Amino acid composition

Functional annotation of protein sequences with low similarity to well characterized protein sequences is a major challenge of computational biology in the post genomic era. The cyclin protein family is once such important family of proteins which consists of sequences with low sequence similarity making discovery of novel cyclins and establishing orthologous relationships amongst the cyclins, a difficult task. The currently identified cyclin motifs and cyclin associated domains do not represent all of the identified and characterized cyclin sequences. We describe a Support Vector Machine (SVM) based classifier, CyclinPred, which can predict cyclin sequences with high efficiency. The SVM classifier was trained with features of selected cyclin and non cyclin protein sequences. The training features of the protein sequences include amino acid composition, dipeptide composition, secondary structure composition and PSI-BLAST generated Position Specific Scoring Matrix (PSSM) profiles. Re...

Plants constitute an alternative source of proteins in the human diet, with advantages over animal proteins because of their low content of saturated fats and absence of cholesterol. Within the framework of a wider research project on the role of Amaranthus cruentus (Ac) in lipid metabolism, in this work the chemical composition and biological value of the Ac flour and its protein concentrate were compared. Proximate chemical composition, amino acid and fatty acid profiles, some antinutrient factors, and biological values were determined for Ac seed flour and its protein concentrate obtained by extraction at pH 11 and precipitation at pH 4.5. The flour protein content was 16.6 g% while that of the concentrate was 52.56 g%. The content of the soluble dietary fiber with a hypolipemic function was notably higher in the protein concentrate (12.90 g%) than in the seed flour (4.29 g%). The protein concentrate also exhibited a higher content of insoluble dietary fiber. The Ac flour and the...

Two laccase isoenzymes produced by Pleurotus eryngii were purified to electrophoretic homogeneity (42- and 43-fold) with an overall yield of 56.3%. Laccases I and II from this fungus are monomeric glycoproteins with 7 and 1% carbohydrate content, molecular masses (by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of 65 and 61 kDa, and pIs of 4.1 and 4.2, respectively. The highest rate of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) oxidation for laccase I was reached at 65 degrees C and pH 4, and that for laccase II was reached at 55 degrees C and pH 3.5. Both isoenzymes are stable at high pH, retaining 60 to 70% activity after 24 h from pH 8 to 12. Their amino acid compositions and N-terminal sequences were determined, the latter strongly differing from those of laccases of other basidiomycetes. Antibodies against laccase I reacted with laccase II, as well as with laccases from Pleurotus ostreatus, Pleurotus pulmonarius, and Pleurotus floridanus. Different hyd...

The results of microbiological and toxicological tests have proved the safety of the
bone-muscular cod waste (BMW). Waste (humerus with meat cuts) from cod cutting
on fillets contains 18,95 % of a full-grade animal protein and insignificant amount of
fat (0.15 %). Thus, the possibility of using them as a protein raw material for
producing peptones has been proved. The technology of obtaining peptone from the
secondary fish raw material - bone-muscular waste from the cutting of cod fish - has
been developed and optimized. Using the cryoextrusion method in the technology of
peptone production at the stage of grinding waste is proposed. Using of the enzyme
(protosubtilin G3X) in hydrolysis is substantiated; proteolytic activity is established, it
is 560,77 μmol TYR / g, the optimal temperature of enzymatic hydrolysis of BMW is
(45±1) ˚С.
Using the theory of experiment planning and computer modeling, a series of works
was carried out to optimize the stage of enzymatic hydrolysis of fish wastes. Nearly
optimal hydrolysis parameters were found: enzyme concentration of 1,33 % to total
waste weight, duration of hydrolysis process of 3 hours. The chemical and
biochemical quality characteristics of the enzymatic peptone obtained by the
optimized technology have been researched. It was found that the mass fraction of
protein in the product is of 92,27 %, water is of 4,7 %, sodium chloride is of 2,6 %, fat
is of 0,3 %. The amino acid composition has been determined with the method of highperformance liquid chromatography. It made it possible to calculate the biological
value of peptone. Tryptophan has been established to be the only limiting amino acid

Conotoxins are disulfide rich small peptides that target a broad spectrum of ion-channels and neuronal receptors. They offer promising avenues in the treatment of chronic pain, epilepsy and cardiovascular diseases. Assignment of newly sequenced mature conotoxins into ...

Grains of most cereal species, like wheat, maize and sorghum, which represent the world's largest providers of food and consequently important economical commodities, contain inadequate levels of some essential amino acids, particularly lysine, threonine, tryptophan and methionine. These deficiencies arise from the amino acid composition of the grain storage proteins, called prolamins, which account for up to 80% of the total grain proteins. In sorghum these deficiencies are also exacerbated by cooking, which reduces sorghum protein digestibility. Similarly, binding of tannins to proteins can also reduce digestibility in high tannin lines. Our ability to improve the nutritional quality (defined as the content of essential amino acids) of sorghum grain protein by classical plant breeding is limited by the low level of variation in the gene pool available for crossing. Genetic engineering offers an opportunity to overcome this limitation by introducing wild type or mutant genes fr...

Two novel type I ribosome-inactivating proteins (RIPs) were found in the storage roots of Mirabilis expansa, an underutilized Andean root crop. The two RIPs, named ME1 and ME2, were purified to homogeneity by ammonium sulfate precipitation, cationexchange perfusion chromatography, and C4 reverse-phase chromatography. The two proteins were found to be similar in size (27 and 27.5 kD) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their isoelectric points were determined to be greater than pH 10.0. Amino acid N-terminal sequencing revealed that both ME1 and ME2 had conserved residues characteristic of RIPs. Amino acid composition and western-blot analysis further suggested a structural similarity between ME1 and ME2. ME2 showed high similarity to the Mirabilis jalapa antiviral protein, a type I RIP. Depurination of yeast 26S rRNA by ME1 and ME2 demonstrated their ribosome-inactivating activity. Because these two proteins were isolated from roots, their antimicrobial...

Humans have had a historic and cherished association with silk. The lustre, handle, and draping qualities of silk fibers are definitely superior to those of other textile fibers.1 Because of this, efforts are ongoing to manufacture silklike fibers. Silk is an animal fiber secreted as a continuous ...

Functional annotation of protein sequences with low similarity to well characterized protein sequences is a major challenge of computational biology in the post genomic era. The cyclin protein family is once such important family of proteins which consists of sequences with low sequence similarity making discovery of novel cyclins and establishing orthologous relationships amongst the cyclins, a difficult task. The currently identified cyclin motifs and cyclin associated domains do not represent all of the identified and characterized cyclin ...

Purification of extracellular α-amylase from Bacillus subtilis KIBGE HAS was carried out by ultrafiltration, ammonium sulfate precipitation and gel filtration chromatography. The enzyme was purified to homogeneity with 96.3-fold purification with specific activity of 13011 U/mg. The molecular weight of purified α-amylase was found to be 56,000 Da by SDS-PAGE. Characteristics of extracellular α-amylase showed that the enzyme had a Km and

Maximum likelihood (ML) phylogenies based on 9,957 amino acid (AA) sites of 45 proteins encoded in the plastid genomes of Cyanophora, a diatom, a rhodophyte (red algae), a euglenophyte, and five land plants are compared with respect to several properties of the data, including between-site rate variation and aberrant amino acid composition in individual species. Neighbor-joining trees from AA LogDet distances and ML analyses are seen to be congruent when site rate variability was taken into account. Four feasible trees are identified in these analyses, one of which is preferred, and one of which is almost excluded by statistical criteria. A transition probability matrix for the general reversible Markov model of amino acid substitutions is estimated from the data, assuming each of these four trees. In all cases, the tree with diatom and rhodophyte as sister taxa was clearly favored. The new transition matrix based on the best tree, called cpREV, takes into account distinct substitut...

Amaranth was a major crop among the Aztecs. In Mexico the seed is popped and eaten with brown sugar. The crude protein content of the seed is 14 +/- 2% but its contents of lysine and tryptophan are 6.2 and 1.6 g/16 g N respectively. We developed a popping method based on a fluid bed system (FBS) whereas the traditional method (TM) is just to pop the seeds manually in a hot plate. Assays carried out were evaluation of racemization of the amaranth protein due to heat treatment, amino acid composition of the raw and heat treated seeds and a biological experiment testing whether leucine was the most limiting amino acid of amaranth protein. Male rats were fed both popped amaranths and roasted amaranth. Parboiled amaranth and casein were controls. The results were: (a) Lys, Arg and Cys were damaged in the heat treated seeds; (b) Asp, Met, Glu, Ala and Phe were racemized in that decreasing order in the seeds popped and roasted by the TM; (c) the estimated net protein retention (NPR) and estimated net protein utilization (NPU) of popped amaranths by either method were not different, but were lower than for the parboiled amaranth. The parboiled amaranth was not different from casein; (d) Leu was not the most limiting amino acid in any of the amaranth seeds tested. After Lys, sulfur amino acids appear to be the next most limiting in severely heat treated amaranth. The FBS seems to be a promising method for popping amaranth at industrial level.

Oligodeoxynucleotides complementary to the deduced mRNA sequence of soybean Kunitz trypsin inhibitor (KTI) were used to prime the synthesis of cDNA from soybean cotyledon total poly(A) RNA. The primed cDNA was used to select clones from a Glycine max cotyledon cDNA library. Two out of twelve hybridizing clones were shown to contain KTI cDNA. The nucleotide sequence of one clone, pSTI 9-2, was determined and it was found to encompass the complete protein coding region of KTI excet for three C-terminal residues. Trypsin inhibitor is synthesized with a 25 amino acid hydrophobic N-terminal sequence presumed to be a signal peptide. The mature polypeptide encoded by pSTI 9-2 agrees with the published amino acid composition of KTI, but contains two discrepancies at the peptide sequence level.

Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular 'adaptive' strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using ...

The active vaccine component recombinant chimeric IgE Fc-fragment opossum-human-opossum (OSO) has been expressed in CHO-K1 cells. It contains two identical polypeptide chains with 338 amino acid residues in each chain connected by two disulfide bridges. The cell lines were adapted to suspension culture in a serum-free medium. An expression level of 60 mg/L was obtained after 8 days in a shaking flask at a temperature of 31.5 degrees C. The OSO protein has been purified to homogeneity by a combination of three chromatographic steps. Virus inactivation and reduction by solvent detergent treatment and nano-filtration were included in the process. The residual host cell protein content was less than 50 ng/mg OSO as analyzed by ELISA. Purity was analyzed by SDS-PAGE under reducing and non-reducing conditions and was estimated by densitometry to be above 99.0%. The dimer content was less than 0.1% as estimated by analytical size exclusion chromatography. The molecular mass, as estimated b...