Amino acid composition and protein dimension

There is indirect evidence that the amino acid composition of proteins depends on their dimension. The amino acid composition of a nonredundant set of about 550,000 proteins was determined and it was observed that, in the range of 50-200 residues, the percentage of occurrence of most of the residue types significantly depends on protein dimension. This result should prove useful in analyzing protein sequences and genomics.     

Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera

The honeybee (Apis mellifera) has a genome with a wide variation in GC content showing 2 clear modal GC values, in some ways reminiscent of an isochore-like structure. To gain insight into causes and consequences of this pattern, we used a comparative approach to study the genome-wide alignment of primarily coding sequence of A. mellifera with Drosophila melanogaster and Anopheles gambiae. The latter 2 species show a higher average GC content than A. mellifera and no indications of bimodality, suggesting that the GC-poor mode is a derived condition in honeybee. In A. mellifera, synonymous sites of genes generally adopt the GC content of the region in which they reside. A large proportion of genes in GC-poor regions have not been assigned to the honeybee assembly because of the low sequence complexity of their genome neighborhood. The synonymous substitution rate between A. mellifera and the other species is very close to saturation, but analyses of nonsynonymous substitutions as well as amino acid substitutions indicate that the GC-poor regions are not evolving faster than the GC-rich regions. We describe the codon usage and amino acid usage and show that they are remarkably heterogeneous within the honeybee genome between the 2 different GC regions. Specifically, the genes located in GC-poor regions show a much larger deviation in both codon usage bias and amino acid usage from the Dipterans than the genes located in the GC-rich regions.     

Understanding the recognition of protein structural classes by amino acid composition

Knowledge of amino acid composition, alone, is verified here to be sufficient for recognizing the structural class, α, β, α+β, or α/β of a given protein with an accuracy of 81%. This is supported by results from exhaustive enumerations of all conformations for all sequences of simple, compact lattice models consisting of two types (hydrophobic and polar) of residues. Different compositions exhibit strong affinities for certain folds. Within the limits of validity of the lattice models, two factors appear to determine the choice of particular folds: 1) the coordination numbers of individual sites and 2) the size and geometry of non-bonded clusters. These two properties, collectively termed the distribution of non-bonded contacts, are quantitatively assessed by an eigenvalue analysis of the so-called Kirchhoff or adjacency matrices obtained by considering the non-bonded interactions on a lattice. The analysis permits the identification of conformations that possess the same distribution of non-bonded contacts. Furthermore, some distributions of non-bonded contacts are favored entropically, due to their high degeneracies. Thus, a competition between enthalpic and entropic effects is effective in determining the choice of a distribution for a given composition. Based on these findings, an analysis of non-bonded contacts in protein structures was made. The analysis shows that proteins belonging to the four distinct folding classes exhibit significant differences in their distributions of non-bonded contacts, which more directly explains the success in predicting structural class from amino acid composition. Proteins 29:172–185, 1997. Published 1997 Wiley-Liss, Inc.

1 This article is a US Goverment work and, as such, is in the public domain in the United States of America.

     

Distribution and amino acid composition of protein fractions in opaque-2 maize grains

Immature opaque 2 (o2) maize grains were compared with mature grains of o2 and normal maizes to determine the distribution and amino acid composition of protein fractions isolated by selective extraction. All the fractions are accumulated in o2 grains on development, except the albumins whose concentration decreases in the last stage of maturation. Each fraction has a nearly constant amino acid composition which is similar to that of the corresponding fractions present in normal grains. The data confirm that the main effect of the o2 gene is to alter the distribution of protein fractions by decreasing the proportion of accumulated zein and by increasing the proportions of salt-soluble proteins and G₃-glutelins.     

Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation

Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores, we develop a maximum-likelihood approach to determine the history of substitution patterns in the human genome. This approach utilizes the vast amount of repetitive sequence deposited in the human genome over the past approximately 250 Myr. Using this approach, we estimate the frequencies of seven types of substitutions: the four transversions, two transitions, and the methyl-assisted transition of cytosine in CpG. Comparing substitutional patterns in repetitive elements of various ages, we reconstruct the history of the base-substitutional process in the different isochores for the past 250 Myr. At around 90 MYA (around the time of the mammalian radiation), we find an abrupt fourfold to eightfold increase of the cytosine transition rate in CpG pairs compared with that of the reptilian ancestor. Further analysis of nucleotide substitutions in regions with different GC content reveals concurrent changes in the substitutional patterns. Although the substitutional pattern was dependent on the regional GC content in such ways that it preserved the regional GC content before the mammalian radiation, it lost this dependence afterward. The substitutional pattern changed from an isochore-preserving to an isochore-degrading one. We conclude that isochores have been established before the radiation of the eutherian mammals and have been subject to the process of homogenization since then.     

The amino acid composition of tissue protein is affected by the total sulfur amino acid supply in growing pigs

The factorial approach to assess the amino acid (AA) requirements of pigs is based on the assumption that the AA composition of body protein is constant. However, there are indications that this assumption may not be valid because the AA composition of body protein can be affected by the AA supply. The extent to which different tissues are affected by an AA deficiency is unknown. The objective of this study was to investigate the effect of feeding pig diets with a deficient or sufficient total sulfur AA supply (TSAA; Met+Cys) from 6 to 23 weeks of age on tissue composition and meat quality. The deficient diet (TSAA–) provided 24% Met : Lys and 51% TSAA : Lys on a standardized ileal digestible basis, which are 19% and 16% below the recommended requirements, respectively. The sufficient diet (TSAA+) provided 33% Met : Lys and 60% TSAA : Lys. Diets were offered slightly below the ad libitum feed intake capacity of the pigs. Pigs offered diet TSAA– had a lower average daily gain, lower weights of the longissimus dorsi (LM) and rhomboideus muscles (RM), and of selected skin sections (P<0.05). The weight of different sections of the small intestine and the liver was not affected by the diet. The protein content of the LM and RM decreased in pigs offered diet TSAA– (P<0.05), whereas the protein content of other tissues was not affected. The TSAA supply affected the AA composition (g/16 g N) of protein in all tissues, but the Met content was changed only in the liver (P<0.05). Pigs receiving diet TSAA– had a lower Cys content in the RM and in the distal jejunum and ileum (P<0.01). The deficient TSAA supply resulted in a lower carcass weight and higher muscle glycogen stores (P<0.05), but did not affect other meat quality traits. The results of this study indicate that the muscles, jejunum and ileum respond more to a prolonged AA deficiency than the liver. In addition, the observed changes in AA composition of tissue protein question the use of a constant AA profile of retained protein to assess AA requirements.     

Mutation-biased adaptation in a protein NK model

Evolutionary trends responsible for systematic differences in genome and proteome composition have been attributed to GC:AT mutation bias in the context of neutral evolution or to selection acting on genome composition. A possibility that has been ignored, presumably because it is part of neither the Modern Synthesis nor the Neutral Theory, is that mutation may impose a directional bias on adaptation. This possibility is explored here with simulations of the effect of a GC:AT bias on amino acid composition during adaptive walks on an abstract protein fitness landscape called an "NK" model. The results indicate that adaptation does not preclude mutation-biased evolution. In the complete absence of neutral evolution, a modest GC:AT bias of realistic magnitude can displace the trajectory of adaptation in a mutationally favored direction, to such a degree that amino acid composition is biased substantially and persistently. Thus, mutational explanations for evolved patterns need not presuppose neutral evolution.     

Adaptation of model proteins from cold to hot environments involves continuous and small adjustments of average parameters related to amino acid composition

The growth temperature adaptation of six model proteins has been studied in 42 microorganisms belonging to eubacterial and archaeal kingdoms, covering optimum growth temperatures from 7 to 103 degrees C. The selected proteins include three elongation factors involved in translation, the enzymes glyceraldehyde-3-phosphate dehydrogenase and superoxide dismutase, the cell division protein FtsZ. The common strategy of protein adaptation from cold to hot environments implies the occurrence of small changes in the amino acid composition, without altering the overall structure of the macromolecule. These continuous adjustments were investigated through parameters related to the amino acid composition of each protein. The average value per residue of mass, volume and accessible surface area allowed an evaluation of the usage of bulky residues, whereas the average hydrophobicity reflected that of hydrophobic residues. The specific proportion of bulky and hydrophobic residues in each protein almost linearly increased with the temperature of the host microorganism. This finding agrees with the structural and functional properties exhibited by proteins in differently adapted sources, thus explaining the great compactness or the high flexibility exhibited by (hyper)thermophilic or psychrophilic proteins, respectively. Indeed, heat-adapted proteins incline toward the usage of heavier-size and more hydrophobic residues with respect to mesophiles, whereas the cold-adapted macromolecules show the opposite behavior with a certain preference for smaller-size and less hydrophobic residues. An investigation on the different increase of bulky residues along with the growth temperature observed in the six model proteins suggests the relevance of the possible different role and/or structure organization played by protein domains. The significance of the linear correlations between growth temperature and parameters related to the amino acid composition improved when the analysis was collectively carried out on all model proteins.     

Amino acid composition, protein content and calculation of nitrogen-to-protein conversion factors for 19 tropical seaweeds

The use of nitrogen‐to‐protein conversion factors (N‐Prot factors) is the most practical way of determining protein content. The accuracy of protein determination by this method depends on the establishment of N‐Prot factors specific to individual species. Experimental data are needed to allow the use of this methodology with seaweeds. The present study was designed to characterize the amino acid composition and to establish specific N‐Prot factors for six green, four brown and nine red marine algae. Mean values for individual amino acids tended to be similar among the three groups, but some differences were found. Green algae tended to show lower percentages of both aspartic acid and glutamic acid than the other two groups of algae. The percentages of both lysine and arginine were higher in red algae, while brown algae tended to show more methionine than green and red algae. The actual protein content of the species, based on the sum of amino acid residues, varied from 10.8% (Chnoospora minima, brown algae) to 23.1% (Aglaothamnion uru‐guayense, red algae) of the dry weight. Nitrogen‐to‐protein conversion factors were established for the species studied, based on the ratio of amino acid residues to total nitrogen, with values ranging from 3.75 (Cryptonemia seminervis, red algae) to 5.72 (Padina gymnospora, brown algae). The relative importance of non‐protein nitrogen is greater in red algae, and consequently lower N‐Prot factors were calculated for these species (average value 4.59). Conversely, protein nitrogen content in both green and brown algae tends to be higher, and average N‐Prot factors were 5.13 and 5.38, respectively. An overall average N‐Prot factor for all species studied of 4.92 ± 0.59 (n = 57) was established. This study confirms that the use of the traditional factor 6.25 is unsuitable for seaweeds, and the use of the N‐Prot factors proposed here is recommended.     

Changes in chemical composition of Zilla spinosa Forssk. medicinal plants grown in Saudi Arabia in response to spatial and seasonal variations

Extracts of different medicinal plants had been used to control several diseases in both traditional medicine and modern drugs. In the current study, we aimed to examine the changes in chemical composition of Zilla spinosa Forssk. plants collected from different habitats in Saudi Arabia in response to spatial and seasonal variations. Z. spinosa samples were collected from two different sites in Riyadh and Eastern regions in Saudi Arabia to examine the spatial variations effects on the studied parameters. Samples were collected from both sites at two different times (3:00 PM and 3:00 AM) to examine the effect of light on the chemical content and composition of these plants. Samples was, also, collected from the same sites at two different seasons (on start of January 2018 “winter season” and end of May 2018 “summer season”) to examine the effect of temperature changes (seasonal variations) on the chemical content and composition of the different studied plants. In Z. spinosa plants collected from Riyadh region, squalene was found to be the major constitute of 3 samples; however, surprisingly, the sample collected in Winter at 3:00 AM showed the presence of mome inositol and (Z)-5-(formylmethylene)-4-methoxy-2(5 h)-furanone as the dominant components. Similarly, chemical compositions of essential oils extracted from Z. spinosa samples collected from Eastern region in the Summer season was dominated by squalene. Z. spinosa plants showed that all collected samples had high carbohydrate and protein contents with very low content of fats.     

Amino acid balancing for the prediction and evaluation of protein concentrations in cell-free protein synthesis systems

Cell-free protein synthesis (CFPS) systems are an attractive method to complement the usual cell-based synthesis of proteins, especially for screening approaches. The literature describes a wide variety of CFPS systems, but their performance is difficult to compare since the reaction components are often used at different concentrations. Therefore, we have developed a calculation tool based on amino acid balancing to evaluate the performance of CFPS by determining the fractional yield as the ratio between theoretically achievable and experimentally achieved protein molar concentration. This tool was applied to a series of experiments from our lab and to various systems described in the literature to identify systems that synthesize proteins very efficiently and those that still have potential for higher yields. The well-established Escherichia coli system showed a high efficiency in the utilization of amino acids, but interestingly, less considered systems, such as those based on Vibrio natriegens or Leishmania tarentolae, also showed exceptional fractional yields of over 70% and 90%, respectively, implying very efficient conversions of amino acids. The methods and tools described here can quickly identify when a system has reached its maximum or has limitations. We believe that this approach will facilitate the evaluation and optimization of existing CFPS systems and provides the basis for the systematic development of new CFPS systems.     

Chemical composition of labile fractions in DOM

Dissolved organic matter in natural water was classified into a labile and a refractory fraction according to the decomposition properties for microorganisms. In decomposition experiments of dissolved organic matter from an eutrophic small lake in Japan, dissolved amino acids and dissolved carbohydrates fractions could be confirmed to be the labile fractions of dissolved organic matter.Tokyo Metropolian University, Department of Chemistry, Faculty of Science     

The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis

Several studies have highlighted the leading role of the sequence periodicity of polar and nonpolar amino acids (binary patterns) in the formation of regular secondary structures (RSS). However, these were based on the analysis of only a few simple cases, with no direct mean to correlate binary patterns with the limits of RSS. Here, HCA‐derived hydrophobic clusters (HC) which are conditioned binary patterns whose positions fit well those of RSS, were considered. All the HC types, defined by unique binary patterns, which were commonly observed in three‐dimensional (3D) structures of globular domains, were analyzed. The 180 HC types with preferences for either α‐helices or β‐strands distinctly contain basic binary units typical of these RSS. Therefore a general trend supporting the “binary pattern preference” assumption was observed. HC for which observed RSS are in disagreement with their expected behavior (discordant HC) were also examined. They were separated in HC types with moderate preferences for RSS, having “weak” binary patterns and versatile RSS and HC types with high preferences for RSS, having “strong” binary patterns and then displaying nonpolar amino acids at the protein surface. It was shown that in both cases, discordant HC could be distinguished from concordant ones by well‐differentiated amino acid compositions. The obtained results could, thus, help to complement the currently available methods for the accurate prediction of secondary structures in proteins from the only information of a single amino acid sequence. This can be especially useful for characterizing orphan sequences and for assisting protein engineering and design. Proteins 2016; 84:624–638. © 2016 Wiley Periodicals, Inc.     

Comparative multivariate analysis of codon and amino acid usage in three Leishmania genomes

Multivariate analysis of codon and amino acid usage was performed for three Leishmania species, including L. donovani, L. infantum and L. major. It was revealed that all three species are under mutational bias and translational selection. Lower GC 12 and higher GC 3S in all three parasites suggests that the ancestral highly expressed genes (HEGs), compared to lowly expressed genes (LEGs), might have been rich in AT-content. This also suggests that there must have been a faster rate of evolution under GC-bias in LEGs. It was observed from the estimation of synonymous/non-synonymous substitutions in HEGs that the HEG dataset of L. donovani is much closer to L. major evolutionarily. This is also supported by the higher d N value as compared to d S between L. donovani and L. major, suggesting the conservation of synonymous codon positions between these two species and the role of translational selection in shaping the composition of protein-coding genes.     

Complete nutrient composition of commercially raised invertebrates used as food for insectivores

A variety of invertebrates are commonly fed to insectivorous animals by both zoos and hobbyists, but information as to the nutrient composition of most commercially raised species is limited. Adult house crickets, house cricket nymphs (Acheta domesticus), superworms (Zophobas morio larvae), giant mealworm larvae, mealworm larvae and adult mealworms (Tenebrio molitor), waxworm larvae (Galleria mellonella), and silkworm larvae (Bombyx mori) were analyzed for moisture, crude protein, crude fat, ash, acid detergent fiber (ADF), neutral detergent fiber (NDF), minerals, amino acids, fatty acids, and vitamins. Earthworms (Lumbricus terresstris) were analyzed for moisture, crude protein, crude fat, ash, ADF, NDF, minerals, amino acids, and vitamins A and D₃. Proximate analyses were variable, with wide ranges found for moisture (57.9–83.6%), crude protein (9.3–23.7%), crude fat (1.6–24.9%), ADF (0.1–7.4%), NDF (0.0–11.5%), and ash (0.6–1.2%). Energy content ranged from a low of 674 kcal/kg for silkworms to 2,741 kcal/kg for waxworms.Using an amino acid scoring pattern for rats, the first limiting amino acid for all invertebrates tested was the total sulfur amino acid methionine+cystine. Deficiencies by nutrient (% of samples deficient vs. NRC requirements for rats on a dry matter (DM) basis) were as follows: calcium (100%), vitamin D₃ (100%), vitamin A (89%), vitamin B₁₂ (75%), thiamin (63%), vitamin E (50%), iodine (44%), manganese (22%), methionine‐cystine (22%), and sodium (11%). Deficiencies by invertebrate species (number of nutrients deficient vs. the NRC requirements for rats on a DM basis) were as follows: waxworms (9), superworms (8), giant mealworm larvae (7), adult mealworms (6), mealworm larvae (5), adult house crickets (4), house cricket nymphs (4), silkworms (4), and earthworms (4). These data provide a basis for determining nutrient intake of captive insectivores, and will aid in the development of gut‐loading diets to provide captive insectivorous animals with appropriate levels of necessary nutrients. Zoo Biol 21:269–285, 2002. © 2002 Wiley‐Liss, Inc.     

Standardised ileal crude protein and amino acid digestibilities in protein supplements for piglets

Standardised ileal digestibilities (SID) of crude protein and amino acids (AA) originating from 24 different feed ingredients, including 11 feed ingredients produced from soybeans, seven by-products of starch processing, four whey products and two fish meals, were determined in piglets by means of the difference method. For the indispensable AA, the highest SID values were obtained in three out of four whey proteins (SID ≥90% for most indispensable AA), one out of two fish meals (SID ≥86%), soy protein concentrate, hydrolysed soy protein isolate (SID ≥86% for most indispensable AA), and by-products of starch processing (SID ≥84% for most indispensable AA). The lowest SID values were obtained in extruded soybeans and microbially fermented soy protein (SID ≤78% for most indispensable AA), whereas the SID values for high-protein soybean meal were intermediate (SID 80–89% for indispensable AA except for Thr). The SID values in the three enzymatically fermented soy proteins (SID 80–94% for most indispensable AA) were similar to those in high-protein soybean meal and soy protein concentrate. The results of the present study indicate that SID values of AA in feed ingredients for piglets differ considerably from those reported for grower-finisher pigs, thus there may be a need for separate feed tables for piglets.     

Black soldier fly as dietary protein source for broiler quails: meat proximate composition,fatty acid and amino acid profile,oxidative status and sensory traits

In the perspective of improving the sustainability of meat production, insects have been rapidly emerging as innovative feed ingredient for some livestock species, including poultry. However, at present, there is still limited knowledge regarding the quality and sensory traits of the derived meat. Therefore, the present study tested the effect of a partial substitution of soya bean meal and oil with defatted black soldier fly (Hermetia illucens) larvae meal (H) in the diet for growing broiler quails (Coturnix coturnix japonica) on meat proximate composition, cholesterol, amino acid and mineral contents, fatty acid profile, oxidative status and sensory characteristics. To this purpose, three dietary treatments were designed: a control diet (C) and two diets (H1 and H2) corresponding to 10% and 15% H inclusion levels, respectively, were fed to growing quails from 10 to 28 days of age. At 28 days of age, quails were slaughtered and breast meat was used for meat quality evaluations. Meat proximate composition, cholesterol content and oxidative status remained unaffected by H supplementation as well as its sensory characteristics and off-flavours perception. Differently, with increasing the dietary H inclusion, the total saturated fatty acid and total monounsaturated fatty acid proportions raised to the detriment of the polyunsaturated fatty acid fraction thus lowering the healthiness of the breast meat. The H2 diet increased the contents of aspartic acid, glutamic acid, alanine, serine, tyrosine and threonine thus further enhancing the biological value of the meat protein. As a direct result of the dietary content of Ca and P, the meat of quails fed with the highest H level, displayed the highest Ca and the lowest P values. Therefore, meat quality evaluations confirmed H to be a promising insect protein source for quails. The only potential drawback from feeding H to broiler quails regarded the fatty acid profile of the meat, therefore requiring further research efforts to understand to what extent the fatty acid profile of H can be improved.     

The amino acid composition of gum exudates from Prosopis species

The amino acid compositions of the proteinaceous components of the gum exudates from Prosopis alba, P. chilensis, P. glandulosa, P. laevigata, P. torreyana and P. velutina, and for a sample of commercial gum mesquite, are presented. In agreement with data published previously for the polysaccharide components of their gums, only minor differences in composition are shown by these species. The amino acid compositions are characterized by very high proportions of hydroxyproline and by high proportions of proline and serine; these three amino acids account for 62.5% of those present in the gum from Prosopis velutina. The amino acid compositions of these Prosopis gums are remarkably similar to that established recently for the gum from Acacia senegal (gum arabic).     

Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae

We sequenced nucleosomal DNA fragments of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae and then mapped those sequences on their genomes. We compared the GC content and nucleosome density in the exonic and intronic regions in the genes of A. nidulans and A. oryzae. Although the GC content and nucleosome density in the exonic regions tended to be higher than those in the intronic regions, the difference in the distribution of the GC content was more notable than that of the nucleosome density. Next, we compared the GC content and nucleosome density in the exonic regions of 9616 orthologous gene pairs. In both Aspergillus species, the GC content did not correlate with the nucleosome density. In addition, the Spearman's rank correlation coefficient (ρ = 0.51) between the GC content of the exonic regions of the 9616 orthologous gene pairs was higher than that (ρ = 0.31) of the nucleosome densities of A. nidulans and A. oryzae. These results strongly suggest that the GC content in the exons of the orthologous gene pairs has been conserved during evolution but the nucleosome density has varied throughout.     

Influence of branched-chain amino acid composition of culture media on the synthesis of plasma proteins by serum-free cultured rat hepatocytes

Summary Supplementation of Ham's F12 culture medium with essential amino acids (EAA) up to the rat plasma levels increased the rates of synthesis of albumin and transferrin by cultured rat hepatocytes by 1.3 and 1.7, respectively. Fifty percent of this increase could be attributed to three of the EAA: the branched-chain amino acids (BCAA: Leu Ile and Val). Non-branched-chain essential amino acids (non-BC-EAA) stimulated only 25% of the increase produced by the whole EAA mixture. When each EAA was tested individually, none of them caused an appreciable increase in albumin and transferrin in culture medium. When the concentrations of all EAA were raised to rat postprandial portal levels, albumin and transferrin synthesis rates reached a maximum, increasing by 3.2 and 3.5, respectively. Supplementation with BCAA at postprandial portal concentrations increased albumin and transferrin synthesis rates by 2.2 and 2.0, respectively, and had no noteworthy effect on the synthesis of cellular proteins. Non-BC-EAA at their postprandial portal concentrations increased albumin and transferrin synthesis rates by 1.7 and 1.9, respectively. Supplementation with alanine to reach a nitrogen content equal to that of the modified EAA-enriched medium had no stimulatory effect. Our results show that EAA have a specific effect on the synthesis of plasma proteins by cultured hepatocytes, and that BCAA at physiologic concentrations account for the major part of this stimulatory effect. Consequently, EAA and particularly BCAA concentration should be elevated in serum-free nutrient media to sustain maximum plasma protein synthesis.