Reversed-phase liquid chromatography of peptides for direct micro-sequencing

Purity evaluation of aprotinin by high performance liquid chromatography

A separation to the baseline isocratic technique has been developed for the evaluation of the purity of aprotinin by internal normalization. The column used was a 30 nm pore diameter butyl-bonded silica stationary phase. An exact relationship was found to give an adequate description of the retention of aprotinin using acetonitrile concentrations of 17-22% and NaClO4 concentrations of 5-50 mmol. It can be used to optimize the mobile phase content for the particular user column and to compensate for possible variations in the retention time of aprotinin, analysed on different batches of butyl-bonded stationary phases.

A mammalian tryptophanyl-tRNA synthetase shows little homology to prokaryotic synthetases but near identity with mammalian peptide chain release factor

Determination of the amino acid sequence of beef pancreas tryptophanyl-tRNA synthetase was undertaken through both cDNA and direct peptide sequencing. A full-length cDNA clone containing a 475 amino acid open reading frame was obtained. The molecular mass of the corresponding peptide chain, 53,728 Da, was in agreement with that of beef tryptophanyl-tRNA synthetase, as determined by physicochemical methods (54 kDa). Expression of this clone in Escherichia coli led to tryptophanyl-tRNA synthetase activity in cell extracts. The open reading frame included two sequences analogous to the consensus sequences, HIGH and KMSKS, found in class I aminoacyl-tRNA synthetases. The homology with prokaryotic and yeast mitochondrial tryptophanyl-tRNA synthetases was low and was limited to the regions of the consensus sequences. However, a 90% homology was observed with the recently described rabbit peptide chain release factor (eRF) [Lee et al. (1990) Proc. Natl. Acad. Sci. 87, 3508-3512]. Such a strong homology may reveal a new group of genes deriving from a common ancestor, the products of which could be involved in tRNA aminoacylation (tryptophanyl-tRNA synthetase) or translation termination (eRF).

The three cysteine residues of cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae are not essential for its activity

Cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae is a dimer made up of identical subunits (Mr 63,000) each of these containing three cysteines (residues 255, 512 and 519 in the amino acid sequence). Thiol-specific probes were used to label these cysteines and study the resulting effect of the modification on the kinetic parameters of both the ATP/PPi exchange and tRNA aminoacylation reactions. Using the classical techniques of protein chemistry it was shown that none of the three cysteines was labelled with iodoacetic acid, whilst N-ethylmaleimide and 5,5'-dithiobis(2-nitrobenzoate) reacted with Cys512 and Cys255, respectively. Only the latter modification was accompanied by a decrease in the rates of both enzyme activities whilst the Km values for the various substrates remained unaffected. Site-directed mutagenesis was also used to replace each of the three cysteines by other residues, either individually or simultaneously. For these experiments the enzyme was expressed in Escherichia coli using an expression vector bearing the structural gene in which the first 13 codons were replaced by the first 14 of the CII lambda gene. The resulting substitution in the amino-terminal part of the expressed enzyme had no effect on the kinetic parameters, compared to those of the enzyme purified from S. cerevisiae. Taking into account the consequences of such substitutions, as well as those of chemical modifications on the two reactions catalysed by the enzyme. ATP/PPi exchange and tRNA aminoacylation, it could be concluded that none of these three cysteines plays any essential role in either substrate binding or catalysis.

Isolation and characterization of thirteen new salt-soluble proteins from barley by reversed-phase high-performance liquid chromatography

Thirteen new proteins from barley (Hordeum vulgare L.) have been isolated and characterized. These proteins and seven other previously known components were isolated from a 0.5-M NaCl extract of endosperm by single-step, reversed-phase, high-performance liquid chromatography, using a Vydac C4 semi-preparative column. The purity of the isolated proteins was analyzed by polyacrylamide gel electrophoresis at pH 3.2 or in sodium dodecyl sulfate, by two-dimensional gel electrophoresis and was further confirmed by partial NH2-terminal sequencing. The NH2-terminal amino-acid sequences of fourteen of the components were determined, from 5 to 27 cycles, by automated liquid-phase sequencing. According to the sequence data and predictions of secondary structure, different groups of homologous proteins were established. Based on the presented results, two thionins, one trypsin inhibitor and one α-amylase/subtilisin inhibitor are included among the purified proteins.

Analytical strategy for determination of active site sequences in aminoacyl-tRNA synthetases

Affinity labelling with radioactive, periodate-oxidized tRNA has been used to investigate the structures of tRNA-binding sites in Escherichia coli aminoacyl-tRNA synthetases. Labelled peptides were isolated by means of a combination of techniques involving chymotryptic digestion of the enzyme, gel filtration, ribonuclease digestion of tRNA, chromatography on a TSK 2000 column and reversed-phase chromatography. An isocratic phenylthiohydantoin identification system has been interfaced to a sequencer, allowing the characterization of modified lysine residues by means of both chromatographic retention and liquid scintillation counting.

Affinity labeling of Escherichia coli phenylalanyl-tRNA synthetase at the binding site for tRNAPhe

Periodate-oxidized tRNA(Phe) (tRNA(oxPhe)) behaves as a specific affinity label of tetrameric Escherichia coli phenylalanyl-tRNA synthetase (PheRS). Reaction of the alpha 2 beta 2 enzyme with tRNA(oxPhe) results in the loss of tRNAPhe aminoacylation activity with covalent attachment of 2 mol of tRNA dialdehyde/mol of enzyme, in agreement with the stoichiometry of tRNA binding. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the PheRS-[14C]tRNA(oxPhe) covalent complex indicates that the large (alpha, Mr 87K) subunit of the enzyme interacts with the 3'-adenosine of tRNA(oxPhe). The [14C]tRNA-labeled chymotryptic peptides of PheRS were purified by both gel filtration and reverse-phase high-performance liquid chromatography. The radioactivity was almost equally distributed among three peptides: Met-Lys[Ado]-Phe, Ala-Asp-Lys[Ado]-Leu, and Lys-Ile-Lys[Ado]-Ala. These sequences correspond to residues 1-3, 59-62, and 104-107, respectively, in the N-terminal region of the 795 amino acid sequence of the alpha subunit. It is noticeable that the labeled peptide Ala-Asp-Lys-Leu is adjacent to residues 63-66 (Arg-Val-Thr-Lys). The latter sequence was just predicted to resemble the proposed consensus tRNA CCA binding region Lys-Met-Ser-Lys-Ser, as deduced from previous affinity labeling studies on E. coli methionyl- and tyrosyl-tRNA synthetases [Hountondji, C., Dessen, P., & Blanquet, S. (1986) Biochimie 68, 1071-1078].

Amyloid fibrils derived from V-region together with C-region fragments from a lambda II-immunoglobulin light chain (HAR)

Amyloid fibril proteins were isolated from the spleen of a patient with IgD(lambda)-plasmocytoma by extraction and gel filtration in 5M guanidine hydrochloride. The molecular mass of the predominant polypeptide chain was approximately 5000 Da. Its complete amino-acid sequence was elucidated by stepwise automated degradation of the carboxymethylated polypeptide chain and by structural studies of tryptic and thermolysinolytic cleavage products. The length of the polypeptide chain was 58 to 59 residues and it was homologous to the amino acids in positions 8 through 65 of the variable part of an lambda-type immunoglobulin light chain, which was most closely related to the lambda II subgroup. The N-terminal sequence of this amyloid fibril protein proved to be heterogeneous, indicating cleavage after the amino acids in positions 7 and 8. Peptides from the constant part of the lambda-chain were unexpectedly found in the tryptic digest of the denatured amyloid protein HAR. One polypeptide derived from the constant region was separated from the main component by high performance liquid chromatography. Its amino-acid sequence commenced at position 111 and could be traced in 41 steps. In this case, at least two constant region fragments were shown to be constituents of the amyloid fibril protein. The association of fragments from the variable as well as the constant region is discussed with respect to amyloid formation.

Complete complementary DNA of rat tyrosine aminotransferase messenger RNA. Deduction of the primary structure of the enzyme

The primary structure of rat tyrosine aminotransferase (L-tyrosine:2-oxoglutarate aminotransferase; EC 2.6.1.5), a liver-specific enzyme involved in gluconeogenesis, has been deduced from the nucleotide sequence of a cloned full-length cDNA. The mRNA is 2362 nucleotides long (excluding the poly(A) tail) and codes for a polypeptide of 454 amino acids with a molecular weight of 50634. Unambiguous identification was obtained by comparison of this sequence with the amino acid sequences of several peptides obtained from the purified enzyme.

General method for the separation of cyanogen bromide digests of proteins by high-performance liquid chromatography. Rabbit skeletal troponin I

In this study, we have demonstrated the necessity for a combination of size-exclusion, ion-exchange and reversed-phase high-performance liquid-chromatography to resolve completely a protein digest. Our approach minimizes the number of steps, and the column order provides the maximum information about the properties of the fragments. The order is: (1) size-exclusion (Bio-Rad TSK-250 column), (2) strong cation-exchange (Synchropak S300 column), and finally (3) reversed-phase chromatography (Ultrapore C3). It was desirable for the first step of the procedure to be size-exclusion chromatography to produce the least number of fractions. The volatile eluent used in size-exclusion eliminated the need for subsequent sample desalting. Volatile buffers were not necessary for the ion-exchange chromatography, since the fractions were both desalted and purified in the final reversed-phase step. All column effluents were compatible with absorbance measurements at 210 nm to provide maximum sensitivity for peptide detection. The results obtained in this study strongly suggest that the combined use of three methods of separation, which utilize different selectivities (size, charge, hydrophobicity), can provide excellent resolving power for peptide separations. We believe this fast, efficient procedure should be generally applicable to other protein digests.

Purification of Escherichia coli 30S ribosomal proteins by high performance liquid chromatography

High performance liquid chromatography was applied to the separation of proteins derived from the Escherichia coli 30S ribosomal subunit. Several methods of separating this protein mixture has been tested: size-exclusion chromatography on hydrophilic phases; ion exchange and reversed phase chromatography (on C2 to C18 hydrocarbon-bonded supports). Various elution systems were examined in order to obtain pure proteins suitable for micro-sequence analysis. The resolution and yields of the proteins varied considerably, depending on the type of support and gradient system used. The best results were achieved with uniformly globular-shaped supports of large pore size, and by combining high performance size exclusion with rechromatography on reversed phase columns. Purification conditions for the individual proteins are listed. The methods employed avoid any precipitation step and allow easy identification of the proteins by one or two-dimensional gel electrophoresis, amino-acid analysis or direct manual or automatic micro-sequencing. Since the isolation time is much reduced compared with conventional purification procedures, the proteins obtained by the techniques described here are well suited for topographical and immunological studies or reconstitution assays. Ribosomal proteins of other organisms can be separated under similar conditions.