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.

Amino acid composition of some Mexcan foods

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

Plasma excitatory amino acids in autism / Aminoácidos excitatorios en niños autistas

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

Métodos microbiológicos para determinacao nutricional da proteina - artigo de revisäo / Microbiological methods for the determination of the nutritional value on the protein- review article

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.