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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.

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Date palm sap (Phoenix dactylifera L.), also known as legmi, is a fresh juice extracted from date palm trees. The present study aimed to elucidate the effects of collection time (at the beginning of the tapping period and after seven days of collection) on the amino acid profile and physico-chemical properties of date palm sap from both male and female trees. Dry matter, protein, amino acid, and sugar profiles were determined using the Kjeldahl method, High-Performance Liquid Chromatography (HPLC), and High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD), respectively. Date palm sap from both male and female trees contained high levels of carbohydrates. HPLC analysis showed that this fraction was dominated by sucrose in the sap sample from female trees compared to that from male trees. Male date palm sap was noted to exhibit lower dry matter content than female date palm sap but higher protein, total polyphenol, ash, and amino acid contents. While the major essential amino acids in the sap from male trees consisted of valine and threonine, they were represented by lysine and phenylalanine in sap samples from female trees. Further, Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) analysis showed the presence of a proteinic band of 30 kDa only for the sap from male trees. Taken together, the sap from both male and female date palm trees had a number of properties that are highly valued by the functional food industry.(AU)

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Date palm sap (Phoenix dactylifera L.), also known as legmi, is a fresh juice extracted from date palm trees. The present study aimed to elucidate the effects of collection time (at the beginning of the tapping period and after seven days of collection) on the amino acid profile and physico-chemical properties of date palm sap from both male and female trees. Dry matter, protein, amino acid, and sugar profiles were determined using the Kjeldahl method, High-Performance Liquid Chromatography (HPLC), and High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD), respectively. Date palm sap from both male and female trees contained high levels of carbohydrates. HPLC analysis showed that this fraction was dominated by sucrose in the sap sample from female trees compared to that from male trees. Male date palm sap was noted to exhibit lower dry matter content than female date palm sap but higher protein, total polyphenol, ash, and amino acid contents. While the major essential amino acids in the sap from male trees consisted of valine and threonine, they were represented by lysine and phenylalanine in sap samples from female trees. Further, Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) analysis showed the presence of a proteinic band of 30 kDa only for the sap from male trees. Taken together, the sap from both male and female date palm trees had a number of properties that are highly valued by the functional food industry.

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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.

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Here we describe the cloning and characterization of the Schistosoma mansoni Alkaline Phosphatase(SmAP), previously identified in the tegument of adult worms. SmAP encodes a complete sequence composedof 536 amino acids containing an N-terminal signal peptide, five N-glycosylation sites, and a GPIanchor signal, similar to that described for mammalian orthologs. Real-time RT-PCR and Western blotexperiments suggest a rapid translation as soon as cercariae are transformed into schistosomula. Immunolocalizationanalysis shows that the protein is widely distributed in the worm tissues, with increased concentration in the vitelline glands of female parasites. Furthermore, the surface localization of thisenzyme was quantitatively supported by its enzymatic activity in live ex vivo or cultured parasites throughout the life cycle stages. The fact that cercariae accumulate large amounts of SmAP mRNA, which rapidly translates into protein upon schistosomula transformation, indicates it may have an important role in host invasion.

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Thimet oligopeptidase (EC 3.4.24.15; EP24.15) is a thiol-rich metallopeptidase ubiquitously distributed in mammalian tissues and involved inoligopeptide metabolism both within and outside cells. Fifteen Cys residues are present in the rat EP24.15 protein, seven are solvent accessible, andtwo are found inside the catalytic site cleft; no intraprotein disulfide is described. In the present investigation, we show that mammalianimmunoprecipitated EP24.15 is S-glutathionylated. In vitro EP24.15 S-glutathionylation was demonstrated by the incubation of bacterialrecombinant EP24.15 with oxidized glutathione concentration as low as 10 ìM. The in vitro S-glutathionylation of EP24.15 was responsible for itsoxidative oligomerization to dimer and trimer complexes. EP24.15 immunoprecipitated from cells submitted to oxidative challenge showedincreased trimeric forms and decreased S-glutathionylation compared to immunoprecipitated protein from control cells. Our present data also showthat EP24.15 maximal enzymatic activity is maintained by partial S-glutathionylation, a mechanism that apparently regulates the proteinoligomerization. Present results raise the possibility of an unconventional property of protein S-glutathionylation, inducing oligomerization byinterprotein thiol–disulfide exchange.

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Reduced or simplified amino acid alphabets group the 20 naturally occurring amino acids into a smaller number of representative protein residues. To date, several reduced amino acid alphabets have been proposed, which have been derived and optimized by a variety of methods. The resulting reduced amino acid alphabets have been applied to pattern recognition, generation of consensus sequences from multiple alignments, protein folding, and protein structure prediction. In this work, amino acid substitution matrices and statistical potentials were derived based on several reduced amino acid alphabets and their performance assessed in a large benchmark for the tasks of sequence alignment and fold assessment of protein structure models, using as a reference frame the standard alphabet of 20 amino acids. The results showed that a large reduction in the total number of residue types does not necessarily translate into a significant loss of discriminative power for sequence alignment and fold assessment. Therefore, some definitions of a few residue types are able to encode most of the relevant sequence/structure information that is present in the 20 standard amino acids. Based on these results, we suggest that the use of reduced amino acid alphabets may allow to increasing the accuracy of current substitution matrices and statistical potentials for the prediction of protein structure of remote homologs.

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La composición de aminoácidos es esencial para calcular la calificación química de un alimento, calificación que se utiliza para predecir la calidad de la proteína cuando se ingiere sola o como parte de la dieta. No obstante es necesario determinar la composición de aminoácidos de los alimentos consumidos diariamente en diferentes regiones y países. El presente artículo muestra la composición de aminoácidos en alimentos crudos y procesados en distintas presentaciones, que se consumen o procesan en México. La composición de aminoácidos de los distintos alimentos se determinó usando analizadores marca Beckman (modelos 116 y 6300). La determinación de triptofano se realizó con el método de Spies and Chambers. De los alimentos analizados, merecen una mención especial los siguientes: alga spirulina es limitante en lisina con una calificación química de 67 por ciento pero que es buena fuente de triptofano (1.16 g/16 gN), el amaranto alto en aminoácidos azufrados (4.09 a 5.34 g/16 gN) con un contenido de proteína de 15 g/100g y el pulque una bebida prehispánica, que tiene un alto contenido en triptofano (2.58 g/16 gN) y aminoácidos azufrados (2.72 g/16 gN). Finalmente, los insectos son una buena fuente de aminoácidos azufrados y lisina

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UNLABELLED: Amino acid contacts in terms of atomic interactions are essential factors to be considered in the analysis of the structure of a protein and its complexes. Consequently, molecular biologists do require specific tools for the identification and visualization of all such contacts. Graphical contacts (GC) and interface forming residue graphical contacts (IFRgc) presented here, calculate atomic contacts among amino acids based on a table of predefined pairs of the atom types and their distances, and then display them using number of different forms. The inventory of currently listed contact types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge-charge interactions, aromatic stacking and disulfide bonds. Such extensive catalog of the interactions, representing the forces that govern protein folding, stability and binding, is the key feature of these two applications. GC and IFRgc are part of STING Millennium Suite. AVAILABILITY: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).

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Osmotic stress constitutes a major bacterial stress factor in the soil and during industrial fermentation. In this paper, we quantified the metabolic response, in terms of metabolic flux redistribution, of a lysine-overproducing strain of Corynebacterium glutamicum grown under continuous culture, to gradually increasing osmolality. Oxygen and carbon dioxide evolution rates, and the changes in concentration of extracellular, as well as intracellular, metabolites were measured throughout the osmotic gradient. The metabolic fluxes were estimated from these measurements and from the mass balance constraints at each metabolite-node of the assumed metabolic reaction network. Our results show that formation rates of compatible solutes--trehalose first and proline at a later stage of the gradient--increased with osmotic stress to equilibrate the external osmotic pressure. Estimated flux distributions indicate that the observed increase in the glucose specific uptake rate with osmotic stress is channeled through the main energy generating pathways-- glycolysis and the tricarboxylic acid cycle--while the flux through the pentose phosphate pathway remains constant throughout the gradient. This results in a significant increase in the net specific ATP production rate, which may possibly be used to support the higher energy requirements required for cellular maintenance at high osmolalities. Finally, nodal analysis confirmed that the PEP/pyruvate node is essentially rigid and that the glucose-6-phosphate, oxaloacetate and alpha-ketoglutarate nodes are flexible and therefore adaptable to changes in osmotic pressure in C. glutamicum.

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The milk composition of women on a typical rural Mexican diet was compared with that secreted by American women, consuming a diet typical of affluent countries. Milk concentrations of free fatty acids, cholesterol, total amino acids, and selected key minerals were analyzed at 4 or 6 months postpartum. The total milk fat concentration was lower in the Otomi (22.7 +/- 6.7 mg/g milk) than in the American women (31.3 +/- 5.4 mg/g milk, p = 0.001). Although the absolute concentration did not differ, cholesterol, expressed in terms of total lipid, was higher in the Otomi milk (3.9 +/- 1.1 vs. 3.1 +/- 0.7 mg/g fat, p = 0.005). Saturated medium-chain (C10:0-C14:0) and unsaturated intermediate-chain fatty acids (C16:1 and C18:2) were higher in the Otomi than in the American milk (p < 0.03). The concentrations of C16:0, C18:0, and C18:1 were significantly lower in Otomi than in American milk. The milk concentrations of protein and nonprotein nitrogen were comparable between the two groups. The concentrations of serine, proline, cystine, methionine, and tryptophan were higher in the Otomi than in the American milk (p < 0.05-0.001). The concentrations of valine and isoleucine were significantly lower in the Otomi milk (p = 0.05). Expressed per gram of milk protein, the cystine, methionine, lysine, and tryptophan concentrations were higher, and the glutamine/glutamate, valine, isoleucine, and arginine levels were lower in the Otomi milk. The concentrations of phosphorus and copper were lower in the Otomi than in the American milk at 4 months postpartum (p = 0.05). These differences in milk fatty acid and amino acid patterns and mineral content are unlikely to affect infant growth, but may have other biological consequences yet to be ascertained.

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Plasma amino acid levels were measured by high pressure liquid chromatography (HPLC) in fourteen autistic children, all bellow 10 years of age. Mean glutamic and aspertic acid values were elevated (169 ñ 142 uM and 22.1 ñ 113 uM respectively) together with taurine (90.1 ñ 78.7 uM) ( p>0.1). All affected children had low levels of glutamine (241 ñ 1166 uM; p<0.01) and asparagine (22.9 ñ uM respectively); eleven children had increased aspartic acid and eight children had high levels of glutamate; seven of these children had a concomitant increment of taurine. The increment of the three above mentioned compounds was observed at the same time in five children. These findings demostrate that abnormal plasmatic levels of neurotransmitter amino acids may be found in some autistic children. Increased glutamatemia may be dietary in origen or may arise endogenously for several reasons, among others, metabolic derrangements in glutamate metabolism perhaps involving vitamin B6, defects or blockage of the glutamate receptor at the neuronal compartment, or alterations in the function of the neurotransmitters transporters. Increments of taurine, an inhibitor, is likely compensatory and calcium dependent

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As proteínas tem como funçäo fornecer ao organismo quantidades adequadas e balanceadas de aminoácidos. O valor nutritivo de cada proteína difere em funçäo da composiçäo dos seus aminoácidos. Essas diferenças podem ser observadas quando se estabelece recomendaçöes ou necessidade de proteína. A qualidade de uma proteína pode ser medida por métodos biológicos e microbiológicos.O método biológico geralmente e usado em experimentos com animais e o microbiológico utiliza microrganismo. Este último e o mais barato e simples, diminuindo o espaço físico necessário para o desenvolvimento do experimento. Entretanto, alguns problemas säo lembrados: alguns compostos näo säo tóxicos para o rato ou para o homem (fungos, condimentos, etc), porém impedem o crescimento do microrganismo, pois cada um deles tem sua especificidade na disponibilidade para determinados aminoácidos essenciais ou quantidade protéica.

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