Comparison Of Amino Acid Composition Research Articles

Isolation and characterization of an iron-containing superoxide dismutase from tomato leaves, Lycopersicon esculentum.

A cyanide-insensitive superoxide dismutase was purified from tomato leaves (Lycopersicon esculentum, Mill., var. Venture) to apparent homogeneity. The enzyme had twofold higher specific activity (about 4000 standard units) than ferric superoxide dismutases purified from Brassica campestris [Salin, M. L. and Bridges, S. M. (1980) Arch. Biochem. Biophys. 201, 369-374] and Nuphar luteum [Salin, M.L. and Bridges, S. M. (1982) Plant Physiol. 69, 161-165]. The protein had a relative molecular mass of about 42000 and was composed of two equal subunits noncovalently joined. It was negatively charged (pI = 4.6) and contained about 1.45 mol Fe/mol dimer and negligible amounts of Mn, Cu and Zn. Absorption spectrum and sensitivity to NaN3, H2O2 and temperature are also reminiscent of other ferric superoxide dismutases. Comparison of amino acid composition indicated, however, a closer relationship to the Mn-containing enzymes rather than to other Fe-containing superoxide dismutases. Two possible ways of Fe-containing superoxide dismutase acquisition by vascular plants were suggested.

Relationship of lipoamide dehydrogenases from Pseudomonas putida to other FAD-linked dehydrogenases

Pseudomonas putida produces two lipoamide dehydrogenases, LPD-glc and LPD-val. LPD-val is specifically required as the lipoamide dehydrogenase of branched-chain keto acid dehydrogenase and LPD-glc fulfills all other requirements for lipoamide dehydrogenase. Both proteins are dimers with one FAD per subunit. LPD-glc has an absorption maximum at 455 nm, but LPD-val has a maximum at 460 nm. Comparison of amino acid compositions revealed that LPD-glc was more closely related to Escherichia coli and pig heart lipoamide dehydrogenase than to LPD-val. LPD-val did not appear to be closely related to any of the proteins compared with the possible exception of mercuric reductase.

山羊乳および牛乳酸性ホスファターゼのアミノ酸組成と炭水化物の比較

山羊乳および牛乳酸性ホスファターゼのアミノ酸組成と炭水化物の比較

Involvement of arginine residues in catalysis by rat brain hexokinase

Inactivation of rat brain hexokinase (ATP: d-hexose 6-phosphotransferase, EC 2.7.1.1) by the arginine-specific reagent, phenylglyoxal, has been studied. Inactivation did not follow pseudo-first-order kinetics, suggesting the involvement of two or more arginine residues in catalytic function. Using [ 14C]phenylglyoxal, it was found that 5 of the 55 arginines per molecule of hexokinase react with this reagent, with an accompanying loss of over 90% of the catalytic activity. Virtually all of the activity loss occurs during derivatization of four relatively slower reacting arginines, with essentially no activity loss during derivatization of one rapidly reacting arginine. Inactivation by phenylglyoxal was not due to reaction with critical sulfhydryl groups in brain hexokinase since reactivity of the enzyme with the sulfhydryl reagent, 5,5′-dithiobis(2-nitrobenzoic acid) was not affected by prior treatment with phenylglyoxal. Comparison of amino acid composition, before and after reaction with phenylglyoxal, indicated that only the arginine content had been affected by phenylglyoxal treatment. The decrease in arginine content, measured by amino acid analysis, and the incorporation of phenylglyoxal, measured with [ 14C]phenylglyoxal, was consistent with the phenylglyoxal:arginine stoichiometry of 2:1 originally reported by K. Takahashi (1968, J. Biol. Chem. 243, 6171–6179). Several ligands were tested and found to provide varying degrees of protection of hexokinase activity against phenylglyoxal. ATP and ADP alone provided only slight protection, but were highly effective in the presence of N-acetylglucosamine which itself gave only moderate protection. Glucose 6-phosphate and 1,5-anhydroglucitol 6-phosphate, both good inhibitors of brain hexokinase, were very effective while poorly inhibitory hexose 6-phosphates were not. Glucose was very effective, with protection afforded by other hexoses being correlated with their ability to serve as substrates (i.e., poor substrates also provided little protection against phenylglyoxal). The effectiveness of hexose 6-phosphates and hexoses in protecting the enzyme against inactivation by phenylglyoxal was related to their ability to induce conformational change in the enzyme. None of the ligands tested appreciably affected the reactivity of the rapidly reacting arginine residue. There was no correlation between the inhibition observed in the presence of various ligands and the number of arginines reacted with phenylglyoxal. The results were interpreted as indicating the involvement of two to four arginine residues in the catalytic function of brain hexokinase, possibly in the binding of anionic ligands such as ATP, ADP, or glucose 6-phosphate.

Overlapping evolutionary affinities revealed by comparison of amino acid compositions.

Comparison of the amino acid compositions of purified proteins indicates the presence of overlapping evolutionary affinities among enzymes of the beta-ketoadipate pathway. Isofunctional enzymes from different bacterial genera share a common evolutionary origin. Moreover, enzymes that mediate isofunctional or chemically analogous reactions within an organism appear to be evolutionarily homologous. Most remarkably, closely similar amino acid compositions are found in enzymes that mediate the following consecutive metabolic steps: lactonization, decarboxylation, hydrolysis, and transfer of a thioester bond.

Comparison of yeast mitochondrial Phe-tRNA synthetase subunits to their cytoplasmic counterparts: Isolation and determination of amino acid compositions

The α and β subunits of yeast mitochondrial Phe-tRNA synthetase are separated and isolated by means of chromatography on DEAE-cellulose, after enzyme alkylation with iodoacetate. The comparison of amino acid compositions of yeast mitochondrial and cytoplasmic native Phe-tRNA synthetases and their components shows significant differences. Results indicate that the two enzymes are coded for by different nuclear genes.

The proteins of living psoriatic epidermis

Psoriatic epidermis has a rapid rate of tunrover and produces a stratum corneum with an abnormal tonofilament composition. One polypeptide chain, ( M r 70 000) is absent or greatly decreased in relative amount and two other chains, ( M r 63 000 and 55 000), which are normally modified in the living cells, persists into the stratum corneum. Increasing the turnover of normal epidermis has been shown to cause the persistence of 63 and 55 kilodalton chains in the stratum corneum but does not affect the relative amount of 70 kilodalton chain. It has, therefore, been suggested that, in psoriasis, the deficiency of the 70 kilodalton chain may occur prior to or simultaneuously with the induction of increased tissue turnover. In the present study, the polypeptide chain composition of living psoriatic epidermis has been examined. It is shown that the relative amounts of 70 kilodalton chain in psoriatic stratum corneum and involved living epidermis from the same site are not significantly different. The abnormality is therefore, already present in the living cells and it appears that, in psoriasis, the synthesis of the 70 kilodalton chain is defective. The uninvolved epidermis of psoriatics is intermediate between normal and involved psoriatic epidermis both in the ability to synthesise the 70 kilodalton chain and to modify the 63 and 55 kilodalton chains. Comparisons of amino acid compositions of proteins containing different proportions of 70 kilodalton chain suggest that it has a considerably higher content of glycine and serine than the other tonofilament chains. These studies suggest that the 70 kilodalton chain may be functionally different from the other tonofilament chains. The defect in its synthesis in psoriasis is a relatively early event and may be involved with the induction of increased tissue turnover or induced by the same abnormal conditions as the increased tissue turnover.

Protein adsorption on glass surfaces using porous glass

Comparison of amino acid composition and other properties of proteins (horseradish peroxidase, bovine serum albumin, hemoglobin, catalase, and aldolase), which are separable on controlled-pore glass, showed that the elution order of proteins did not depend on their molecular weights, isoelectric points, hydrophobicity indices, and acidic and basic amino acid contents. The turbidity of the proteins bound on glass at 660 nm indicated the precipitated state of the proteins.

How reliably do amino acid composition comparisons predict sequence similarities between proteins?

A method for comparing amino acid compositions of proteins (Cornish-Bowden, 1977) has been extended to allow proteins of unequal lengths to be compared. The method has been tested by applying it to proteins of known sequence. It tends to exaggerate the amount of difference between unrelated proteins. It is therefore a reliable guide to possible sequence similarities, in that it does not suggest that sequences are similar when they are not, though it sometimes fails to detect genuine similarities. When applied to related proteins the method gives results in good agreement with those predicted. A phylogenetic tree for 37 snake venom toxins has been constructed from their compositions and is similar in most important respects to one constructed from the corresponding sequences.

Comparison of amino acid compositions of mitochondrial and cytoplasmic ribosomal proteins of Saccharomyces cerevisiae

The amino-acid compositions of the mitochondrial ribosomal subunits of Saccharomyces cerevisiae have been determined and compared to those of cytoplasmic ribosomal subunits. For the large subunits, the mitochondrial and cytoplasmic ribosomes showed major differences in the proportions of arginine, alanine and methionine. For the small subunits, arginine, aspartic acid, alanine, valine and methionine showed marked differences. We have compared these amino-acid compositions with those already published of bacterial and eukaryotic ribosomes by a statistical method of data analysis. It appeared clearly that the yeast mitoribosomes are more distant from bacterial ribosomes than from eukaryotic cytoribosomes.

IMMUNOGLOBULIN GAMMA CHAINS OF A MONOTREME MAMMAL, THE ECHIDNA (TACHYGLOSSUS ACULEATUS): AMINO ACID COMPOSITION AND PARTIAL AMINO ACID SEQUENCE

The echidna represents the lowest stage in phylogeny at which molecules clearly homologous to IgG antibodies appear to occur. We provide evidence that a fraction of gamma chains possess an unblocked N terminal sequence comparable to the VHIII sub-group of human gamma chains and that glycine is the C-terminal residue. Statistical comparison of amino acid composition of the component chains with other immunoglobulin heavy chains suggests that echidna gamma chains are more closely related to eutherian gamma chains than to the 7S Ig heavy chains from amphibia or aves. The results are consistent with our view that true gamma-type heavy chains did not appear in evolution until after the mammalian line diverged from the stem reptiles.

Subunit and chemical composition of citrate lyase from Klebsiella pneumoniae.

Citrate lyase from Klebsiella pneumoniae (previously called Klebsiella aerogenes) is shown by amino acid sequencing techniques to contain equimolar amounts of three nonidentical subunits. Together with the molecular weight of the enzyme, this finding is interpreted to indicate that there are 6 mol of each of these subunits per mol of native enzyme. A partial amino acid sequence of each of the three subunits is presented. The pure enzyme with a specific activity of 73 units/mg of dry protein has an absorbance index (E1% 1 cm at 278 nm) of 6.2. The amino acid composition of the native enzyme is presented. In addition, the amounts of adenine, phosphate, taurine (from cysteamine), and "ribose," present as a bound cofactor of unknown structure, have been estimated. A comparison of amino acid compositions and the partial amino acid sequences of two of the subunits reveals some resemblance between them.

Sporogenicity of yeast autolyzates and casein hydrolyzates for Bacillus popilliae in liquid cultures

Bacillus popilliae NRRL B-2309S forms several million refractile spores/ml in liquid shaken cultures. A suitable medium includes glucose, K 2HPO 4, water, and three selected ingredients-activated carbon, a yeast autolyzate, and a casein hydrolyzate. Only 4 out of 26 lots of commercial yeast autolyzates tried were sporogenic. However, spore formation in the presence of the four was poor and erratic unless a compatible casein hydrolyzate also was present. Five of eight lots of casein hydrolyzates improved the sporogenicity of selected yeast products to various degrees. A comparison of amino acid compositions of yeast and casein lysates sheds no light on differences between suitable and unsuitable ones. Less refined yeast and casein products seem preferable.

Isolation and characterization of cytoplasmic L-glycerol-3-phosphate dehydrogenase from rabbit-renal-adipose tissue and its comparison with the skeletal-muscle enzyme.

Cytoplasmic NAD‐linked l‐glycerol‐3‐phosphate dehydrogenase was isolated from rabbit renal adipose tissue in a preparation that was apparently homogeneous by preparative isoelectric focusing and polyacrylamide‐disc‐gel electrophoresis. The adipose tissue and skeletal muscle enzymes were indistinguishable by disc‐gel electrophoresis, immunological comparisons, apparent Km, values for substrates and coenzymes, isoelectric point in preparative isoelectric‐focusing runs, and apparent molecular weight and Stokes radius on polyacrylamide‐gel‐filtration columns. The ultraviolet spectrum of the adipose tissue enzyme was identical to that of the muscle enzyme including the broad maximum at 275 nm indicative of the non‐protein component characteristic of the muscle enzyme. Crude homogenates of rabbit adipose tissue and muscle electro‐focused in polyacrylamide gels and stained for glycerol‐3‐P dehydrogenase activity showed four major zones present in slightly different proportions in the two homogenates, but fully superimposable in runs on mixed tissue homogenates.Comparison of amino acid composition of the adipose tissue enzyme with analyses of the muscle done in five different laboratories showed that the adipose tissue enzyme cannot be distinguished from the muscle enzyme by this criterion. Similar comparison of the adipose tissue and muscle enzymes with the liver enzyme suggests that the liver enzyme is not identical to the muscle‐adipose form of the enzyme. Possible similarity in physiological role for the muscle‐adipose form of glycerol‐3‐P dehydrogenase in these two tissues and a rationale for their absence in rapidly growing cancer cells is suggested.

Structural Comparisons between the Class I Fructose Diphosphate Aldolases from Micrococcus aerogenes and Rabbit

It has been previously shown that the fructose-P2 aldolase isolated from Micrococcus aerogenes is a Class I (Schiff base) enzyme. All other prokaryotic organisms so far studied contain Class II (metallo) aldolases. Studies were undertaken to investigate whether or not this bacterial aldolase is structurally related to the Class I aldolases of higher organisms. 1. A comparison of amino acid compositions gives no indication of homology between M. aerogenes and mammalian aldolases. 2. The NH2-terminal residue of this enzyme was found to be methionine in contrast to proline which is found at the NH2 terminus of the rabbit enzymes. 3. The M. aerogenes enzyme contains lysine rather than tyrosine at the COOH terminus. 4. The tryptic peptide containing the active site lysyl residue of M. aerogenes aldolase was isolated and partially characterized. The peptide contains 28 amino acids as do the peptides of rabbit aldolases A and B. The amino acids of the M. aerogenes peptide may be aligned to obtain the maximum of 48% homology with the corresponding rabbit aldolase peptides. 5. Several of the structural distinctions between M. aerogenes and rabbit aldolases are discussed in relation to the proposed functions of tyrosine, and cysteine in the catalytic process of Class I fructose-P2 aldolases. Our results suggest extensive and perhaps fundamental differences between the M. aerogenes enzyme and the Class I aldolases of mammals. The extent of relationship between this prokaryotic enzyme and the fructose-P2 aldolases of higher organisms must await more thorough structural analyses.

Estimation of primary sequence homology from amino acid composition of evolutionary related proteins

The amino acid compositions of many of the known sequenced proteins were compared to determine if a relationship exists between the amino acid composition and the amount of sequence homology of these proteins. For this purpose, a function, the composition divergence, was defined. A computer program based on relatively simple assumptions has been successfully used to simulate the data distribution found in comparing composition divergence with the sequence dissimilarity. From this characterization of known proteins, it is possible to predict the sequence homology of unsequenced proteins, based on amino acid composition comparisons. The power and limitations of this technique are discussed.

Cyanogen bromide peptides from the alpha 1-chain of cod skin collagen.

The α1‐chain of cod skin collagen has been cleaved with cyanogen bromide. The resulting peptides have been isolated and purified by chromatography on phosphocellulose and CM‐cellulose and gel filtration on Sephadex. The amino acid composition and molecular weights of eight of these peptides, accounting for about 70% of the whole α1‐chain, are presented. Comparison of amino acid compositions suggests a homology between three of these peptides and cyanogen bromide peptides from rat skin and chick bone α1‐chains.

Modifications in the Heterogeneity of the Antibody Response

It is now generally accepted that the specificity of antibody is consequent to its amino acid sequence and mediated through the effects of sequence on the conformation of the combining site. Evidence for this has been obtained from reversible denaturation experiments on specific antibodies (Haber, 1964; Whitney and Tanford, 1965; Freedman and Sela, 1966) and has been inferred from comparisons of amino acid compositions of purified antibodies (Koshland, 1966), as well as from sequence studies on myeloma proteins (Hilschman and Craig, 1965; Titani et al., 1966; Milstein, 1966). Myeloma proteins have provided an excellent model for the study of antibody structure. These studies have revealed the regions of sequence common to all globulins of a given class as well as regions which are unique to each member. In this way they have pointed to the portions of the molecule which are likely to be responsible for forming the antibody combining...

貝殻コンキオリンのアミノ酸組成にみられる分類学的差異

A comparison of amino acid composition was made on the proteins from different structur-al units of two shells of Cephalopoda, of three shells of Gastropoda, and of five shells of Bivalvia for exploring the taxonomic and ecological modifications in the amino acid pattern. The conchiolin matrix obtained from a decalcified shell was put in a glass tube containing 2ml. of a 6N hydrochloric acid solution, sealed and then hydrolysed for 22 hours at 110°C. The hydrolyzate of conchiolin was treated according to an usual way for an automatic amino acid analysis. The conchiolin of any given species appears to have a specific amino acid pattern, though the pattern varied considerably between non-mineralized and mineralized layers of a same shell (Fig. 1). They may be clearly classified in amino acid composition under the three groups of Cephalopoda, Gastropoda and Bivalvia. Such ecological elements as food habits and environments do not seem to disturb the proper amino acid patterns which the groups of animals possess.