Synthetic tyrosine polymers as substrates and inhibitors of tyrosine-specific protein kinases

Several synthetic random polymers of tyrosine containing glutamic acid, alanine, and lysine in various proportion served as substrates for tyrosine-specific protein kinases. The Km values for these substrates were much lower than for small polypeptides such as angiotensin. For the protein kinase coded by Fujinami virus, the best substrates (with the lowest Km) were polymers containing glutamic acid, alanine, and 8 to 10% tyrosine; for the insulin receptor protein kinase, the best substrate was a polymer containing 80% glutamic acid and 20% tyrosine. These polymers serve as inexpensive and tyrosine-specific substrates that can be used even with crude extracts and analyzed by the convenient filter paper assay. Several synthetic polymers with ordered sequences were found to be potent inhibitors of these tyrosine-specific protein kinases.     

Immune responses of inbred guinea pigs against random terpolymers containing L glutamic acid and L alanine.

The immune responses of the inbred guinea pig strains 2 and 13 have been determined against random terpolymers of L glutamic acid and L alanine and a third amino acid. Strain 2 guinea pigs responded against GAT10, GAT20(LLD), GAT10(NO2)15, GAT4, and GAL10. However, strain 13 guinea pigs responded only against GAT10. The explanation offered is that strain 2 guinea pigs, which have the Ir-GA gene, recognize the polymers via random GA determinants present in sufficient concentration in all of the above polymers. However, strain 13 guinea pigs recognize the GAT10 via the Ir-GT gene, and reduction in the concentration of tyrosyl residues below 10 mole % by various procedures alters the concentration of available random GT determinants necessary for interaction with the gene product of the Ir-GT gene.     

Sequence,Packing and Nanometer Scale Structure in STM Images of Nucleic Acids Under Water

Abstract

Scanning tunneling microscope (STM) images of random-sequence nucleic acid polymers under water show internal structure which depends strongly on the packing density of the polymer. Images of dense aggregates have a semicrystalline order with the individual polymers adopting simple periodic structures. Loose aggregates (or isolated molecules) show structural variability with considerable local bending and curving on a nanometer scale. It is not clear to what extent this structure is induced by the operation of the microscope. In order to investigate the possibility that the structure is sequence directed, we have imaged various DNA and RNA polymers at low packing densities. We present results here for random sequence DNA, poly(dAT) · poly(dAT), poly(dA) · poly(dT), poly(dCG) · poly(dCG) and for random sequence RNA and poly(U). In contrast to loose aggregates of the random sequence material, the homopolymers show few sharp bends. Furthermore, the homopolymers appear to yield characteristic backbone patterns, usually at resolutions in excess of that obtained with random sequence polymers. The random sequence polymers show much more evidence of image distortion due to tip-molecule interactions, suggesting that they are, on average, mechanically less stable in the STM tunnel-gap than the homopolymers. Thus, while some of the structure observed in STM images is a consequence of tip-molecule interactions, it is related to sequence-directed properties of the polymer.     

Recognition site directing vitamin K-dependent gamma-carboxylation resides on the propeptide of factor IX

Posttranslational processing of vitamin K-dependent proteins includes gamma-carboxylation of specific glutamic acid residues to form gamma-carboxyglutamic acids. To determine whether carboxylation is directed by the propeptide sequence, homologous among the precursors of these proteins, alterations were made in the Factor IX propeptide cDNA. The extent of gamma-carboxylation of recombinant Factor IX was assessed using conformation-specific antibodies directed against the gamma-carboxyglutamic acid-dependent, metal-stabilized structure. Deletion of the propeptide (residues -18 to -1) abolished carboxylation, but not secretion, of Factor IX. Substitution of alanine for phenylalanine -16 or glutamic acid for alanine -10 also impaired carboxylation. These results indicate that the Factor IX propeptide participates in defining a recognition site that designates an adjacent glutamic acid-rich domain for gamma-carboxylation. The association of the propeptide with the gamma-carboxylation recognition site provides the first demonstration of a specific function served by a propeptide in posttranslational protein processing.     

Synthesis and characterization of six sequential polypeptides containing tyrosine, glutamic acid, alanine, and glycine by circular dichroism and difference spectroscopy

Six sequential polytetrapeptides containing equimolar amounts of tyrosine, glutamic acid, alanine, and glycine were characterized by CD and difference spectroscopy over a wide range of pH. As the pH was lowered from physiological values, each of the polymers underwent pH-sensitive transitions. The CD spectra indicated that two polymers, poly(Tyr-Glu-Ala-Gly) and poly(Tyr-Ala-Glu-Gly), had some α-helical conformation at pH 7.0 and approached maximum helicity around pH 6.0; two others, poly(Ala-Tyr-Glu-Gly) and poly(Glu-Ala-Tyr-Gly), had no α-helical conformation at pH 7.0 and about one-third of the ellipticities of the above two polymers at pH 5.5; and the remaining two, poly(Ala-Glu-Tyr-Gly) and poly(Glu-Tyr-Ala-Gly) had little or no α-helix, even at pH 5.5. Difference spectroscopy at 286 nm yielded results quite different. The molar extinction coefficients for poly(Tyr-Glu-Ala-Gly) and poly(Tyr-Ala-Glu-Gly) continued to change, even below pH 5.5, and the total changes in absorbance between pH 8.0 and 4.5 were of intermediate magnitudes among the six polymers. Poly(Ala-Tyr-Glu-Gly) and poly(Glu-Ala-Tyr-Gly), which had similar CD spectra, had the lowest and highest pH-related changes in the molar extinction coefficients. It thus appears that amino acid composition alone cannot account for the apparent differences in conformation among the polytetrapeptides. Other factors, such as amno acid sequence, must play a major role in the determination of conformation. The intrinsic viscosity of poly(Tyr-Glu-Ala-Gly) increased markedly between pH 6.0 and 5.5, which was below the pH of the CD transition but above the pH at which the largest absorption perturbation change, at 286 nm, took place. The model that can best account for the relatively low pH at which the absorption transition of tyrosine occurred is a progressive immobilization of side chains in the α-helix as the pH decreases.     

Genetic control of the immune response in rats to the known sequential polypeptide (Tyr-Glu-Ala-Gly)n. I. Antibody responses.

In inbred rats, the antibody response to the known sequential polypeptide (Tyr-Glu-Ala-Gly)n (T-G-A-Gly)n is under the control of two independently assorting loci; (co) dominant, Ag-B-linked Ir-(T-G-A-Gly) I, controlling qualitative responsivenss, and a non-Ag-B-linked modifier locus termed Ir-(T-G-A-Gly) II, controlling the level of antibody produced. The antibody response to (T-G-A-Gly)n was solely IgG and the level of antibody produced was dependent upon Ir-(T-G-A-Gly) II for phenotypic response type.     

Analysis of Z-DNA in fixed polytene chromosomes with monoclonal antibodies that show base sequence-dependent selectivity in reactions with supercoiled plasmids and polynucleotides

Five monoclonal anti-Z-DNA antibodies were characterized with respect to their binding of synthetic nucleic acid polymers and of supercoiled circular plasmid DNA. All of the antibodies reacted only with DNA in the Z-conformation; however, they fell into two classes on the basis of sequence specificity. One class, with broad specificity, reacted well with all sequences in the Z-form, including poly(dG-dC), poly(dG-dm5C), and poly (dG-dBr5C) in linear polymers and poly(dG-dC)n and poly[(dC-dA)n.(dT-dG)n] sequences in supercoiled plasmids. The other class bound only Z-DNA formed by poly(dG-dC). Binding of the monoclonal antibodies specifically to inserts of Z-DNA-forming sequences in plasmids was mapped directly by cross-linking of antibody to the DNA, digestion with restriction nuclease, and electrophoretic analysis of both the unbound fragments and the bound fragments recovered from immune complexes. The monoclonal antibodies were used for indirect immunofluorescence staining of Drosophila polytene chromosomes fixed by two procedures. One procedure yielded chromosomes with Z-specific antibody binding in many interbands, a few specific bands, and parts of some puffs. On chromosomes fixed by the second procedure, antibody staining appeared to follow the DNA concentration, staining all bands brightly. For each fixation procedure, chromosomes showed the same staining pattern with each of the broad specificity monoclonal antibodies that had been seen with polyclonal antibodies. The antibodies that reacted only with poly(dG-dC) and poly (dG-dC)n plasmid inserts did not stain chromosomes fixed by either protocol. We conclude that stretches of poly(dG-dC)n sequences do not contribute significantly to the presence of Z-DNA in fixed polytene chromosomes of Drosophila melanogaster.     

Sequence, packing and nanometer scale structure in STM images of nucleic acids under water

Scanning tunneling microscope (STM) images of random-sequence nucleic acid polymers under water show internal structure which depends strongly on the packing density of the polymer. Images of dense aggregates have a semicrystalline order with the individual polymers adopting simple periodic structures. Loose aggregates (or isolated molecules) show structural variability with considerable local bending and curving on a nanometer scale. It is not clear to what extent this structure is induced by the operation of the microscope. In order to investigate the possibility that the structure is sequence directed, we have imaged various DNA and RNA polymers at low packing densities. We present results here for random sequence DNA, poly(dAT).poly(dAT), poly(dA).poly(dT), poly(dCG).poly(dCG) and for random sequence RNA and poly(U). In contrast to loose aggregates of the random sequence material, the homopolymers show few sharp bends. Furthermore, the homopolymers appear to yield characteristic backbone patterns, usually at resolutions in excess of that obtained with random sequence polymers. The random sequence polymers show much more evidence of image distortion due to tip-molecule interactions, suggesting that they are, on average, mechanically less stable in the STM tunnel-gap than the homopolymers. Thus, while some of the structure observed in STM images is a consequence of tip-molecule interactions, it is related to sequence-directed properties of the polymer.     

Exploring antibody recognition of sequence space through random-sequence peptide microarrays

A universal platform for efficiently mapping antibody epitopes would be of great use for many applications, ranging from antibody therapeutic development to vaccine design. Here we tested the feasibility of using a random peptide microarray to map antibody epitopes. Although peptide microarrays are physically constrained to ～10(4) peptides per array, compared with 10(8) permitted in library panning approaches such as phage display, they enable a much more high though put and direct measure of binding. Long (20 mer) random sequence peptides were chosen for this study to look at an unbiased sampling of sequence space. This sampling of sequence space is sparse, as an exact epitope sequence is unlikely to appear. Commercial monoclonal antibodies with known linear epitopes or polyclonal antibodies raised against engineered 20-mer peptides were used to evaluate this array as an epitope mapping platform. Remarkably, peptides with the most sequence similarity to known epitopes were only slightly more likely to be recognized by the antibody than other random peptides. We explored the ability of two methods singly and in combination to predict the actual epitope from the random sequence peptides bound. Though the epitopes were not directly evident, subtle motifs were found among the top binding peptides for each antibody. These motifs did have some predictive ability in searching for the known epitopes among a set of decoy sequences. The second approach using a windowing alignment strategy, was able to score known epitopes of monoclonal antibodies well within the test dataset, but did not perform as well on polyclonals. Random peptide microarrays of even limited diversity may serve as a useful tool to prioritize candidates for epitope mapping or antigen identification.     

Maintenance of D-alanine ester substitution of lipoteichoic acid by reesterification in Staphylococcus aureus.

Toluene-treated Staphylococcus aureus cells did not synthesize teichoic acid and lipoteichoic acid under the conditions used. The organism displayed, however, a high capacity of incorporating D-[14C]alanine into previously formed polymers. The reaction was dependent on ATP and enhanced by magnesium ions. The incorporation rate into lipoteichoic acid correlated with the rate of loss of alanine ester which occurred through transfer to teichoic acid and base-catalyzed hydrolysis. At pH 6.5 the loss (20% within 4 h) was completely compensated for by reesterification. At pH 7.5 the loss was 60%, but by accelerated incorporation it was reduced to 10%. Incorporation was also enhanced when the original substitution of lipoteichoic acid was lowered by previous growth of S. aureus at high salt concentration. The newly added alanine was randomly distributed along the poly(glycerophosphate) chain. The decreased alanine substitution of lipoteichoic acid after growth at high salt concentration was shown to result from a direct inhibition of alanine incorporation.     

Synthesis and physicochemical properties in aqueous solution of the sequential polypeptide poly(Tyr-Ala-Glu)

A polypeptide having the repealing sequence (Tyr-Ala-Glu)_n was synthesized by the polymerization of the N-hydroxysuccinimide ester of O-benzyl-L -tyrosyl-L -alanyl-γ-benzyl-L -glutamate, followed by the removal of the benzyl groups by means of hydrogen bromide. The main fraction obtained on gel filtration had an average molecular weight of over 60, 000, corresponding to over 500 amino acid residues per polypcptide chain. The polymer is soluble in water above pH 5.5, and precipitates on lowering the pH. The x-ray powder photographs show features of an α-helical structure. The dependence of the ultraviolet absorption spectrum, the optical rotatory dispersion, and the fluorescence of poly(Tyr-Ala-Glu) on pH, in salt-free as well as in salt-containing aqueous solutions, was compared with the corresponding properties of a copolymer containing equimolar proportions of tyrosine, alanine, and glutamic acid in a random sequence. From these measurements it was concluded that poly(Tyr-Ala-Glu ) has a helical con formation at low pH and a random coil conformation at high pH, the transition taking place at pH 6 in the absence of salt and pH II in the presence of salt. Thus, in the range pH 7 to l0. random coil-to-helix transition can be achieved by merely increasing the ionic strength. A model is proposed for the structure of the helical poly peptide which accounts for the Stability of the helical conformation by assuming hydrogen bonding between the carboxylate group of the ith glutamic acid residue and the hydroxyl group of the (i + 4 )th tyrosine residue. The complex ORD of helical poly(Tyr-Ala-Glu) is explained as being due to a superposition of the ORD of an α-helix and that of a regular array of phenolic ehroniopholes originating from the immobilization of the aromatic rings in the specific structure of the polymer.     

Shared idiotypes on anti-DNA and anti-poly (ADP-ribose) antibodies

Hed 10 is a ssDNA-specific mAb derived from an NZB/W autoimmune mouse. ADP 1 is a poly(ADP-ribose)-specific mAb derived from a C57BL/6 mouse. Rabbit anti-idiotypic sera were raised against Hed 10 and ADP 1. By affinity chromatography it was shown that at least 20 to 30% of DNA-binding antibodies contained these idiotypes. The sera were also used to evaluate idiotypic cross-reactivity among 26 diverse, predominantly anti-nucleic acid, murine mAb. Each serum bound directly to several mAb and in addition inhibited the binding of several antibodies to their appropriate Ag. The anti-Hed 10 serum detected an idiotype which was restricted to antibodies that bound to poly(dT) and/or poly(ADP-ribose). The anti-ADP 1 serum detected a more widely distributed idiotype contained in antibodies which bound to a variety of nucleic acids. Although both sera bound directly to Hed 10, only the anti-Hed 10 serum could compete for the binding of Hed 10 to poly(dT). On the other hand, both sera could compete for the binding of ADP 1 to poly(ADP-ribose) as well as bind directly to ADP 1. In addition anti-ADP 1 serum appeared to enhance, rather than inhibit, the binding of one mAb to native calf thymus DNA and poly[d(AT)] but had no effect on the binding to several ssDNA. These results demonstrate that many antibodies which recognize DNA and poly(ADP-ribose) have shared idiotypes. This may be of relevance to the development of autoimmunity because poly(ADP-ribose) is ubiquitous and immunogenic.     

Immune responses of mice to poly(L-Tyr-L-Glu-L-Ala-Gly) and its oligomers

C57BL/6 (H-2 ^b) mice, when immunized with the sequential polymer (T-G-A-Gly)_n and its low-molecular-weight oligomers, respond only to theα-helical oligomers with molecular weights of 9700 and above. Only the sameα-helical oligomers were able to inhibit the homologous antigen-antibody reaction. Random copolymers of GA, GT, and GAT¹⁰ did not inhibit. In vitro stimulation of peritoneal exudate lymphocyte (PETLES) cultures showed that the cellular response (T-cell) against (T-G-A-Gly)_n is antigen-specific. In vitro antigen-induced stimulation of whole spleen or lymph node lymphocytes indicated that (T-G-A-Gly)_n might also be a B-cell mitogen.     

Topographic antigenic determinants on cytochrome c. Immunoadsorbent separation of the rabbit antibody populations directed against horse cytochrome.

Seven populations of site-specific antibodies were isolated from each of three sera of rabbits immunized against glutaraldehyde-polymerized horse cytochrome c. The antibodies were separated using an immunoadsorption scheme which employed the following cytochromes c: horse, beef, guanaco, rabbit, mouse testicular, pigeon, and the cyanogen-bromide cleaved fragment of the rabbit protein containing residues 1 to 65. The monovalent, antigen-binding fragments of the antibodies (Fab') gave 1:1 stoichiometries with native horse cytochrome c in fluorescence quenching assays. Cross-reactivities with heterologous cytochromes c using fluorescence quenching and a modified Farr assay demonstrated that the antigenic determinants are situated around residues 44, 60, and 89/92, four of the six amino acid sequence positions where horse and rabbit cytochromes c differ. The remaining two differences occur at residues 47 and 62. The apparent lack of immunogenicity of these two substitutions may result from the presence of the more immunogenic residues 44 and 60 nearby. Of the seven antibody populations isolated, four were shown to bind in the region of residues 89 and 92. Since several cytochromes c have amino acid sequence differences from the horse protein at either of these two residue positions, it was possible to fractionate the antibodies directed against this complex site on the basis of subtle specificity differences between them. Two antibody populations bind in the region of residue 44. One of these is specific for proline at that position, while the other antibody population also binds to cytochrome c containing glutamic acid at position 44. The remaining antibody population binds in the region of the lysine residue at position 60. Each of the seven site-specific antibody populations binds effectively to any cytochrome c having a suitable amino acid sequence in the antigenic determinant regardless of any residue differences from the immunogen outside of that area. It was also demonstrated that these seven antibody populations represent the totality of the antibodies elicited in rabbits against horse cytochrome c, since the immunoadsorbants bound all the antibodies specific for the native protein. Furthermore, the rabbit antisera contained no other antibody population that could bind to the conformationally disturbed, cyanogen bromide-cleaved fragment of horse cytochrome c containing residues 1 to 65, making it appear that there were no antibodies elicited against a "processed" form of cytochrome c.     

Antibodies against synthetic peptides as a tool for functional analysis of the transforming protein pp60src

To study the function of pp60src, the transforming protein encoded for by Rous sarcoma virus, we have raised antibodies against synthetic oligopeptides corresponding to the primary structure of pp60src. All eight investigated peptides were immunogenic in rabbits, and four induced pp60src-specific antibodies. We screened tumor-bearing rabbit (TBR) sera for antibodies against the peptides; this revealed that five out of six of the peptides, chosen according to a high hydrophilicity plot, were related to epitopes of native pp60src, in contrast to two peptides of low hydrophilicity, which contained a cleavage site for protease. Antibodies against three of the peptides appeared to react with the kinase-active site of pp60src, as these antibodies were phosphorylated in their heavy chain upon immune precipitation. Antibodies against two of the peptides, in contrast to the others, did not precipitate pp60src when this molecule was complexed with two cellular proteins, pp50 and pp90. This observation allows speculation about the location of the pp60src site involved in the formation of this complex.     

Site-directed mutagenesis of a soluble recombinant fragment of platelet glycoprotein Ib alpha demonstrating negatively charged residues involved in von Willebrand factor binding.

We have expressed in mammalian cells a fragment (residues 1-302) of the alpha chain of platelet glycoprotein (GP) Ib containing the von Willebrand factor- (vWF) binding site. The secreted soluble protein had an apparent molecular mass of 45 kDa and reacted with conformation-dependent monoclonal antibodies that bind only to native GP Ib, thus demonstrating its proper folding. After insolubilization on nitrocellulose membrane, the recombinant GP Ib alpha fragment bound soluble vWF in the presence of ristocetin or botrocetin with a dissociation constant similar to that exhibited by GP Ib.IX complex on platelets. Moreover, the interaction was blocked by anti-GP Ib monoclonal antibodies known to inhibit vWF binding to platelets. The sequence of GP Ib alpha between residues 269-287 has a strong net negative charge due to the presence of 10 glutamic or aspartic acid residues; 5 of these are contained in the sequence of a synthetic peptide (residues 251-279) previously shown to inhibit vWF-platelet interaction. In order to evaluate the possible functional role of these acidic residues, we employed site-directed mutagenesis to express two mutant GP Ib alpha fragments containing asparagine or glutamine instead of aspartic or glutamic acid, respectively. Mutant 1, with substitutions between residues 251-279, failed to bind vWF whether in the presence of ristocetin or botrocetin; in contrast, vWF binding to Mutant 2, with substitutions between residues 280-302, was nearly normal in the presence of ristocetin, but markedly decreased in the presence of botrocetin. Thus, mammalian cells transfected with a truncated cDNA sequence encoding the amino-terminal domain of GP Ib alpha synthesize a fully functional vWF-binding site; acidic residues in the sequence 252-287 are essential for normal function.     

Identification and expression of haponin, a new protein from HL-60 cells

We found a new protein haponin (an HLDF-alike protein) in promyelocyte HL-60 cells that is immunoreactive to polyclonal antibodies against HLDFbeta. Determination of the partial primary structure of the protein allowed us to reveal an immunogenic peptide of haponin and, on the basis of the amino acid sequence of this peptide, the degenerate primers were synthesized, which enabled us to clone the full-size cDNA of haponin. The stable heterologous expression of this cDNA in E. coli cells (Rosetta strain) was obtained. Preparations of natural and recombinant proteins exhibited antigenic cross-reactivity to polyclonal antibodies against this peptide.     

Trigramin. A low molecular weight peptide inhibiting fibrinogen interaction with platelet receptors expressed on glycoprotein IIb-IIIa complex

Trigramin, a highly specific inhibitor of fibrinogen binding to platelet receptors, was purified to homogeneity from Trimeresurus gramineus snake venom. Trigramin is a single chain (approximately 9 kDa) cysteine-rich peptide with the Glu-Ala-Gly-Glu-Asp-Cys-Asp-Cys-Gly-Ser-Pro-Ala NH2-terminal sequence. Chymotryptic fragmentation showed the Arg-Gly-Asp sequence in trigramin. Trigramin inhibited fibrinogen-induced aggregation of platelets stimulated by ADP (IC50 = 1.3 X 10(-7)M) and aggregation of chymotrypsin-treated platelets. It did not affect the platelet secretion. Trigramin was a competitive inhibitor of the 125I-fibrinogen binding to ADP-stimulated platelets (Ki = 2 X 10(-8) M). 125I-Trigramin bound to resting platelets (Kd = 1.7 X 10(-7) M; n = 16,500), to ADP-stimulated platelets (Kd = 2.1 X 10(-8) M; n = 17,600), and to chymotrypsin-treated platelets (Kd = 8.8 X 10(-8) M; n = 13,800) in a saturable manner. The number of 125I-trigramin binding sites on thrombasthenic platelets amounted to 2.7-5.4% of control values obtained for normal platelets and correlated with the reduced number of GPIIb-GPIIIa molecules on the platelet surface. EDTA, monoclonal antibodies directed against the GPIIb-GPIIIa complex, and synthetic peptides (Arg-Gly-Asp-Ser and Tyr-Gly-Gln-Gln-His-His-Leu-Gly-Gly-Ala-Lys-Gln-Ala-Gly-Asp-Val) blocked both 125I-fibrinogen binding and 125I-trigramin binding to platelets. Fibrinogen binding was more readily inhibited by these compounds than was trigramin binding. Monoclonal antibodies directed either against GPIIb or GPIIIa molecules did not block the interaction of either ligand with platelets. Reduced, S-pyridylethyl, trigramin did not inhibit platelet aggregation and fibrinogen binding to platelets and it did not bind to platelets, suggesting that the secondary structure of this molecule is critical for expression of its biological activity.     

Initiation factor 2 of Myxococcus xanthus, a large version of prokaryotic translation initiation factor 2

We have isolated the structural gene for translation initiation factor IF2 (infB) from the myxobacterium Myxococcus xanthus. The gene (3.22 kb) encodes a 1,070-residue protein showing extensive homology within its G domain and C terminus to the equivalent regions of IF2 from Escherichia coli. The protein cross-reacts with antibodies raised against E. coli IF2 and was able to complement an E. coli infB mutant. The M. xanthus protein is the largest IF2 known to date. This is essentially due to a longer N-terminal region made up of two characteristic domains. The first comprises a 188-amino-acid sequence consisting essentially of alanine, proline, valine, and glutamic acid residues, similar to the APE domain observed in Stigmatella aurantiaca IF2. The second is unique to M. xanthus IF2, is located between the APE sequence and the GTP binding domain, and consists exclusively of glycine, proline, and arginine residues.