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H Nika

Publications and source records attributed to H Nika.

16 recordsLinked to original sources
PubMed1995

Synthesis of the protein-sequencing reagent 4-(3-pyridinylmethylaminocarboxypropyl) phenyl isothiocyanate and characterization of 4-(3-pyridinylmethylaminocarboxypropyl) phenylthiohydantoins.

We report the synthesis and structural characterization of the novel Edman-type protein-sequencing reagent 4-(3-pyridinylmethylaminocarboxypropyl) phenyl isothiocyanate. A panel of thiohydantoins prepared from this reagent were found stable during liquid chromatography-electrospray mass spectrometry and were detectable at the low femtomole sensitivity level. Furthermore, the signal detected for these compounds in the mass spectrometer was linear from the low femtomole to the low picomole range. The derivatives showed uv absorbance spectra comparable to their phenylthiohydantoin counterparts. The extinction coefficient for the 4-(3-pyridinylmethylaminocarboxypropyl) phenyl thiohydantoin tyrosine was determined by adsorptive sequence analysis of a synthetic pentapeptide featuring an N-terminal 125I-labeled tyrosine. The sequence data suggest that the reagent will be useful for extended sequence analysis of proteins and peptides using commercially available gas-liquid-phase sequencers.

Amino Acid Sequence↗
PubMed1995

Liquid chromatography-electrospray ionization mass spectrometry of 4-(3-pyridinylmethylaminocarboxypropyl) phenylthiohydantoins.

We report the separation of 4-(3-pyridinylmethylaminocarboxypropyl) phenylthiohydantoins by microbore reverse-phase high-performance liquid chromatography and their detection by on-line electrospray ionization mass spectrometry. These compounds are the products of the chemical stepwise degradation of polypeptides using 4-(3-pyridinylmethylaminocarboxypropyl) phenyl isothiocyanate. We describe chromatographic conditions for on-column concentration of the analytes and for baseline separation of the isobaric amino acid derivatives of leucine and isoleucine. A commercially available protein sequencer was readily interfaced with the described analytical system and used for adsorptive sequence analysis of a panel of synthetic peptides containing collectively all 20 naturally occurring amino acids. On-line mass analysis of derivatives generated by automated sequencing confirmed that the derivatives were of the predicted mass and were detectable at comparable signal strength and sensitivity. Finally, we demonstrate that the additional selectivity in data interpretation provided by mass analysis dramatically improves the signal-to-noise ratio and therefore enhances the ability to conclusively interpret protein and peptide sequence data.

Amino Acid Sequence↗
PubMed1990

Covalent attachment of peptides for high sensitivity solid-phase sequence analysis.

We have developed a method for the high efficiency covalent immobilization of picomole to nanomole quantities of peptides in a form compatible with high sensitivity gas-liquid or solid-phase sequence analysis. Glass fiber filter paper was derivatized with amino-phenyltriethoxysilane and peptides were applied to circular disks cut to 1-cm diameters. Peptides were covalently immobilized on the aminophenyl-glass fiber paper through their terminal alpha-carboxyl groups and amino acid side-chain carboxyl groups by activation with the water-soluble reagent N-ethyl-N'-(3-dimethylaminopropyl)carbodiimide. Disks containing the covalently attached peptide were directly inserted into the cartridge of an automated sequenator for sequence analysis by the Edman degradation. Peptides prepared in this way could be routinely sequenced through to and including the C-terminal amino acid residue, at extraordinarily low backgrounds. The covalent immobilization of peptide fragments allowed far more flexibility in sequencing conditions, including the use of polar extraction solvents to increase the yield of phenylthiohydantoin (PTH)-His and PTH-Arg and the use of alternative Edman-type sequencing reagents with enhanced detectability, such as the chromophoric compound 4- (N,N'-dimethylamino)azobenzene-4'-isothiocyanate. The potential of this high efficiency immobilization method for contributing to the development of sequencing chemistries with enhanced sensitivity is discussed.

Amino Acid Sequence↗
PubMed1989

Biochemical characteristics and partial amino acid sequence of the receptor-like human B cell and carcinoma antigen CDw40.

The Ag CDw40 (p50, Bp50) is a phosphoprotein expressed on the surface of both B lymphocytes and on certain malignant cell types of nonhemopoietic origin. Antibodies to this Ag have been shown to act as a potent co-mitogen for B cells. In order to elucidate the function of this Ag, we have now investigated some of its biochemical characteristics as well as the relationship of B cell derived CDw40 to that derived from urinary bladder carcinoma (transitional cell carcinoma, TCC) cells. CDw40 from normal B cells or from the Burkitt lymphoma line Raji showed a characteristic pattern of three bands when analyzed by SDS-PAGE and Western blotting: a main band of 47 kDa, a degradation product of 43 kDa, and a dimer of 85 kDa. The dimer was disrupted by reduction with 2-ME but was reformed spontaneously from the purified monomers under nonreducing conditions. CDw40 from two bladder cancer cell lines gave a similar pattern but formed little or no dimer. Thirty amino acids of the amino terminal end of CDw40 from Raji and 22 amino acids of that from TCC cells (HU549) were sequenced. The sequences were unusually rich in cysteines and differed only in that the cysteine in position 6 in Raji CDw40 had been replaced by glutamine in HU549. In addition there were two conservative changes in positions 15 and 19. Taken together these results show that CDw40 derived from B cells or from TCC cells are the same or closely related molecules. Comparisons of the amino acid sequence and biochemical characteristics of CDw40 with proteins having receptor functions indicated a close structural resemblance of CDw40 to the nerve growth factor-receptor.

Amino Acid Sequence↗
PubMed1988

Covalent immobilization of proteins for high-sensitivity sequence analysis: electroblotting onto chemically activated glass from sodium dodecyl sulfate-polyacrylamide gels.

We report a new method for the preparation of proteins in a form suitable for high-sensitivity N-terminal amino acid sequence analysis. Proteins separated by polyacrylamide gel electrophoresis were electrophoretically transferred onto glass fiber filter paper chemically activated by the introduction of phenyl isothiocyanate functional groups. The proteins became covalently coupled to the matrix during the electrotransfer process. Bands containing transferred proteins were detected by fluorescent staining or autoradiography, cut out from the glass fiber filter, and directly loaded into the cartridge of a gas-phase sequenator. The covalent nature of the interactions between protein and glass fiber support permitted the use of more vigorous solid-phase sequencing protocols and of alternative sequencing reagents. This high-efficiency isolation and covalent coupling method provides the essential first step toward enhanced-sensitivity protein sequence analysis. The method has been successfully applied to the isolation of a wide variety of proteins from SDS-polyacrylamide gels, and was shown to be compatible with both the standard Edman reagent phenyl isothiocyanate and alternative sequencing reagents such as 4-(N,N'-dimethylamino)azobenzene-4'-isothiocyanate (DABITC).

Amino Acid Sequence↗
PubMed1986

Selective high-efficiency cross-linking of mammalian ribosomal proteins with cleavable thiol-directed heterobifunctional reagents: separation and identification of contact sequences of neighboring proteins after CNBr fragmentation.

Mammalian ribosomal proteins were cross-linked in situ with the primarily cysteine-selective heterobifunctional reagents N-succinimidyl 2-(4-hydroxy-2-maleimidophenylazo)benzoate (reagent A, maximum range approx. 8 A) and N-succinimidyl 4-(4-hydroxy-3-maleimidophenylazo)[carboxyl-14C]benzoate (reagent B, maximum range approx. 12 A). With reagent B the secondarily attached (N-aryolated) protein becomes labelled specifically at the receptor amino group (lysine). The cross-linked proteins were fragmented with CNBr in attempts to isolate and identify sequences involved in the next-neighbor contacts. Two experimental schemes were adopted. Heavy complexes containing the large protein L4 cross-linked to protein L14 and/or L18 were isolated and treated with CNBr. The split products were submitted to diagonal electrophoresis for separation and identification of the two pairs of contact fragments. Proteins cross-linked with the radiolabelled reagent B were submitted to diagonal electrophoresis. The labelled receptor proteins were excised and treated with CNBr. Fragments carrying the contact sequences were separated by gradient gel electrophoresis and identified by autoradiography. By use of these methods CNBr fragments were isolated containing one or the dual contact sites of the following binary protein complexes: L4-L14, L4-L18, L4-L13a/L18a, L6'-L23, L6-L29, L7-L29, L14-L13a, L21-L18a, and L27-L30 (asterisks indicate the labelled receptor proteins). By varying the site of labelling of the heterobifunctional reagents and the methods of protein fragmentation a complete analysis of the contact sequences of these proteins should be possible.

Animals↗
PubMed1984

Reaction detector system for the simultaneous monitoring of primary amino groups and sulfhydryl groups in peptides eluted by high-performance liquid chromatography.

A reaction detector system is described which can be used for simultaneous analysis of primary amino groups and sulfhydryl groups in peptides separated by high-performance liquid chromatography. By use of an automatic split valve system, well-defined portions of the effluent are diverted alternately into one of the two reaction detectors, based on the ninhydrin and Ellman assay, respectively. In the latter case the dithioerythritol included in the elution buffers for thiol preservation is eliminated with arsenite. For selective recovery of eluted peptides the amino/thiol group analyser can easily be converted into a high-yield monitoring system compatible with volatile, UV-opaque gradient buffers. In this version an automatic sample valve is used for the thiol assay, removing picomole amounts of material from the effluent destined for collection. In preparative applications there is a progressive net gain in sensitivity with increasing proportion of collected material. Under conditions of optimum recovery ca. 90% of the material could be recovered at a total consumption in the two detectors of less than 100 pmol. Experimental conditions are described which would allow for the additional identification of tryptophan, tyrosine and lysine-containing peptides. The monitoring system may also be used without modification for the assessment of key residues in polypeptides and proteins.

Amines↗
PubMed1984

Location of the sulfhydryl groups involved in disulfide interaction between the neighboring proteins L6 and L29 in mammalian ribosomes. S-cleavage of the cyanylated proteins in polyacrylamide gels after separation by dodecylsulfate gel electrophoresis.

Proteins L6 and L29 occupy closely adjacent sites in mammalian 60-S ribosomal subparticles and are easily cross-linked by intermolecular disulfide bond formation. For locating the interacting thiols within the polypeptide chains the dissociated proteins L6 and L29 obtained from the isolated disulfide complex were subjected to S-cleavage following [14C]cyanylation of the two cysteine residues. Four split products of the [14C]cyanylated proteins were isolated by dodecylsulfate gel electrophoresis. Two of these could be identified by autoradiography as the selectively labeled C-terminal fragments. For unequivocal assignment of the fragments to the parent proteins, a simple and generally applicable method of cleaving cyanylated proteins in polyacrylamide gel for subsequent diagonal analysis was developed. The experiments indicated that the sulfhydryl group of L6 interacting with L29 is located at a distance of approximately 80 amino acid residues from the N-terminus. In the intact ribosome this sequence contains a clostripain-sensitive and trypsin-sensitive portion of the protein more or less exposed at the ribosomal surface. In the case of protein L29, the interacting sulfhydryl group was located at a distance of approximately 40 amino acid residues from the C-terminal.

Amino Acid Sequence↗
PubMed1984

Isolation of the contact regions of the neighboring mammalian ribosomal proteins L6 and L29. Cyanogen bromide cleavage of the disulfide complex after preparative electrophoresis in non-oxidative polyacrylamide gels.

Proteins L6 and L29 in the 60-S subparticle of mammalian ribosomes interact in situ under gentle conditions by intermolecular disulfide bond formation. For identifying the contact regions of the two proteins the disulfide complex was isolated from whole ribosomes by preparative polyacrylamide gel electrophoresis and subjected to cyanogen bromide cleavage. For effective cleavage non-oxidizing conditions had to be maintained throughout the preparation. A simple and generally applicable method of high-efficiency gel pre-electrophoresis with anionic and cationic thiols was developed. Under these conditions reversibly cross-linked CNBr fragments of L6 and L29 could be isolated in high yield (Mr approx. 13 000 and 7000, respectively). After [14C]carboxymethylation of the reduced disulfide links smaller contact sequences were obtained by pepsin digestion and characterized by two-dimensional peptide mapping. These smaller contact peptides were contained within the corresponding CNBr fragments. Both contact peptides were hydrophilic and relatively basic.

Animals↗
PubMed1982

Identification by RNA-protein cross-linking of ribosomal proteins located at the interface between the small and the large subunits of mammalian ribosomes.

Protein constituents at the subunit interface of rat liver ribosomes were analysed by cross-linking with the bifunctional reagent, diepoxybutane (distance between reactive groups 4 A). Isolated 40S and 60S subunits were labelled with 125I and recombined with unlabelled complementary subunits. The two kinds of selectively labelled 80S ribosomes were treated with diepoxybutane at low concentration. Radioactive ribosomal proteins covalently attached to the rRNA of the unlabelled complementary subparticles were isolated by repeated gradient centrifugation. The RNA-bound, labelled proteins were identified by two-dimensional gel electrophoresis. The experiments showed that proteins S2, S3, S4, S6, S7, S13, and S14 in the small subunit of rat liver ribosomes are located at the ribosomal interface in close proximity to 28S rRNA. Similarly, proteins L3, L6, L7, and L8 were found at the the interface of the large ribosomal subunit in the close vicinity of 18S rRNA.

Animals↗
PubMed1982

Identification and characterization of sulfhydryl-containing proteolytic fragments involved in the Ca2+-induced conformational change of beef brain S-100.

The Ca2+-dependent conformational alteration of the brain-specific S-100 protein was studied by reacting the protein with N-ethyl[2,3-14C]maleimide in the absence and presence of Ca2+ and under denaturing conditions. Peptic hydrolysates of the 14C-labeled protein were analyzed and fractionated by high-performance liquid chromatography. Labeled peptide fractions were characterized by high-voltage electrophoresis and TLC. A clear distinction could be made between two classes of sulfhydryl-containing fragments: (a) neutral, hydrophobic, and (b) acidic. Ca2+ markedly favored 14C incorporation into the former components, whereas the latter were readily available only under denaturing conditions.

Animals↗
PubMed1979

Disulfide interaction in situ between two neighbouring proteins in mammalian 60-S ribosomal subunits. Isolation of the contact region of the larger protein.

A disulfide complex is formed in situ under gentle conditions between two neighbouring proteins in the 60-S subunits of mammalian ribosomes. The proteins have been identified as L 4 and L 29. The complex is easily isolated from whole ribosomes, and can be utilized for preparing the two proteins in a very pure state for further characterization. Chymotryptic cleavage of the complex or the isolated larger protein (L 4) in the presence of SDS produces two unequal fragments of this protein in nearly quantitative yield. The smaller fragment (approx. 12 000 daltons) contains the contact sequence. Only this fragment of protein L 4 is labelled when rat liver ribosomes are incuabted with iodo[14C]acetate under conditions of complex formation. Protein L 29 is resistant to chymotrypsin in the presence of sodium dodecyl sulfate.

Animals↗