Search results for "Amino acid composition"

Amino acid composition in eyes from zebrafish (Danio rerio) and sardine (Sardina pilchardus) at the larval stage

2016

A comparative study was performed to identify differences in the amino acid composition of the eyes from zebrafish (Danio rerio) and sardine (Sardina pilchardus) larvae and their link to the environmental adaption of the species. Amino acids in the acidic hydrolysates of eyes from 11 zebrafish and 12 sardine were determined with the use of high-performance liquid chromatography involving precolumn derivatization with ortho-phthalaldehyde. Differences in the content of most amino acids were detected between zebrafish and sardine. These amino acids were aspartate, glutamate, serine, glycine, threonine, arginine, methionine, valine, phenylalanine, isoleucine, leucine and lysine. Of particular …

2018

Amino acid composition is a sequence feature that has been extensively used to characterize proteomes of many species and protein families. Yet the analysis of amino acid composition of protein domains and the linkers connecting them has received less attention. Here, we perform both a comprehensive full-proteome amino acid composition analysis and a similar analysis focusing on domains and linkers, to uncover domain- or linker-specific differential amino acid usage patterns. The amino acid composition in the 38 proteomes studied showcase the greater variability found in archaea and bacteria species compared to eukaryotes. When focusing on domains and linkers, we describe the preferential u…

Avoided motifs: short amino acid strings missing from protein datasets.

2020

Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins…

Protein data condensation for effective quaternary structure classification

2007

Many proteins are composed of two or more subunits, each associated with different polypeptide chains. The number and the arrangement of subunits forming a protein are referred to as quaternary structure. The quaternary structure of a protein is important, since it characterizes the biological function of the protein when it is involved in specific biological processes. Unfortunately, quaternary structures are not trivially deducible from protein amino acid sequences. In this work, we propose a protein quaternary structure classification method exploiting the functional domain composition of proteins. It is based on a nearest neighbor condensation technique in order to reduce both the porti…

Proteome-wide comparison between the amino acid composition of domains and linkers

2018

Objective Amino acid composition is a sequence feature that has been extensively used to characterize proteomes of many species and protein families. Yet the analysis of amino acid composition of protein domains and the linkers connecting them has received less attention. Here, we perform both a comprehensive full-proteome amino acid composition analysis and a similar analysis focusing on domains and linkers, to uncover domain- or linker-specific differential amino acid usage patterns. Results The amino acid composition in the 38 proteomes studied showcase the greater variability found in archaea and bacteria species compared to eukaryotes. When focusing on domains and linkers, we describe …

Polymer-coated reversed-phase packings with controlled hydrophobic properties

1992

Abstract We have designed and synthesized novel reversed-phase packings of non-porous and porous polymethacrylate-coated silicas. By varying the hydrophobicity of the polymer coating, selective unfolding of polypeptides may be achieved, thus enabling manipulation of the chromatographic profile. This study characterizes these packings through their employment for separations of model synthetic peptides of defined secondary, tertiary and quaternary structure. Thus, the packings were applied to the reversed-phase separation α-helical amphipathic and non-amphipathic peptides of the same amino acid composition but different sequences. In addition, selective unfolding of model to-stranded α-helic…

Relationships between metabolic fluxes and enzyme amino acid composition

2013

AbstractMetabolic fluxes are a key parameter of metabolic pathways being closely related to the kinetic properties of enzymes and could be conditional on their sequence characteristics. This study examines possible relationships between the metabolic fluxes and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. Metabolic fluxes were quantified by the COPASI tool using the kinetic models of Hynne and Teusink at 25 mM, 50 mM, and 100 mM of external glucose or employing literature data for cognate kinetic or stoichiometric models. The enzyme sequences were taken from the UniProtKB, and the AAC computed by the ExPASy/ProtParam tool. Mul…

Amino Acid Contents of Infant Formulas

1999

Abstract The amino acid supply in an infant's first month of life must be sufficient in quantity and quality to fulfil the needs of this period of life. Guidelines, recommendations and minimum and maximum values have been established regarding to amino acid composition of infant formulas. The aim of this study was to determine the amino acid profile of infant formulas of different types marketed in Spain in order to assess the compliance with the recommendations (ESPGAN) and to detect possible differences in the amino acid profiles depending on the protein source. Amino acids were determined by HPLC in ion-pair reversed phase after hydrolysis and derivatization with phenylisothiocyanate. Ne…

Engraulis encrasicolus larvae from two different environmental spawning areas of the Central Mediterranean Sea: first data on amino acid profiles and…

2020

Early life stages of marine fish populations may be strongly affected by environmental factors. Changes in the physical environment or the availability of food resources could lead to stress-related physiological responses affecting larval fitness, growth and survival. In the present study, we determined, for the first time, amino acid composition (AAC), lipid, and carbohydrate content, as well as alkaline phosphatase and peroxidase activities in larvae from the European anchovy Engraulis encrasicolus. Fishes were caught in two different spawning areas of the Strait of Sicily, characterized by different environmental conditions, including a coastal upwelling with a lower temperature (Advent…