ABSTRACT
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.
Subject(s)
Hydrophobic and Hydrophilic Interactions , Amino Acids/chemistry , Membrane Proteins/chemistry , Reference Values , Time Factors , Weights and Measures , Algorithms , Predictive Value of Tests , Reproducibility of Results , Amino Acid Sequence , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Amino Acids/classificationABSTRACT
Velvet worm taxonomy from Santander, Colombia and thermogravimetry, differential scanning calorimetry and infrared spectroscopy of the adhesive secretion (Onychophora: Peripatidae). Onychophoran worms are terrestrial organisms that have changed relatively little since the mid-Cambrian. We collected Macroperipatus geagy in coffee plantations at "Hacienda El Roble", Santander, Colombia, and here redescribe the species based on 15 individuals. A digital three-dimensional reconstruction of the ventral side of the body indicates that the primary and accessory papillae lack a defined distribution pattern. Diagnostic characters: one main tooth and one accessory tooth in the outer jaw, and one main tooth, one accessory tooth and seven denticles in the internal jaw. Measurements: length (X=45.66 mm; SD=26.10), weight (X= 0.95 g; SD= 2.21) and number of lobopods (X= 28.13 pairs; SD= 1.30). We present a taxonomic key for six species of Macroperipatus. The liquid adhesive secretion lost 60% of the initial weight at 70 oC (solid: 13% close to 90 oC). The stability phase of the liquid secretion was within 90-280 oC (100 oC -205 oC in the solid secretion). The starting degradation temperature of the sample was 355 oC. Heat flow changes in the solid and liquid secretions were confirmed by the sample behavior during thermogravimetric analysis. The percentage of β sheets calculated by infrared spectrum was 59%. In comparison with Nephila spiders, the onychophoran secretion lost more weight and entered the phase of degradation at lower temperatures. This secondary structure of proteins gives the onychophoran adhesive secretion a tensile strength and extensibility similar to those of the silk produced by spiders for prey-capture. Rev. Biol. Trop. 57 (3): 567-588. Epub 2009 September 30.
Redescribimos taxonómicamente el gusano Macroperipatus geagy Bouvier 1899, a partir de 15 especímenes recolectados en los cafetales de hacienda El Roble, Santander, Colombia. De acuerdo con la reconstrucción en tres dimensiones de la superficie dorsal del cuerpo, las papilas primarias y accesorias de M. geagy se distribuyen sin formar un patrón determinado. Características diagnósticas: un diente accesorio y un diente principal en la mandíbula externa; y un diente principal, un diente accesorio y siete dentículos en la sierra de la mandíbula interna. Cuerpo: longitud (X=45.66; S=26.10 mm), peso (X= 0.95; S= 2.21) y pares de lobopodos (X= 28.13; S= 1.30). Se elaboró una clave para seis especies de Macroperipatus. La secreción adhesiva en estado líquido perdió 60% del peso inicial al alcanzar los 70 ºC, la muestra sólida perdió el 13% del peso cerca de los 90 ºC, la fase de estabilidad térmica de la secreción estuvo entre los 90 y 280 ºC en la secreción líquida y entre los 100 y 205 ºC en la sólida. La temperatura de inicio de la degradación de las muestras se registró a los 355 ºC. En comparación con la araña Nephila sp., el onicóforo perdió mayor porcentaje de peso y alcanzó la fase de degradación a temperaturas más bajas. Los cambios en el flujo de calor en la secreción adhesiva sólida y líquida de M. geagy fueron confirmados con el comportamiento de las muestras en el análisis de termogravimetría. La proporción de láminas beta calculado en el espectro infrarrojo de la secreción adhesiva fue del 59%. La presencia de este tipo de conformación de la estructura secundaria de las proteínas en la secreción adhesiva de M. geagy conferiría extensibilidad y resistencia a la tracción, en similitud con las fibras de seda tejidas por las arañas para depredación.