Asymmetric amino acid compositions of transmembrane beta-strands

In contrast to water-soluble proteins, membrane proteins reside in a heterogeneous environment, and their surfaces must interact with both polar and apolar membrane regions. As a consequence, the composition of membrane proteins' residues varies substantially between the membrane core and the interfacial regions. The amino acid compositions of helical membrane proteins are also known to be different on the cytoplasmic and extracellular sides of the membrane. Here we report that in the 16 transmembrane beta-barrel structures, the amino acid compositions of lipid-facing residues are different near the N and C termini of the individual strands. Polar amino acids are more prevalent near the C termini than near the N termini, and hydrophobic amino acids show the opposite trend. We suggest that this difference arises because it is easier for polar atoms to escape from the apolar regions of the bilayer at the C terminus of a beta-strand. This new characteristic of beta-barrel membrane proteins enhances our understanding of how a sequence encodes a membrane protein structure and should prove useful in identifying and predicting the structures of trans-membrane beta-barrels.     

Antarctic fish tubulins: heterogeneity, structure, amino acid compositions and charge

1. Tubulins purified from the brain tissues of three Antarctic fishes (Notothenia gibberifrons, Notothenia coriiceps neglecta, and Chaenocephalus aceratus) contain equimolar quantities of the alpha and beta chains and are free of microtubule-associated proteins (MAPs) and other non-tubulin proteins. 2. When examined by isoelectric focusing and by two-dimensional electrophoresis, brain tubulins from the Antarctic fishes were found to be highly heterogeneous; each was resolved into 15-20 distinct variants. The range of isoelectric points displayed by the Antarctic fish tubulins (5.30-5.75) is slightly more basic than that of bovine brain tubulin (5.25-5.60). 3. Peptide mapping demonstrated that tubulins from the Antarctic fishes and the cow differ in structure. 4. The amino acid compositions of piscine and mammalian tubulins are similar, but the Antarctic fish tubulins apparently contain fewer glutamyl and/or glutaminyl residues than do tubulins from the temperate channel catfish (Ictalurus punctatus) and the cow. 5. Native tubulin from N. coriiceps neglecta possesses 1-2 fewer net negative charges per tubulin dimer than does bovine tubulin. 6. We suggest that the enhanced assembly of Antarctic fish tubulins at low temperatures (-2 to +2 degrees C) results from adaptive, perhaps subtle, changes in their tubulin subunits.     

Foldability and the amino acid compositions of exons and introns

Various procedures are employed to relate the structural tendencies of polypeptide chain fragments to amino acid residues that in general have low background frequencies. A numerical evaluation of the content of these amino acids, named amino acid diversity, is defined. Distributions of the amino acid diversity parameter in databases containing exons, introns, and randomized exons show that there is a small difference between exons and shuffled exons, a detectable difference between exons and introns, and a large difference between exons and totally randomized exons.     

N-terminal amino acid sequences and amino acid compositions of the Spirochaeta aurantia flagellar filament polypeptides.

The amino-terminal sequences and amino acid compositions of the three major and two minor polypeptides constituting the filaments of Spirochaeta aurantia periplasmic flagella were determined. The amino-terminal sequence of the major 37.5-kDa outer layer polypeptide is identical to the sequence downstream of the proposed signal peptide of the protein encoded by the S. aurantia flaA gene. However, the amino acid composition of the 37.5-kDa polypeptide is not in agreement with that inferred from the sequence of flaA. The 34- and 31.5-kDa major filament core polypeptides and the 33- and 32-kDa minor core polypeptides show a striking similarity to each other, and the amino-terminal sequences of these core polypeptides show extensive identity with homologous proteins from members of other genera of spirochetes. An additional 36-kDa minor polypeptide that occurs occasionally in preparations of S. aurantia periplasmic flagella appears to be mixed with the 37.5-kDa outer layer polypeptide or a degradation product of this polypeptide.     

Antiradiation effectiveness of amino acid mixtures of various compositions

Radioprotective efficacy of differently composed amino acid mixtures (e. g. swine brain hydrolyzate, mixtures of several crystalline amino acids, etc.) was estimated. The survival rate and average life of exposed animals increased after the administration of amino acid preparations. The most pronounced effect was produced by the mixtures composed of several crystalline amino acids.     

Systematic variation in amino acid compositions of grass caryopses

Variation in amino acid patterns of 121 species (72 genera) of grass caryopses is extensively consistent with taxonomic groupings. The patterns of pooids and chloridoids are distinguishable from one another and from those of eu-panicoids and andropogonoids; the bamboos, Oryza, Stipeae, Ehrharta and Microlaena, which share certain morphological and anatomical features, also share a characteristic amino acid profile, while profiles of danthonoioids, Triodia and Aristida are clearly non-pooid. Caryopsis amino acid patterns vary independently of photosynthetic pathway. Embryos from taxonomically diverse genera all show very similar amino acid profiles, which differ strikingly from those of the endosperms, and the amino acid patterns of whole caryopses are dominated by their endosperms, which are responsible for the taxonomic variation. ‘Chemical scores’ of the caryopsis proteins, but not total protein contents, correlate to some extent with taxonomic groupings.     

Sexual dimorphism in amino acid compositions of mouse prolactin

Sexual dimorphism was found in amino acid compositions and immunogenecity of variant types of prolactin (PRL) purified from the pituitary gland of normal adult C57BL mice by a high performance liquid chromatography. From the pituitary gland of female mice, three female variant types of PRL were isolated, whereas from the pituitary gland of male mice, two male variant types of PRL (M1-PRL and M3-PRL) and a female variant type of PRL (M2-PRL) were obtained. The amino acid composition of M3-PRL was different from any of female variant types which were very similar to each other and contained less varine, isoleucine, leucine, tyrosine and lysine but more alanine than the latter. Immunoreactivity of any of female variant types of PRL against anti-PRL serum was 100%, whereas that of M1-PRL was as much as 85% and that of M3-PRL was nearly undetectable.     

Host ranges and serological properties of eight isolates of parsnip yellow fleck virus belonging to the two major serotypes

Isolates of parsnip yellow fleck virus (PYFV) from parsnip (P-121), celery (CV506 and CV065) and Heracleum sphondylium (Hs2) were serologically close to each other but distant from isolates from carrot (Dc2 and Dc5) and Anthriscus sylvestris (A-421 and As2), which were in turn close to each other serologically. The two groups of isolates also differed from each other in host range. Minor differences in immunological reactions and in host range and symptomatology were observed between isolates in each group. Particles of all eight isolates had similar RNA and protein compositions. The data confirm that PYFV isolates fall into two major serotypes, those from parsnip, celery and H. sphondylium belonging to the P-121 serotype and those from carrot and A. sylvestris belonging to the A-421 serotype.     

Correlation between prebiotic amino acid compositions and contemporary proteins.

A method of energy minimization for conformational energy calculations using the least-squares technique has been reported. The method has been tested in the simple case of a pair of alanyl peptide units using the non-bonded potential energy. Starting from any point in the (φ, ψ) energy map (not necessarily near a minimum), convergence to one of the energy minima is achieved rapidly, within a few cycles of iteration.     

Calculation of subunit stoichiometry of large, multisubunit proteins from amino acid compositions

The subunit stoichiometry of a large, multisubunit protein can be determined from the molar amino acid compositions (i amino acids) of the protein and its subunits. The number of copies of the subunits (1, 2, ... j) is calculated by solving all possible combinations of simultaneous equations in j unknowns (i!/j!(i - j)!). Calculations carried out using the published amino acid compositions determined by analysis and the compositions calculated from the sequences for two proteins of known stoichiometry provided the following results: Escherichia coli aspartate transcarbamoylase (R6C6, Mr = 307.5 kDa), R = 5.6 to 6.6 and C = 5.8 to 6.3, and spinach ribulose-bisphosphate carboxylase (L8S8, Mr = 535 kDa), L = 7.3 to 9.1 and S = 5.6 to 10.6. Calculations were also carried out with the amino acid compositions of two much larger proteins, the E. coli pyruvate dehydrogenase complex, Mr = 5280 kDa, subunits E1 (99.5 kDa), E2 (66 kDa), and E3 (50.6 kDa), and the extracellular hemoglobin of Lumbricus terrestris, Mr = 3760 kDa, subunits M (17 kDa), D1 (31 kDa), D2 (37 kDa), and T (51 kDa); the results for PDHase were E1 = 20 to 24, E2 = 18 to 31, E3 = 21 to 33 and those for Lumbricus hemoglobin were M = 34 to 46, D1 = 13 to 19, D2 = 13 to 18, and T = 34 to 36. Although the sample standard deviations of the mean values are generally high, the proposed method works surprisingly well for the two smaller proteins and provides physically reasonable results for the two larger proteins.     

Variations in free protein amino acid compositions of grass leaves

Total free protein amino acids in grass leaves varied from 0.02 to 0.76 g % fr. wt and were present in greater amounts in grasses (especially C₃ forms) collected from the field during a hot, dry summer (for 31 species/28 genera; 0.28 ± 0.21 g % fr. wt) than those grown in the greenhouse (for 48 species/36 genera; 0.10 ± 0.08 g % fr. wt). Variation in free proline was generally greater in field-collected grasses (0.5–47.0% total free amino acids) than in greenhouse-grown grasses (0.4−8.4%). Taxonomic patterns are detectable in the free protein amino acid compositions of grasses grown in the greenhouse. Among the taxa, chloridoids, danthonioids, Aristida, eu-panicoids and andropogonoids exhibit closely similar free protein amino acid profiles which are distinguishable from those of pooids, while Oryza, Stipeae and Ehrharteae share certain features of their free protein amino acid patterns. Variation in free alanine is clearly associated with the different photosynthetic pathways, C₃ grasses being generally lower in alanine than C₄ grasses, irrespective of taxonomic groupings and growing conditions.     

Systematic variation in leaf amino acid compositions of leguminous plants

The leaf protein content for 17 species of legumes ranges from 2.8 to 9.4 g% fr. wt, with an average of 5.3 g % fr. wt. Taxonomic pattern is detectable in leaf amino acid patterns, those of the Mimosoideae being distinguishable from those of the Papilionoideae and Caesalpinioideae.     

Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.     

Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins

A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitochondrium, amino acid compositions of mitochondrial proteins (mt-proteins) were examined in the 20-dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt-proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G-C-rich base composition.     

Taxonomic variation in total leaf protein amino acid compositions of grasses

Leaves of greenhouse grown grasses had free protein amino acid contents of generally less than 5 % total amino acids, while field collected grasses averaged 14.7 % free protein amino acid contents. Taxonomic patterns are detectable in the total leaf amino acid profiles of grasses from both sources, those of pooids being distinguishable from those of chloridoids and panicoids, and those of danthonioids showing an intermediate pattern. Leaf profiles of Oryza, Stipeae, and Ehrharteae resemble one another, and are more like those of pooids than those of panicoids. Variations in Thr and Leu are apparently associated with differences in photosynthetic pathway. Grass leaves are generally low in total amino acid contents (2.2 ? 1.0 g % fr. wt), with Ile, Val and Met + Cys identified as the limiting essential amino acids. However, the nutritional ‘chemical scores’ of grass leaf proteins are high (75 %, based on the WHO scoring pattern).     

Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria

One of the well-known observations of proteins from thermophilic bacteria is the bias of the amino acid composition in which charged residues are present in large numbers, and polar residues are scarce. On the other hand, it has been reported that the molecular surfaces of proteins are adapted to their subcellular locations, in terms of the amino acid composition. Thus, it would be reasonable to expect that the differences in the amino acid compositions between proteins of thermophilic and mesophilic bacteria would be much greater on the protein surface than in the interior. We performed systematic comparisons between proteins from thermophilic bacteria and mesophilic bacteria, in terms of the amino acid composition of the protein surface and the interior, as well as the entire amino acid chains, by using sequence information from the genome projects. The biased amino acid composition of thermophilic proteins was confirmed, and the differences from those of mesophilic proteins were most obvious in the compositions of the protein surface. In contrast to the surface composition, the interior composition was not distinctive between the thermophilic and mesophilic proteins. The frequency of the amino acid pairs that are closely located in the space was also analyzed to show the same trend of the single amino acid compositions. Interestingly, extracellular proteins from mesophilic bacteria showed an inverse trend against thermophilic proteins (i.e. a reduced number of charged residues and rich in polar residues). Nuclear proteins from eukaryotes, which are known to be abundant in positive charges, showed different compositions as a whole from the thermophiles. These results suggest that the bias of the amino acid composition of thermophilic proteins is due to the residues on the protein surfaces, which may be constrained by the extreme environment.