authors, and it would allow the detection of key residues and regions that are proposed in this article as essential for the structure and function of PsbO.


Subject(s)
Models, Molecular , Photosynthetic Reaction Center Complex Proteins/chemistry , Photosystem II Protein Complex , Algorithms , Conserved Sequence , Methods , Protein Structure, Tertiary , Sequence Alignment , Structure-Activity Relationship
17.
Protein Eng ; 14(9): 609-14, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11707606

ABSTRACT

Deciphering the network of protein interactions that underlines cellular operations has become one of the main tasks of proteomics and computational biology. Recently, a set of bioinformatics approaches has emerged for the prediction of possible interactions by combining sequence and genomic information. Even though the initial results are very promising, the current methods are still far from perfect. We propose here a new way of discovering possible protein-protein interactions based on the comparison of the evolutionary distances between the sequences of the associated protein families, an idea based on previous observations of correspondence between the phylogenetic trees of associated proteins in systems such as ligands and receptors. Here, we extend the approach to different test sets, including the statistical evaluation of their capacity to predict protein interactions. To demonstrate the possibilities of the system to perform large-scale predictions of interactions, we present the application to a collection of more than 67 000 pairs of E.coli proteins, of which 2742 are predicted to correspond to interacting proteins.


Subject(s)
Computational Biology/methods , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Phylogeny , Chaperonin 60/chemistry , Chaperonin 60/genetics , Chaperonin 60/metabolism , Escherichia coli Proteins/chemistry , Evolution, Molecular , GTP-Binding Proteins/chemistry , GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Genome, Bacterial , Glutamate-tRNA Ligase/chemistry , Glutamate-tRNA Ligase/genetics , Glutamate-tRNA Ligase/metabolism , Protein Structure, Tertiary , Proteome/chemistry , Proteome/genetics , Proteome/metabolism , Ribosomal Proteins/chemistry , Ribosomal Proteins/genetics , Ribosomal Proteins/metabolism , Sequence Alignment , Sequence Analysis, Protein , Statistics as Topic
18.
Toxicon ; 39(10): 1547-60, 2001 Oct.
Article in English | MEDLINE | ID: mdl-11478962

ABSTRACT

Sticholysins I and II are two highly hemolytic polypeptides purified from the Caribbean Sea anemone Stichodactyla helianthus. Their high sequence homology (93%) indicates that they correspond to isoforms of the same hemolysin. The spectroscopic measurements show a close similarity in the secondary structure content, conformation and stability of both toxins. Exposure of the toxins to high pHs (>11), a free radical source (AAPH), urea or temperature produce permanent changes in the toxin that lead to a significant loss of HA. It is significant to note that this loss of hemolytic activity occurs when other indicators, probably with the only exception of near-UV CD spectra, barely detect changes in the protein structure. This emphasizes the sensitivity of the protein function to changes in the macromolecule conformation. The most noticeable difference between both toxins is the considerably higher activity of St II, both measured in terms of erythrocyte internal K(+) exit or hemolysis; which is related to enthalpic factors. This difference is not due to an incomplete association of St I to the membrane. We consider then that the different pore forming capacity of both toxins in erythrocytes can be explained in terms of the difference in charge of the N-terminal fragment, than can considerably reduce the St I insertion rate in the membrane probably due to the negatively charged outer leaflet of the red blood cell, without a significant reduction of its capacity to bind to the cell membrane. This electrostatic effect, together with a slightly more relaxed structure in St II, could explain the higher pore forming capacity of St II in the red blood cell membrane.


Subject(s)
Amidines/metabolism , Cnidarian Venoms/chemistry , Erythrocytes/physiology , Hemolysin Proteins/metabolism , Liposomes/chemistry , Liposomes/metabolism , Neurotoxins/chemistry , Neurotoxins/metabolism , Potassium/physiology , Protein Isoforms/chemistry , Protein Isoforms/metabolism , Sea Anemones/pathogenicity , Animals , Circular Dichroism , Cnidarian Venoms/toxicity , Erythrocytes/drug effects , Hemolysin Proteins/drug effects , Humans , Hydrogen-Ion Concentration , Oxidants/metabolism , Potassium/analysis , Protein Conformation , Protein Structure, Secondary , Sequence Homology, Amino Acid , Spectrometry, Fluorescence , Temperature , Time Factors
19.
Biophys J ; 80(6): 2761-74, 2001 Jun.
Article in English | MEDLINE | ID: mdl-11371451

ABSTRACT

Sticholysin I and II (St I and St II), two basic cytolysins purified from the Caribbean sea anemone Stichodactyla helianthus, efficiently permeabilize lipid vesicles by forming pores in their membranes. A general characteristic of these toxins is their preference for membranes containing sphingomyelin (SM). As a consequence, vesicles formed by equimolar mixtures of SM with phosphatidylcholine (PC) are very good targets for St I and II. To better characterize the lipid dependence of the cytolysin-membrane interaction, we have now evaluated the effect of including different lipids in the composition of the vesicles. We observed that at low doses of either St I or St II vesicles composed of SM and phosphatidic acid (PA) were permeabilized faster and to a higher extent than vesicles of PC and SM. As in the case of PC/SM mixtures, permeabilization was optimal when the molar ratio of PA/SM was ~1. The preference for membranes containing PA was confirmed by inhibition experiments in which the hemolytic activity of St I was diminished by pre-incubation with vesicles of different composition. The inclusion of even small proportions of PA into PC/SM LUVs led to a marked increase in calcein release caused by both St I and St II, reaching maximal effect at ~5 mol % of PA. Inclusion of other negatively charged lipids (phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), or cardiolipin (CL)), all at 5 mol %, also elicited an increase in calcein release, the potency being in the order CL approximately PA >> PG approximately PI approximately PS. However, some boosting effect was also obtained, including the zwitterionic lipid phosphatidylethanolamine (PE) or even, albeit to a lesser extent, the positively charged lipid stearylamine (SA). This indicated that the effect was not mediated by electrostatic interactions between the cytolysin and the negative surface of the vesicles. In fact, increasing the ionic strength of the medium had only a small inhibitory effect on the interaction, but this was actually larger with uncharged vesicles than with negatively charged vesicles. A study of the fluidity of the different vesicles, probed by the environment-sensitive fluorescent dye diphenylhexatriene (DPH), showed that toxin activity was also not correlated to the average membrane fluidity. It is suggested that the insertion of the toxin channel could imply the formation in the bilayer of a nonlamellar structure, a toroidal lipid pore. In this case, the presence of lipids favoring a nonlamellar phase, in particular PA and CL, strong inducers of negative curvature in the bilayer, could help in the formation of the pore. This possibility is confirmed by the fact that the formation of toxin pores strongly promotes the rate of transbilayer movement of lipid molecules, which indicates local disruption of the lamellar structure.


Subject(s)
Cell Membrane Permeability , Cnidarian Venoms/metabolism , Hemolysin Proteins/metabolism , Liposomes/chemistry , Liposomes/metabolism , Membrane Lipids/metabolism , Sea Anemones , Animals , Cardiolipins/metabolism , Fluoresceins/metabolism , Hemolysis , Models, Biological , Organic Chemicals , Osmolar Concentration , Phosphatidic Acids/metabolism , Phosphatidylglycerols/metabolism , Phosphatidylinositols/metabolism , Phosphatidylserines/metabolism , Spectrometry, Fluorescence , Static Electricity
20.
Toxicon ; 39(2-3): 187-94, 2001.
Article in English | MEDLINE | ID: mdl-10978735

ABSTRACT

Two hemolysins, Sticholysin I (St I) and Sticholysin II (St II) were purified from the sea anemone Stichodactyla helianthus combining gel filtration and ion exchange chromatography. The amino acid composition of both cytolysins was determined revealing a high proportion of glycine, lysine, tyrosine and non-polar amino acids (alanine, leucine and valine). Cysteine was not found in either polypeptide. Molecular masses of St I and St II were 19401 and 19290 Da, respectively. N-terminal sequence analysis of St I and St II showed a high homology between them suggesting they are isoforms of the same cytolysin. Compared with other sea anemone cytolysins, St I and St II contain a 22 amino acid insertion fragment also present in Eq T II/Tn C and probably in CaT I and Hm T and absent in C III, the major hemolysin previously reported in this anemone.


Subject(s)
Cnidarian Venoms/isolation & purification , Hemolysin Proteins/isolation & purification , Peptides/isolation & purification , Sea Anemones , Amino Acid Sequence , Animals , Chromatography, Gel , Chromatography, High Pressure Liquid , Cnidarian Venoms/analysis , Hemolysin Proteins/analysis , Molecular Sequence Data , Organic Chemicals , Peptides/analysis
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