Expression and immunochemical analysis of rat and human fibroblast growth factor receptor (flg) isoforms

Potentially 96 splice variants among four genes that code for the human heparin-binding fibroblast growth factor receptor family complicate study of structure, metabolism, and function of single isoforms in mammalian cells. As an alternative, we expressed structural subdomains and isoforms of the flg receptor gene in bacteria and baculoviral-infected insect cells. We developed and characterized a panel of 16 isoform and domain-specific polyclonal and monoclonal antibodies. The panel of antibodies was used to distinguish mature glycosylated ligand-binding and kinase-active and -inactive recombinant isoforms in baculoviral insect cells and transfected mammalian cells and natural isoforms in rat prostate and human liver cells. The results revealed a cell type-specific expression of the flg gene and isoforms that result from combinations of splice variations. Reactive epitopes of monoclonal antibodies against both the three (alpha) and two (beta) immunoglobulin-like disulfide loop extracellular domain isoforms were mapped by cross-reactivity with synthetic polypeptide sequences and deletion mutants expressed in bacteria. The native alpha and beta receptor isoforms differed in display of shared epitopes and suggested that the NH2-terminal Loop I and COOH-terminal Loops II and III of the alpha isoform are interactive. Although the common Loops II and III appear qualitatively sufficient for ligand binding, the results suggest that tertiary relationships among loops in the three and two loop isoforms are distinct and, therefore, the two isoforms may have distinct activities. Spatial models for arrangement of immunoglobulin-like loops in the extracellular domain of the two isoforms are presented.

Serine analogues of hFSH-beta-(33-53) and hFSH-beta-(81-95) inhibit hFSH binding to receptor

Synthetic peptides corresponding to hFSH-beta-(33-53) and hFSH-beta-(81-95) each contain free sulfhydryl groups, inhibit binding of FSH to receptor and are partial agonists of estradiol synthesis in Sertoli cells. Recently, we have reported that sulfhydryl groups are important in FSH- receptor interaction and that peptides containing free sulfhydryl groups or disulfide bridges, such as glutathione, may nonspecifically inhibit FSH binding to receptor. In the present study, Cys residues of hFSH-beta-(33-53) and hFSH-beta-(81-95) were replaced by Ser residues and the peptides tested for their ability to inhibit binding of FSH to receptor. Results similar to those obtained previously with natural sequence peptides were obtained with the Ser analogs, indicating that Cys residues were not essential for binding inhibition. However, the partial agonist activity of the hFSH-beta-(33-53) and (81-95) in cultured Sertoli cells could not be detected when Cys residues were replaced by Ser. Thus, replacement of Cys residues with Ser does not effect receptor binding activity but is deleterious to the agonist activity of these peptides.

Assignment of the gene (RLBP1) for cellular retinaldehyde-binding protein (CRALBP) to human chromosome 15q26 and mouse chromosome 7

Cellular retinaldehyde-binding protein (CRALBP) has properties that suggest that it is involved in the visual process and, therefore, potentially with retinal diseases. A human cDNA probe has been used to map this gene to human chromosome 15q26 (somatic cell hybrids and in situ hybridization) and to mouse chromosome 7 by somatic cell hybrids.

Phosphorylation of the catalytic subunit of type-1 protein phosphatase by the v-abl tyrosine kinase

The catalytic subunit of type-1 protein phosphatase (PP1) was phosphorylated by the tyrosine kinase v-abl as follows: (i) cytosolic PP1 was phosphorylated more (0.73 mol/mol) than PP1 obtained from the glycogen particles (0.076 mol/mol), while free catalytic subunit isolated in the active or inactive form from cytosolic PP1 was phosphorylated even less and catalytic subunit complexed with inhibitor-2 was not phosphorylated; (ii) phosphorylation stoichiometry was dependent on the concentration of PP1 and 3 h incubation at 30 degrees C was required for maximal phosphorylation; (iii) phosphorylation was on a tyrosine residue located in the C-terminal region of PP1 which is lost during proteolysis; (iv) phosphorylation did not affect enzyme activity but allowed conversion from the active to the inactive form upon incubation with inhibitor-2 of a PP1 form that in its dephospho-form did not convert.

Characterization of cDNA clones encoding rabbit and human serum paraoxonase: the mature protein retains its signal sequence

Serum paraoxonase hydrolyzes the toxic metabolites of a variety of organophosphorus insecticides. High serum paraoxonase levels appear to protect against the neurotoxic effects of organophosphorus substrates of this enzyme [Costa et al. (1990) Toxicol. Appl. Pharmacol. 103, 66-76]. The amino acid sequence accounting for 42% of rabbit paraoxonase was determined by (1) gas-phase sequencing of the intact protein and (2) peptide fragments from lysine and arginine digests. From these data, two oligonucleotide probes were synthesized and used to screen a rabbit liver cDNA library. A clone was isolated and sequenced, and contained a 1294-bp insert encoding an open reading frame of 359 amino acids. Northern blot hybridization with RNA isolated from various rabbit tissues indicated that paraoxonase mRNA is synthesized predominately, if not exclusively, in the liver. Southern blot experiments suggested that rabbit paraoxonase is coded by a single gene and is not a family member of closely related genes. Human paraoxonase clones were isolated from a liver cDNA library by using the rabbit cDNA as a hybridization probe. Inserts from three of the longest clones were sequenced, and one full-length clone contained an open reading frame encoding 355 amino acids, four less than the rabbit paraoxonase protein. Each of the human clones appeared to be polyadenylated at a different site, consistent with the absence of the canonical polyadenylation signal sequence. Of potential significance with respect to the paraoxonase polymorphism, the derived amino acid sequence from one of the partial human cDNA clones differed at two positions from the full-length clone. Amino-terminal sequences derived from purified rabbit and human paraoxonase proteins suggested that the signal sequence is retained, with the exception of the initiator methionine residue [Furlong et al. (1991) Biochemistry (preceding paper in this issue)]. Characterization of the rabbit and human paraoxonase cDNA clones confirms that the signal sequences are not processed, except for the N-terminal methionine residue. The rabbit and human cDNA clones demonstrate striking nucleotide and deduced amino acid similarities (greater than 85%), suggesting an important metabolic role and constraints on the evolution of this protein.

Purification of rabbit and human serum paraoxonase

Rabbit serum paraoxonase/arylesterase has been purified to homogeneity by Cibacron Blue-agarose chromatography, gel filtration, DEAE-Trisacryl M chromatography, and preparative SDS gel electrophoresis. Renaturation (Copeland et al., 1982) and activity staining of the enzyme resolved by SDS gel electrophoresis allowed for identification and purification of paraoxonase. Two bands of active enzyme were purified by this procedure (35,000 and 38,000). Enzyme electroeluted from the preparative gels was reanalyzed by analytical SDS gel electrophoresis, and two higher molecular weight bands (43,000 and 48,000) were observed in addition to the original bands. This suggested that repeat electrophoresis resulted in an unfolding or other modification and slower migration of some of the purified protein. The lower mobility bands stained weakly for paraoxonase activity in preparative gels. Bands of each molecular weight species were electroblotted onto PVDF membranes and sequenced. The gas-phase sequence analysis showed that both the active bands and apparent molecular weight bands had identical amino-terminal sequences. Amino acid analysis of the four electrophoretic components from PVDF membranes also indicated compositional similarity. The amino-terminal sequences are typical of the leader sequences of secreted proteins. Human serum paraoxonase was purified by a similar procedure, and ten residues of the amino terminus were sequenced by gas-phase procedures. One amino acid difference between the first ten residues of human and rabbit was observed.

Topological and epitope mapping of the cellular retinaldehyde-binding protein from retina

Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes. As a first approach to identifying functional domains and protein recognition sites in CRALBP, a low resolution topological and epitope map has been developed using monoclonal and polyclonal antibodies and limited proteolysis. Fifteen peptides of 8-31 residues spanning 99% of the 316-residue bovine CRALBP were synthesized and used to prepare 13 anti-peptide polyclonal antibodies. Using a competitive ELISA procedure, peptide epitopes were classified as either accessible or inaccessible in the native protein based on the extent of their recognition by these site-specific antibodies. Use of the synthetic peptides to map the epitopes of a polyclonal antibody to intact CRALBP confirmed that the amino terminus and carboxyl terminus are immunodominate regions and hence likely to be exposed, at least in part. Limited tryptic proteolysis of native CRALBP produced three major fragments which were shown by microsequence and Western analysis to be derived from sequential loss of short peptides from the amino terminus. None of these major fragments reacted with four monoclonal antibodies (mAbs) to intact CRALBP although each mAb immunoprecipitated native CRALBP. These results and the lack of mAb recognition of any of the synthetic peptides indicates that the amino terminus of the protein is exposed and contains part of an assembly epitope recognized by the mAbs. Overall this study indicates that residues 1-30, 100-124, and 257-285 contain highly exposed segments in the native protein and therefore constitute potential interaction domains for CRALBP and visual cycle enzymes. Residues 30-99 and 176-229 are inaccessible in the native structure and may be involved with retinoid binding. These results provide a basis for a systematic higher resolution mutagenesis study directed toward correlating CRALBP structural domains with function.

Enhanced inhibition of tissue factor by the extended form of an endothelial cell glycoprotein (an extrinsic pathway inhibitor)

We have identified, in the supernatant medium of cultured endothelial cells, an additional inhibitor of tissue factor that is eluted at higher salt concentrations during heparin-Sepharose chromatography and is a much more potent inhibitor of the activation of the coagulation cascade than the species we studied earlier (Colburn and Buonassisi: In Vitro Cellular and Developmental Biology 24: 1133-1136, 1988). The inhibitor we described earlier has been shown to be functionally and immunologically identical to a rabbit plasma extrinsic pathway inhibitor, EPI (Warn-Cramer et al.: Thrombosis Research 61:515-527, 1991). The new species (molecular mass, 47 kDa) is susceptible to proteolytic cleavage which results in a sharp reduction of its ability to inhibit tissue factor and an increase in electrophoretic mobility compatible with a molecular mass of 45 kDa, the same as that of the inhibitor reported earlier. Based on these data, we suggest that the new inhibitor yields, through proteolytic cleavage of an amino acid sequence of about 25 residues, the N-glycan-sulfated compound previously described.

Mechanism of rhodopsin kinase activation

The role of the cytoplasmic loops and C-terminal region of bovine rhodopsin (Rho) in binding and activating rhodopsin kinase was investigated. The ability of various enzymatically truncated forms of photolyzed rhodopsin (Rho*) to stimulate rhodopsin kinase activity was quantified. Following endopeptidase Asp-N cleavage of all phosphorylation sites on the C-terminal, the resulting truncated Rho* (329G-Rho*) was not phosphorylated by rhodopsin kinase. This suggests that rhodopsin kinase only phosphorylates C-terminal sites of Rho*. However 329G-Rho* could bind rhodopsin kinase and stimulate phosphorylation of exogenous peptide. Kinase stimulation was investigated for other truncated forms of Rho* in which the C-terminal region was either partially or completely eliminated, and the V-VI loop was either cleaved or left intact (339K-Rho*, 341E239E-Rho*, 329G239E-Rho*, 327P240S-Rho*). Results suggest that the V-VI loop is crucial for kinase binding (similar to the binding of GT). Mastoparan, a model peptide for G-protein-coupled receptors, was found to stimulate rhodopsin kinase in a mechanism similar to that of truncated Rho*. We conclude that rhodopsin kinase binds to the cytoplasmic loops of Rho* to cause a stimulation of its catalytic activity.

A synthetic peptide encompassing two discontinuous regions of hFSH-beta subunit mimics the receptor binding surface of the hormone

Synthetic peptides corresponding to discontinuous segments of the hFSH-beta subunit, amino acids 33-53 and 81-95, have been shown to interact with the follicle-stimulating hormone (FSH) receptor. In this study, we demonstrate that hFSH-beta-(33-53)-(81-95)-peptide amide, a synthetic peptide encompassing these binding regions, possesses higher affinity for the FSH receptor than either synthetic hFSH-beta-(33-53) or hFSH-beta-(81-95). This increased affinity suggests that each binding component is effectively interacting with the receptor, providing evidence that these two separate receptor binding regions of hFSH-beta form a continuous binding surface on the native molecule. These results also suggest that binding surfaces of very complex proteins, such as the heterodimeric glycoprotein hormone FSH, may be mimicked by a linear arrangement of its binding domains. A model based on energetics of the peptide-receptor interaction is also described. The results indicate that the affinity (Ka) of a peptide containing different binding domains can be approximated utilizing the product of the affinity constant of each binding domain (Ka = k1.k2...kn).

Stimulation of FA and casein kinase II by insulin in 3T3-L1 cells

Insulin stimulates protein phosphatase-1 and FA, assayed as phosphatase-1 activator, in 3T3-L1 cells. Since other kinases, such as casein kinase-II may also contribute to such FA activity, we assayed casein kinase-II and FA as peptide kinase on extracts from 3T3-L1 cells that had been exposed to insulin for various times. Under such conditions FA, assayed as phosphatase-1 activator, was stimulated 2-3-fold within 1-2 min. Casein kinase-II was stimulated about 2-fold but at a slightly later time (2-3 min) than FA, making it unlikely that casein kinase-II contributes to FA stimulation. Insulin slightly stimulated also the kinase activity of FA towards a synthetic peptide at 2 min, thus confirming the FA activation seen when FA was assayed as activator of phosphatase-1.

Structural analysis of bovine pancreatic thread protein

Pancreatic thread protein (PTP) forms double helical threads in the neutral pH range after purification, undergoing freely reversible, pH-dependent globule-fibril transformation. The purified bovine PTP consists on SDS gels of two carbohydrate-free polypeptide chains (Gross et al., 1985). Plasma desorption mass spectrometry and amino acid sequence analysis now confirm that bovine PTP contains two disulfide-bonded polypeptides, an A chain of 101 amino acid residues with a molecular weight of 11,073 and a B chain of 35 residues with a molecular weight of 3970. The intact protein exhibits a molecular weight of 15,036, agreeing greater than 99.9% with the molecular weight calculated from the sequence. The B chain sequence was determined by gas-phase Edman degradation of the intact polypeptide. The A chain sequence was determined from overlapping peptides generated by cleavage at lysyl, tryptophanyl, and aspartyl-prolyl residues. Based upon the bovine PTP cDNA structure, the two chains of the protein result from cleavage of a single polypeptide with removal of a dipeptide between the NH2-terminal A chain and COOH-terminal B chain. Comparison of bovine PTP with other proteins reveals significant structural relatedness with the single-chain homologues from human and rat pancreas and with the motif associated with Ca2(+)-dependent carbohydrate recognition domains. The physiological role of PTP has not yet been resolved. The protein is present in very high concentration in pancreatic secretion and it has been detected in brain lesions in Alzheimer's disease and Down syndrome and in regenerating rat pancreatic islets. The present results provide a firm protein base for ongoing molecular, physical-chemical, and structure-function studies of this unusual protein.

Purification and characterization of catalytic fragments of phosphorylase kinase gamma subunit missing a calmodulin-binding domain

A catalytic fragment preparation of rabbit muscle phosphorylase kinase produced by limited chymotryptic digestion was isolated and identified as the NH2-terminal region of the gamma subunit by Edman degradation. Mass spectral analysis, gas phase sequence analysis, and amino acid analysis of the active fragment carboxyl-terminal peptides revealed multiple COOH termini generated at residues Tyr290, Arg296, and Phe298 in the gamma subunit sequence. These active fragment species are about 24% smaller than the gamma subunit (Mr 44,673) and range in size from Mr 33,279 to Mr 34,275. The active fragment preparation exhibits a specific activity about 6-fold higher than that of the gamma subunit-calmodulin complex. Calmodulin confers calcium sensitivity to the gamma subunit but has no effect on the enzymatic properties of active fragment. Affinity measurements demonstrated a dissociation constant of 0.7 microM for active fragment binding to dansylcalmodulin, a value about 28-fold weaker than reported for the gamma subunit. These data support the presence of a calmodulin binding domain in the COOH-terminal region of the gamma subunit.

Analysis of the DNA of patients with retinitis pigmentosa with a cellular retinaldehyde binding protein cDNA

We used a cDNA fragment corresponding to the human cellular retinaldehyde binding protein (CRALBP) gene to search for mutations at this locus in patients with autosomal dominant, autosomal recessive, or isolate retinitis pigmentosa, and Usher's syndrome, type I. No gene deletions or rearrangements could be detected in any patient by Southern blotting. We identified a Pvu II restriction fragment length polymorphism (RFLP) defining two alleles at the CRALBP locus in the normal population. We used this RFLP to analyze the genomic DNA of large sets of unrelated patients with autosomal dominant, autosomal recessive, or isolate retinitis pigmentosa. Within each of these groups, RFLP alleles at the CRALBP locus showed no linkage disequilibrium (departure from Hardy-Weinberg equilibrium). In addition, two autosomal dominant, two autosomal recessive, and three Usher's syndrome, type I pedigrees each showed no cosegregation of the CRALBP locus and the disease locus. We could find no evidence that mutations of the CRALBP gene are associated with the common forms of retinitis pigmentosa or Usher's syndrome, type I.

Structural characterization of the rat seminal vesicle secretion II protein and gene

The gene encoding rat seminal vesicle secretion II (SVS II) protein has been cloned from a rat genomic DNA library using a cDNA probe generated from rat dorsal prostate androgen-dependent mRNA. The cloned 7.3-kilobase pair genomic fragment contains approximately 5000 base pairs (bp) of the 5'-flanking region and the entire coding region of the SVS II protein within two exons. A sequence of 4156 bp of the rat SVS II gene has been determined, including 2037 bp of the 5'-flanking region, exon 1 (95 bp), intron 1 (236 bp), exon 2 (1171 bp), and 614 bp of the 3'-flanking region. The 5'-flanking region contains three conserved elements found in other seminal vesicle secretion genes (SVS IV-VI proteins) within 250 bp of the transcription start site as well as a glucocorticoid response element at position -314 in the SVS II gene. The first exon encodes a 22-amino acid leader peptide plus the first 2 amino acids of the secreted protein. The second exon encodes the remaining amino acids in the SVS II protein sequence. The mature protein contains 392 residues and has an Mr of 43,116. Concomitant with the gene analysis, the rat SVS II protein was purified to homogeneity, and 333 residues (85%) of the amino acid sequence were determined by automated Edman degradation. The DNA-deduced sequence and that determined by direct analysis of the protein are in complete agreement. The blocked NH2-terminal amino acid was identified as pyroglutamic acid by mass spectrometry and aminopeptidase digestion. A 13-residue structure with the consensus sequence GSQLKSFGQVKSS is repeated 13 times within the SVS II protein and appears to be involved in the formation of the rat copulatory plug via a transglutaminase reaction cross-linking glutamine and lysine residues. Overall, the SVS II protein sequence exhibits little structural relatedness to any other known protein sequence; however, some similarity can be found between the 13-residue repeat and another repeating structure and apparent transglutaminase substrate in the guinea pig seminal vesicle clotting protein.

Electrophoretic purification of the alpha and beta subunits of phosphorylase kinase and evidence in support of the deduced amino acid sequences

A simple, rapid sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) method is presented for isolating the alpha, alpha' and beta subunits of rabbit muscle phosphorylase kinase. The SDS-PAGE procedure can yield milligram amounts of alpha and beta from a single preparative gel and also allows isolation of the alpha' isozyme free of alpha. Notably the method provides the purified subunits in a form amenable to structural analysis. Edman degradation of alpha and alpha' reveal identical NH2-terminal structures. Amino acid analysis of the electrophoretically purified alpha and beta subunits are in good agreement with their deduced primary structures. The amino acid sequence of 488 residues in alpha and 713 residues in beta were determined by gas phase Edman degradation. The data support the recently deduced primary structures of alpha (Zander et al., Proc. Natl. Acad. Sci. USA, 1988, 85, 9381-9385).

Human epidermal growth factor (EGF) receptor sequence recognized by EGF competitive monoclonal antibodies. Evidence for the localization of the EGF-binding site

Epitopes recognized by three epidermal growth factor (EGF) competitive monoclonal antibodies, LA22, LA58, and LA90, have been localized to a 14-amino acid region in the extracellular domain of the human EGF receptor. The binding of each of these mutually competitive antibodies to A431 epidermoid carcinoma cells was inhibited up to 87% by EGF. Furthermore, binding to A431 cells was inhibited 100% by the EGF competitive monoclonal antibody 528 IgG. The EGF receptor monoclonal antibody 455 IgG, which recognizes a blood group A-related carbohydrate modification of A431 receptors and does not inhibit EGF binding, did not inhibit the binding of these three antibodies to A431 cells. Antibodies LA22, LA58, and LA90 were unusual in that they bound to recognized denatured and endoglycosidase F-treated antigenic determinants in Western blots. This suggested that the antibodies recognized continuous peptide epitopes. The epitopes for these antibodies were first localized in cyanogen bromide- and V8 protease-generated fragments of a truncated form of the EGF receptor secreted by A431 cells. In experiments with synthetic peptides, all three antibodies were found to bind to the 14 amino acids from Ala-351 to Asp-364 of the mature human EGF receptor. These amino acids are located between the two Cys-rich regions of the extracellular domain of the receptor, and they include an Arg-Gly-Asp-Ser recognition site for adhesion molecule receptors. The homologous sequence in the chicken EGF receptor, which binds mouse EGF with a 100-fold lower affinity than the human EGF receptor, contains four amino acid differences including two in the Arg-Gly-Asp-Ser tetramer. The mutually competitive binding of EGF and antibodies LA22, LA58, and LA90 implied that the amino acids between Ala-351 and Asp-364 participated in the formation of the EGF-binding site of the human EGF receptor.

Glycogen-bound type-1 phosphatase: isolation and dissociation of a complex containing undegraded G-subunit

A high molecular mass type-1 phosphatase complex can be isolated from muscle glycogen particles by a fast procedure that preserves the glycogen-binding subunit of phosphatase called G from proteolysis. G can be dissociated from such complex by ion exchange chromatography on FPLC SI column, with recovery of unproteolyzed G completely separated from phosphatase catalytic subunit.

Reaction of fluorescein isothiocyanate with an ATP-binding site on the phosphorylase kinase alpha subunit

Phosphorylase kinase can be labeled specifically on the alpha subunit with fluorescein 5'-isothiocyanate (FITC) which concomitantly inactivates the enzyme (T. G. Sotiroudis and S. Nikolaropoulus (1984) FEBS Lett. 176, 421-425). Labeled peptides have been purified and their primary structure has been determined. The amino acid sequence of the fluorescein-labeled tryptic peptide is Lys-Met-Gln-Asp-Gly-Tyr-Phe-Gly-Gly-Ala-Arg. The environment of this fluorescein-labeled lysine has been determined by sequencing peptides isolated from a Staphylococcus aureus V8 digest and two further cyanogen bromide fragments of the purified [14C]carboxymethylated alpha subunit. The partial sequences obtained have then been localized in the primary structure of the alpha subunit [Zander et al. (1988) Proc. Natl Acad. Sci. USA 85, 2929-2933]. Both the incorporation of the fluorescent label and enzymatic inactivation are inhibited by ATP only at pH 7.0; ADP and AMP do not protect. Kinetic analysis reveals a competition between ATP and FITC; a Ki for ATP of 728 +/- 100 microM has been determined.

The androgen-dependent rat prostate protein, probasin, is a heparin-binding protein that co-purifies with heparin-binding growth factor-1

Rat prostate extracts contain an abundant 20-22 kilodalton heparin-binding protein with near identical chromatographic properties, but only 0.2-1% of the mitogenic activity, of bovine brain heparin-binding growth factor-1 (acidic fibroblast growth factor). Amino terminal amino acid sequence (met-met-thr-asp-lys-asn-leu-lys-lys-lys-ile-glu-gly-asn-trp-arg-thr-val -tyr- leu-ala-ala-ser-?-val-glu-lys-ile-asn-glu-gly-ser-pro) and immunochemical analysis revealed that the protein is identical to the androgen-dependent protein "probasin".

Cloning of the cDNAs encoding the cellular retinaldehyde-binding protein from bovine and human retina and comparison of the protein structures

A 1173-base pair cDNA encoding bovine cellular retinaldehyde-binding protein (CRALBP) was cloned from a bovine retinal cDNA expression library using as probes both anti-CRALBP polyclonal and monoclonal antibodies. The amino acid sequence deduced from the cDNA corresponds exactly to that determined by direct analysis of NH2-terminally acetylated bovine CRALBP (Crabb, J. W., Johnson, C. M., Carr, S. A., Armes, L. G., and Saari, J. C. (1988) J. Biol. Chem. 263, 18678-18687). Nick-translated bovine CRALBP cDNA probes were then used to clone from a human retinal cDNA library a 1317-base pair cDNA encoding human CRALBP. Bovine and human CRALBP are 92% identical in amino acid sequence and not related to any other known protein sequence. Both the bovine and human proteins contain 316 residues and have calculated molecular weights of 36,378 and 36,347, respectively, exclusive of the NH2-terminal blocking groups. The CRALBP cDNA clones should prove valuable as tools for studying the physiological role of the protein in vision and visual disorders.

The complete primary structure of the cellular retinaldehyde-binding protein from bovine retina

Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol and 11-cis-retinaldehyde as endogenous ligands and may be a functional component of the visual cycle. The complete amino acid sequence of CRALBP from bovine retina has been determined by direct microanalysis of the protein. Bovine CRALBP contains 316 residues in a single amino-terminal-blocked chain corresponding to a molecular weight of 36,421, inclusive of the blocking group. Overlapping peptides were generated by cleavage of lysyl, arginyl, methionyl, glutamyl, and one tryptophanyl bond and sequenced by gas-phase Edman degradation. Analysis of amino-terminal arginyl and methionyl peptides by fast atom bombardment mass spectrometry identified the N alpha-blocking group as an acetyl moiety, and tandem mass spectrometry provided the sequence of the first 9 residues. Comparison of CRALBP with other known protein sequences reveals no significant structural relatedness. The present results provide a basis for relating CRALBP domains with physiological function and for the future development of a more detailed three-dimensional model of the interaction of 11-cis-retinaldehyde with protein.

Structure of Saccharomyces cerevisiae mating hormone a-factor. Identification of S-farnesyl cysteine as a structural component

Mating type a cells of the yeast Saccharomyces cerevisiae produce a mating hormone, the a-factor, that we have previously characterized as a very hydrophobic, modified dodecapeptide (Betz, R., Crabb, J. W., Meyer, H. E., Wittig, R., and Duntze, W. (1987) J. Biol. Chem. 262, 546-548). We have investigated the molecular structure in detail using mass spectrometry and proton NMR spectrometry of the intact hormone and authentic component molecules. Tandem mass spectrometry confirms the previously determined peptide sequence of the hormone and shows that it contains additional structural components with masses of 205 and 15 daltons. These were identified by proton NMR and mass spectrometry as a farnesyl (C15H25) residue and a terminal methyl ester group. The farnesyl moiety is attached to the sulfur atom of the carboxyl-terminal cysteine residue, as revealed by NMR of synthetic S-farnesyl cysteine methyl ester. The stereochemical configuration of the farnesyl moiety was determined to be trans,trans by comparison of gas chromatography retention times, mass spectra, and NMR spectra with those of standards. These results define the structure of a-factor as: (Sequence: see text). Replacement of the farnesyl by a methyl group leads to a partial reduction in specific biological activity of the a-factor, whereas hydrolysis of the carboxyl-terminal methyl ester causes a complete loss of activity.

The alpha and beta subunits of phosphorylase kinase are homologous: cDNA cloning and primary structure of the beta subunit

We have cloned cDNA molecules encoding the beta subunit of phosphorylase kinase (ATP:phosphorylase-b phosphotransferase; EC 2.7.1.38) from rabbit fast-twitch skeletal muscle and have determined the complete primary structure of the polypeptide by a combination of peptide and DNA sequencing. In the mature beta subunit, the initial methionine is replaced by an acetyl group. The subunit is composed of 1092 amino acids and has a calculated molecular mass of 125,205 Da. Alignment of its sequence with the alpha subunit of phosphorylase kinase reveals extensive regions of homology, but each molecule also possesses unique sequences. Two of the three phosphorylation sites known for the beta subunit and all seven phosphorylation sites known for the alpha subunit are located in these unique domains.

cDNA cloning and complete primary structure of skeletal muscle phosphorylase kinase (alpha subunit)

We have isolated and sequenced a cDNA encoding the alpha subunit of phosphorylase kinase from rabbit fast-twitch skeletal muscle. The cDNA molecule consists of 388 nucleotides of 5'-nontranslated sequence, the complete coding sequence of 3711 nucleotides, and 342 nucleotides of 3'-nontranslated sequence followed by a poly(dA) tract. It encodes a polypeptide of 1237 amino acids and a deduced molecular mass of 138,422 Da. Nearly half of the deduced amino acid sequence is confirmed by peptide sequencing. Seven positions of endogenously phosphorylated serine residues and autophosphorylation sites, identified by peptide sequencing, could be assigned. They cluster in a segment of only 60 amino acids. RNA blot hybridization analysis demonstrates a predominant RNA species of approximately equal to 4500 nucleotides and a less abundant RNA of 8700 nucleotides.

Isolation and characterization of different molecular and chromatographic forms of heparin-binding growth factor 1 from bovine brain

Bovine brain heparin-binding growth factor 1 (HBGF-1), a single polypeptide (Mr 17,400) with an amino-terminal acetylalanine and three cysteines within the sequence, isolates in multiple truncated and chromatographic forms. The relative yields of the various forms of HBGF-1 depend upon the methods used for purification. Extraction of brain tissue at neutral pH in the presence of protease inhibitors yielded intact acetylala-HBGF-1 and Asn21-HBGF-1 in a ratio of 2.3 to 1. Omission of the protease inhibitors during extraction markedly reduced the yield of acetylala-HBGF-1 and generated predominantly a mixture of Asn21-HBGF-1 and Phe15-HBGF-1. Acetylala-HBGF-1 and Asn21-HBGF-1 can be separated by cation-exchange chromatography prior to further purification. Isolated acetylala-HBGF-1 and Asn21-HBGF-1 distributed into three chromatographic peaks each on reverse-phase high-performance chromatography. Reduction of samples with dithiothreitol prior to reverse-phase chromatography reduced the three peaks of each molecular species into a single peak. Exposure of a single chromatographic peak of HBGF-1 to pH 8 in the absence of a reducing agent generated two or more additional chromatographic peaks upon subsequent chromatography. Although each chromatographic form of different molecular species of HBGF-1 exhibited potent mitogenic activity, reduction of HBGF-1 forms prior to reverse-phase chromatography appeared to increase the specific mitogenic activity of both purified molecular forms.

Amino acid sequences of a-factor mating peptides from Saccharomyces cerevisiae

The molecular structure of a-factor, the mating hormone produced by mating type a cells of Saccharomyces cerevisiae, has been investigated. In culture filtrates of a cells four oligopeptides (a1 to a4) exhibiting a-factor activity have been found. These peptides have been isolated and their amino acid sequences have been determined. The a-factor peptides comprise two (apparently identical) pairs, a1/a2 and a3/a4, which differ in an interchange at position 6 of a valine in a1/a2 for a leucine in a3/a4. a1 and a4, which can be obtained by oxidation with H2O2 of purified a2 and a3, respectively, obviously represent oxidation artifacts formed under the conditions of culture. The amino acid sequences determined for the a-factor peptides are Tyr-Ile-Ile-Lys-Gly-Val Leu-Phe-Trp-Asp-Pro-Ala-Cys. Several lines of evidence suggest that the carboxyl-terminal cysteine residue is S-alkylated by a hydrophobic moiety.

Complete primary structure of prostatropin, a prostate epithelial cell growth factor

Bovine brain prostatropin is a potent and essential mitogen for prostate epithelial cell growth. The major form of prostatropin contains 154 amino acid residues in a single amino terminally blocked chain corresponding to a molecular weight of 17,400. The amino acid sequence of the 150 carboxy-terminal residues of prostatropin was derived by Edman degradation of overlapping peptides primarily generated by cleavage at lysyl and glutamyl residues. Analysis of the amino-terminal tetradecapeptide by fast atom bombardment mass spectrometry identified the blocking group as an acetyl moiety, and tandem mass spectrometry provided the sequence of the first 12 residues. Prostatropin residues 15-154 contain the sequence of bovine brain polypeptides recently described as acidic fibroblast growth factor and class I heparin-binding growth factor. The sequence of the first 25 residues of prostatropin is acetyl-Ala-(Gly, Glu)-Glu-Thr-Thr-Thr-Phe-Thr-Ala-Leu-Thr-Glu-Lys-Phe-Asn-Leu-Pro-Leu-Gly -Asn-Tyr-Lys-Lys-Pro. Reduced and carboxymethylated prostatropin exhibits mitogenic activity, suggesting that disulfide bonds among cysteine residues 30, 61, and 97 are not functionally essential. These results demonstrate by rigorous structural analysis that the brain-derived polypeptide previously described only as a mesenchymal and neuroectodermal cell mitogen is also an epithelial cell growth factor that may be involved in support of prostate hyperplasia and adenocarcinoma.

Characterization of multiple forms of prostatropin (prostate epithelial cell growth factor) from bovine brain

Two molecular forms of prostatropin distributed among five chromatographic peaks have been isolated from bovine brain by heparin-Sepharose affinity and reverse phase high performance liquid chromatography. One form has an apparent molecular weight of 16000 and an amino terminal sequence of asn-tyr-lys-lys-pro-lys-leu-leu-tyr-x-ser-asn-gly. The other form has an apparent molecular weight of 18000 and a blocked amino terminus. Both forms are similar in amino acid composition. The sequence of a proteolytic fragment from the blocked form overlaps the NH2-terminal sequence of the unblocked form, therefore, the smaller form may be derived from the larger form through proteolytic processing. Both forms contain regions identical in sequence to brain-derived, heparin-binding growth factors that have been isolated on the basis of mitogenic activity for fibroblasts and endothelial cells. Both forms of prostatropin exhibit potent mitogenic activity for normal and tumor prostate epithelial cells.

The complete amino acid sequence of the cellular retinoic acid-binding protein from bovine retina

The complete amino acid sequence of cellular retinoic acid-binding protein from bovine retina was obtained by Edman degradation of peptides obtained from enzymatic and CNBr digests. The 136 residue sequence is identical to that reported recently for the protein from bovine adrenal tissue indicating that the same gene is expressed in both tissues.

T4-induced alpha- and beta-glucosyltransferase: cloning of the genes and a comparison of their products based on sequencing data

Bacteriophage T4 alpha- and beta-glucosyltransferases link glucosyl units to the 5-HMdC residues of its DNA. The monoglucosyl group in alpha-linkage predominates over the one in beta linkage. Having recently reported on the nucleotide sequence of gene alpha gt (1) we now determined the nucleotide sequence of gene beta gt. The genes were each cloned on a high expression vector under the control of the lambda pL promoter. After thermo-induction the proteins were isolated and purified to homogeneity. To verify that the translational starting sites and the proposed reading frames are effective in vivo the sequence of the first 31 amino acid residues from gp alpha gt and the first 30 amino acid residues from gp beta gt were determined by Edman degradation. The primary structures of the two proteins seem to have only limited structural similarities. The results are discussed comparing secondary structure predictions and homologies with other proteins from the protein sequence database of the Protein Identification Resource.

High performance liquid chromatography purification and amino terminal sequence analysis of the subunits of bovine heart mitochondrial F1-ATPase

All five subunits of bovine heart mitochondrial F1-ATPase have been isolated by reverse-phase HPLC and NH2-terminal sequences determined by gas phase Edman degradations. Bovine gamma exhibits 16 identities in the first 30 residues compared with the NH2-terminus of gamma from E.coli F1. Bovine delta exhibit about 27% identity with residues 28-59 of precursor delta from N.crassa and in the first six residues is identical with delta from S.cerevisiae. Approximately half of bovine epsilon has been sequenced. Possibly significant sequence similarities exist between bovine gamma and epsilon and kinase-related gene and oncogene products. The bovine alpha subunit has a blocked NH2-terminus.

Peroxisomal beta-oxidation system of Candida tropicalis. Purification of a multifunctional protein possessing enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and 3-hydroxyacyl-CoA epimerase activities

A multifunctional protein from oleate-grown cells of Candida tropicalis has been purified and partially characterized. A simple two-step purification has been developed involving ion-exchange chromatography followed by dye-ligand chromatography on blue Sepharose CL-6B. Homogeneous enzyme with a subunit Mr of 102 000 is obtained in 60% yield. The native relative molecular mass, determined by three different methods, yielded values which suggest that the enzyme is dimeric. Sodium dodecyl sulfate/polyacrylamide gel electrophoresis of the purified protein revealed a single polypeptide band and reverse-phase high-performance liquid chromatography indicated a single component suggesting that this protein may consist either of two identical or very similar subunits. Three beta-oxidation activities, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and 3-hydroxyacyl-CoA epimerase, co-purified with this protein. The ratio of the three beta-oxidation enzyme activities remained constant during purification and was unchanged by additional chromatographic methods (adsorption and affinity chromatography), thus indicating the multifunctional nature of this protein. Enzymatic staining of the purified protein for 3-hydroxyacyl-CoA dehydrogenase and epimerase, following electrophoresis in a polyacrylamide density gradient, further supported the multifunctionality of this protein. After isopycnic centrifugation of a particulate fraction from oleate-grown cells in a linear sucrose gradient the activities of all individual beta-oxidation enzymes cosedimented with catalase and with the glyoxylate bypass enzymes. This result demonstrated the peroxisomal localization of the multifunctional enzyme. The relationship of this multifunctional protein to the two bifunctional beta-oxidation enzymes isolated from peroxisomes of rat liver and from glyoxysomes of cucumber seeds is discussed.

Bovine heart mitochondrial F6: HPLC purification, NH2-terminal sequence and the possible structural relatedness to other components of ATPase complexes

The mitochondrial factor F6 has been purified by reverse-phase HPLC and the molecular weight (8500), amino acid composition and about 25% of the amino acid sequence determined. In the NH2-terminal sequence of the first 18 amino acids (NKELDPVQKLFVDKIREY), six identities with the NH2-terminal sequence of the oligomycin-sensitivity conferring protein (OSCP) are apparent, as well as less striking similarities with the OSCP related subunit delta of E. coli F1. The possibility that F6, OSCP and subunit delta of E. coli F1 could have evolved from a common ancestral gene is supported by apparent gene duplication within the OSCP and subunit delta sequences.

Properties of an interphotoreceptor retinoid-binding protein from bovine retina

Washes and extracts of frozen and fresh cattle retina contain a water-soluble high-molecular-weight, retinoid-binding protein that is distinct from three other retinoid-binding proteins previously isolated from this tissue. The protein can be purified to apparent homogeneity from retinal homogenates by a combination of gel filtration, lectin, and ion-exchange chromatography. Overestimation of the protein molecular weight was observed in several systems involving migration of the protein through a porous network. The approximate molecular weight obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was 140,000, a value consistent with those reported by other laboratories. However, a more detailed analysis using the method of Ferguson revealed the protein to behave anomalously relative to several proteins used as sodium dodecyl sulfate-polyacrylamide gel electrophoresis standards. The apparent radius of the native protein, estimated from calibrated gel filtration, corresponded to a globular protein with a molecular weight of 240,000-280,000, suggesting that the protein was a dimer. However, when the molecular weight of native interphotoreceptor retinoid-binding protein (IRBP) was determined by a method with no shape dependence, sedimentation equilibrium, a value of 131,700 +/- 3,900 g/mol, was obtained. Sedimentation equilibrium in a dissociating solvent (6 M guanidine HCl) yielded a molecular weight of the smallest component of 120,100 +/- 2,300 g/mol. The similarity of values for the denatured and native molecular weight by sedimentation equilibrium demonstrates that the protein is a monomer. In further support of this, no evidence for a dimer was observed in cross-linking experiments with dimethyl suberimidate. The sedimentation coefficient (S0(20),w = 5.73 +/- 0.15 S) and molecular weight from sedimentation equilibrium were employed to calculate the frictional coefficient and Stokes radius of IRBP (f/f0 = 1.64, Rs = 55 A). The high value of f/f0 of the protein provides a reasonable explanation for the over-estimation of the molecular weight of native IRBP on gel filtration. Approximately 2 mol of exogenous all-trans- or 11-cis-retinol were bound per mol of protein (131,000). Approximately 7% of the binding sites were saturated with endogenous ligand (11-cis-retinol, 88%; all-trans-retinol, 12%) following isolation from partially bleached cattle eyes.(ABSTRACT TRUNCATED AT 400 WORDS)

Micropreparative protein purification by reversed-phase high-performance liquid chromatography

Micropreparative purification of the four subunits of phosphorylase kinase (molecular weights 16,680, 43,000, 113,000 and 132,000) by reversed-phase high-performance liquid chromatography has provided quantities sufficient for some of the first structural studies of these proteins. The best yield from a 25 X 0.46 cm I.D. column was obtained on a packing material (5-microns C18) bonded under conditions resulting in a relatively low ligand density; of a total 250 micrograms of protein applied, 76% was recovered. Low recoveries from 5-30-micrograms sample loads suggest partial irreversible adsorption. Retention of protein by the column after an initial micropreparative separation adversely affects resolution and recovery on subsequent separations. Incorporation of gradient wash steps between sample injections was necessary to maintain column performance and to prolong usable column lifetime. The use of a short column with a large diameter (6 X 1 cm) gave increased loading capacity above 400 micrograms protein and enhanced recovery while maintaining good resolution. A less expensive reversed-phase support (17-micron C18) provided adequate resolution for this separation.

Xylose isomerase from Escherichia coli. Characterization of the protein and the structural gene

The gene that codes for xylose isomerase in Escherichia coli has been cloned by complementation of a xylose isomerase-negative E. coli mutant. The structural gene is 1320 nucleotides in length and codes for a protein of 440 amino acids. An additional 209 nucleotides 5' and 82 nucleotides 3' to the structural gene were also sequenced. To verify that the cloned gene encodes E. coli xylose isomerase, the enzyme was purified to homogeneity and the sequence of the first 25 amino acid residues was determined by a semimicromanual Edman procedure. These results establish that the NH2-terminal methionine of xylose isomerase is specified by an ATG which is 7 nucleotides downstream from a Shine-Dalgarno sequence.

High performance liquid chromatography purification and structural characterization of the subunits of rabbit muscle phosphorylase kinase

A rapid reverse-phase high performance liquid chromatography (HPLC) method is presented for isolating the alpha, beta, gamma, and delta subunits of rabbit muscle phosphorylase kinase. The HPLC separation allows micropreparative purification of all the subunits with 66-88% recoveries. Relative molecular weights of the subunits as determined by sodium dodecyl sulfate gel electrophoresis in 4, 5, 7, and 10% acrylamide are alpha 132,000, alpha' 127,000, beta 113,000 and gamma 43,000. Amino acid compositions are reported for the HPLC purified subunits. alpha contains about 2 mol of endogenous phosphate/mol of protein and beta, gamma, and delta each contain about 1 mol of phosphate/mol of protein. Despite the identity of delta and calmodulin, essentially no protein-bound phosphate was found associated with bovine brain calmodulin. Holophosphorylase kinase contains about 20 mol of endogenous phosphate/mol of protein. The first NH2-terminal sequence analyses of the alpha, beta, and gamma subunits were determined by Tarr manual Edman degradation. Within the NH2-terminal 23 residues of gamma ( TRDAALPGSHSTHGFYENYESKE . . . ) there are six identities and one conservative interchange with the catalytic subunit of bovine cAMP-dependent protein kinase. The first 17 residues of the NH2-terminal sequence of alpha ( MRSRSNSGVRLDSYARL . . . ) exhibit six identities and one conservative interchange with the transforming protein from the Rous sarcoma virus (Schmidt- Rupin strain) provided a single gap is inserted in the src gene product. Further structural information is required to evaluate the significance of these sequence similarities. The beta subunit has a blocked NH2 terminus.

Reverse-phase high-performance liquid chromatography of hydrophobic proteins and fragments thereof

Reverse-phase high-performance liquid chromatography (HPLC) resolution and recovery of cytochrome P-450 and bovine rhodopsin, both integral membrane proteins, and large peptides derived from P-450 LM2 were enhanced by utilizing ternary solvents. Surprisingly, most test materials eluted later in the gradient when using mixtures of acetonitrile and propanol in the mobile phase compared to using either solvent alone. Of the supports tested, the best recovery of hydrophobic cytochrome P-450 LM4 was experienced on the less retentive CN-bonded phase. Two alternate solvents for HPLC of polypeptides are proposed: (1) 0.02-0.1 M hexafluoroacetone/NH3, pH 7.2 for highly acidic peptides; and (2) 6 M formic acid/0.13 M trimethylamine, pH 1.5, vs 4 M formic acid/0.09 M trimethylamine in propanol for relatively insoluble peptides. Anomalous side reactions between formic acid and peptides can cause HPLC peak broadening, increased retention, and decreased resolution. These deleterious effects are thought to be due in part to formyl esterification of serine and threonine residues and appear to be reversible by aminoethanol treatment.

Sequence homology in the amino-terminal and active-site regions of thermolabile glyceraldehyde-3-phosphate dehydrogenase from a thermophile

The unusual thermolability of glyceraldehyde-3-phosphate dehydrogenase from the facultative thermophile Bacillus coagulans KU (Crabb et al., Biochemistry 16:4840-4847, 1977) has provided the first opportunity to study a homologous enzyme from the same genus that exhibits a marked difference in thermostability. In pursuit of the structural bases for the thermostability of proteins, the sequences of the amino terminus (residues 1 through 27) and the active-site cysteine cyanogen bromide peptide (residues 130 through 167) of this enzyme have been determined and compared with sequences of the enzyme from other sources. The importance of comparing phylogenetically related proteins is evident from the 87% identity found between these sequences in the enzyme from B. coagulans and Bacillus stearothermophilus, versus only 45% identity for all other known sequences. The marked sequence identity of the enzyme from the two Bacillus species drew attention to the variable region (residues 138 through 140a) which is exposed to the exterior of the quaternary structure of this enzyme. Based on the reported crystallographic structures of the enzyme from lobster muscle and B. stearothermophilus and space-filling models of the variable region, the segment Asp-Pro-Lys-Ala in B. stearothermophilus should be more thermostable than the analogous sequence, Asp-Ala-Ala-Asn, from B. coagulans. In addition, the space-filling models suggested that the spatial relationship of an amino acid side chain and its potential for close packing and interactions with neighboring side chains may be more important than the type of amino acid substituted.