Sequenator Analysis Research Articles

Identification of the essential cysteine residue of NADH-cytochrome b5 reductase.

The soluble catalytic domain of NADH-cytochrome b5 reductase was radiolabeled with [14C]N-ethylmaleimide. Reaction for a limited time resulted in incorporation of 0.41 eq of N-ethylmaleimide and loss of 36% of the enzyme activity. Chromatography on a 5'-ADP affinity column separated the reductase which was modified with N-ethylmaleimide from the unreacted enzyme; the isolated derivative constituted 37% of the total material, was completely inactivated, and contained 1.00 eq of N-ethylmaleimide. Cyanogen bromide cleavage of the derivative demonstrated that radioactivity was limited to a single peptide which contained both Cys-283 and Cys-297. Tryptic hydrolysis of this cyanogen bromide peptide showed that the radioactivity was associated with Cys-283. Automated sequenator analysis confirmed that Cys-283 was the radiolabeled residue. These data demonstrate unambiguously that Cys-283 provides the essential thiol group of cytochrome b5 reductase.

Evolution of alpha-lactalbumins. The complete amino acid sequence of the alpha-lactalbumin from a marsupial (Macropus rufogriseus) and corrections to regions of sequence in bovine and goat alpha-lactalbumins.

alpha-Lactalbumin was purified from a whey protein fraction of the milk of the red-necked wallaby (Macropus rufogriseus). The complete amino acid sequence was determined from the results of automatic sequenator analyses of the intact protein, the three cyanogen bromide fragments, and of peptides generated from the larger, COOH-terminal CNBr fragment by digestion with trypsin or staphylococcal protease. This is the first sequence to be determined of an alpha-lactalbumin from a marsupial and differs from known eutherian alpha-lactalbumins in size and locations of deletions in alignments with the homologous type c lysozymes, as well as in having amino acid substitutions at 8 sites that are invariant in known eutherian proteins. Some corrections are also reported for two regions of sequence in both bovine and goat alpha-lactalbumins. The new and previously published information on alpha-lactalbumin sequences is analyzed in relation to the evolutionary history of the alpha-lactalbumin line as well as the relationship of structure to function in these proteins.

Amino acid sequence of the light chain of bovine protein C.

The amino acid sequence of the light chain of the vitamin K-dependent protein C from bovine plasma is reported together with the supporting data. The sequence was determined by sequenator analysis of intact light chain, which contains 155 amino acid residues, and fragments obtained by chemical and enzymatic degradation of the light chain. All 11 glutamyl residues up to position 44 are carboxylated as gamma-carboxyglutamic acid residues. This part of the molecule proved very homologous to the other vitamin K-dependent plasma proteins. The remaining part (111 residues) is homologous to the corresponding parts in factor IX and factor X but not to prothrombin.

Composition and sequence studies show that A/duck/Ukraine/1/63 haemagglutinin (Hav7) belongs to the Hong Kong (H3) subtype.

The haemagglutinin chains HA1 and HA2 from the avian influenza virus A/duck/Ukraine/1/63 (Hav7, Neq2) have been subjected to amino acid analysis and N-terminal sequencing. Automated sequenator analysis of HA1 (40 cycles), after enzymic removal of the N-terminal pyroglutamic acid blocking group, and HA2 (43 cycles) showed that the Hav7 haemagglutinin closely resembled the human Hong Kong (H3) haemagglutinins including the presence of the characteristic extended 10 residue sequence at the N-terminus of HA1. These findings, together with the amino acid compositions for both chains, demonstrate that the Hav7 haemagglutinin is structurally similar to the Hong Kong (H3) haemagglutinins.

The complete covalent structure of protein B. The third major protein degraded during germination of Bacillus megaterium spores.

The complete covalent structure of Protein B, the third major protein degraded during germination of Bacillus megaterium spores, has been determined. The intact protein was cleaved with the specific B. megaterium spore protease into three peptides, residues 1 to 31 (B-III), 32 to 66 (B-I), and 67 to 96 (B-II). Cleavage of the intact protein with trypsin allowed isolation of the peptide encompassing residues 61 to 77 (T-11) as well as the COOH-terminal peptide, residues 94 to 96 (T-4). Cleavage of Peptide B-I with trypsin or chymotrypsin allowed isolation of peptides encompassing residues 53 to 60 (B-I-T-2) and residues 52 to 66 (B-I-C-4), respectively. Subtractive Edman degradation of Peptide T-4, automated sequenator analysis of Peptides B-I, B-II, T-11, B-I-T-2, and B-I-C-4, previously published partial sequence data on the intact B-protein and carboxypeptidase V digestion of the intact protein provided the data from which the following unique sequence was deduced: NH2-Ala-Lys-Gln-Thr-Asn-Lys-Thr-Ala-Ser-Gly-Thr-Ser-Thr-Gln-His-15 Val-Lys-Gln-Gln-Asp-Ala-Gln-Ala-Ser-Lys-Asn-Asn-Phe-Gly-Thr-30 Glu-Phe-Gly-Ser-Glu-Thr-Asn-Val-Gln-Glu-Val-Lys-Gln-Gln-Asn-45 Ala-Gln-Ala-Ala-Asn-Lys-Ser-Gln-Asn-Ala-Gln-Ala-Ser-Lys-60 Asn-Asn-Phe-Gly-Thr-Glu-Phe-Ala-Ser-Glu-Thr-Ser-Ala-Gln-Glu-75 Val-Arg-Gln-Gln-Asn-Ala-Gln-Ala-Gln-Lys-Lys-Asn-Gln-Asn-90 Ser-Gly-Lys-Tyr-Gln-Gly-COOH. The primary sequence of the B-protein contains a large internal duplication (residues 17 to 50 and 52 to 85), and shows significant sequence homology with the A- and C-proteins, the other major proteins degraded during B. megaterium spore germination.

Covalent structure of protein C. A second major low molecular weight protein degraded during germination of Bacillus megaterium spores.

The complete covalent structure of protein C, a protein degraded during germination of Bacillus megaterium spores, has been determined. The intact protein was cleaved with a highly specific spore protease into two peptides, residues 1 to 30 and 31 to 71. The intact protein was also cleaved by cyanogen bromide into two peptides, residues 1 to 27 and 28 to 71. Cleavage of the larger cyanogen bromide peptide with trypsin allowed isolation of the COOH-terminal peptide, residues 59 to 71. Automated sequenator analysis of the intact protein and peptide fragments, together with previously published partial sequence data on this protein and carboxypeptidase A digestion of the intact protein provided data from which the following unique sequence was deduced: (formula: see text). The primary sequence of the C protein shows an extremely high degree of homology with that of the A protein--another protein degraded during germination of B. megaterium spores.

Completion of the amino acid sequence of a Hong Kong influenza hemagglutinin heavy chain: Sequence of cyanogen bromide fragment CN1

The amino acid sequence of cyanogen bromide fragment CN1 from the hemagglutinin heavy chain (HA 1) of the Hong Kong influenza virus A/Memphis/102/72 has been determined by manual Edman degradation of tryptic and chymotryptic peptides and automated sequenator analysis of whole HA 1 after removal of the N-terminal pyroglutamic acid blocking group with calf liver pyroglutamate aminopeptidase. CN1 is the N-terminal cyanogen bromide peptide of HA 1 and extends from residues 1 to 168. The elucidation of the sequence of CN1 completes the amino acid sequence of A/Memphis/102/72 HA 1. This Hong Kong heavy chain contains a total of 328 amino acid residues and when compared with the HA 1 polypeptides of other influenza strains has an additional 10 residues at its N terminus including a glycosylated asparagine residue. It contains six glycosylated asparagine residues, five of which occur in CN1 at residues 8, 22, 38, 81, and 165 and one in CN3 at residue 285. No carbohydrate groups were found attached to serine or threonine residues. The Hong Kong HA 1 contains nine half-cystine residues, six of which are in CN1 at positions 14, 52, 64, 76, 97, and 139 and three in CN3 at positions 277, 281, and 305. The structure is discussed in relation to the available published data on the hemagglutinins from other strains of influenza virus and recent developments in the analysis of antigenic shift and drift.

Amino acid sequence of the sulfate-binding protein from Salmonella typhimurium LT2.

The amino acid sequence of the sulfate-binding protein from Salmonella typhimurium LT2 was determined by automated sequenator analysis of whole protein and fragments derived by chemical and enzymatic cleavage of whole protein. The fragments were products of limited trypsin digestion at arginine, cleavage at tryptophan by BrNps-skatole and o-iodosobenzoic acid, digestion with the protease from Staphylococcus aureus V8 at Glu-X bonds, cleavage by hydroxylamine at Asn-Gly bonds, and subdigestion with trypsin, chymotrypsin, and the Staphylococcus protease. The COOH-terminal sequence was confirmed using carboxypeptidase B and amino acid analysis. The sulfate-binding protein was determined to contain a single polypeptide of 310 residues with a molecular weight of 34,667 calculated from the sequence.

Covalent structure of protein A. A low molecular weight protein degraded during germination of Bacillus megaterium spores.

The complete covalent structure of Protein A, a protein degraded during bacterial spore germination, has been determined. The intact protein was cleaved with a highly specific spore protease into two peptides, residues 1 to 21 and 22 to 61. The larger peptide was further cleaved into two fragments with either cyanogen bromide or by trypsin cleavage following arginine modification with cyclohexanedione. The peptides derived from cyanogen bromide fragmentation encompassed residues 22 to 53 and 54 to 61 while trypsin hydrolysis yielded overlapping fragments comprising residues 22 to 48 and 49 to 61. Automated sequenator analysis together with carboxypeptidase Y digestion of the intact protein and the peptide fragments provided data from which the following unique amino acid sequence was deduced. NH2-Ala-Asn-Thr-Asn-Lys-Leu-Val-Ala-Pro-Gly10-Ser-Ala-Ala-Ala-Ile-Asp-Gln-Met-Lys-Tyr20-Glu-Ile-Ala-Ser-Glu-Phe-Gly-Val-Asn-Leu30-Gly-Pro-Glu-Ala-Thr-Ala-Arg-Ala-Asn-Gly40-Ser-Val-Gly-Gly-Glu-Ile-Thr-Lys-Arg-Leu50-Val-Gln-Met-Ala-Glu-Gln-Gln-Leu-Gly-Gly60-Lys-COOH.

Primary structure of rabbit alpha-lactalbumin.

Rabbit alpha-lactalbumin was purified from the milk of New Zealand White rabbits. It was found to exist predominantly as a glycoprotein, containing 5 mol of glucosamine per mol of protein, as well as other sugars. The amino acid sequence of the protein was determined by sequenator analysis and carboxypeptidase digestion. There are 122 amino acids in the protein and a single carbohydrate moiety, probably attached to an asparagine residue at position 45. The C terminus of rabbit alpha-lactalbumin is one residue shorter than that of the other alpha-lactalbumins. Sequence comparisons indicate that the alpha-lactalbumin gene has been undergoing more frequent mutation than had previously been thought. A new method of preparative peptide mapping using 2,5-diphenyloxazole (PPO) fluor to detect peptides is described.

Amino acid sequence of the biotinyl subunit from transcarboxylase.

The complete amino acid sequence of the biotinyl subunit from the enzyme transcarboxylase of Propionibacterium shermanii has been determined from the structures of overlapping tryptic and cyanogen bromide peptides together with sequenator analysis on the whole subunit. The subunit contains 123 amino acid residues. Eleven of nineteen residues in the region of biotin attachment, when compared to pyruvate carboxylase from avian liver (Rylatt, D. B., Keech, D. B., and Wallace, J. C. (1977) Arch. Biochem. Biophys. 183, 113-122), were found to be in identical positions relative to biocytin. There was less homology with acetyl-CoA carboxylase from Escherichia coli (Sutton, M. R., Fall, R. R., Nervi, A. M., Alberts, A. W., Vagelos, P. R., and Bradshaw, R. A. (1977) J. Biol. Chem. 252, 3934-3940), but in all of these biotin enzymes there was an alanylmethionyl-biocytinyl-methionine sequence. The secondary structure of the biotinyl subunit has been estimated using the method of Chou and Fasman (Chou, P. Y., and Fasman, G. D. (1978) Adv. Enzymol. 47, 45-148) and considered in relationship to the role of the biotinyl subunit in the structure and function in transcarboxylase.

The Complete Amino‐Acid Sequence of the Sweet Protein Thaumatin I

The primary structure of the sweet-tasting protein thaumatin has been elucidated. The protein consists of a single polypeptide chain of 207 residues. The sequence of the N-terminal part of the chain was determined by sequenator analysis. As the protein contains only one methionine residue, it was possible to deduce the N-terminal sequence of the C-terminal cyanogen bromide fragment by automatic sequencing of the cyanogen-bromide-cleaved, succinylated protein. To arrive at the sequence of the whole protein tryptic and Staphylococcus protease peptides, together with chymotryptic peptides and a 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine (BNPS-skatole) fragment were also sequenced. Comparing the amino acid sequence of thaumatin with that of the other sweet-tasting protein, monellin, we have located five sets of identical tripeptides. Since immunological cross-reactivity of thaumatin antibodies with monellin has recently been described, one or more of these tripeptides might be part of a common antibody recombination site and possibly be involved in the interaction with the sweet-taste receptor.

New evidence for glutamic acid as an iron ligand in hemerythrin

The amino acid sequence of the respiratory protein, hemerythrin, from Phascolopsis gouldii was reinvestigated in the region of residue 58. Sequenator analyses were performed on peptide 50–113, obtained by trypsin digestion of the intact protein, and on peptide 50–62, obtained by cyanogen bromide cleavage of peptide 50–113. In both peptides residue 58 was unambiguously identified as glutamic acid and residue 59 as glutamine. This corrects a previous mistake in the assignment of residue 58 and makes its proposed role as an iron ligand more plausible.

Amino acid sequence of a peptide containing an essential cysteine residue of Escherichia coli GMP synthetase.

The amino acid sequence of a 51-residue tryptic peptide of citraconylated [1-14C]carboxamidomethyl-labeled Escherichia coli GMP synthetase was determined by sequenator analyses of the intact peptide and fragments obtained by cleavage of the peptide with cyanogen bromide, trypsin, and Staphylcoccus aureus strain V8 protease. The cysteine residue of this peptide fragment is essential for glutamine-dependent GMP synthesis activity and is implicated in formation of a hypothetical covalent glutamyl-enzyme intermediate. There is essentially cysteine-containing regions of two other glutamine amidotransferases, Pseudomonas putida anthranilate synthetase Component II and chicken liver formylglycinamide ribonucleotide amidotransferase. There is, however, a cluster of amino acids with "antipathy" for helix formation and a "nonessential" cysteine of anthranilate synthetase Component II.

Bovine protein C: amino acid sequence of the light chain.

The amino acid sequence of the light chain of bovine protein C was determined by sequenator analysis of the carboxymethylated light chain and fragments obtained by cyanogen bromide treatment, tryptic digestion after blocking of lysine residues, and cleavage with 2-(2-nitrophenylsulfenyl)-3-methyl-3-bromoindolenine (BNPS-skatole). The sequence was (in the standard one-letter code) A-N-S-F-L-X-X-L-R-P-G-N-V-X-R-X-C-S-X-X-V-C-X-F-X-X-A-R-X-I-F-Q-N-T-X-D-T-M-A-F-W-S-K-Y-S-D-G-D-Q-C-E-D-R-P-S-G-S-P-C-D-L-P-C-C-G-R-G-K-C-I-H-G-L-G-G-F-R-C-D-C-A-E-G-W-E-G-R-F-C-L-H-E-V-R-F-S-N-C-S-A-E-B-G-G-C-A-H-Y-C-M-E-E-E-G-R-R-H-C-S-C-A-P-G-Y-R-L-E-D-D-H-Q-L-C-V-S-K-V-T-F-P-C-G-R-L-G-K-R-M-E-K-K-R-K-T-L. The first eleven glutamic acid residues were carboxylated to gamma-carboxyglutamic acid (X). The NH2-terminal, vitamin K-dependent part showed an extensive homology to both prothrombin and factor X, whereas the rest of the chain showed a strong homology to factor X but little similarity to prothrombin.

Amino acid sequence of hemerythrin from Themiste dyscritum

The amino acid sequence of hemerythrin from the sipunculid worm, Themiste dyscritum, was determined by sequenator analyses of the S-pyridylethylated protein and fragments derived by further chemical and enzymatic cleavages. The fragments were obtained by cleavage of the intact protein with hydroxylamine, trypsin digestion of citraconylated intact protein, and subdigestion with Staphylococcal protease V8. The COOH-terminal sequence was determined using carboxypeptidases A and B and amino acid analyses. The polypeptide chain was found to contain 113 amino acids. Since heterogeneity was observed at no more than two positions in the amino acid sequence, the native octameric protein appears to be composed of identical subunits. By combining information derived from sequence analyses and x-ray crystallographic studies, it has been possible to identify amino acids responsible for the tertiary and quaternary structure of the protein as well as amino acids serving as iron ligands at the oxygen-binding site.

Covalent structure of the membranous segment of horse cytochrome b5. Chemical cleavage of the native hemoprotein

The complete covalent structure of the membranous segment of horse liver cytochrome b5 has been determined. This peptide spans residues 91 to 133 of the cytochrome molecule, and contains the segment responsible for the association of the hemoprotein with microsomal or synthetic vesicles. Two peptides, residues 91 to 127 and 128 to 133, comprising the entire membranous moiety were isolated from a tryptic digest of urea-denatured apoprotein. The membranous segment (residues 91 to 127) could be separated from all other tryptic peptides by a single gel filtration step. Trypsin digestion of succinylated cytochrome produced similar peptides, residues 89 to 127 and 128 to 133. The covalent structures for residues 89 to 127 and 128 to 133 were derived from automated sequenator analysis of tryptic peptides. Chemical cleavage at tryptophanyl, or methionyl residues, or both, by the method of Ozols and Gerard ((1977) J. Biol. Chem. 252, 5986-5989) provided the overlapping peptides from which the following unique sequence was deduced: (formula: see text).

The amino acid sequence of Clostridium pasteurianum iron protein, a component of nitrogenase. II. Cyanogen bromide peptides.

A total of 10 cyanogen bromide peptides were isolated from the S-beta-carboxymethyl iron protein of nitrogenase. Purification of these peptides was performed mainly by gel filtration on Sephadex G-50; by ascending paper chromatography using the solvent system of pyridine, isoamyl alcohol, 0.1 M ammonium hydroxide; and also, in some cases, with additional steps such as anion exchange column chromatography on Dowex 1-X2 or ascending paper chromatography in an acidic solvent system or by pyridine precipitation of the cyanogen bromide fragment. Sequenator analyses of three large cyanogen bromide peptides (53 to 72 residues) provided tryptic peptide overlap data for the inner portion of the protein. The cyanogen bromide peptides accounted for all of the 273 amino acid residues which were present in the tryptic peptides isolated from carboxymethyl-iron protein (Tanaka, M., Haniu, M., Yasunobu, K. T., and Mortenson, L. E. (1977) J. Biol. Chem. 252, 7081-7088).

Amino acid sequence of the L-arabinose-binding protein from Escherichia coli B/r.

The amino acid sequence of the L-arabinose-binding protein of Escherichia coli B/r was determined by sequenator analyses of reduced and S-pyridylethylated L-arabinose-binding protein and fragments derived by chemical and enzymatic cleavage of the native protein. The fragments were the products of cleavage by cyanogen bromide. BNPS-skatole, hydroxylamine, mild acid hydrolysis, limited trypsin digestion, chymotrypsin subdigestion, and subdigestion with Staphylococcus aureus protease V8. The COOH-terminal sequence was determined using bovine carboxypeptidases A and B and amino acid analyses. The L-arabinose-binding protein was determined to contain 306 amino acid residues, the sequence of which is presented below.

Amino acid sequence of Escherichia coli biotin carboxyl carrier protein (9100).

The amino acid sequence of a proteolytic fragment of Escherichia coli biotin carboxyl carrier protein was determined from the structures of overlapping tryptic, thermolytic, and staphylococcal protease peptides together with automated sequenator analyses on the intact protein. The fragment, 82 residues in length, contains the single residue of biocytin of the protein. The relationship of the Mr = 9100 fragment to the native Mr = 22,500 subunit is discussed.