Use of fluorescamine as an effective blocking reagent to reduce the background in protein sequence analyses by the Beckman automated sequencer

Location and nucleotide sequence of the gene for the proton-translocating subunit of wheat chloroplast ATP synthase

The proton-translocating subunit of wheat chloroplast ATP synthase is encoded by a chloroplast gene that has been accurately mapped and whose nucleotide sequence has been determined. The predicted sequence of 81 amino acids has been confirmed in part by determination of the sequence of the first 40 amino acids from the NH(2) terminus of the protein, and it shows 100% homology with the known amino acid sequence of the spinach protein but no more than 35% homology with the amino acid sequences of bacterial and mitochondrial proteins. The gene shows no deviation from the "universal" genetic code and is not split. A potential ribosome binding site is located 12 nucleotides upstream from the initiation codon, but sequences homologous to prokaryotic promotors and transcription terminators are not apparent.

Atrial pronatriodilatin: a precursor for natriuretic factor and cardiodilatin

Numerous peptides isolated from rat heart atria, including two containing 33 and 73 amino acids, were isolated and shown to exhibit natriuretic activities. Here, we describe the purification and partial amino acid sequence of a 106-residue peptide containing the previously sequenced 33- and 73-amino-acid ANF peptides. The determined sequence is a novel one and is not significantly homologous to any known protein or segment thereof. In fact, this sequence shows significant homology only to another novel partial sequence obtained from sequence analysis of a porcine peptide, called cardiodilatin, also found in heart atria. This relationship is taken as evidence that ANF and cardiodilatin are part of the same precursor molecule which would contain at the very least 126 amino acids.

Heterogeneous expression of protein and mRNA in pyruvate dehydrogenase deficiency

Deficiency of pyruvate dehydrogenase [pyruvate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-acetylating), EC 1.2.4.1], the first component of the pyruvate dehydrogenase complex, is associated with lactic acidosis and central nervous system dysfunction. Using both specific antibodies to pyruvate dehydrogenase and cDNAs coding for its two alpha and beta subunits, we characterized pyruvate dehydrogenase deficiency in 11 patients. Three different patterns were found on immunologic and RNA blot analyses. (i) Seven patients had immunologically detectable crossreactive material for the alpha and beta proteins of pyruvate dehydrogenase. (ii) Two patients had no detectable crossreactive protein for either the alpha or beta subunit but had normal amounts of mRNA for both alpha and beta subunits. (iii) The remaining two patients also had no detectable crossreactive protein but had diminished amounts of mRNA for the alpha subunit of pyruvate dehydrogenase only. These results indicate that loss of pyruvate dehydrogenase activity may be associated with either absent or catalytically inactive proteins, and in those cases in which this enzyme is absent, mRNA for one of the subunits may also be missing. When mRNA for one of the subunits is lacking, both protein subunits are absent, suggesting that a mutation affecting the expression of one of the subunit proteins causes the remaining uncomplexed subunit to be unstable. The results show that several different mutations account for the molecular heterogeneity of pyruvate dehydrogenase deficiency.

Identification of a cDNA clone for the beta-subunit of the pyruvate dehydrogenase component of human pyruvate dehydrogenase complex

We report the isolation of a 1.5 kb cDNA clone for the beta subunit of human pyruvate dehydrogenase (E1) from a human liver lambda gt11 cDNA library using anti-E1 serum. We generated a peptide sequence of 24 amino acids starting from the N-terminus of bovine heart mature E1 beta. The identity of the E1 beta cDNA clone was confirmed by the similarity between the amino acid sequence deduced from the cDNA nucleotide sequence and the known amino acid sequence of bovine heart E1 beta. In Northern analysis of total RNA extracted from human heart, the E1 beta cDNA clone hybridized to a major 1.6 kb and a minor 5.2 kb RNA species.

Partial primary structures of human and murine macrophage colony stimulating factor (CSF-1)

Approximately 40 amino-terminal residues and 20 internal residues of CSF-1 purified from the media of cultured human pancreatic carcinoma (MIA PaCa) cells and of cultured murine L cells have been identified. Results indicated that the two subunits in each molecule of biologically active CSF-1 are identical in their amino-terminal portions. The twelve amino-terminal residues of MIA PaCa CSF-1 were found to be identical to those of human-urinary CSF-1, suggesting that the polypeptide portions of the two human proteins may be identical. Approximately 75% of the amino acids identified in both MIA PaCa CSF-1 and murine CSF-1 were found to be common to both. No homology to other proteins was observed. This study suggests a subunit polypeptide Mr nearer to 17K than to 26K predicted from cDNA.

Amino acid sequence determination of guanyl-specific ribonuclease Sa from Streptomyces aureofaciens

Using automated Edman degradation of two nonfractionated peptide mixtures of tryptic and staphylococcal protease digests of the protein, the complete amino acid sequence of the guanyl-specific ribonuclease Sa from Streptomyces aureofaciens was established. Ribonuclease Sa contains 96 amino acid residues (Mr 10,566). A 50% sequence homology of ribonuclease Sa to the guanyl-specific ribonuclease St from S. erythreus was found.

Amino acid sequence and S-S bonds of Penicillium brevicompactum guanyl-specific ribonuclease

The primary structure of Penicillium brevicompactum guanyl-specific RNase was determined. The enzyme consists of 102 amino acid residues, Mr 10801. The 4 cysteine residues of the RNase are linked in pairs by disulfide bonds: Cys2-Cys10, Cys6-Cys101. P. brevicompactum RNase structure is similar to RNase T1; the degree of homology is 66%.

Solid-phase protein and peptide sequencing using either 4-N,N-dimethylaminoazobenzene 4'-isothiocyanate or phenylisothiocyanate

Automated solid-phase sequencing using 4-N,N-dimethylaminoazobenzene 4'-isothiocyanate (DABITC) double coupling or regular phenylisothiocyanate (PITC) degradation procedures have been investigated. Employing sensitive high-performance liquid chromatography for the identification of amino acid thiohydantoin derivatives (PTH and DABTH), both methods were capable of sequencing immobilized peptides or proteins at the subnanomole levels. In the sequencing program using DABITC, alternate methanol and dichloroethane washes and automated conversion using methanolic HCl containing dithiothreitol were introduced to obtain clean thiazolinones and to ensure high recovery yields of the thiohydantoins. Using regular PITC degradation with a 59-min program, the background peaks of the side products could be reduced to enhance HPLC identification. Peptides or proteins attached to the glass beads or resins via the carboxyl terminii or epsilon-amino groups of lysyl residues could be readily sequenced up to 30 identifiable degradation cycles, where the sequencing is generally terminated due to the increased background components.

Use of o-phthalaldehyde to reduce background during automated Edman degradation

Background generated during the cleavage step of the Edman degradation is a major obstacle to extended automated amino acid sequencing. It was demonstrated recently by A. S. Bhown, J. C. Bennett, P. H. Morgan, and J. E. Mole (1981, Anal. Biochem. 112, 158-162) that introduction of fluorescamine into the spinning cup reduced background by blocking primary amino groups at cycles where a proline residue is at the exposed amino terminus. A convenient blocking reaction program using o-phthalaldehyde which can be intercalated into the sequencing format of an automated Beckman liquid-phase sequencer is presented. The advantages of o-phthalaldehyde in blocking of primary amines when proline is amino terminal arise from its stability in aqueous solution and the ease of programmed metering of delivery to the sequencer spinning cup. The blocking reaction proved successful not only in extending sequence analyses but also in the elimination of unwanted sequences in selected peptide mixtures without the necessity of purification of the target peptide.

Amino acid sequence of the heavy chain variable region from the A/J mouse anti-arsonate monoclonal antibody 36-60 bearing a minor idiotype

In addition to the predominant idiotype family (IdCR) associated with the murine A/J anti-azophenylarsonate response, a second idiotype family (Id36-60) was defined on the basis of serologic cross-reactivity and amino acid sequence homology among monoclonal antibodies [Marshak-Rothstein, A., Margolies, M.N., Benedetto, J.D., & Gefter, M.L. (1981) Eur. J. Immunol. 11, 565-572]. The complete variable region amino acid sequence of the A/J IgG2a hybridoma protein 36-60 heavy chain was obtained by automated Edman degradation of the intact chain and fragments generated by cleavage with CNBr and by tryptic digestion of a succinylated CNBr peptide. A comparison of the Id36-60 heavy chain sequence to that of the IdCR heavy chain variable region reveals only 45% homology between them. The structural data indicate that different genes encode the VH, D, and JH gene-encoded sequences in the two idiotypes.

Sequence analysis of rat hypothalamic corticotropin-releasing factor with the o-phthalaldehyde strategy

Sequence analysis was performed on a 41-residue polypeptide that has been identified as the predominant form of high intrinsic corticotropin-releasing activity of rat hypothalamus. The sequence of residues 1-39 of this corticotropin-releasing factor (CRF) was determined by Edman degradation of a partially purified peptide in a highly sensitive spinning cup sequencer after selective blocking of CRF or its main contaminant with o-phthalaldehyde. This approach was validated by peptide mapping of CRF of a highly purified preparation. Peptide mapping was accomplished with reverse-phase high-pressure liquid chromatography of CRF fragments obtained by digestion with clostripain. The identities of the fragments cleaved from CRF were established by chromatographic comparison with synthetic peptides, amino acid analysis, and Edman degradation. On the basis of these experiments, the primary structure of rat hypothalamic CRF was established to be H-Ser-Glu-Glu-Pro-Pro-Ile-Ser-Leu-Asp-Leu-Thr-Phe-His-Leu- Leu-Arg-Glu-Val-Leu-Glu-Met-Ala-Arg-Ala-Glu-Gln-Leu-Ala-Gln-Gln-Ala-His-Ser-Asn - Arg-Lys-Leu-Met-Glu-Ile-Ile-NH2. It is expected that the o-phthalaldehyde strategy will facilitate the sequence analysis of partially purified peptides containing proline residues.

Isolation and characterization of the CNBr peptides from the proteolytically derived N-terminal fragment of ovine opsin

Ovine rhodopsin may be cleaved in situ by Staphylococcus aureus V8 proteinase into two membrane-bound fragments designated V8-L (27 000 mol.wt.) and V8-S (12 000 mol.wt.). After purification of the proteolysed complex by affinity chromatography in detergent using concanavalin A immobilized on Sepharose 4B, the two polypeptide fragments may be separated by gel-permeation chromatography on Sephadex LH-60. Digestion of the N-terminal-derived V8-L fragment with CNBr in 70% (v/v) trifluoroacetic acid resulted in a peptide mixture that could be fractionated by procedures involving gel-permeation chromatography in organic and aqueous solvents and the use of differential solubility. The complete or partial sequences of all ten peptides are reported.

A comparison of fluorescamine and o-phthaldialdehyde as effective blocking reagents in protein sequence analyses by the Beckman sequencer

Use of o-phthaldialdehyde to chemically reduce the newly generated amino termini responsible for the progressively increasing background during an extended amino acid sequence analysis in a liquid phase sequencer has been described. The results have been compared with Fluram blocking using apomyoglobin and rabbit C-reactive protein as standard and unknown samples, respectively.

Prosimian hemoglobins I. The primary structure of the beta-globin chain of Lemur catta

The primary structure of the beta chain from the hemoglobin of a prosimian primate, Lemur catta, has been determined by automated Edman degradation of intact polypeptide chain and fragments produced by tryptic, cyanogen bromide and acid cleavage, and by homology with the sequence of Lemur fulvus. The sequence presented here differs from the human beta-globin sequence at 26 sites. This is the same degree of divergence previously reported for the beta-globin chain of Lemur fulvus. The sequences of the two congeneric lemuroid beta-globin chains are surprisingly divergent, differing at 18 sites. Of the 26 positions where L. catta differs from Homo sapiens, 7 are at positions with defined function. Of these 7 positions, 4 (2-Phe, 54-Ile, 94-Val, 112-Ile) are unique to L. catta among the primate beta-globin chains of established sequence. Residue 112-Ile is consistent with the prediction of Beard and Goodman (19) of an isoleucyl residue in this position in the ancestral primate beta-globin chain.

Isolation, characterization and N-terminal sequences of the CNBr-cleavage peptides from human complement Factor B. Localization of a free thiol group and a sequence defining the site cleaved by factor D

Nine CNBr-cleavage peptides from Factor B (a component of the alternative pathway of complement) were isolated. Each was characterized by amino acid analysis and automated Edman degradation. One peptide contained a methionyl bond resistant to cleavage by CNBr. The number of CNBr-cleavage peptides is in agreement with the results of amino acid analysis of Factor B and the fragments Ba and Bb. A total of 358 unique residues were identified from the N-terminal sequences of the CNBr-cleavage peptides. These represent approx. 50% and 60% of the total residues of Factor B and fragment Bb respectively. Alignment of two CNBr-cleavage peptides (CB-VIc and CB-IV) provided a continuous segment of 140 residues. This sequence contained the site cleaved by Factor D to generate the Ba and Bb fragments during the activation of complement. Peptide CB-IV contained a free thiol group at a position corresponding to residue 33 of fragment Bb. Amino sugar analyses of Factor B and of fragments Bb and Ba indicated that all the carbohydrate structures of factor B are N-linked to asparagine through N-acetylglucosamine. The two carbohydrate-attachment sites of the Bb fragment were identified.