50 years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification

BACKGROUND: Physicochemical properties are frequently analyzed to characterize protein-sequences of known and unknown function. Especially the hydrophobicity of amino acids is often used for structural prediction or for the detection of membrane associated or embedded ß-sheets and α-helices. For this purpose many scales classifying amino acids according to their physicochemical properties have been defined over the past decades. In parallel, several hydrophobicity parameters have been defined for calculation of peptide properties. We analyzed the performance of separating sequence pools using 98 hydrophobicity scales and five different hydrophobicity parameters, namely the overall hydrophobicity, the hydrophobic moment for detection of the α-helical and ß-sheet membrane segments, the alternating hydrophobicity and the exact ß-strand score. RESULTS: Most of the scales are capable of discriminating between transmembrane α-helices and transmembrane ß-sheets, but assignment of peptides to pools of soluble peptides of different secondary structures is not achieved at the same quality. The separation capacity as measure of the discrimination between different structural elements is best by using the five different hydrophobicity parameters, but addition of the alternating hydrophobicity does not provide a large benefit. An in silico evolutionary approach shows that scales have limitation in separation capacity with a maximal threshold of 0.6 in general. We observed that scales derived from the evolutionary approach performed best in separating the different peptide pools when values for arginine and tyrosine were largely distinct from the value of glutamate. Finally, the separation of secondary structure pools via hydrophobicity can be supported by specific detectable patterns of four amino acids. CONCLUSION: It could be assumed that the quality of separation capacity of a certain scale depends on the spacing of the hydrophobicity value of certain amino acids. Irrespective of the wealth of hydrophobicity scales a scale separating all different kinds of secondary structures or between soluble and transmembrane peptides does not exist reflecting that properties other than hydrophobicity affect secondary structure formation as well. Nevertheless, application of hydrophobicity scales allows distinguishing between peptides with transmembrane α-helices and ß-sheets. Furthermore, the overall separation capacity score of 0.6 using different hydrophobicity parameters could be assisted by pattern search on the protein sequence level for specific peptides with a length of four amino acids.

Effect of glycemic index on obesity control

Objective Evaluate the effect of glycemic index (GI) on biochemical parameters, food intake, energy metabolism, anthropometric measures and body composition in overweight subjects.Materials and methods Simple blind study, in which nineteen subjects were randomly assigned to consume in the laboratory two daily low GI (n = 10) or high GI (n = 9) meals, for forty-five consecutive days. Habitual food intake was assessed at baseline. Food intake, anthropometric measures and body composition were assessed at each 15 days. Energy metabolism and biochemical parameters were evaluated at baseline and the end of the study.Results Low GI meals increased fat oxidation, and reduced waist circumference and HOMA-IR, while high GI meals increased daily dietary fiber and energy intake compared to baseline. There was a higher reduction on waist circumference and body fat, and a higher increase on postprandial fat oxidation in response to the LGI meals than after high GI meals. High GI meals increased fasting respiratory coefficient compared to baseline and low GI meals.Conclusion The results of the present study showed that the consumption of two daily low GI meals for forty-five consecutive days has a positive effect on obesity control, whereas, the consumption of high GI meals result has the opposite effect. Arch Endocrinol Metab. 2015;59(3):245-51.

Physical inactivity and anthropometric measures in schoolchildren from Paranavaí, Paraná, Brazil / Inatividade física e medidas antropométricas em escolares de Paranavaí, Paraná, Brasil

OBJECTIVE: To investigate the association between physical inactivity and anthropometric measures in schoolchildren from Paranavaí-Parana, Brazil. METHODS: Cross-sectional survey, carried out in July and August 2013. Sample of 566 students (287 boys and 279 girls) from 6th to 9th grade, aged 10 to 14 years, from public and private schools of Paranavaí - PR, Southern Brazil. The variables analyzed were: time of weekly physical activity through a questionnaire (physical inactivity <300 minutes/week), body mass index (BMI) and waist circumference (WC). In the statistical analysis, the U Mann-Whitney and Student's t tests were used for comparison between genders. To identify factors associated with insufficient levels of physical activity, univariate and multivariate logistic regression analysis was applied and expressed in Odds ratio (OR) and 95% confidence interval (95%CI). RESULTS: There was an association between physical inactivity and anthropometric measurements for BMI (p<0.001) and WC (p<0.001), with a prevalence rate of 56.1% and 52.7% of inactive adolescents, respectively. In the multivariate analysis, there was significant association of physical inactivity and overweight (OR 1.8, 95%CI: 1.1-3.0) and with increased waist circumference (OR 2.8, 95%CI: 1.4-3.8). CONCLUSIONS: Inadequate levels of physical activity is a determining factor for overweight and abdominal adiposity. Accordingly, preventive measures should be taken, especially in schools, emphasizing the importance of exercise for body composition control and weight reduction. .

OBJETIVO: Investigar a associação entre a inatividade física e medidas antropométricas em escolares de Paranavaí, Paraná, Brasil. MÉTODOS: Pesquisa com delineamento transversal, feita em julho e agosto de 2013. Amostra composta por 566 escolares (287 meninos e 278 meninas), de 10 a 14 anos, do 6° ao 9° ano da rede pública e privada de Paranavaí (PR). As variáveis analisadas foram: tempo de atividade física semanal, por meio de questionário (inatividade física: < 300 min/semanal), índice de massa corporal (IMC) e circunferência de cintura (CC). Na análise estatística foram usados os testes U de Mann-Whitney e t de Student para comparar os sexos. Para verificar os fatores associados ao nível insuficiente de atividade física aplicou-se o modelo de regressão logística binária univariada e multivariada, expressa em odds ratio (OR), e intervalo de confiança de 95% (IC95%). RESULTADOS: Houve associação entre inatividade física e as medidas antropométricas para IMC (p<0,001) e CC (p<0,001), com prevalências de 56,1% e 52,7% de inativos, respectivamente. Na análise multivariada, foram observadas associações significativas de inatividade física nos alunos que apresentaram excesso de peso (OR 1,8; IC95%: 1,1-3,0) e circunferência de cintura aumentada (OR 2,2; IC95%: 1,4-3,8). CONCLUSÕES: Nível inadequado de atividade física é fator determinante no excesso de peso e na adiposidade abdominal. Nesse sentido, medidas preventivas devem ser tomadas, principalmente nas escolas, e enfatizar-se a importância do exercício físico no controle da composição corporal e redução do pesoe. .

Gephyrin: a central GABAergic synapse organizer

Gephyrin is a central element that anchors, clusters and stabilizes glycine and gamma-aminobutyric acid type A receptors at inhibitory synapses of the mammalian brain. It self-assembles into a hexagonal lattice and interacts with various inhibitory synaptic proteins. Intriguingly, the clustering of gephyrin, which is regulated by multiple posttranslational modifications, is critical for inhibitory synapse formation and function. In this review, we summarize the basic properties of gephyrin and describe recent findings regarding its roles in inhibitory synapse formation, function and plasticity. We will also discuss the implications for the pathophysiology of brain disorders and raise the remaining open questions in this field.

First Report on Familial Hemophagocytic Lymphohistiocytosis with an Abnormal Immunophenotype and T Cell Monoclonality in Korea

No abstract available.

MAPS: An interactive web server for membrane annotation of transmembrane protein structures.

The exact positioning of the membrane in transmembrane (TM) proteins plays important functional roles. Yet, the structures of TM proteins in protein data bank (pdb) have no information about the explicit position of the membrane. Using a simple hydrophobic lipid-protein mismatch energy function and a flexible lipid/water boundary, the position of lipid bilayer for representative TM proteins in pdb have been annotated. A web server called MAPS (Membrane Annotation of Protein Structures; available at: http://www.boseinst.ernet.in/gautam/maps) has been set up that allows the user to interactively analyze membrane-protein orientations of any uploaded pdb structure with user-defined membrane flexibility parameters.

Culture & characterisation of limbal epithelial cells & oral mucosal cells.

Background & objectives: Sources of autologous tissue that can functionally replace the corneal epithelium have been considered as an alternative to allogenous limbal transplants for limbal stem cells deficiency (LSCD). The aim of the present study was to compare the characterization of oral mucosa with limbal epithelial cells by markers using reverse transcriptase polymerase chain reaction (RT-PCR). Methods: Experiments were performed using oral tissue (n=6) obtained from patients who underwent oral mucosal graft for LSCD. Confluent cultures of limbus and oral mucosa epithelial cells were characterized by the pututative stem cell markers using RT-PCR. The morphological characteristics of cultivated epithelial cells were analyzed by haematoxylin and eosin staining and phase contrast microscopy. Results: Confluent sheets of epithelial cells were seen at the end of 14th day resembling the morphological features of limbal epithelia. RT–PCR analysis showed that cultured oral epithelial cells expressed markers such as ABCG2, p63, delta Np63, isoforms of p63, Keratin 3 (K3), membrane protein – Mucin (MUC 1, 4 and 16) and Antimicrobial Peptide - AMP (Human β Defensin – hBD 1, 2 and 3). Interpretation & conclusions: Oral epithelial cultures have morphological features resembling corneal and limbal epithelial cells by expressing similar marker genes. Thus, feasibility of clinical use of oral epithelial cells need be evaluated for allogenous limbal transplants.

Characterization of arylsulphatase A in a 70 kDa protein isolated from goat spermatozoa having Na+, K+-ATPase inhibitory activity.

A protein having inhibitory effect on Na+, K+-ATPase as well as showing arylsulphatase A activity (ASA) was isolated from the cytosolic fraction of goat spermatozoa and characterized biochemically. The molecular mass of the protein was found to be 70 kDa (P70) on 10% SDS-PAGE after 35% ammonium sulphate precipitation, followed by hydroxyapatite column chromatographic separation. The isoelectric point (pI) of the protein was found to be 4.9. The sequencing results of first ten N-terminal amino acid residues of protein showed 100%, 90%, and 80% homology with N-terminal 18-27 amino acid residues of mice, pig and human testicular ASA, respectively. The optimum pH, temperature and incubation time for maximum ASA activity of the protein was 5.5, 37°C and 30 min respectively. The ASA activity of protein and AS from a commercial source was studied with respect to the sensitivity to different metal ions, vanadate, carbonyl compounds and ascorbate. Inhibition of AS activity of P70 by silver nitrate suggested that it was related to ASA. Comparable effects of different polyunsaturated fatty acids (eicosapentaenoic and docosahexaenoic acids) and purified anti P70-antibody on P70 and AS from commercial source were observed. The findings suggested that protein was novel in nature, having both regulatory and catalytic functions and showed similarities with the ASA reported from different sources.

Determinação do perfil protéico da membrana externa da Leptospira interrogans sorovariedade Hardjoprajitno / Protein profile of the outer membrane of Leptospira interrogans serovar Hardjoprajitno

Estudou-se o perfil das proteínas da membrana externa (PME) da Leptospira interrogans sorovariedade Hardjoprajitno por meio da eletroforese bidimensional. Foram utilizadas técnicas de extração das PME com Triton x114 e precipitação com acetona. Os géis foram corados com nitrato de prata e as imagens analisadas para determinação da massa molecular das proteínas detectadas. Foram visualizadas 35 bandas protéicas, sendo que cinco delas se destacaram por estarem em maior quantidade: 22,54KDa (LipL22), 30/26KDa (LipL32), 34,41KDa (PME34), 42,75KDa (LipL41) e 58,59KDa (LipL63).

The protein profile of the outer membrane of Leptospira interrogans serovar Hardjoprajitno was determined by two-dimensional gel electrophoresis. The outer membrane was extracted with Triton x 114 and the proteins were precipitated with acetone. The images were analyzed for the determination of the molecular weight of the detected proteins. Thirty-five spots for the proteins that are predominant in the outer membrane of this Leptospira were observed and five proteins were found in higher quantities: 22.54KDa (LipL22), 30/26KDa (LipL32), 34.41KDa (PME34) (2), 42.75KDa (LipL41), and 58.59KDa (LipL63).

Protein-mediated surface structuring in biomembranes

The lipids and proteins of biomembranes exhibit highly dissimilar conformations, geometrical shapes, amphipathicity, and thermodynamic properties which constrain their two-dimensional molecular packing, electrostatics, and interaction preferences. This causes inevitable development of large local tensions that frequently relax into phase or compositional immiscibility along lateral and transverse planes of the membrane. On the other hand, these effects constitute the very codes that mediate molecular and structural changes determining and controlling the possibilities for enzymatic activity, apposition and recombination in biomembranes. The presence of proteins constitutes a major perturbing factor for the membrane sculpturing both in terms of its surface topography and dynamics. We will focus on some results from our group within this context and summarize some recent evidence for the active involvement of extrinsic (myelin basic protein), integral (Folch-Lees proteolipid protein) and amphitropic (c-Fos and c-Jun) proteins, as well as a membrane-active amphitropic phosphohydrolytic enzyme (neutral sphingomyelinase), in the process of lateral segregation and dynamics of phase domains, sculpturing of the surface topography, and the bi-directional modulation of the membrane biochemical reactivity.

The effect of hydrostatic pressure on membrane-bound proteins

Many cellular proteins are bound to the surfaces of membranes and participate in various cell signaling responses. Interactions between this group of proteins are in part controlled by the membrane surface to which the proteins are bound. This review focuses on the effects of pressure on membrane-associated proteins. Initially, the effect of pressure on membrane surfaces and how pressure may perturb the membrane binding of proteins is discussed. Next, the effect of pressure on the activity and lateral association of proteins is considered. We then discuss how pressure can be used to gain insight into these types of proteins.

Detergent-resistant membranes in human erythrocytes and their connection to the membrane-skeleton.

In cell membranes, local inhomogeneity in the lateral distribution of lipids and proteins is thought to exist in vivo in the form of lipid 'rafts', microdomains enriched in cholesterol and sphingolipids, and in specific classes of proteins, that appear to play specialized roles for signal transduction, cell-cell recognition, parasite or virus infection, and vesicular trafficking. These structures are operationally defined as membranes resistant to solubilization by nonionic detergents at 4 degree C (detergent-resistant membranes, DRMs). This definition appears to be necessary and sufficient, although additional manoeuvres, not always described with sufficient detail, may be needed to ensure isolation of DRMs, like mechanical homogenization, and changes in the pH and/or ionic strength of the solubilization medium. We show here for the human erythrocyte that the different conditions adopted may lead to the isolation of qualitatively and quantitatively different DRM fractions, thus contributing to the complexity of the notion itself of lipid raft. A significant portion of erythrocyte DRMs enriched in reported lipid raft markers, such as flotillin-1, flotillin-2 and GM1, is anchored to the spectrin membrane-skeleton via electrostatic interactions that can be disrupted by the simultaneous increase in pH and ionic strength of the solubilization medium.

Identification of a Dysferlin Gene Mutation in a Korean Case with Miyoshi Myopathy

Recent genetic and immunohistochemical analyses have shown that Miyoshi myopathy (MM) is caused by a mutation in the DYSF gene, which induces dysfunction of dysferlin. The author described one patient showing characteristic MM phenotype with deficiency of dysferlin on immunohistochemistry. Direct DNA sequencing of whole exons of DYSF gene revealed one homozygous missense mutation (G1165C) on exon 12, which let to an amino acid substitution from the glutamic acid to glutamine at the 389 of the peptide sequence in this patient. This is the first reported case of MM confirmed by immunohistochemical and genetic analyses in Korea.

Esferocitosis hereditaria: aspectos clínicos, bioquímicos y moleculares / Hereditary spherocytosis: Clinical, biochemical and molecular aspects

La esferocitosis hereditaria (EH) es una enfermedad caracterizada por anemia hemolítica de severidad variable, con presencia de esferocitos en sangre periférica y una respuesta clínica favorable a la esplenectomía. Con el desarrollo de nuevas técnicas se encontraron las primeras alteraciones bioquímicas de las proteínas de la membrana eritrocitaria, y posteriormente, se han podido precisar las alteraciones moleculares mediante las técnicas del ADN recombinante. La EH es una enfermedad muy heterogénea que se produce por un defecto intrínseco del glóbulo rojo, y existen otras alteraciones secundarias a esta afección. La prueba más utilizada para el diagnóstico de la EH es la fragilidad osmótica del glóbulo rojo. Se ha demostrado que esta enfermedad es producida por defectos de las proteínas que intervienen en las interacciones verticales entre el esqueleto de la membrana y la bicapa lipídica. El tratamiento de elección en la EH es la esplenectomía, ya que es el más efectivo en el control de la anemia, aunque la sobrevida de los glóbulos rojos permanece acortada y los esferocitos no desaparecen. Este proceder se indica en pacientes con anemia hemolítica severa o en individuos moderadamente asintomáticos pero que presentan litiasis vesicular

Apical membrane antigen-1 (AMA-1) gene sequences of re-emerging Plasmodium vivax in South Korea

Plasmodium vivax malaria re-emerged in South Korea in 1993, and epidemics continue since then. We examined genetic variation in the region encompassing the apical membrane antigen-1 (PvAMA-1) of the parasites by DNA sequencing of the 22 re-emerging P. vivax isolates. The genotype of the PvAMA-1, which was based on sequence data previously reported for the polymorphic regions, showed that two haplotypes were present at one polymorphic site. Compared with reported data, the two types, SKOR type I and type II, were similar to Chinese CH-10A and CH-05A isolates, respectively. Thus, the present study showed that two genotypes of AMA-1 genes coexist in the re-emerging Korean P. vivax.

Cloning of BNIP3h, a member of proapoptotic BNIP3 family genes

Apoptosis is regulated by interaction of antiapoptotic Bcl-2 family proteins with various proapoptotic proteins, several of which are also members of the Bcl-2 family. BNIP3 (formerly NIP3) is a proapoptotic mitochondrial protein classified in the Bcl-2 family based on limited sequence homology-3 (BH3) domain and COOH-terminal transmembrane domain. Sequence comparison of BNIP3 has indicated that there are several BNIP3 human homologs of this protein, like BNIP3L, Nix and BNIP3. We have cloned a new member of BNIP3 family from the cDNA library prepared from human dermal papilla cells and designated as BNIP3h. BNIP3h shows substantial homology with other BNIP3 family proteins. BNIP3h induced apoptosis from 24 hours after transfection in MCF7 cell lines and its apoptosis inducing activity is extended until 72 hours after transfection.

Cell-free expression and functional reconstitution of CALM in clathrin assembly

Clathrin-mediated vesicle formation is an essential step in the intracellular trafficking of the protein and lipid. Binding of clathrin assembly protein to clathrin triskelia induces their assembly into clathrin-coated vesicles (CCVs). In order to better understand a possible role of post-translational modification of CALM (clathrin assembly protein lymphoid myeloid), the homologue of AP180, in the assembly of CCVs, CALM was expressed in the cell-free reticulocyte translation system that is capable of carrying out post-translational modification. The apparent molecular weight of the expressed recombinant CALM was estimated as 105 kD. Alkaline phosphatase treatment of CALM resulted in a mobility shift on SDS-PAGE. We found that CALM was associated with the proteins harboring SH3 domain, promote assembly of clathrin triskelia into clathrin cage and bound to the preformed clathrin cage. CALM was also proteolyzed by caspase 3 and calpain but not by caspase 8. These results indicated that the post-translationally modified CALM, expressed in the eukaryotic cell-free reticulocyte translation system was able to mediate the assembly of clathrin and the coated-vesicle formation.

Characterization of the pili isolated from Vibrio parahaemolyticus O3:K6.

Pilus of Vibrio parahaemolyticus O3:K6 strain LVP9 belonging to the newly identified clone was purified and characterized. The molecular mass of the pilin was estimated to be about 18 kDa by SDS-PAGE, and the isoelectric point of the pilin was 5.0 +/- 0.2. The LVP9 pili were antigenically different from the other V. parahaemolyticus Na2 pili and Ha7 pili as previously reported, nevertheless all three had indistinguishable morphology and shared a high degree of homology in their N-terminal amino acid sequences. Strain LVP9 and its purified pili did not agglutinate human and rabbit erythrocytes. The LVP9 organisms and the purified pili were adhesive to the rabbit intestine. The adhesion was inhibited by pretreatment of the rabbit intestine with the purified pili or by pretreatment of the organisms with the Fab fractions of anti-pilus antibody. These results indicate that the LVP9 pilus is an adherent factor to the rabbit intestine.

Resolution of mitochondrial and chloroplast membrane protein complexes from green leaves of potato on blue-native polyacrylamide gels.

Purification of mitochondria and mitochondrial protein complexes from green tissues is often severely impaired by the presence of chloroplasts and their proteins. Here we present a method which allows analysis of respiratory protein complexes from potato leaves. The procedure includes the preparation of an organellar fraction specifically enriched in mitochondria and the separation of organellar protein complexes by blue-native polyacrylamide gel electrophoresis (BN-PAGE). For the first time mitochondrial and chloroplast protein complexes have been resolved simultaneously in a native gel. BN-PAGE allowed the separation of eleven bands, including the mitochondrial NADH-dehydrogenase, the bc1 complex and the mitochondrial F1-ATP synthase as well as the chloroplast F1-ATP synthase, the cytochrome b6f complex, the two photosystems and the light harvesting complex. The resolution of the protein complexes in the first dimension was good enough to allow identification of all subunits of individual complexes in the second dimension under denaturing conditions. Thus, BN-PAGE offers an opportunity to analyze mitochondrial and chloroplast protein complexes from a single preparation from very small amounts of tissue. The implications of our findings, for studies on protein expression and turnover in different tissues and developmental stages, are discussed.