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After CNBr cleavage of p-hydroxybenzoate hydroxylase from Pseudornonas fluorescens, five peptides and free homoserine were isolated (see preceding paper in this journal). The amino acid sequences of the three smallest peptides, viz. CB3, CB4 and CB5, were determined by automated Edman degradation and analysis of enzymatic subdigests. These peptides form a continuous stretch of 110 residues from the N terminus: [This equation can not be represent in ASCII.TXT]. [ABSTRACT FROM AUTHOR]

This paper is the fifth of a series devoted to the primary structure of the bovine β-casein A². The first two communications dealt with the isolation, analysis and positioning in the peptide chain of the tryptic and “CNBr” peptides [1,2]. The last two described the sequence of 65 residues from the carboxyl-terminus and of 32 residues from the amino-terminus [3,4]. We report here a partial sequence which includes 156 residues (out of the 209 residues of the β-casein A²) exactly positioned in the peptide chain. Two segments including 53 residues (from position 36 to 68 and from 73 to 92) remain to be analyze. In addition to the tryptic and “CNBr” peptides originating from β-casein A², two peptides issued from a tryptic digest of β-casein B were used as starting material. The position of the substitution His→Gln which differentiates the β-casein A² from the β-casein A³, already given in a preliminary communication [5], is indicated, as it is for the substitution Ser→Arg which represents one of the two differences occurring between the β-casein A² and the β-casein B. Four of the five phosphorus atoms of the β-casein A² have been previously located in the NH2-terminal tryptic peptide [4]. The fifth has been located at position 35. All the phosphorus atoms of the β-casein A² occur as phosphoserine. The complete structure of the β-casein A² will be given and discussed in the next and last paper. [ABSTRACT FROM AUTHOR]

Protein sequences evolve through random mutagenesis with selection for optimal fitness. Cooperative folding into a stable tertiary structure is one aspect of fitness, but evolutionary selection ultimately operates on function, not on structure. In the accompanying paper, we proposed a model for the evolutionary constraint on a small protein interaction module (the WW domain) through application of the SCA, a statistical analysis of multiple sequence alignments. Construction of artificial protein sequences directed only by the SCA showed that the information extracted by this analysis is sufficient to engineer the WW fold at atomic resolution. Here, we demonstrate that these artificial WW sequences function like their natural counterparts, showing class-specific recognition of proline-containing target peptides. Consistent with SCA predictions, a distributed network of residues mediates functional specificity in WW domains. The ability to recapitulate natural-like function in designed sequences shows that a relatively small quantity of sequence information is sufficient to specify the global energetics of amino acid interactions. [ABSTRACT FROM AUTHOR]

Protein kinase (PK) A catalytic (PKAcat) subunit was purified to homogeneity from bovine lens using a 100-kDa cut-off membrane filtration followed by different chromatographic procedures. The molecular weight of PKAcat was found to be 41 kDa. The kinase phosphorylates histone IIIs and other synthetic modified peptides of VRKRTLRRL with different amino acid environment. The extent of phosphorylation depends not only on the presence of Ser or Thr (phosphorylating residues) but also on other surrounding amino acid residues. Although some peptides compete in phosphorylating histone, they are not very significant. The result suggests that the extent of phosphorylation depends on the amino acid residue(s) surrounding phosphorylable residue(s) on the peptide. [ABSTRACT FROM AUTHOR]

The complete amino acid sequence of CNBr fragment H4 of the murine immunoglobulin MOPC 173 (IgG2a,χ) has been determined, thus completing the sequence determination of the entire heavy chain. The H4 fragment contains 150 residues, and extends from residue 105 to residue 254 of the heavy chain, which appears thus to be composed of 447 amino acids residues. This fragment contains the end of the V region, the switch peptide, the CH1 domain, the hinge region and the beginning of CH2. Sequence comparisons suggest that the CH1 domain is highly conserved in evolution, and allows the definition of two additional isotypic-specific regions. [ABSTRACT FROM AUTHOR]

Using automated stepwise Edman degradation of suitable overlapping peptides, the complete amino acid sequence of the 268 residue peptida α1-CB7 from calf skin collagen was determined. The preparation and ordering of the chymotryptic, tryptic and thermolytic peptides is described in the preceding paper. As shown previously for other peptides from the helical region of collagen, glycine appears in every third position and proline is present in high amount. Hydroxylation of proline to 4-hydroxyproline and lysine to hydroxylysine only occurred in the Y position of the tripeptide unit Gly-X-Y. Non-random distribution of other amino acids between the X and Y positions was also observed. [ABSTRACT FROM AUTHOR]

Repeat length disease thresholds vary among the 10 expanded polyglutamine (polyQ) repeat diseases, from about 20 to about 50 glutamine residues. The unique amino acid sequences flanking the polyQ segment are thought to contribute to these repeat length thresholds. The specific portions of the flanking sequences that modulate polyQ properties are not always clear, however. This ambiguity may be important in Huntington's disease (HD), for example, where in vitro studies of aggregation mechanisms have led to distinctly different mechanistic models. Most in vitro studies of the aggregation of the huntingtin (HTT) exon1 fragment implicated in the HD mechanism have been conducted on inexact molecules that are imprecise either on the N-terminus (recombinantly produced peptides) or on the C-terminus (chemically synthesized peptides). In this paper, we investigate the aggregation properties of chemically synthesized HTT exon1 peptides that are full-length and complete, containing both normal and expanded polyQ repeat lengths, and compare the results directly to previously investigated molecules containing truncated C-termini. The results on the full-length peptides are consistent with a two-step aggregation mechanism originally developed based on studies of the C-terminally truncated analogues. Thus, we observe relatively rapid formation of spherical oligomers containing from 100 to 600 HTT exon1 molecules and intermediate formation of short protofibril-like structures containing from 500 to 2600 molecules. In contrast to this relatively rapid assembly, mature HTT exon1 amyloid requires about one month to dissociate in vitro, which is similar to the time required for neuronal HTT exon1 aggregates to disappear in vivo after HTT production is discontinued. [ABSTRACT FROM AUTHOR]

The porcine anti-dinitrophenyl antibody was subjected to affinity labeling by m-nitrobenzenediazonium fluoroborate. From the S-sulfo derivative of the labeled antibody light (λ and ...) and heavy chains were isolated. It was found by spectral analysis of the polypeptide chains that the m-nitrobenzenediazonium reagent labeled tyrosine residues. In the light chains 10% molecules, in the heavy chains 21% molecules were labeled. Tryptic digest of labeled λ-chains was resolved by gel chromatography. The label was found to be distributed in two peasks at a ratio of 7: 3. From the labeled peptides of the tryptic digest shorter peptides were prepared by hydrolysis with subtilisin and purified by gel chromatography, paper chromatography and affinity chromato- labeled se peptides with known sections of the amino acid sequence of the λ-chains of porcine nonspecific immunoglobulin showed that the main portion of the label is attached to the tyrosine in position 33, s lesser portion to the tyrosine in position 93. [ABSTRACT FROM AUTHOR]

From the tryptic hydrolyzate of pig immunoglobulin &kappa-chains 6 cystine-containing fragments were isolated. Amino acids analysis showed that they contained 37-70 amino acid residues and were of a variable nature. There exists a linear relationship between the specific electrical charge of the fragment and the ionic strength of the buffer by which the fragment is eluted from a column of QAE-Sephadex. Fragments, the disulfide bond of which was split by oxidative sulfitolysis, were split by thermolysin and the hydrolyzates were compared by the method of peptide maps. All the maps of fragments tested contained the peptide Ile-ThrSerCysSSO3-Arg (where CysSSO3 = S-sulfo-cysteine) which represents the vicinity of the half-cystine 24 of pig κ-chains, as shown by us previously. The nature of the peptide maps indicates that the individual fragments originate in the same section of the primary structure of the N-terminal half of the κ-chains. Each of the isolated fragments was a mixture of variants with an identical specific charge but with some amino acid replacements. [ABSTRACT FROM AUTHOR]

The section which represents a part of a larger fragment of the variable part of pig immunoglobulin λ-chains is constituted by two peptides (18 residues and 4 residues)of variable character. These peptides were fractionated and their amino acid sequence determined. At certain positions two to four different amino acids were found. There is a close relation between the found amino acid sequence ... and the amino acid sequence of the corresponding region of human type L Bence-Jones proteins. [ABSTRACT FROM AUTHOR]

Proteomic analyses provide essential information on molecular pathways of cellular systems and the state of a living organism. Mass spectrometry is currently the first choice for proteomic analysis. However, the requirement for a large amount of sample renders a small-scale proteomics study challenging. Here, we demonstrate a proof of concept of single-molecule FRET-based protein fingerprinting. We harnessed the AAA+ protease ClpXP to scan peptides. By using donor fluorophore-labeled ClpP, we sequentially read out FRET signals from acceptor-labeled amino acids of peptides. The repurposed ClpXP exhibits unidirectional processing with high processivity and has the potential to detect low-abundance proteins. Our technique is a promising approach for sequencing protein substrates using a small amount of sample. [ABSTRACT FROM AUTHOR]

Motivation: In any macromolecular polyprotic system—for example protein, DNA or RNA—the isoelectric point—commonly referred to as the pI—can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge—and thus the electrophoretic mobility—of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machinelearning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. [ABSTRACT FROM AUTHOR]

Background: Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the trans conformation. In spite of their infrequent occurrence, cis peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes. Results: We perform a systematic analysis of regions in protein sequences that contain a proline cis peptide bond in order to discover non-random associations between the primary sequence and the nature of proline cis/trans isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are over-represented (i.e. appear frequently repeated) in a set of sequences. Four types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, iii) pattern discovery using a structural equivalency set and iv) pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate) indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of cis proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of cis prolyl bonds. Conclusion: Cis patterns with matches in the PROSITE database fell mostly into two main functional clusters: family signatures and protein signatures. However considerable propensity was also observed for targeting signals, active and phosphorylation sites as well as domain signatures. [ABSTRACT FROM AUTHOR]

We developed a composite machine-learning based algorithm, called ANGLOR, to predict real-value protein backbone torsion angles from amino acid sequences. The input features of ANGLOR include sequence profiles, predicted secondary structure and solvent accessibility. In a large-scale benchmarking test, the mean absolute error (MAE) of the phi/psi prediction is 28°/46°, which is ∼10% lower than that generated by software in literature. The prediction is statistically different from a random predictor (or a purely secondary-structure-based predictor) with p-value <1.0×10-300 (or <1.0×10-148) by Wilcoxon signed rank test. For some residues (ILE, LEU, PRO and VAL) and especially the residues in helix and buried regions, the MAE of phi angles is much smaller (10-20°) than that in other environments. Thus, although the average accuracy of the ANGLOR prediction is still low, the portion of the accurately predicted dihedral angles may be useful in assisting protein fold recognition and ab initio 3D structure modeling. [ABSTRACT FROM AUTHOR]

Predicting the function of a protein from its sequence is a long-standing goal of bioinformatic research. While sequence similarity is the most popular tool used for this purpose, sequence motifs may also subserve this goal. Here we develop a motif-based method consisting of applying an unsupervised motif extraction algorithm (MEX) to all enzyme sequences, and filtering the results by the four-level classification hierarchy of the Enzyme Commission (EC). The resulting motifs serve as specific peptides (SPs), appearing on single branches of the EC. In contrast to previous motif-based methods, the new method does not require any preprocessing by multiple sequence alignment, nor does it rely on over-representation of motifs within EC branches. The SPs obtained comprise on average 8.4 ± 4.5 amino acids, and specify the functions of 93% of all enzymes, which is much higher than the coverage of 63% provided by ProSite motifs. The SP classification thus compares favorably with previous function annotation methods and successfully demonstrates an added value in extreme cases where sequence similarity fails. Interestingly, SPs cover most of the annotated active and binding site amino acids, and occur in active-site neighboring 3-D pockets in a highly statistically significant manner. The latter are assumed to have strong biological relevance to the activity of the enzyme. Further filtering of SPs by biological functional annotations results in reduced small subsets of SPs that possess very large enzyme coverage. Overall, SPs both form a very useful tool for enzyme functional classification and bear responsibility for the catalytic biological function carried out by enzymes. [ABSTRACT FROM AUTHOR]

C-Terminal protein labeling allows non-radioactive detection of proteins by using fluorescent puromycin derivatives and cell-free translation systems. However, yields of some labeled proteins are low. Here, we report that the yield of labeled protein mainly depends on the C-terminal amino acid sequence. The short peptide tag sequence, RGAA, at the C-terminus increased not only the labeling efficiency (more than 80%) but also the synthesis yield of labeled proteins. To examine the relationship between the C-terminal amino acid sequence and the yield of labeled proteins, we synthesized C-terminally labeled glutathione S-transferase (GST) containing four identical amino acid residues at the C-terminus. The results demonstrated that 4 × Ala, 4 × His, 4 × Gln, and 4 × Cys produced over 200% of the yield of wild-type GST. In addition, the two Ala residues produced almost the same synthesis activity as 4 × Ala and RGAA. Similar results were obtained with various proteins and cell-free translation systems. [ABSTRACT FROM AUTHOR]

The amino acid sequence of the hemocyanin subunit c from the spiny lobster, Panulirus interruptus, has been determined. The elucidation was mainly based on three digests, with CNBr, trypsin and endoproteinase Glu-C, respectively. Additional evidence was obtained by sequencing of peptides from an endoproteinase Lys-C digest. Subunit c is a polypeptide with 661 amino acid residues and with a carbohydrate group attached to residue 476 in the third domain. No heterogeneity was observed. The degree of identity with subunit a is 59%. Some differences with subunit a are an N-terminal extension of six residues, a one-residue C-terminal extension, and a three-residue deletion. Furthermore, carbohydrate attachment is in a different position, as are most half-cystine residues. Limited trypsinolysis resulted in cleavage at the same site as in subunits a and b. [ABSTRACT FROM AUTHOR]

A statistical analysis of the autocorrelation characteristics of active polypeptides has been carried out by means of the correlogram method. It is shown that the amino acid sequences of the analysed proteins, considered as a whole, are autocorrelated and that the correlograms characterize each protein reflecting its three-dimensional structure. [ABSTRACT FROM AUTHOR]

The primary structure of rat β2-microglobulin (β2m) was determined. It is a polypeptide of 99 amino acids with the following sequence: IQKTPQIQVY SRHPPENGKP NFLNCYVSQF HPPQIETELL KNGKKIPNIE MSDLSFSKDW SFYLLAHTEF TPTETDVYAC RVKHVTLKEP KTVTWDRDM. The primary structure was determined by NH2 terminal sequence analysis together with sequence determination of one cyanogen bromide fragment and one tryptic peptide. Of other known β2m sequences, rat β2m is most homologous to mouse β2m (83% identity). The rabbit, human, and guinea pig sequences are more distant, with 24,27, and 31% differences, respectively. [ABSTRACT FROM AUTHOR]

Troponin T isolated from chicken fast skeletal muscle has been shown to be present in three different molecular forms, one in breast and two in leg muscle. The three forms differ in both size and charge. Troponin T from breast muscle has a molecular mass of 33.5 kDa and a pi of about 7. Of the two leg muscle forms the larger has a molecular mass of 30.5 kDa and a pi of about 8.5 and the smaller a molecular mass of 29.8 kDa and a pi of about 10. Considerably more heterogeneity has been found in the leg than in the breast muscle proteins although this is not reflected in their N-terminal sequences. The reason for this is not clear. Troponin T from breast or leg muscle can be phosphorylated with troponin T kinase at the single serine residue at the N-terminus. No difference in the rate or extent of phosphorylation could be found between proteins from breast or leg muscle. The three proteins have been shown to differ only in the amino acid sequence of their N-terminal tryptic peptides. These peptides are of different length, that from breast troponin T being 58 residues and those from leg troponin T being 36 and 42 residues, these differences account for the difference in molecular mass of the parent proteins. Despite this difference the sequence of the first 12 and last 14 residues is identical in all three N-terminal peptides. The remainder of the sequence of the smallest peptide is also repeated in the other two but they each contain an extra piece of unique sequence. On the basis of these sequences it is proposed that chicken troponin T is coded for by a single gene containing, at the 5′ end, a number of small exons and that three different mRNA molecules may be produced by alternative pathways of RNA splicing. The possible significance of these N-terminal sequence variations is discussed. [ABSTRACT FROM AUTHOR]

Partial amino acid sequences of six major subunits of bovine β-crystallin have been determined by automatic liquid-phase Edman degradation and the dansyl-Edman procedure, complemented by amino acid analyses of peptides. The results show that, including the previously established βBp sequence [H. P C. Driessen et al. (1981) Eur. J. Biochein. 121, 83-91], there exist at least seven primary gene products in bovine β-crystallin, which exhibit 40% or more sequence homology. Two of the gene products are completely identical except for the presence in one of them of 17 additional residues at the N terminus, possibly caused by differential splicing of the same primary RNA transcript. The rate of evolutionary change of the β chains (4% sequence change per 100 × 106 years) is about equally slow as that of α-crystallin, and the gene duplications giving rise to the different chains must have occurred very early in vertebrate evolution. The β chains can be divided into two groups, according to sequence homology and presence of deletions/insertions and C-terminal extension, on which basis a new, rational nomenclature for the β subunits is introduced. The N-terminal extensions of all β chains are very different in length and sequence, even between homologous β chains in different species. Possible explanations for this finding are discussed. [ABSTRACT FROM AUTHOR]

The sequence determination of the aA chains of α-crystallin from pig, horse, dog, cat, rabbit, rat and rhesus monkey is described. Most residues were placed by homology with the known bovine sequence, after amino acid analyses of tryptic and thermolytic peptides. Sequences were established, using the dansyl-Edman method, whenever peptides differed in composition from the homologous bovine peptides. The number of observed amino acid replacements among these mammalian αA chains is relatively small, but the rate at which substitutions have occurred varies greatly between the different evolutionary lineages. The amino acid replacements are not randomly distributed along the aA chain, most substitutions occurring in the C-terminal part of the chain. The rabbit, rat and monkey αA chains have four substitutions in common, indicating a polygenetic relationship between these species. [ABSTRACT FROM AUTHOR]

A method for amino acid analysis by double isotope labeling has been developed using ⊃3H-labelled dansyl chloride, and 14C-labelled amino acids as internal standards. As little as 20 pmol of an amino acid can be accurately measured by this method. The amino acid compositions of several peptides, determined using about 50pmol peptide, are reported and compared with the results obtained using conventional high-sensitivity ion-exchange chromatography. The correspondence is very good. The amino acid composition of a tryptic peptide containing the active site disulphide bridge of the lipoamide dehydrogenase component of the pyruvate dehydrogenase multienzyme complex of Escherichia coli has been shown to be identical to that of the corresponding peptide from the 2-oxoglutarate dehydrogenase complex of the same organism. This result is consistent with the view that the lipoamide dehydrogenase components of both complexes have a common amino acid sequence. [ABSTRACT FROM AUTHOR]

A methionine-containing tryptic peptide from acetamidinated human carbonic anhydrase B has been isolated. This peptide has been shown to bridge a previously known carboxyl-terminal fragment prepared by CNBr degradation with the rest of the enzyme molecule. Sequence studies on the methionine-containing peptide have extended the previous knowledge of the carboxyl-terminal sequence of the enzyme. Corresponding bridge peptides from human carbonic anhydrase C and acetamidinated bovine carbonic anhydrase B have also been isolated and their amino acid compositions have been determined. [ABSTRACT FROM AUTHOR]

Red palm weevil (Rhynchophorus ferrugineus Olivier, 1791, Coleoptera: Curculionidae) is a destructive pest of palms, rapidly extending its native geographical range and causing large economic losses worldwide. The present work describes isolation, identification, and bioinformatic analysis of antibacterial proteins and peptides from the immunized hemolymph of this beetle. In total, 17 different bactericidal or bacteriostatic compounds were isolated via a series of high-pressure liquid chromatography steps, and their partial amino acid sequences were determined by N-terminal sequencing or by mass spectrometry. The bioinformatic analysis of the results facilitated identification and description of corresponding nucleotide coding sequences for each peptide and protein, based on the recently published R. ferrugineus transcriptome database. The identified compounds are represented by several well-known bactericidal factors: two peptides similar to defensins, one cecropin-A1-like peptide, and one attacin-B-like protein. Interestingly, we have also identified some unexpected compounds comprising five isoforms of pheromone-binding proteins as well as seven isoforms of odorant-binding proteins. The particular role of these factors in insect response to bacterial infection needs further investigation. [ABSTRACT FROM AUTHOR]