Intraspecific variability in fractional composition of the serum proteins of the sturgeon Acipenser stellatus]

Comparative studies on fractional composition of the blood serum proteins in two sympatric populations of the sturgeon A. stellatus (South-Caspian and North-Caspian) have been made by means of polyacrylamide gel disc-electrophoresis. Serum proteins are fractionated into 13-18 electrophoretic components, the heterogeneity of proteins being somewhat higher in the North-Caspian population than in the South-Caspian one. Most pronounced differences were found in the relative content of albumins and beta-globulins. Special interest is attracted to different heterogeneity of albumins and beta-globulins (transferrins) in the two populations of the Caspian sturgeon.     

Existence of transferrin polymorphism in a species of sturgeon from the Caspian Sea: Acipenser stellatus

Though various subdivisions have been proposed in literature for species of sturgeon from the Caspian Sea, these subdivisions still remain hypothetical. Research on the erythrocyte antigens of four species of anadrome sturgeons, caught off the Iranian coast has not evidenced any erythrocyte antigenic differentiations among these four species. After marking serum with 59Fe, doing paper and starch electrophoreses and revealing the marked serum proteins by autoradiography, we have shown that a transferrin polymorphism exists in Acipenser stellatus. This isotopic marking also enabled us to identify by starch electrophoresis marked proteins corresponding to transferrins in the serum of three other species of sturgeon: Acipenser guldenstadti, Acipenser nudiventris and Huso huso. It has not however been possible to determine with certainty the existence of a transferrin polymorphism in these three species.     

The effect of food deprivation on the plasma free amino acid levels of sturgeon,Acipenser transmontanus

Synopsis Plasma levels of free amino acids were compared in recently fed sturgeon and in those deprived of food for over two weeks. Fed animals had elevated levels of branched chain amino acids. It is suggested that the higher levels of these amino acids are due to reduced metabolism of these amino acids as well as high levels in the food.     

Purification and partial amino acid sequences of an esterase from tomato

Screening of 18 suspension plant cell cultures of taxonomically distant species revealed that a methyl jasmonate hydrolysing enzyme activity (0.21-5.67 pkat/mg) occurs in all species so far analysed. The methyl jasmonate hydrolysing esterase was purified from cell cultures of Lycopersicon esculentum using a five-step procedure including anion-exchange chromatography, gel-filtration and chromatography on hydroxylapatite. The esterase was purified 767-fold to give an almost homogenous protein in a yield of 2.2%. The native enzyme exhibited a M(r) of 26 kDa (gel-filtration chromatography), which was similar to the M(r) determined by SDS-PAGE and MALDI-TOF analysis (M(r) of 28547 kDa). Enzyme kinetics revealed a K(m) value of 15 microM and a V(max) value of 7.97 nkat/mg, an pH optimum of 9.0 and a temperature optimum of 40 degrees C. The enzyme also efficiently hydrolyzed methyl esters of abscisic acid, indole-3-acetic acid, and fatty acids. In contrast, methyl esters of salicylic acid, benzoic acid and cinnamic acid were only poor substrates for the enzyme. N-Methylmaleimide, iodacetamide, bestatin and pepstatin (inhibitors of thiol-, metal- and carboxyproteases, respectively) did not inactivate the enzyme while a serine protease inhibitor, phenylmethylsulfonyl fluoride, at a concentration of 5 mM led to irreversible and complete inhibition of enzyme activity. Proteolysis of the pure enzyme with endoproteinase LysC revealed three peptide fragments with 11-14 amino acids. N-Terminal sequencing yielded an additional peptide fragment with 10 amino acids. Sequence alignment of these fragments showed high homologies to certain plant esterases and hydroxynitrile lyases that belong to the alpha/beta hydrolase fold protein superfamily.     

Prediction of beta-turns from amino acid sequences using the residue-coupled model.

We evaluated the prediction of beta-turns from amino acid sequences using the residue-coupled model with an enlarged representative protein data set selected from the Protein Data Bank. Our results show that the probability values derived from a data set comprising 425 protein chains yielded an overall beta-turn prediction accuracy 68.74%, compared with 94.7% reported earlier on a data set of 30 proteins using the same method. However, we noted that the overall beta-turn prediction accuracy using probability values derived from the 30-protein data set reduces to 40.74% when tested on the data set comprising 425 protein chains. In contrast, using probability values derived from the 425 data set used in this analysis, the overall beta-turn prediction accuracy yielded consistent results when tested on either the 30-protein data set (64.62%) used earlier or a more recent representative data set comprising 619 protein chains (64.66%) or on a jackknife data set comprising 476 representative protein chains (63.38%). We therefore recommend the use of probability values derived from the 425 representative protein chains data set reported here, which gives more realistic and consistent predictions of beta-turns from amino acid sequences.     

Characterization of vitellogenin from white sturgeon,Acipenser transmontanus

Sturgeon are an ancient family (Acipenseridae) of fishes that lie close to the divergence of fish that eventually evolved into terrestrial animals and those that evolved into modern teleost species. Therefore, white sturgeon vitellogenin sequences fill a gap in the current understanding of the functional domains of this protein family. Vitellogenin cDNA was sequenced and used to investigate gene expression in white sturgeon, Acipenser transmontanus. Estrogen-induced vitellogenin mRNA was detected in the livers of both males and females and was also detected in undifferentiated gonads of estrogen-treated fish. Low levels of vitellogenin mRNA were also detected in the testis of both control and estrogen-treated males. The cDNA encoded a 186-kDa protein that was missing only six to seven of the amino-terminal amino acids. Comparisons to silver lamprey, Xenopus, and chicken vitellogenin sequences indicate that the overall structure of the yolk protein domains were highly conserved. There was considerable homology in three regions of the lipovitellin I domain. These conserved sequences are likely to be involved in vitellogenin receptor binding. The phosvitin domain of white sturgeon vitellogenin contained fewer and shorter serine repeats as predicted from yolk protein phosphate content of fish compared to Xenopus and chicken. However, the vitellogenin of white sturgeon had a lower serine content as compared with silver lamprey, indicating that an increased serine content is not strictly a function of evolutionary age. Correspondence to: C. A. Bidwell     

Rainbow trout protamines. Amino acid sequences of six distinct proteins from a single testis

All the protamines present in detectable amounts in a single mature testis from rainbow trout have been purified to homogeneity using acid extraction, gel filtration chromatography on Bio-Gel P-10, ion-exchange chromatography on carboxymethylcellulose and reverse-phase high-pressure liquid chromatography. Each of the six purified protamines was completely sequenced using automated gas-phase Edman degradation. Each protamine is two-thirds arginine and also contains proline, serine, valine and glycine. Three protamines also contain alanine while two contain isoleucine. Four of the protamines have 32 amino acids while the remaining two have 30. The six protamines have been classified into three families on the basis of their amino acid sequences.     

Aligning amino acid sequences: Comparison of commonly used methods

Summary We examined two extensive families of protein sequences using four different alignment schemes that employ various degrees of weighting in order to determine which approach is most sensitive in establishing relationships. All alignments used a similarity approach based on a general algorithm devised by Needleman and Wunsch. The approaches included a simple program, UM (unitary matrix), whereby only identities are scored; a scheme in which the genetic code is used as a basis for weighting (GC); another that employs a matrix based on structural similarity of amino acids taken together with the genetic basis of mutation (SG); and a fourth that uses the empirical log-odds matrix (LOM) developed by Dayhoff on the basis of observed amino acid replacements. The two sequence families examined were (a) nine different globins and (b) nine different tyrosine kinase-like proteins. It was assumed a priori that all members of a family share common ancestry. In cases where two sequences were more than 30% identical, alignments by all four methods were almost always the same. In cases where the percentage identity was less than 20%, however, there were often significant differences in the alignments. On the average, the Dayhoff LOM approach was the most effective in verifying distant relationships, as judged by an empirical jumbling test. This was not universally the case, however, and in some instances the simple UM was actually as good or better. Trees constructed on the basis of the various alignments differed with regard to their limb lengths, but had essentially the same branching orders. We suggest some reasons for the different effectivenesses of the four approaches in the two different sequence settings, and offer some rules of thumb for assessing the significance of sequence relationships.     

Prediction of gamma-turns from amino acid sequences.

We predicted gamma-turns from amino acid sequences using the first-order Markov chain theory and enlarged representative data sets corresponding to protein chains selected from the Protein Data Bank (PDB). The following data sets were used for training and deriving the probability values: (1) an initial data set containing 315 protein chains comprising 904 gamma-turns and (2) a later data set in order to include new entries in the PDB, containing 434 protein chains and comprising 1053 gamma-turns. By excluding 93 protein chains that were common to these two training data sets, we generated two mutually exclusive data sets containing 222 and 341 protein chains for testing our predictions. Applying amino acid probability values derived from training data sets on to testing data sets yielded overall prediction accuracies in the range 54-57%. We recommend the use of probability values derived from the data set comprising 315 protein chains that represents more gamma-turns and also provides better predictions.     

DNA-repair modulation using derivatives of 1,4-dihydroisonicotinic acid as an example

The influence of two derivatives of 1,4-dihydroisonicotinic acid on DNA-repair involved in chemical mutagenesis in Drosophila germ cells has been investigated. The compounds tested decreased the level of EMS-induced chromosome breakage and point mutations due to stimulation of maternal repair of DNA primary damage induced in spermatozoa as well as due to activation of DNA-repair in larvae and imago premeiotic stages of Drosophila males. Deficiency of DNA-repair systems leads to decrease in female and male germ-cell sensitivity to antimutagen action.     

Efficient recognition of immunoglobulin domains from amino acid sequences using a neural network

A neural network was trained using back propagation to recognizeimmunoglobulin domains from amino acid sequences. The programwas designed to identify proteins exhibiting such domains withminimal rates of false positives and false negatives. The NationalBiomedical Research Foundation NEW protein sequences databasewas scanned to evaluate the performance of the program in recognizingmouse immunoglobulin sequences. The program correctly recognized55 out of 56 mouse immunoglobulin sequences, corresponding toa recognition efficiency of 98.2% with an overall false positiverate of 7.3%. These data demonstrate that neural network-basedsearch programs are well suited to search for sequences characterizedby only a few well-conserved subsequences. Received on November 11, 1989; accepted on May 31, 1990     

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

Background

Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D) protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP); the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction.

Results

The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM) and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are characterized by accuracies below 70%. Finally, the Naïve Bayes method is shown to provide the highest sensitivity for the prediction of flexible regions, while FlexRP and SVM give the highest sensitivity for rigid regions.

Conclusion

A new sequence representation that uses k-spaced amino acid pairs is shown to be the most efficient in the prediction of the flexible/rigid regions of protein sequences. The proposed FlexRP method provides the highest prediction accuracy of about 80%. The experimental tests show that the FlexRP and SVM methods achieved high overall accuracy and the highest sensitivity for rigid regions, while the best quality of the predictions for flexible regions is achieved by the Naïve Bayes method.     

Neisseria pili proteins: amino-terminal amino acid sequences and identification of an unusual amino acid.

The amino-terminal amino acid sequences of the pili proteins from four antigenically dissimilar strains of Neisseria gonorrhoeae, from Neisseria meningiditis, and from Escherichia coli were determined. Although antibodies raised to the pili protein from a given strain of gonococcus cross-reacted poorly or not at all with each of the other strains tested, the amino-terminal sequences were all identical. The meningococcal protein sequence was also identical with the gonococcal sequence through 29 residues, and this sequence was highly homologous to the sequence of the pili protein of Moraxella nonliquifaciens determined by other workers. However, the sequence of the pili protein from E. coli showed no similarity to the other sequences. The gonococcal and meningococcal proteins have an unusual amino acid at the amino termini, N-methylphenylalanine. In addition, the first 24 residues of these proteins have only two hydrophilic residues (at positions 2 and 5) with the rest being predominantly aliphatic hydrophobic amino acids. The preservation of this highly unusual sequence among five antigenically dissimilar Neisseria pili proteins implies a role for the amino-terminal structure in pilus function. The amino terminus may be directly or indirectly (through preservation of tertiary structure) important for the pilus function of facilitating attachment of bacteria to human cells.     

Analysis of neutral sugars as glycamines using an amino acid analyzer.

A new method of the analysis of neutral sugars was developed based on the separation of their corresponding glycamines. Sugars and ammonia were combined by means of the reduction with sodlum cyanoborohydride. The glycamines thus obtained were quantitatively analyzed by an automatic amino acid analyzer. Satisfactery results were obtained in the analyses of the constituent sugars of several polysaccharides and glycoconjugates.