Elucidation of the sequence-specific third-strand recognition of four Watson-Crick base pairs in a pyrimidine triple-helix motif: T.AT, C.GC, T.CG, and G.TA.

We report a specific pattern of recognition by third-strand bases for each of the four Watson-Crick base pairs within a pyrimidine triple-helix motif as determined by PAGE: T.AT, C.GC, T.CG, and G.TA. Our recognition scheme for base triplets is in agreement with previous studies. In addition, we identified another triplet, T.CG, under physiological conditions, in which formation of triple helix was observed at equimolar ratios of the third strand and duplex target. Although different nearest-neighbor effects are expected, this finding extends the base-recognition code to all 4 base pairs in double-stranded DNA under physiological conditions. Base-composition analysis of putative triplex species provided independent evidence for the formation of triplex and confirmed the base-recognition code determined by PAGE. Moreover, the formation of triplex, as detected by gel electrophoresis, was seen to be an all-or-none phenomenon, dependent upon a single-base mismatch among 21 nucleotides. This result suggests a high specificity for the recognition of double-stranded DNA by a third strand. In addition, we report the surprising finding that triplex stability depends on the length and sequence of the target duplex DNA.

The size, operation, and technical capabilities of protein and nucleic acid core facilities.

A survey of 40 protein and nucleic acid chemistry facilities has provided data about the capabilities of core facilities and the cost of the services they provide. Approximately 43% of the +158,000 average annual operating budget for a typical university facility is derived from service charges. After correcting for the various degrees of subsidization of the different facilities, it was found that it costs a typical university facility +65 to carry out an acid hydrolysis and amino acid analysis on a protein. A 25-residue peptide can be synthesized and cleaved for +2078, whereas sequencing the same peptide costs +874. A 25-residue oligonucleotide can be synthesized for +258. The total work output per month of an average facility corresponds to 65 amino acid analyses, 15 amino acid sequencing runs, three peptide syntheses, and 16 oligonucleotide syntheses. Depending on the approach used, from 85 to nearly 200 pmol of protein are required to obtain an accurate amino acid composition. To sequence the first 15 amino acids in a protein typically requires 150 pmol compared with 1.2 nmol of protein required to first carry out a tryptic digest and then isolate and sequence the first 15 residues in one of the resulting tryptic peptides.

Sequence of the phosphothreonyl regulatory site peptide from inactive maize leaf pyruvate, orthophosphate dikinase.

The regulatory site peptide sequence of phosphorylated inactive pyruvate, orthophosphate dikinase from maize leaf tissue was determined by automated Edman degradation analysis of 32P-labeled peptides purified by reversed-phase high performance liquid chromatography. The overlapping phosphopeptides were products of a digestion of the [beta-32P]ADP-inactivated dikinase with either trypsin or Pronase E. The sequence is Thr-Glu-Arg-Gly-Gly-Met-Thr(P)-Ser-His-Ala-Ala-Val-Val-Ala-Arg. The phosphothreonine residue, which appeared as either an anomalous proline or an unidentifiable phenylthiohydantoin derivative during sequencing, was verified by two-dimensional phosphoamino acid analysis of the phosphopeptides and by resequencing the tryptic peptide after dephosphorylation with exogenous alkaline phosphatase. This sequence, starting at position 4, is completely homologous to the previously published sequence of the tryptic dodecapeptide harboring the catalytically essential (phospho)histidyl residue in the active-site domain of the dikinase from the nonphotosynthetic bacterium, Bacteroides symbiosus (Goss, N.H., Evans, C.T., and Wood, H.G. (1980) Biochemistry 19, 5805-5809). These comparative results indicate that the regulatory phosphothreonine causing complete inactivation of maize leaf dikinase is separated from the critical active-site (phospho)histidine by just one intervening residue in the primary sequence.

A 15-kDa interferon-induced protein is derived by COOH-terminal processing of a 17-kDa precursor.

An interferon-induced 15-kDa protein is synthesized from a precursor of higher molecular weight; the precursor contains 165 amino acids (17 kDa), whereas the stable product (15 kDa) contains 156 amino acids. The stable 15-kDa form is derived from the precursor 17-kDa form by the removal of eight amino acids from the COOH terminus and the methionine from the NH2 terminus. The existence of the precursor 17-kDa protein can be demonstrated after brief periods of in vivo labeling with [35S]methionine and by translation of mRNA in vitro.

Structure-function relationships for the IL-2 receptor system. V. Structure-activity analysis of modified and truncated forms of the Tac receptor protein: site-specific mutagenesis of cysteine residues.

IL-2R on activated lymphocytes contain the Tac protein. As part of an effort to characterize this molecule, we examined the structure-activity relationship for each of its 12 Cys residues. A preliminary map of intramolecular disulfide bonding was derived by analysis of cystine-linked enzymatic fragments of the Tac protein. The results indicated that disulfide bonds linked Cys-3 with Cys-147, Cys-131 with Cys-163, and Cys-28,30 with Cys-59,61. The contribution of the Cys residues to an active protein conformation was tested by site-specific mutagenesis, followed by expression of the modified molecules in murine L cells. The results indicated that Cys-192 and -225 could be replaced without affecting ligand binding. In contrast, modification of any of the other 10 Cys residues, either singly or in combinations corresponding to the predicted disulfide bonds, greatly reduced the ability of the corresponding protein to bind IL-2 or either of two mAb (anti-Tac and 7G7/B6) which recognize the Tac protein. Each of the latter mutations also interfered with the molecule's post-translational modification and cell-surface expression. Consistent with these findings, transfection of the L cells with vectors containing truncated Tac cDNA inserts resulted in secretion of Tac fragments capable of ligand binding when the polypeptide chains terminated after Cys-163 (the 10th Cys residue in the full length molecule), but resulted in inactive fragments of Tac which were poorly secreted when they terminated before Cys-163. These findings emphasize the remarkable sensitivity of the active conformation of the Tac molecule to each of the postulated intramolecular disulfide bonds.

Structural and mechanistic properties of E. coli adenosylmethionine decarboxylase.

Adenosylmethionine decarboxylase catalyzes one of the first committed steps in polyamine biosynthesis. It is a member of a small class of decarboxylases that use a pyruvovyl prosthetic group rather than the more common pyridoxal cofactor. We have recently shown that AdoMet decarboxylase from E. coli is composed of stoichiometric amounts of two types of subunits; alpha (Mr = 19,000), and beta (Mr = 14,000). The NH2-terminal of the alpha subunit is blocked by the pyruvoyl group and can be sequenced only after reductive amination, which converts this to an alanine residue. The beta subunit, on the other hand, has an unblocked NH2-terminal and sequences normally. The molecular weight of the holoenzyme, estimated by gel filtration, is 136,000 suggesting that the enzyme is an alpha 4 beta 4 octamer. AdoMet decarboxylase undergoes a time dependent inactivation during turnover. The mechanism of this inactivation involves a transamination from the product, decarboxylated AdoMet, and the pyruvoyl group generating an NH2-terminal alanine. The nascent product aldehyde then eliminates methylthioadenosine, resulting in the formation of acrolein, which covalently labels the alpha subunit. How this mechanism may explain AdoMet decarboxylase turned over, and how AdoMet decarboxylase inhibitors can affect its half life will be discussed.

Mechanism of substrate inactivation of Escherichia coli S-adenosylmethionine decarboxylase.

S-Adenosylmethionine decarboxylase, a pyruvoyl-containing decarboxylase, is inactivated in a time-dependent process under turnover conditions. The inactivation is dependent on the presence of both substrate and Mg2+, which is also required for enzyme activity. The rate of inactivation is dependent on the concentration of substrate and appears to be saturable. Inactivation by [methionyl-3,4-14C]-adenosylmethionine results in stoichiometric labeling of the protein. In contrast, when either S-[methyl-3H]adenosylmethionine or [8-14C]adenosylmethionine is used, there is virtually no incorporation of radioactivity. Automated Edman degradation of the alpha (pyruvoyl-containing) subunit reveals that substrate inactivation results in the conversion of the pyruvoyl group to an alanyl residue. These data suggest a mechanism of inactivation which involves the transamination of the nascent product to the pyruvoyl group, followed by the elimination of methylthioadenosine and the generation of a 2-propenal equivalent which could undergo a Michael addition to the enzyme. This is the first evidence for a transamination mechanism for substrate inactivation of a pyruvoyl enzyme.

Structure-function relationships for the IL 2-receptor system. IV. Analysis of the sequence and ligand-binding properties of soluble Tac protein.

The Tac protein is one of at least two glycoproteins known to bind the growth and differentiation factor interleukin 2 (IL 2). In addition to its location on the cell surface, where it plays a part in high and low affinity IL 2 receptors, Tac is released from activated lymphocytes in a soluble form. We observed this release both for Tac protein labeled biosynthetically and for Tac protein labeled by surface iodination of intact cells. Competitive binding studies indicated that the soluble Tac protein retained an ability to bind IL 2 with a low affinity (Kd of 11.1 nM). In addition, structural analysis revealed that the polypeptide chain began at position 1 and ended at or just before Cys-192 of the full-length molecule. Thus, the protein was missing its normal transmembrane and intracytoplasmic segments, accounting for its solubility and cellular release. The apparent lack of modification in the amino acid sequence and the termination at Cys-192 are inconsistent with a mechanism of cellular release dependent only on alternate mRNA splicing. Instead, the results suggest that proteolysis may accompany the release of soluble Tac protein from cells expressing IL 2 receptors.

Escherichia coli S-adenosylmethionine decarboxylase. Subunit structure, reductive amination, and NH2-terminal sequences.

S-Adenosylmethionine decarboxylase is one of a small group of enzymes that use a pyruvoyl residue as a cofactor. Histidine decarboxylase from Lactobacillus 30a, the best studied pyruvoyl-containing enzyme, has an (alpha beta)6 subunit structure with the pyruvoyl moiety linked through an amide bond to the NH2-terminal of the larger alpha subunit (Recsei, P. A., Huynh, Q. K., and Snell, E. E. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 973-977). To examine potential structural analogies between the two enzymes, we have isolated and partially characterized S-adenosylmethionine decarboxylase. The purified enzyme comprises equimolar amounts of two subunits of Mr = 14,000 and 19,000 (by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and has a native molecular weight of 136,000 (by gel filtration). Approximately 4 mol of [methyl-3H] adenosylmethionine are incorporated per mol of enzyme (Mr = 136,000) when the enzyme is inactivated with this substrate and NaCNBH3. These data suggest an (alpha beta)4 structure with 1 pyruvoyl residue for each alpha beta pair. The two subunits have been separated by reversed-phase high performance liquid chromatography after reduction and carboxymethylation. The smaller subunit (beta) has a free amino terminus. The amino terminus of the larger subunit (alpha) appears to be blocked by a pyruvoyl group; this subunit can be sequenced only after this group is converted to an alanyl residue by reduction with sodium cyanoborohydride in the presence of ammonium acetate. This work suggests that S-adenosylmethionine decarboxylase is structurally much more similar to histidine decarboxylase than previously thought.

Molecular characterization of the interferon-induced 15-kDa protein. Molecular cloning and nucleotide and amino acid sequence.

We have isolated a cDNA clone for an interferon-induced 15-kDa protein. The cDNA clone was prepared from mRNA isolated from interferon-beta-treated human Daudi cells. The clone of 635 base pairs contains an open reading frame coding for a protein of 145 amino acids, and suggests for the mRNA a 75-base pair 5' untranslated and a 125-base pair 3' untranslated region. Approximately 85% of the amino acid sequence of the 15-kDa protein has been independently obtained from 2 nmol of material using microsequencing technology on the N terminus of the intact protein and on tryptic and chymotryptic peptides. The amino acid sequence of the isolated protein is identical to the amino acid sequence deduced from the cDNA. Northern blot analysis confirmed that the mRNA for the 15-kDa protein is undetectable in untreated cells, but is greatly induced following interferon treatment.

Purification and properties of Salmonella typhimurium acetolactate synthase isozyme II from Escherichia coli HB101/pDU9.

A facile purification has been devised for recombinantly produced Salmonella typhimurium acetolactate synthase isozyme II. Purification of the enzyme was made possible by determining the complex set of factors that lead to loss of enzymic activity with this rather labile enzyme. When complexed with thiamin pyrophosphate, FAD, and magnesium, acetolactate synthase is subject to oxygen-dependent inactivation, a property not shared by the enzyme-FAD complex. When divorced from all of its tightly bound cofactors, losses of the enzymic activity are encountered at low ionic strength, especially at low protein concentrations. If purified and stored as the enzyme-FAD complex, acetolactate synthase is quite stable. The enzyme is composed of two types of subunits, a result that was not anticipated from previous studies of ilvG (the gene that codes for the large subunit of acetolactate synthase). These subunits were determined to be in equal molar ratio in the purified enzyme from the distribution of radioactivity between the two subunits after carboxymethylation with iodo[14C]acetate and their respective amino acid compositions. Besides the expected ilvG gene product (59.3 kDa), purified acetolactate synthase contained a smaller subunit (9.7 kDa; designated here as the ilvM gene product). On the basis of sequence homology of the small subunit with that coded for by the corresponding Escherichia coli gene sequence [Lawther, R. P., Calhoun, D. H., Adams, C. W., Hauser, C. A., Gray, J., & Hatfield, G. W. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 922-925], it is encoded by the region between ilvG and ilvE, beginning at base-pair (bp) 1914 (relative to the point of transcription initiation).(ABSTRACT TRUNCATED AT 250 WORDS)

Amino acid sequence and post-translational modification of human interleukin 2.

Human interleukin 2 was separated into multiple molecular forms by selective immunoaffinity chromatography and chromatofocusing. For the most part, this heterogeneity was attributed to variations in glycosylation of the threonine residue in position 3 of the polypeptide chain. The various molecular forms of interleukin 2 had nearly identical specific activities in the in vitro proliferation assay, indicating that the glycosylation had no significant effect on this response. The entire primary sequence of interleukin 2, including the location of the intramolecular disulfide bridge, was determined by a combination of peptide mapping and protein sequencing. This information should aid in the determination of the active site(s) of the molecule.

Posttranslational modification of human T-cell growth factor.

Amino-terminal sequence analysis of human T-cell growth factor indicated that the amino acid in position 3 of the polypeptide chain was modified. Examination of the N-terminal octapeptide using the amino acid analyzer and mass spectrometry demonstrated that position 3 was a threonine which was linked to N-acetyl-D-galactosamine. This site of glycosylation is of practical significance since it appears to play a role in the selectivity of a monoclonal antibody for the factor.

Purification and partial sequence analysis of human T-cell growth factor.

A murine monoclonal antibody directed against human T-cell growth factor (TCGF) from the JURKAT cell line was used for affinity column purification of the factor. Bound TCGF was eluted nearly quantitatively at low pH, and the recovered factor appeared homogeneous by two-dimensional gel electrophoresis. The molecule is markedly hydrophobic, with a high content of leucine. A single NH2-terminal sequence of 36 residues was obtained by automated Edman degradation, further supporting the homogeneity of the material. Thus, significant quantities of purified TCGF have been prepared in a single step, making possible detailed analysis of its molecular structure and biological role.

Preparation of protected peptide hydrazides from the acids and hydrazine by dicyclohexylcarbodiimide-hydroxybenzotriazole coupling.

A mild procedure for preparing protected peptide hydrazides directly from the corresponding carboxylic acids and equivalent amounts of hydrazine, N-hydroxybenzotriazole and dicyclohexylcarbodiimide is described. Side reactions frequently encountered in hydrazinolysis are thus totally avoided. The process is especially useful for the preparation of aspartic acid and glutamic acid containing peptide hydrazides. No racemization of the amino acid residue was observed.