Glyceraldehyde-3-phosphate dehydrogenase. Investigation on the regions responsible for self-assembly of subunits

1. In glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (EC 1.2.1.12) the four S-loop form the core of the tetramer. 2. Amino acid sequence of the S-loop of the regions of GAPDH from carp muscle was established through the analysis of tryptic digests of the enzyme treated alternatively with bromocyanate and o-iodosobenzoic acid. 3. Enzyme had been oxidized with performic acid. After treatment with trypsin the peptide mixture was fractionated into fragments. 4. CNBr cleavage of this enzyme was performed after S-carboxymethylation. The respective cyanogen bromide fragments have been isolated and characterized. 5. The procedure of protein fragmentation by o-iodosobenzoic acid used to split tryptophanyl peptide bonds. 6. Each peptide obtained after enzymatic or chemical fragmentation was purified to homogeneity by Bio-Gel or Sephadex chromatography, high voltage electrophoresis and descending paper chromatography and characterized by electrochromatography, N- and C-terminal sequence and amino acid composition. 7. The results are compared with those obtained from studies on GAPDH from other sources.     

Prereplicative modulation of nuclear protein kinases in the regenerating rat liver

Treatment of carboxymethylated actin with o-iodosobenzoic acid (Mahoney, W.C., and Hermodson, M.A. (1979) Biochemistry, $\text{18}$, 3810–3814) did not produce the peptide pattern expected on the basis of specific peptide bond cleavage at tryptophanyl bonds. Isolation and amino acid sequence characterization of peptides from the digest indicated that in addition to cleavage at Trp residues, cleavages occurred at Tyr-53, Tyr-198, Tyr-218, Tyr-239 and probably at Tyr-91. These results indicate that the specificity of o-iodosobenzoic acid as a reagent for peptide bond cleavage is wider than previously reported. A simple explanation for the different susceptibilities of tyrosyl-containing peptide bonds to cleavage was not apparent from inspection of the sequences adjacent to these residues.     

Comparative studies of the neurofilament triplet protein peptide mapping by chemical cleavage

Peptide mapping of the three neurofilament protein subunits with apparent mol. weights of 210 kDa, 160 kDa and 70 kDa was performed with two different reagents: CNBr, BNPS-Skatole leading to the cleavage of methionyl and tryptophanyl bonds respectively. With BrCN we obtained two large fragments resistant to the cleavage, with mol. wts of 85 kDa for the 160 kDa and 135 kDa for the 210 kDa neurofilament proteins respectively. These fragments were located on the C-terminal part of the proteins (the tails) and correspond to specific regions responsible for their physiological identity. On the other hand, the cleavage with BNPS-Skatole at the tryptophanyl bonds gave similar patterns. The 210 kDa and 160 kDa neurofilament proteins gave a doublet of high mol. wt resistant to the cleavage, corresponding very likely to the C-terminal part and 4 fragments of mol. wt between 30 and 40 kDa corresponding to the N-terminal part. The neurofilament triplet share a common 30.5 kDa fragment located on the N-terminal part. From these peptide mapping studies, we conclude that the two neurofilament subunit proteins with mol. wts of 160 kDa and 210 kDa are different but related structures and that the CNBr characterized cleavage fragments of mol. wt 85,000 and 135 kDa are suitable polypeptides for sequence and immunological studies of the C-terminal part of these proteins.     

Use of N-chlorosuccinimide/urea for the selective cleavage of tryptophanyl peptide bonds in proteins. Cytochrome c.

The conditions and utility of the N-chlorosuccinimide/urea (NCS/urea) reagent for the selective cleavage of tryptophanyl peptide bonds in proteins is demonstrated with cytochrome c. At low concentrations of NCS/urea the oxidation of thioether side chains in cytochrome c is the predominant reaction. Methionyl residues are oxidized to sulfoxide and the heme-thioether bridge is partially cleaved. At 10-fold excess of NCS/urea reagent, cleavage of the tryptophanyl peptide bond is optimal at approximately 50% yield in several species of cytochrome c studied. Analytical data on isolated horse cytochrome c peptide fragments demonstrate lack of modification and cleavage at tyrosyl and histidyl residues. However, at high concentrations of NCS/urea reagent (30-fold) unexpected conversions of methionine to sulfone and cysteine to cysteic acid in intact proteins are observed. This is in contradistinction to the absence of sulfone in NCS/urea-reacted amino acid mixtures. The mechanisms of halogenation and cleavage by N-bromosuccinimide, N-iodosuccinimide, and N-chlorosuccinimide are discussed. It is porposed that the selectivity with respect to halogenation by N-chlorosuccinimide is due to the insignificant participation of molecular chlorine in the NCS/urea reaction. A mechanism of halogenation and cleavage by NCS at tryptophan is also offered.     

Causes of the decrease in fluorescence due to proteolysis of alpha-casein

Fluorescence decrease in casein solutions induced by proteolytic enzymes is mainly due to cleavage of alpha-casein, and in particular to alpha S1-casein, which is quantitatively the main component of commercial casein. Treatment of alpha-casein with o-iodosobenzoic acid, diminished its intrinsic fluorescence considerably and abolished the decrease in fluorescence induced by proteolytic cleavage. The carboxyterminal Trp at position 199 in alpha S1-casein contributes approximately 30% to the overall effect, while the Trp at position 164 contributes about 70%. Treatment of alpha-casein with cyanogen bromide lowered the initial fluorescence of the preparation, but, in the resulting fragment, trypsin still diminished some of the residual fluorescence. The velocity of decrease in fluorescence correlates with the distance from the Trp in position 164 at which the peptide bond is broken. This effect seems to be rather unique for the caseins, but particularly for alpha S1-casein; this is due to the existence of a Trp that is in the vicinity of hydrophobic amino acids and which upon hydrolysis, becomes exposed to a more hydrophilic environment.     

The complete amino acid sequence of chicken skeletal-muscle enolase.

The complete amino acid sequence of chicken skeletal-muscle enolase, comprising 433 residues, was determined. The sequence was deduced by automated sequencing of hydroxylamine-cleavage, CNBr-cleavage, o-iodosobenzoic acid-cleavage, clostripain-digest and staphylococcal-proteinase-digest fragments. The presence of several acid-labile peptide bonds and the tenacious aggregation of most CNBr-cleavage fragments meant that a commonly used sequencing strategy involving initial CNBr cleavage was unproductive. Cleavage at the single Asn-Gly peptide bond with hydroxylamine proved to be particularly useful. Comparison of the sequence of chicken enolase with the two yeast enolase isoenzyme sequences shows that the enzyme is strongly conserved, with 60% of the residues identical. The histidine and arginine residues implicated as being important for the activity of yeast enolase are conserved in the chicken enzyme. Secondary-structure predictions are analysed in an accompanying paper [Sawyer, Fothergill-Gilmore & Russell (1986) Biochem. J. 236, 127-130].     

Chemical Cleavage of Bovine β-Lactoglobulin by BNPS-Skatole for Preparative Purposes: Comparative Study of Hydrolytic Procedures and Peptide Characterization

A comparative study of various procedures for tryptophanyl peptide bond cleavage by BNPS-skatole [2-(2-nitrophenyl)-3-methyl-3-bromoindolenine] was carried out on native and on reduced and alkylated bovine β-lactoglobulin (BLG). The reaction yield and the composition of the derived products were studied in acetic acid, trifluoroacetic acid (TFA), and ethanol/TFA. For BNPS-skatole removal, extraction by water or ethyl ether was compared with dialysis and gel filtration. The three expected peptides (1–19, 20–61, 62–162) and incomplete cleaved fragments (1–61, 20–162) were separated and characterized by electrophoresis, reverse-phase high-performance liquid chromatography, and mass spectrometry. The highest hydrolysis yield (67.4%) occurred with native BLG cleaved in 88% acetic acid at 47°C for 60 min. Subsequent water extraction and gel filtration led to total recovery of the material, but reagent elimination was only quantitative after gel filtration. Cleavage specificity was ensured by mass spectrometry and the amino acid composition of peptides 1–19 and 62–162. The chemical side reactions identified are discussed.     

Structure and function of L-lactate dehydrogenases from thermophilic and mesophilic bacteria, IV. The primary structure of the mesophilic lactate dehydrogenase from Bacillus subtilis

The complete amino-acid sequence of lactate dehydrogenase from the mesophilic Bacillus subtilis (B. X1) was determined. Approximately 70% of the sequence was obtained by sequence analysis of intact protein (N-terminal sequence) and of four CNBr fragments (CNBr3, CNBr4, CNBr5 and CNBr6). Sequences overlapping the CNBr fragments were determined from polypeptide fragments obtained by cleavage using o-iodosobenzoic acid (cleavage at Trp) or clostripain (cleavage at Arg). The C-terminal amino-acid residue (Asn) was detected by carboxypeptidase Y-degradation. Lactate dehydrogenase from B. subtilis shows a 69% sequence homology to that from the thermophilic strain B. stearothermophilus, and a 34% sequence homology to those from higher organism. The homology of these enzymes is particularly high at the active site regions (the coenzyme and substrate binding sites). The relatively high sequence conservation of the lactate dehydrogenases from B. subtilis and B. stearothermophilus (and from other bacilli) allows a structural comparison of this temperature variants.     

Oxidation of reactive sulfhydryl groups of sarcoplasmic reticulum ATPase

The role of reactive sulfhydryl groups of sarcoplasmic reticulum ATPase has been investigated. Incubation of ATPase with 17 mol o-iodosobenzoic acid per mol ATPase results in a 15% inhibition of Ca2+ uptake with only a 5% loss of ATPase activity. When ATPase is treated with 15 mol KMnO4 per mol ATPase, Ca2+ uptake is completely inhibited. From the measurement of remaining SH groups using 5,5'-dithiobis-(2-nitrobenzoic acid), it is found that the oxidation of approximately four SH groups per ATPase molecule with KMnO4 leads to a complete loss of Ca2+ uptake, while the oxidation of five SH groups per ATPase with o-iodosobenzoic acid results in only 15% inhibition of Ca2+ uptake. The results of amino acid analysis indicate that KMnO4 oxidizes the reactive SH groups to sulfonic acid groups. Among the five o-iodosobenzoic acid-reactive SH groups, at least one shows a distinct Ca2+ dependence. Addition of o-iodosobenzoic acid to the reaction medium containing KMnO4 does not increase the number of oxidized SH groups, indicating that both o-iodosobenzoic acid and KMnO4 oxidize the same SH groups of the enzyme. The different effects of two oxidizing agents on sarcoplasmic reticulum ATPase eliminate the possibility of direct involvement of SH group(s) in the ATPase reaction.     

Structure and function of L-lactate dehydrogenases from thermophilic and mesophilic bacteria, V. The complete amino-acid sequence of the mesophilic L-lactate dehydrogenase from Bacillus megaterium

The complete amino-acid sequence of L-lactate-dehydrogenase from the mesophilic Bacillus megaterium was determined. 92% of the 318 amino acids were established by sequence analysis of the N-terminus, of four CNBr fragments and of one fragment obtained by cleavage with BNPS-skatole. The primary structure was completed by sequencing overlapping fragments obtained by further cleavage of suitable CNBr fragments and BNPS fragments with either trypsin, endoproteinase Lys-C, o-iodosobenzoic acid or hydroxylamine. The C-terminal amino acids were determined by degradation with carboxypeptidase A. The sequence homology between lactate dehydrogenases from B. megaterium and those from other Bacilli is 59-61% and 35-37% to those from higher organisms. The high sequence homology among lactate dehydrogenases from Bacilli, adapted to different temperatures, allows comparative studies of the structural basis of protein thermostability.     

Complete amino acid sequences of the heavy and light chain variable regions from two A/J mouse antigen nonbinding monoclonal antibodies bearing the predominant p-azophenyl arsonate idiotype

The immune response to p-azophenyl arsonate (Ars) in A/J mice is dominated by a cross-reactive idiotype (CRI or IdCR). IdCR+ hybridoma proteins 1F6 and 3D10 produced in a single mouse by immunization with a monoclonal anti-IdCR antibody did not bind Ars [Wysocki, L., & Sato, V. (1981) Eur. J. Immunol. 11, 832-839]. The preservation of idiotype coupled with lack of antigen binding in the same molecules provoked an examination of their primary structures in order to localize sites involved in binding to antigen and to anti-idiotypes. The VH sequence of antibody 3D10 was determined by Edman degradation of intact chains and fragments generated by CNBr, hydroxylamine, and o-iodosobenzoic acid cleavage, by trypsin and V8 protease digestion, and by sequence analysis of mRNA. The 1F6 VH sequence was reported previously [Smith, J. A., & Margolies, M. N. (1984) Biochemistry 23, 4726-4732]. The VL sequences of 1F6 and 3D10 were determined by Edman degradation of intact chains and peptides generated by cleavage with o-iodosobenzoic acid and digestion with trypsin and chymotrypsin. Both 1F6 and 3D10 are encoded by the same VH, VK, D, and JK gene segments as are IdCR+ Ars-binding antibodies. However, 1F6 and 3D10 employ the JH4 gene segment rather than JH2. Antibodies 1F6 and 3D10 share several somatic mutations, suggesting a common clonal origin, but manifest individual mutations as well. By comparison with Ars-binding IdCR+ molecules, the substitutions in 1F6 and 3D10 likely responsible for the lack of Ars binding are localized to the heavy chain D-JH junction and/or to a substitution in light chain CDR 3.     

Site-specific fragmentation and modification of albumin by sulfite in the presence of metal ions or peroxidase/H2O2: role of sulfate radical.

Exposure of albumin to sulfite in the presence of Co(II) or peroxidase/H2O2 caused site-specific fragmentation, which was not due to cleavage of methionyl nor tryptophanyl peptide bonds. The reaction of GlyPro with sulfite in the presence of Co(II) or peroxidase/H2O2 led to Gly liberation, suggesting the oxidative cleavage of protein at Pro residues. Sulfite plus Co(II) induced bityrosine production, Trp loss and a new Trp-derived fluorescence. ESR-spin trapping method provided evidence for the formation of sulfate radical (SO4.-) during Co(II)-catalyzed autoxidation of sulfite. The order of reactivity with SO4.- seemed to be Trp greater than GlyPro greater than GlyGly approximately Gly approximately Pro. The results suggest that SO4.- plays an important role in fragmentation and modification of albumin.     

Oxidation and oxidative cleavage of tryptophanyl peptide bonds during iodination

Tryptophan peptides are oxidized to the oxindole by various chemical and peroxidase catalyzed iodination procedures in the pH range 4.0–7.5. This oxidation results in significant cleavage of tryptophanyl peptide bonds at pH 4–5. Thus, destruction of some biologically active peptides and proteins during iodination may be due to the modification of essential tryptophan residues.     

Amino acid sequence of the regulatory subunit of bovine type II adenosine cyclic 3',5'-phosphate dependent protein kinase

Evidence is presented that establishes the amino acid sequence of the regulatory subunit of type II cAMP-dependent protein kinase from bovine cardiac muscle. Complementary sets of overlapping peptides were generated primarily by tryptic digestion and by chemical cleavage at methionyl residues. The analysis was augmented by chemical cleavage at a single tryptophanyl residue and at three of the four aspartyl-proline bonds. Several large fragments generated by limited proteolysis contributed to the proof of structure. The subunit is a single chain of 400 residues corresponding to a molecular weight of 45 004. An amino-terminal segment of about 100 residues is believed to include the region responsible for oligomeric association. The remainder of the molecule consists of two tandem homologous domains, each of which is thought to bind a single molecule of cAMP. Comparison of the three domains with corresponding regions of the type I isozyme, of the Escherichia coli catabolite gene activator protein, and of cGMP-dependent protein kinase indicates extensive regions of homology and as much as 50% identity with the sequence of an internal segment of the type I isozyme.     

A new method for partial peptide mapping using N-chlorosuccinimide/urea and peptide silver staining in sodium dodecyl sulfate-polyacrylamide gels

A simple, rapid procedure for obtaining partial peptide maps from nanogram quantities of protein in gel slices using the selective tryptophanyl peptide bond cleavage reagent N-chlorosuccinimide/urea is presented. The generated peptide fragments can be visualized by autoradiography or by a sensitive protein silver-staining technique.     

Chemical cleavage of bovine beta-lactoglobulin by BNPS-skatole for preparative purposes: comparative study of hydrolytic procedures and peptide characterization

A comparative study of various procedures for tryptophanyl peptide bond cleavage by BNPS-skatole [2-(2-nitrophenyl)-3-methyl-3-bromoindolenine] was carried out on native and on reduced and alkylated bovine -lactoglobulin (BLG). The reaction yield and the composition of the derived products were studied in acetic acid, trifluoroacetic acid (TFA), and ethanol/TFA. For BNPS-skatole removal, extraction by water or ethyl ether was compared with dialysis and gel filtration. The three expected peptides (1–19, 20–61, 62–162) and incomplete cleaved fragments (1–61, 20–162) were separated and characterized by electrophoresis, reverse-phase high-performance liquid chromatography, and mass spectrometry. The highest hydrolysis yield (67.4%) occurred with native BLG cleaved in 88% acetic acid at 47°C for 60 min. Subsequent water extraction and gel filtration led to total recovery of the material, but reagent elimination was only quantitative after gel filtration. Cleavage specificity was ensured by mass spectrometry and the amino acid composition of peptides 1–19 and 62–162. The chemical side reactions identified are discussed.     

Expression in Escherichia coli and characterization of human growth-hormone-releasing factor

A chemically synthesized DNA sequence, coding for the 44 amino acid residues of human growth-hormone-releasing factor (GRF) preceded by a tryptophan codon, was cloned in frame with Escherichia coli trpE gene within a pBR322-derived plasmid. GRF was expressed in E. coli as a fused polypeptide chain (TrpE-GRF) and then the GRF amino acid sequence was released from the fused protein by specific chemical cleavage at the tryptophan residue using o-iodosobenzoic acid. The thioether group of the methionine residue of GRF was converted in the sulfonium salt derivative, in order to prevent irreversible oxidation of methionine to the sulfone derivative by the o-iodosobenzoic acid reagent. GRF was purified by HPLC and characterized in terms of amino acid composition after acid hydrolysis, protein sequencing and gel electrophoretic behaviour. These data clearly established that the biosynthetic GRF was identical to the natural one, except for the lack of amidation at the carboxyl-terminal amino acid. Far-ultraviolet circular dichroism measurements established that both biosynthetic and natural GRF are devoid of secondary structure in aqueous solution at neutral pH, whereas both peptide samples achieve a high percentage of helical structure in the presence of trifluoroethanol.     

The primary structure of ribosomal protein L2 from Bacillus stearothermophilus

The complete amino acid sequence of ribosomal protein L2 from the moderate thermophile Bacillus stearothermophilus has been determined. This has been achieved by the sequence analysis of peptides derived by enzymatic digestion with Staphylococcus aureus protease, trypsin and chymotrypsin, as well as by chemical cleavage with o-iodosobenzoic acid. The protein contains 275 amino acid residues and has a calculated molecular mass of 30201 Da. Comparison of this sequence with sequences of the corresponding proteins from Escherichia coli and from spinach and tobacco chloroplasts reveals that 60% of the residues of protein L2 from B. stearothermophilus are identical to those of the protein from E. coli and 45% are identical to those found in the two chloroplast proteins. There are extended regions of totally conserved sequence at positions 54-58 (GGGHK), 81-86 (EYDPNR), and 224-230 (MNPVDHP) in all four proteins.     

Localization of the high molecular weight kininogen binding site in the heavy chain of human factor XI to amino acids phenylalanine 56 through serine 86

We have previously demonstrated that a monoclonal antibody (5F7) directed against the heavy chain region of factor XI inhibits the binding of factor XI to high molecular weight kininogen (high Mr kininogen) and the surface-mediated proteolytic activation of factor XI by factor XIIa in the presence of high Mr kininogen. In order to identify the structural domain of factor XI that binds high Mr kininogen, CNBr-digested factor XI was passed over a 5F7 antibody affinity column. One of two CNBr peptides that bound to this 5F7 affinity column inhibited binding of 125I-factor XI to high Mr kininogen, as did intact factor XI. Polyacrylamide gel electrophoresis in sodium dodecyl sulfate of an inhibitory peptide purified by high performance liquid chromatography revealed an Mr of 10,000-15,000. Gas-phase sequencing of this peptide revealed the following amino-terminal sequence: X-X-Val-Thr-Gln-Leu-Leu-Lys-Asp-Thr. These data together with the amino acid composition of the isolated peptide indicate that both the epitope recognized by antibody 5F7 and at least a portion of the high Mr kininogen binding site are contained within the amino-terminal portion of factor XI comprising residues Glu-1 through Met-102. Further cleavage of this peptide with o-iodosobenzoic acid at a tryptophanyl peptide bond revealed that an Mr 5,000 peptide (with the amino-terminal sequence Trp-Phe-Thr-Cys-Val-Leu) bound to a high Mr kininogen affinity column and inhibited binding of 125I-factor XI to high Mr kininogen. Finally, a synthetic peptide comprising residues Phe-56 through Ser-86 inhibited 125I-factor XI binding to high Mr kininogen. These experiments strongly suggest that the high Mr kininogen binding site is contained within the domain in the heavy chain region of factor XI comprising residues Phe-56 through Ser-86.     

The plane of cleavage in human ferrihemoglobin. I. Ultraviolet difference spectroscopy.

X-ray diffraction studies have shown that hemoglobin has two predominant interfaces in the tetramer at which dissociation to dimers could occur. These interfaces have been designed as alpha1-beta1 and alpha1-beta2. There are 2 tyrosyl residues and 1 tryptophanyl residue in the alpha1-beta2- interface but only 1 tyrosyl residue in the alpha1-beta1 interface exposed to the solvent are perturbed. The ultraviolet difference spectrum between ferrihemoglobin dissociated in 1 M NaClO4 and undissociated hemoglobin revealed two negative peaks, one at 292.5 nm and another at 285 nm. This difference spectrum is due to tyrosyl and tryptophanyl residues which reside on the plane of cleavage and were exposed to 1 M NaClO4 upon dissociation. Hence, dissociation must have occurred along the alpha1-beta2 interface to yield alpha1 beta1 dimers. The deltaF degrees value extrapolated to zero salt concentration calculated on the basis of difference spectroscopy and sedimentation velocity experiments is 8.6 plus or minus 0.7 kcal per mol at pH 7.1 (K equals 4.5 times 10-7.