Stereoselective binding of an enantiomeric pair of stromelysin-1 inhibitors caused by conformational entropy factors.

Isothermal titration calorimetry was used to analyze the binding of an enantiomeric pair of inhibitors to the stromelysin-1 catalytic domain. Differences in binding affinity are attributable to different conformational entropy penalties suffered upon binding. Two possible explanations for these differences are proposed.

Regulatory effects of endogenous protease inhibitors in acute lung inflammatory injury.

Inflammatory lung injury is probably regulated by the balance between proteases and protease inhibitors together with oxidants and antioxidants, and proinflammatory and anti-inflammatory cytokines. Rat tissue inhibitor of metalloprotease-2 (TIMP-2) and secreted leukoprotease inhibitor (SLPI) were cloned, expressed, and shown to be up-regulated at the levels of mRNA and protein during lung inflammation in rats induced by deposition of IgG immune complexes. Using immunoaffinity techniques, endogenous TIMP-2 in the inflamed lung was shown to exist as a complex with 72- and 92-kDa metalloproteinases (MMP-2 and MMP-9). In inflamed lung both TIMP-2 and SLPI appeared to exist as enzyme inhibitor complexes. Lung expression of both TIMP-2 and SLPI appeared to involve endothelial and epithelial cells as well as macrophages. To assess how these endogenous inhibitors might affect the lung inflammatory response, animals were treated with polyclonal rabbit Abs to rat TIMP-2 or SLPI. This intervention resulted in significant intensification of lung injury (as revealed by extravascular leak of albumin) and substantially increased neutrophil accumulation, as determined by cell content in bronchoalveolar lavage (BAL) fluids. These events were correlated with increased levels of C5a-related chemotactic activity in BAL fluids, while BAL levels of TNF-alpha and chemokines were not affected by treatment with anti-TIMP-2 or anti-SLPI. The data suggest that endogenous TIMP-2 and SLPI dynamically regulate the intensity of lung inflammatory injury, doing so at least in part by affecting the generation of the inflammatory mediator, C5a.

Application of electrospray ionization mass spectrometry for studying human immunodeficiency virus protein complexes.

Mass spectrometry (MS) with electrospray ionization (ESI) has shown utility for studying noncovalent protein complexes, as it offers advantages in sensitivity, speed, and mass accuracy. The stoichiometry of the binding partners can be easily deduced from the molecular weight measurement. In many examples of protein complexes, the gas phase-based measurement is consistent with the expected solution phase binding characteristics. This quality suggests the utility of ESI-MS for investigating solution phase molecular interactions. Complexes composed of proteins from the human immunodeficiency virus (HIV) have been studied using ESI-MS. Multiply charged protein dimers from HIV integrase catalytic core (F185K) and HIV protease have been observed. Furthermore, the ternary complex between HIV protease dimer and inhibitor pepstatin A was studied as a function of solution pH. Zinc binding to zinc finger-containing nucleocapsid protein (NCp7) and the NCp7-psi RNA 1:1 stoichiometry complex was also studied by ESI-MS. No protein-RNA complex was observed in the absence of zinc, consistent with the role of the zinc finger motifs for RNA binding.

Bacterial expression and characterization of human recombinant apolipoprotein(a) kringle IV type 9.

Elevated plasma lipoprotein(a) [Lp(a)] is an independent risk factor for several vascular diseases. Lp(a) particles are generated through the formation of a disulfide bond between Cys4057 of kringle IV type 9, (KIVt9), of the multikringle apolipoprotein(a) [apo(a)] and a cysteine in apoB-100 low-density lipoprotein (LDL). To better understand this interaction, we have expressed and purified KIVt9 from Escherichia coli as a His-Tag fusionprotein. Dithiothreitol (DTT)-treated purified KIVt9 migrated as a single approximately 17. 3-kDa band on SDS-PAGE gels. Without DTT, an additional band twice the molecular weight of KIVt9 was observed. The double-size band presumably resulted from dimerization of individual kringles, through their unpaired cysteine residues, since a mutation Cys4057 --> Ser ([Ser4057]KIVt9) abolished dimer formation. Using a gel-shift assay, we showed that KIVt9 could couple to 14-amino-acid apoB-100 synthetic peptides (apoB3732-3745 and apoB4319-4332) containing Cys3734 or Cys4326. Both of these apoB-100 cysteines have been reported to associate with apo(a) to generate Lp(a). In the presence of either apoB-100 peptide, KIVt9 was shifted to a higher molecular weight that was consistent with the covalent addition of a 1.2-kDa apoB-100 peptide. Identical apoB-100 peptides in which the cysteine residues were replaced by alanine ([Ala3734]apoB3732-3745 and [Ala4326]apoB4319-4332) had no effect in the gel-shift assay. Furthermore, [Ser4057]KIVt9 did not covalently interact with apoB3732-3745 or apoB4319-4332. These results indicated that KIVt9 couples to the Cys-apoB-100 peptides through a disulfide linkage. This system may be suitable for further investigating the apo(a)/apoB-100 coupling reaction and the structure of KIVt9 through X-ray crystallographic studies.

Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand.

The specific association of an SH2 domain with a phosphotyrosine (pTyr)-containing sequence of another protein precipitates a cascade of intracellular molecular interactions (signals) which effect a wide range of intracellular processes. The nonreceptor tyrosine kinase Src, which has been associated with breast cancer and osteoporosis, contains an SH2 domain. Inhibition of Src SH2-phosphoprotein interactions by small molecules will aid biological proof-of-concept studies which may lead to the development of novel therapeutic agents. Structure-based design efforts have focused on reducing the size and charge of Src SH2 ligands while increasing their ability to penetrate cells and reach the intracellular Src SH2 domain target. In this report we describe the synthesis, binding affinity, and Src SH2 cocrystal structure of a small, novel, nonpeptide, urea-containing SH2 domain ligand.

Nuclear magnetic resonance solution structure of the growth factor receptor-bound protein 2 Src homology 2 domain.

A family of NMR solution structures of the growth factor receptor-bound protein 2 (Grb2) SH2 domain has been determined by heteronuclear multidimensional NMR. Proton, nitrogen, and carbon chemical shift assignments have been made for the SH2 domain of Grb2. Assignments were made from a combination of homonuclear two-dimensional and 15N- and 13C-edited three-dimensional spectra at pH 6.2 and 298 K. Structure-induced proton and carbon secondary shifts were calculated and used to facilitate the spectral assignment process. NOE, scalar coupling, secondary chemical shift, and amide proton exchange data were used to characterize the secondary structural elements and hydrogen-bonding network in the Grb2 SH2 domain. The three-dimensional structure of the Grb2 SH2 domain was calculated using 1112 restraints obtained from NOE, coupling constant, and amide proton exchange data. The rmsd for the 24 calculated structures to the mean structure of the Grb2 SH2 domain was 0.75 A for backbone and 1.28 A for all heavy atoms. The three-dimensional fold of the Grb2 SH2 domain is similar to that observed for other SH2 domains and consists of two alpha-helical segments and eight beta-strands, six strands that make up two contiguous antiparallel beta-sheets, and two strands that form two short parallel beta-sheets. The structure of the phosphotyrosine binding pocket of Grb2 is similar to that observed for other SH2 domains. The hydrophobic binding pocket of Grb2 is similar to that observed for Src with the exception that tryptophan 121 of Grb2 occupies part of the pY+3 binding pocket. Structural implications for the Grb2 SH2 domain selectivity at the pY+2 and pY+3 sites are discussed.

Development and validation of two solid-phase enzyme immunoassays (ELISA) for quantitation of human epidermal growth factors (hEGFs).

PURPOSE: The purpose of the present investigation was to develop and validate two separate enzyme-linked immunosorbent assays (ELISA) for quantitation of exogenous human epidermal growth factor (hEGF1-53) and its truncated fragment (hEGF1-48) in rat plasma. METHODS: The present assay systems were based on the sandwiching of the antigen between a monoclonal mouse anti-hEGF1-53 antibody, pre-coated on a 96-well polystyrene plate, and a polyclonal rabbit anti-hEGF1-48 antibody, which is then detected with a peroxidase-labeled goat anti-rabbit antibody. RESULTS: The calibration curves for hEGF1-48 and hEGF1-53 in plasma were validated over a concentration range of 7.8-250 and 62.5-1000 pg/ml, respectively. Determined from replicate assays of hEGF1-48 quality control samples, the intra-assay precision and accuracy were < or = 8.8% RSD and within +/- 9.8%; and the inter-assay precision and accuracy were < or = 14.8% RSD and within +/- 9.7% RE, respectively. Determined from replicate assays of hEGF1-53 quality control samples, the intra-assay precision and accuracy were < or = 10.0% RSD and within +/- 8.5%; and the inter-assay precision and accuracy were < or = 10.0% RSD and within +/- 5.7% RE, respectively. The limit of quantitation of the hEGF1-48 and hEGF1-53 assay using 200 microliters plasma per well is 7.8 and 62.5 pg/ml, respectively. These two ELISA methods are specific to hEGFs and do not cross-react with mouse EGF or other growth factors (TGF alpha, TGF beta, PDGF, and FGF) or lymphokines (IL1 beta and TNF alpha). These validated methods have been routinely applied to assay of plasma samples from various pharmacokinetic studies in rats receiving intravenous hEGFs. Both assay methods were also adapted to assay endogenous hEGFs in biological fluids of different animal species. CONCLUSIONS: Two sensitive ELISA methods have been validated for quantitation of hEGF1-53 and hEGF1-48 in rat plasma. Their utility has been demonstrated in the application of assaying immunoreactive concentration of exogenous and endogenous epidermal growth factors.

Impact of receptor downregulation on clearance of two human EGFs with different receptor binding activity.

Human epidermal growth factor [hEGF(1-53)] has been thought to be cleared mainly via an EGF receptor (EGFR) endocytosis pathway. Pretreatment of rats with hEGF(1-53) has been shown previously to cause a dramatic reduction in clearance of the peptide contributable to EGFR downregulation. The impact of receptor downregulation has raised concerns for rational design of dosage regimen for this potential wound-healing therapeutic peptide. However, following a similar protocol, we could not reproduce the dramatic reduction in clearance reported previously mediated by an i.v. bolus acute dose. As EGFR downregulation may be sensitive to the length of exposure and to the activation of the receptor tyrosine kinase activity, two other pretreatment protocols were also evaluated: a 4-h i.v. infusion (prolonged exposure) of the peptide and an i.v. bolus of a potent synthetic kinase inhibitor pretreatment were evaluated for effects on clearance. However, neither pretreatment affected the peptide's clearance profile. Further, no effects on clearance and other kinetic parameters were observed for any pretreatment paradigms with a truncated analogue hEGF (1-48), whose EGF receptor binding activity is much weaker but plasma clearance is much higher than hEGF (1-53). In addition, a study in a second rat strain showed no difference in clearance profile of hEGF-(1-53) following pretreatment. Results of the present investigation suggest that receptor binding does not have a direct relationship with plasma clearance, and that the EGF clearance mechanisms is highly refractory with EGF receptors possibly recovering rapidly from downregulation through the recycling process.

Expression and purification of active recombinant platelet factor 4 from a cleavable fusion protein.

A synthetic gene for human platelet factor 4 (hPF4) has been expressed at high levels as a fusion protein in Escherichia coli. The hPF4 sequence has been cleaved from the fusion protein by cyanogen bromide treatment and purified by column chromatography. Like hPF4, our recombinant hPF4 (rhPF4) is tetrameric under physiological conditions, binds heparin, and inhibits angiogenesis. Extensive purification to remove trace amounts of uncleaved fusion protein completely from the desired product rhPF4 was difficult. We have exploited recombinant DNA technology by modifying the fusion moiety to accomplish separation. This type of modification, which did not affect expression level, could be applied to other recombinant fusion proteins.

Inhibition of chicken liver 5-aminoimidazole-4-carboxamide ribonucleotide transformylase by 5,8-dideaza analogues of folic acid.

A series of fourteen 5,8-dideaza analogues of folic and pteroic acids was evaluated for inhibition of 5-aminoimidazole-4-carboxamide ribonucleotide transformylase (AICAR TFase) from chicken liver. Of the 5,8-dideaza folate derivatives studies, 10-oxa-5,8-dideazafolic acid was the most potent inhibitor. The addition of one L-glutamate moiety to the gamma-carboxyl group caused a 6- to 7-fold reduction in Ki in three instances. Two compounds devoid of an L-glutamate were 4- to 6-fold less inhibitory than their parent counterparts possessing one L-glutamate residue.

HTLV-III/LAV-neutralizing antibodies to an E. coli-produced fragment of the virus envelope.

Immunization with either an Escherichia coli recombinant segment of the human T-cell lymphotropic virus (HTLV-III/LAV) envelope protein (gp 120) or with deglycosylated gp 120 envelope protein produced antibodies that neutralize HTLV-III/LAV infection in vitro. Virus neutralization titers of these antisera were equivalent to those obtained with purified native gp120 as immunogen. This localizes at least one class of neutralizing epitopes to the carboxyl-terminal half of the molecule. In addition, native gp120 prevented HTLV-III/LAV--mediated cell fusion, whereas the recombinant gp120 fragment did not. This shows that although glycosylation is not required for induction of neutralizing antibodies, it may be important for interaction with CD4, the virus receptor. A segment of the HTLV-III/LAV envelope produced in E. coli may be an important ingredient of a vaccine for acquired immune deficiency syndrome.

Evidence that the folate-requiring enzymes of de novo purine biosynthesis are encoded by individual mRNAs.

Isolation of the mRNAs encoding for the three folate-requiring enzymes involved in de novo purine biosynthesis followed by their in vitro translation resulted in three separate proteins electrophoretically identical with those previously isolated. The three enzymes are glycinamide ribonucleotide transformylase, 5-aminoimidazole-4-carboxamide ribonucleotide transformylase, and 5,10-methenyl-, 5,10-methylene-, and 10-formyltetrahydrofolate synthetase. Thus these enzymes do not appear to be derived from large multifunctional proteins that are then subject to proteolysis in vivo or during in vitro purification. The levels of these enzymatic activities were increased by approximately 2-fold after raising the concentration of protein in the chicken's diet. The observed response is similar to that noted for glutamine phosphoribosylpyrophosphate amidotransferase, the presumed rate-limiting enzymatic activity for this pathway. For 5-amino-imidazole-4-carboxamide ribonucleotide transformylase and the trifunctional synthetase but not glycinamide ribonucleotide transformylase the increase in enzymatic activity correlates with higher mRNA levels.

An antibody probe to determine the native species of glycinamide ribonucleotide transformylase in chicken liver.

Antibody probes of Western blots [Renart, J., Reiser, J., & Stark, G. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 3116] of chicken liver homogenates under various conditions revealed that glycinamide ribonucleotide transformylase can be rapidly proteolyzed in such homogenates. These findings, along with molecular weight measurements by ultracentrifugation, identify the true form of glycinamide ribonucleotide transformylase as a monomeric protein of 117000 daltons. This protein has been purified 400-fold in 44% yield from chicken liver in one step on an affinity column of 10-formyl-5,8-dideazafolate-Sepharose. Native glycinamide ribonucleotide transformylase retains full activity after proteolytic cleavage to a form (Mr 55000) similar to fragments seen in the Western blot of the homogenates. This phenomenon may be responsible for the previous identification of glycinamide ribonucleotide (GAR) transformylase as a dimer of 55000-dalton subunits. Similar analyses using antibodies to 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase [Mueller, W. T., & Benkovic, S. J. (1981) Biochemistry 20, 337] and trifunctional enzyme [Smith, G. K., Mueller, W. T., Wasserman, G. F., Taylor, W. D., & Benkovic, S. J. (1980) Biochemistry 19, 4313] confirm that these two proteins were isolated in their native forms.

Direct transfer of one-carbon units in the transformylations of de novo purine biosynthesis.

It is shown that the transfer of formyl units in the de novo purine biosynthetic pathway as catalyzed by glycinamide ribonucleotide (GAR) transformylase and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase probably proceeds through a direct displacement mechanism involving only formyl donor (10-CHO-H4folate) and formyl acceptor (GAR or AICAR). The inability to observe enzyme-catalyzed solvent oxygen incorporation or uncoupling by hydroxylamine of 1:1 stoichiometry between formylated acceptor [formylglycinamide ribonucleotide or 5-(formylamino)imidazole-4-carboxamide ribonucleotide] and deformylated donor implies the absence of an amidine intermediate and suggests that either a formylated enzyme-bound intermediate is not formed or such an intermediate is not accessible to hydroxylamine.

On the cofactor specificity of glycinamide ribonucleotide and 5-aminoimidazole-4-carboxamide ribonucleotide transformylase from chicken liver.

Tests of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) and glycinamide ribonucleotide (GAR) transformylase cofactor specificity were conducted with 5-and/or 8-deazafolate analogues formylated at N-10. Several of these compounds were found to serve as cofactors for both the enzymes. The finding that 10-formyl-8-deazafolate can be used by AICAR transformylase eliminates those mechanisms requiring cyclization to a methenyl derivative prior to carbon unit transfer for this transformylase. Surprisingly, a similar analogue, 10-formyl-5,8-deazafolate, is very effective as a cofactor for GAR transformylase in the presence or absence of the trifunctional protein which is required for 5,10-methenyl-H4-folate activity with this transformylase. This finding suggests that the trifunctional protein modulates GAR transformylase cofactor specificity by supplying the active cofactor as the N10-formyl species, possibly through a transport process that avoids its dissociation into solution.

On the purification and mechanism of action of 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase from chicken liver.

The transformylase from chicken liver catalyzing the formylation of 5-aminoimidazole-4-carboxamide ribonucleotide through the agency of 19-formyltetrahydrofolate has been purified to apparent homogeneity. Inosinicase activity copurifies. This transformylase is not further activated kinetically by the presence of the trifunctional protein in contrast to the glycinamide ribonucleotide transformylase. The enzyme exhibits a greater than 1000-fold preference for the naturally occurring 10-formyltetrahydrofolate cofactor and a sequential reaction pattern. A reinvestigation of the chemical structure of the formylated ribotide product employing 13C and 1H NMR indicated that the imidazole ring remained intact upon formylation, consistent with the originally proposed structure.

Characterization of the enzyme complex involving the folate-requiring enzymes of de novo purine biosynthesis.

Evidence is presented for a functional association of GAR TFase and the trifunctional protein within the protein complex consisting of GAR TFase, AICAR TFase, Ser HMase, and trifunctional protein. Resolution of the trifunctional protein from the remaining enzymes in the complex causes a loss of GAR TFase activity which is regained upon recombination. The minimum stoichiometry for GAR TFase reactivation is 3:1 GAR TFase--trifunctional protein. Determination by ultracentrifugation of the sedimentation coefficient as a function of protein concentration disclosed that the complex is in mobile equilibrium with the individual proteins. However, mixed GAR TFase--trifunctional protein species can be detected by trapping with cleavable bifunctional cross-linking reagents. Additional support for their interaction is found in the kinetic coupling of the trifunctional protein and GAR TFase activities that leads to a fourfold more efficient formation of formylglycinamide ribotide commencing with formate rather than with 5,10-methenyl-H4folate triglutamate.