Amino acids and their metabolites in Eimeria tenella (Coccidiida) oocysts

The amino acid composition of protein in the oocysts of Eimeria tenella has been studied in detail by using the new method of purification of the coccidial oocysts. 35 amino acids and their metabolites have been established for the first time at the exogenous stages of development of E. tenella. The oocyst sporulation is noted to be followed by quantitative changes of the majority of free amino acids and their metabolites.     

Method for the determination of protein evolution rates by amino acid composition. Evolution rate of actins

A method has been developed to determine the actin evolution rate. The method is based on amino acid composition. The actin evolution rate has been established to be extremely low. Only three or less amino acid changes per hundred amino acid residues have accumulated for a 100 million years. One can explain the conservative nature of actin evolution as a sequence of its unique tightly fitted structure rich in biologically active centres at short distances from each other. The peculiar invariability of polar amino acids leads to a conclusion that some given distribution of charges is necessary for the unique functioning of actin molecules.     

Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms

Correlations between genomic GC contents and amino acid frequencies were studied in the homologous sequences of 12 eubacterial genomes. Results show that amino acids encoded by GC-rich codons increases significantly with genomic GC contents, whereas opposite trend was observed in case of amino acids encoded by GC-poor codons. Further studies show all the amino acids do not change in the predicted direction according to their genomic GC pressure, suggesting that protein evolution is not entirely dictated by their nucleotide frequencies. Amino acid substitution matrix calculated among hydrophobic, amphipathic and hydrophilic amino acid groups' shows that amphipathic and hydrophilic amino acids are more frequently substituted by hydrophobic amino acids than from hydrophobic to hydrophilic or amphipathic amino acids. This indicates that nucleotide bias induces a directional changes in proteome composition in such a way that underwent strong changes in hydropathy values. In fact, significant increases in hydrophobicity values have also been observed with the increase of genomic GC contents. Correlations between GC contents and amino acid compositions in three different predicted protein secondary structures show that hydropathy values increases significantly with GC contents in aperiodic and helix structures whereas strand structure remains insensitive with the genomic GC levels. The relative importance of mutation and selection on the evolution of proteins have been discussed on the basis of these results.     

Amino acid production in isolated rat liver mitochondria

Amino acid analyses of mitochondrial membranes are compared with the amino acid composition of whole mitochondria (Alberti, 1964) and found to be very similar except in the cystine content. The composition of the endogenous amino acids found in freshly prepared mitochondria has been established and shown to differ considerably from the amino acid composition of membranes or whole mitochondria. The amino acids produced during anaerobic incubation of mitochondria at pH7.4, on the other hand, resemble the membrane in composition, supporting the view that neutral proteinase activity is responsible for their appearance. Aerobic incubation produces a similar pattern of amino acids except that amino acids such as proline, serine, asparagine, glutamic acid and glutamine, which can be metabolically utilized under aerobic conditions, are present to a smaller extent. The presence of large relative concentrations of endogenous taurine, cysteic acid and oxidized glutathione and the accumulation of taurine during incubation is found. The selective retention of taurine and cysteic acid within the mitochondria is established. It is proposed that the first step in the degeneration of isolated mitochondria results from lipid hydroperoxide accumulation caused by the lack of glutathione reductase in isolated mitochondria.     

The aminoacyl phosphatidyl glycerols of the plastid membrane system in the process of chloroplast biogenesis

The composition of aminoacyl phosphatidyl glycerols in maize plastids at different stages of chloroplast differentiation has been studied. In the course of incubation of 14C amino acids or 14CO2 with maize and bean seedlings in vivo the 14C amino acids were incorporated preferably into the acid phospholipid fraction, forming O-esters of amino acids with phosphatidylglycerols. The rate of lipoamino acid compounds formation increased with the chloroplast differentiation and reached its maximum in the seedlings containing chloroplasts with a developed lamellar system. Changes in the amino acid composition of 14C aminoacyl phosphatidyl glycerols were observed at all stages of chloroplast ultrastructure development.     

What Amino Acid Properties Affect Protein Evolution?

We studied 10 protein-coding mitochondrial genes from 19 mammalian species to evaluate the effects of 10 amino acid properties on the evolution of the genetic code, the amino acid composition of proteins, and the pattern of nonsynonymous substitutions. The 10 amino acid properties studied are the chemical composition of the side chain, two polarity measures, hydropathy, isoelectric point, volume, aromaticity, aliphaticity, hydrogenation, and hydroxythiolation. The genetic code appears to have evolved toward minimizing polarity and hydropathy but not the other seven properties. This can be explained by our finding that the presumably primitive amino acids differed much only in polarity and hydropathy, but little in the other properties. Only the chemical composition (C) and isoelectric point (IE) appear to have affected the amino acid composition of the proteins studied, that is, these proteins tend to have more amino acids with typical C and IE values, so that nonsynonymous mutations tend to result in small differences in C and IE. All properties, except for hydroxythiolation, affect the rate of nonsynonymous substitution, with the observed amino acid changes having only small differences in these properties, relative to the spectrum of all possible nonsynonymous mutations. Received: 2 January 1998 / Accepted: 25 April 1998     

Formation of specific amino acid sequences during carbodiimide-mediated condensation of amino acids in aqueous solution,and computer-simulated sequence generation

Carbodiimide-mediated peptide synthesis in aqueous solution has been studied with respect to self-ordering of amino acids. The copolymerisation of amino acids in the presence of glutamic acid or pyroglutamic acid leads to short pyroglutamyl peptides. Without pyroglutamic acid the formation of higher polymers is favoured.The interactions of the amino acids and the peptides, however, are very complex. Therefore, the experimental results are rather difficult to explain. Some of the experimental results, however, can be explained with the aid of computer simulation programs. Regarding only the tripeptide fraction the copolymerisation of pyroGlu, Ala and Leu, as well as the simulated copolymerisation lead to pyroGlu-Ala-Leu as the main reaction product. The amino acid composition of the insoluble peptides formed during the copolymerisation of Ser, Gly, Ala, Val, Phe, Leu and Ile corresponds in part to the computer-simulated copolymerisation data.     

Formation of specific amino acid sequences during carbodiimide-mediated condensation of amino acids in aqueous solution, and computer-simulated sequence generation

Carbodiimide-mediated peptide synthesis in aqueous solution has been studied with respect to self-ordering of amino acids. The copolymerisation of amino acids in the presence of glutamic acid or pyroglutamic acid leads to short pyroglutamyl peptides. Without pyroglutamic acid the formation of higher polymers is favoured. The interactions of the amino acids and the peptides, however, are very complex. Therefore, the experimental results are rather difficult to explain. Some of the experimental results, however, can be explained with the aid of computer simulation programs. Regarding only the tripeptide fraction the copolymerisation of pyroGlu, Ala and Leu, as well as the simulated copolymerisation lead to pyroGlu-Ala-Leu as the main reaction product. The amino acid composition of the insoluble peptides formed during the copolymerisation of Ser, Gly, Ala, Val, Phe, Leu and Ile corresponds in part to the computer-simulated copolymerisation data.     

Amino acids metabolism by VO 208 hybridoma cells: some aspects of the culture process and medium composition influence

In the present study an approach has been developed in order to examine the consequence of essential and non essential amino acid supplementation on VO208 hybridoma cells behaviour. The effect of amino acid enrichment has been studied taking into account the culture process, i.e., batch or continuous culture mode and the medium composition, i.e., a home made serum-free medium or a serum containing one. A group of 4 amino acids, i.e., Ser, Pro, Gly and Arg presented atypical evolution pattern of their extracellular concentration depending on the type of the medium and on the culture mode. Some amino acids were probably involved in the limitation of the cellular proliferation. Met was one of the amino acids that appears to may have been at limiting concentration in all cases. In continuous culture mode, an enrichment of amino acids resulted in a rapid improvement of the viable cell density in both media, with or without the presence of serum. For most amino acids, supplementation during continuous culture induced an increase of the amino acid uptake rate. A comparative analysis of amino acids utilisation, depending on the culture conditions studied in the present study, has been performed in order to propose an overall picture of amino acids metabolism by VO 208 Hybridoma cell line. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effect of acute intestinal obstruction on erythrocyte membrane function

The amino acid composition of red blood cell membrane proteins had been studied in different stages of acute intestinal obstruction. Hydrophobic amino acids were revealed to increase and glutamate was found to decrease during the early period of acute intestinal obstruction. Later neutral amino acids and some of the main amino acids were stated to decrease. Shifts in the ratio of protein fractions seen in red blood cell membrane of rats with acute intestinal obstruction could be explained by changes followed in the amino acid composition. The data accumulated had demonstrated that such a significant modification of protein component of the red blood cell membrane could be one of the reasons of the erythrocyte membrane penetrability violation and could play the pathogenetic role in the occurrence of irreversibility changes in cases of the intestinal obstruction. All that was mentioned above had shown the necessity to use membrane protectors and antienzyme drugs in the postoperative period.     

Effect of some essential amino acid deficiency in the medium on the action of insulin on primary cultured hepatocytes of rats. Hepatocytes do not respond to insulin in some essential amino acid-deficient medium

1. The effects of insulin, glucagon and dexamethasone on the amino acid consumption by primary cultures of rat hepatocytes were studied in a medium containing all essential amino acids or in those deficient in some essential or nonessential amino acids. 2. The cells which were cultured in a medium containing all the essential amino acids responded to insulin by enhancing the consumption of amino acids and augmenting protein synthesis. 3. However, the cells did not respond to insulin significantly when they were cultured in a medium deficient in lysine or some other essential amino acids. 4. The results suggest that some essential amino acid deficiency impairs the transmission of the signal of insulin to the site of the metabolic changes induced by the hormone.     

Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code

To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code.     

The effect of the antibiotic AL-87 on the amino acid yield from Staphylococcus aureus 209P cells]

Antibiotic AL-87 has been studied for its effect on the composition of intracellular free amino acids and of amino acids in culture fluid of Staphylococcus aureus 209 P. It is established that the content of amino acids in the culture fluid of S. aureus 209 P is doubled due to antibiotics, while the content of intracellular free amino acids considerably decreases. Spectrum of free amino acids of S. aureus 209 P is presented by 17 basic amino acids. When there is a sub-bacteriostatic concentration of the antibiotic in the medium all free amino acids tend to leave the cells, the content of aspartic acid, serine, threonine and leucine in the medium being increased. Data obtained when studying the effect of antibiotic AL-87 on the composition of free amino acids of Staphylococcus agree well with the previously obtained results from the study of the fatty acid composition of cells. In the light of these data it may be supposed that an increase of the membrane permeability and as a result of it an outlet of amino acids into the medium is one of constituents of the mechanism of antibiotic AL-87 action on Staphylococcus cells.     

Effect of 24-hour starvation on amino acid pool composition and enzyme activities of rat brown adipose tissue

The effect of 24-hr starvation on the amino acid pool composition and its concentration ratios with respect to blood and plasma as well as the activities of alanine, aspartate and branched chain amino acid transaminases, glutamate dehydrogenase, glutamine synthetase and adenylate deaminase have been studied in rat brown adipose tissue. Starvation induced a considerable decrease of pool amino acid concentration. Alanine and taurine were the amino acids in which the decrease was more marked. Small changes were observed in the activities of the enzymes studied, with decreases only in glutamate dehydrogenase and adenylate deaminase. These changes agree with a decrease in amino acid utilization in this tissue induced by starvation.     

Biochemical composition of algivorous freshwater ciliates: you are not what you eat

The focus of our study was to determine whether the biochemical composition of two algivorous ciliates, both fed the same alga, resembles that of their diet. By comparing both ciliated protozoa we intended to identify species-specific differences in the metabolic features of these ciliates. Carbon- and cell-specific concentrations of fatty acids and essential amino acids were investigated for the ciliates Balanion planctonicum and Urotricha farcta grown on the cryptomonad Cryptomonas phaseolus. Stepwise discriminant analyses (SDA) indicated differences in the biochemical composition between ciliates and their diet and between the two ciliated protozoa. Carbon-specific fatty acid concentrations were usually higher in the ciliates than in their diet, especially concentrations of monounsaturated and some polyunsaturated fatty acids. Except for tryptophan, valine, and lysine, amino acid concentrations were higher in the ciliates than in C. phaseolus. Furthermore, differences in the polyunsaturated fatty acids accounted for the largest discrepancies between the two ciliated protozoa. The higher concentrations in the ciliates compared to their diet suggest that these species are capable of efficiently ingesting, assimilating or possibly synthesizing some fatty acids and amino acids. We conclude that dietary fatty acid and amino acid composition influences the composition of the two ciliated protozoa to a minor extent, and that species-specific differences in fatty acid and amino acid metabolism may be more important determinants of the biochemical composition of the studied ciliates. Moreover, the metabolism of polyunsaturated fatty acids seems to differ more profoundly between the two ciliated protozoa than the metabolism of other fatty acid classes or amino acids.     

Distribution of amino acid residues in the primary protein structure

The amino acid composition and sequence in primary structure of 180 proteins have been studied. It is shown that the distribution of amino acid residues is near to a random one, i.e. it is determined by the amino acid composition. The ratio between statistical and unique character of protein primary structures has been discussed. The amino acid sequence is suggested to be unique in fibrous proteins. In contrast the amino acid sequence in globular proteins is a statistical one. The statistical character of amino acids distribution in globular proteins explains the possibility of sensible text generation under the frame shift mutations, deletions and insertions.     

RNA editing of wheat mitochondrial ATP synthase subunit 9: direct protein and cDNA sequencing.

RNA editing of subunit 9 of the wheat mitochondrial ATP synthase has been studied by cDNA and protein sequence analysis. Most of the cDNA clones sequenced (95%) showed that editing by C-to-U transitions occurred at eight positions in the coding region. Consequently, 5 amino acids were changed in the protein when compared with the sequence predicted from the gene. Two edited codons gave no changes (silent editing). One of the C-to-U transitions generated a stop codon by modifying the arginine codon CGA to UGA. Thus, the protein produced is 6 amino acids shorter than that deduced from the genomic sequence. Minor forms of cDNA with partial or overedited sequences were also found. Protein sequence and amino acid composition analyses confirmed the results obtained by cDNA sequencing and showed that the major form of edited atp9 mRNA is translated.     

A study of the interaction of human spermatozoa membrane with ATP and cyclic-AMP

The three coat proteins of foot-and-mouth disease virus type O can be separated in milligram amounts using a SE-cellulose ionic exchanger, both from each other and viral RNA not quantitatively precipitated by acetic acid. The amino acid composition of the separated proteins has been determined and a statistical method has been used to calculate, for each, the most probable number of amino acids and molecular weight. The N-terminal amino acids of the three proteins are glycine, asparagine and threonine.     

Individual amino acid balances in young lean and obese Zucker rats fed a cafeteria diet

The amino acid composition of the diet ingested by reference and cafeteria diet-fed lean and obese Zucker rats has been analyzed from day 30 to 60 after birth. Their body protein amino acid composition was measured, as well as the urinary and faecal losses incurred during the period studied. The protein actually selected by the rats fed the cafeteria diet had essentially the same amino acid composition as the reference diet. The mean protein amino acid composition of the rat showed only small changes with breed, age or diet.Cafeteria-fed rats had a higher dietary protein digestion/absorption efficiency than reference diet-fed rats. Obese rats wasted a high proportion of dietary amino acids when given the reference diet, but not on the cafeteria diet. In all cases, the amino acids lost as such in the urine were a minimal portion of available amino acids.In addition to breed, the rates of protein accretion are deeply influenced by diet, but even more by the age — or size — of the animals: cafeteria-fed rats grew faster, to higher body protein settings, but later protein accrual decreased considerably; this is probably due to a limitation in the blueprint for growth which restricts net protein deposition when a certain body size is attained. Obese rats, however, kept accuring protein with high rates throughout.Diet composition — and not protein availability or quality-induced deep changes in amino acid metabolism. Since the differences in the absolute levels of dietary protein or carbohydrate energy ingested by rats fed the reference or cafeteria diets were small, it can be assumed that high (lipid) energy elicits the changes observed in amino acid metabolism by the cafeteria diet. The effects induced in the fate of the nitrogen ingested were more related to the fractional protein energy proportion than to its absolute values. Cafeteria-fed rats tended to absorb more amino acids and preserve them more efficiently; these effects were shown even under conditions of genetic obesity.There were deep differences in handling of dietary amino acids by dietary or genetically obese rats. The former manage to extract and accrue larger proportions of their dietary amino acids than the latter. The effects of both models of amino acid management were largely additive, suggesting that the mechanisms underlying the development of obesity did not run in parallel to those affecting the control of amino acid utilization. Obesity may be developed in both cases despite a completely different strategy of amino acid assimilation, accrual and utilization. (Mol Cell Biochem121: 45–58, 1993)     

Amino acid composition of aragonitic concholin in the shell of Arctica islandica

Haugen, J. E. & Sejrup, H. P. 1990 04 15: Amino acid composition of aragonitic conchiolin in the shell of Arctica islandica. Lethaia , Vol. 23, pp. 133–141. Oslo. ISSN 0024–1164.
The distribution of amino acids within the two aragonitic shell layers of modern specimens of the mollusc Arctica islandica (Linné) has been studied in detail. The mean total hydrolyzed amino acid content was 19 nmol*mg in the inner layer and 15 nmol/mg in the outer layer. No significant difference in amino acid composition could be found between the two layers. The layers contained minor amounts of free amino acids which made up 0.3–0.7% of the total hydrolyzed amino acid content. The composition of the free amino acid fraction was very similar in each of the two layers, but differed somewhat from the total hydrolyzed fraction. The total hydrolyzed fraction was dominated by aspartic acid, glycine. alanine and glutamic acid, which together made up 62% of the total amount of amino acids, whereas the free fraction was dominated by Asp. Ser, Gly and Tyr. Amino acid content and composition within a single layer showed little variation from umbo to the ventral margin. The amino acid composition is in accordance with previously reported data on similar mineral structures which support the theory of structure specific rather than species specific amino acid composition. * Arctica islandica. amino acids. shell structure .