Structure of the spectrin-actin binding site of erythrocyte protein 4.1

The complete primary structure of the functional site of erythrocyte protein 4.1 involved in spectrin-actin associations has been determined. The sequence of this domain, which contains 67 amino acids and has a molecular mass of 8045 daltons, has been obtained by NH2-terminal sequence analysis of an 8-kDa chymotryptic peptide, three endoproteinase lysine C-cleaved peptides and two peptides obtained by Staphylococcus aureus protease V8 cleavage. All peptides including the 8-kDa domain peptide were purified by reverse-phase high performance liquid chromatography. Antibodies against two different synthetic peptides of the 8-kDa domain are able to inhibit the association between protein 4.1, spectrin, and F-actin, corroborating that the 8-kDa domain is responsible for the formation of a ternary complex. A computer search of the 8-kDa sequence with the National Biomedical Research Foundation database did not detect any significant homologies to known sequences. Protein 4.1 is not related to any known proteins and may represent a new protein superfamily.     

Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.     

Modelling the effect of forest cover on shallow landslides at the river basin scale

The potential for reducing the occurrence of shallow landslides through targeted reforestation of critical parts of a river basin is explored through mathematical modelling. Through the systematic investigation of land management options, modelling allows the optimum strategies to be selected ahead of any real intervention in the basin. Physically based models, for which the parameters can be evaluated using physical reasoning, offer particular advantages for predicting the effects of possible future changes in land use and climate. Typically a physically based landslide model consists of a coupled hydrological model (for soil moisture) and a geotechnical slope stability model, along with an impact model, such as basin sediment yield. An application of the SHETRAN model to the 65.8-km² Guabalcón basin in central Ecuador demonstrates a technique for identifying the areas of a basin most susceptible to shallow landsliding and for quantifying the effects of different vegetation covers on landslide incidence. Thus, for the modelled scenario, increasing root cohesion from 300 to 1500 Pa causes a two-thirds reduction in the number of landslides. Useful information can be obtained even on the basis of imperfect data availability but model output should be interpreted carefully in the light of parameter uncertainty.     

Differential phosphorylation of multiple sites in protein 4.1 and protein 4.9 by phorbol ester-activated and cyclic AMP-dependent protein kinases

The phosphorylation of the membrane skeleton components protein 4.1 and protein 4.9 in intact erythrocytes is shown to increase in the presence of either 1 microM 12-O-tetradecanoyl phorbol 13-acetate or 2 mM dibutyryl cAMP. The phosphorylation induced by these protein kinase activators is compared by two-dimensional tryptic peptide mapping. In both proteins, the pattern of peptides phosphorylated in the presence of 12-O-tetradecanoyl phorbol 13-acetate differs from the pattern of peptides phosphorylated in the presence of dibutyryl cAMP. The relative locations of the phosphorylated sites on protein 4.1 have been determined using limited proteolysis by alpha-chymotrypsin.     

Identification of the functional site of erythrocyte protein 4.1 involved in spectrin-actin associations

Peptides produced by mild chymotryptic digestion of human erythrocyte protein 4.1 mimic the ability of intact 4.1 to promote the binding of spectrin to F-actin. This complex-promoting activity was found to reside in an 8-kDa peptide which was fully functional when dissociated from other protein 4.1-derived peptides, indicating that noncovalent complexes of multiple peptides were not essential for activity. The 8-kDa peptide was incorporated into a ternary complex with spectrin and F-actin in approximately stoichiometric amounts. Amino acid composition and two-dimensional peptide mapping show that the 8-kDa active peptide is located within the 10-kDa region of protein 4.1 which contains a cAMP-dependent phosphorylated site.     

Heterogeneous phenotype of human glioblastoma: In vitro study

Glioblastomas (GBMs) are the most lethal primary brain tumours. Increasing evidence shows that brain tumours contain the population of stem cells, so‐called cancer stem cells (CSCs). Stem cell marker CD133 was reported to identify CSC population in GBM. Further studies have indicated that CD133 negative cells exhibiting similar properties and are able to initiate the tumour, self‐renew and undergo multilineage differentiation. GBM is a highly heterogeneous tumour and may contain different stem cell populations with different functional properties. We characterized five GBM cell lines, established from surgical samples, according to the marker expression, proliferation and differentiation potential. CD133 positive cell lines showed increased proliferation rate in neurosphere condition and marked differentiation potential towards neuronal lineages. Whereas two cell lines low‐expressing CD133 marker showed mesenchymal properties in vitro, that is high proliferation rate in serum condition and differentiation in mesenchymal cell types. Further, we compared therapy resistance capacity of GBM cell lines treated with hydroxyurea. Our results suggest that CSC concept is more complex than it was believed before, and CD133 could not define entire stem cell population within GBM. At least two different subtypes of GBM CSCs exist, which may have different biological characteristics and imply different therapeutic strategies. Copyright © 2013 John Wiley & Sons, Ltd.     

Self-association of human erythrocyte glycophorin A. Appearance of low mobility bands on sodium dodecyl sulfate gels

We have examined the self-association of glycophorin A, the major sialoglycoprotein of the human erythrocyte membrane, using sodium dodecyl sulfate (SDS) polyacrylamide gels and circular dichroism. Pure glycophorin A has a tendency to form multiple bands on SDS gels at positions of higher apparent molecular weight than the PAS 1 and PAS 2 bands previously seen. These high molecular weight bands do not have mobilities corresponding to integral polymers of PAS 1 and PAS 2. Circular dichroism spectra of solutions giving rise to these bands or to PAS 1 and PAS 2 bands alone, indicate that these species all have essentially the same peptide conformation.     

Tissue-specific analogues of erythrocyte protein 4.1 retain functional domains

Analogues of the human erythroid membrane skeletal component protein 4.1 have been identified in perfused rat tissues and human T and B lymphocyte cell lines. olyclonal antibodies were used which are specific for all domains of protein 4.1, the spectrin-actin-promoting 8-Kd peptide, the membrane-binding 30-Kd domain, and the 50-Kd domain. Antibody reactivity, by Western blotting of tissue homogenates, shows reactivity with proteins varying in molecular weight from 175 Kd to 30 Kd. Further, these protein 4.1 analogues appear to be expressed in a tissue-specific fashion. Of the analogues detected there appear to be at least three classes: analogues containing all erythroid protein 4.1 domains, analogues containing all domains but with modified antigenic epitopes, and analogues containing only some domains. Chemical cleavage at cysteine linkages indicates that in analogues containing the 30-Kd region the location of cysteine is highly conserved. This datum suggests that in nonerythroid 4.1 isoforms of higher molecular weight the additional protein mass is added to the amino terminal end (30 Kd end).