QSYP peptide sequence is selected from phage display libraries by bovine IgG contaminants in monoclonal antibody preparations.

A consensus peptide sequence, QSYP, appears as an artifact during the mapping of monoclonal antibodies (MAbs) using a random peptide phage display library. Phage bearing this QSYP sequence were independently selected by four different laboratories screening separate MAb preparations with the same phage library. In each case, the QSYP sequence was selected in addition to a consensus sequence specific to the MAb. Phage that displayed the QSYP sequence were not bound by the MAb of interest, but rather bound to bovine IgG derived from the FBS present in the hybridoma growth media. The implications of this finding for the interpretation of phage library screening results and possible methods for the removal of bovine IgG from MAb preparations are discussed.

Phage display mapping for peptide 11 sensitive sequences binding to laminin-1.

We utilized a 9-mer random phage display library to identify sequences which bind to laminin-1 and elute with heparan sulfate or peptide 11 (CDPGYIGSR). Laminin-1 derivatized plates were used for biopanning. Three consecutive rounds of low pH elutions were carried out, followed by three rounds of specific elutions, each consisting of a heparan sulfate elution followed by a peptide 11 elution. The random sequence inserts were sequenced for phage populations eluted at low pH, by heparan sulfate and by peptide 11. Specifically eluted phage populations exhibited three classes of mimotopes for different regions in the cDNA derived amino acid sequence of the 67 kDa laminin binding protein (LBP). These regions were (1) a palindromic sequence known as peptide G, (2) a predicted helical domain corresponding to LBP residues 205-229, and (3) TEDWS-containing C-terminal repeats. All elution conditions also yielded phage with putative heparin binding sequences. We modeled the LBP(205-229) domain, which is strongly predicted to have a helical secondary structure, and determined that this region likely possesses heparin-binding characteristics located to one side of the helix, while the opposite side appears to contain a hydrophobic patch where peptide 11 could bind. Using ELISA plate assays, we demonstrated that peptide 11 and heparan sulfate individually bound to synthetic LBP(205-229) peptide. We also demonstrated that the QPATEDWSA peptide could inhibit tumor cell adhesion to laminin-1. These data support the proposal that the 67 kDa LBP can bind the beta-1 laminin chain at the peptide 11 region, and suggest that heparan sulfate is a likely alternate ligand for the binding interactions. Our results also confirm previous data suggesting that the most C-terminal region of the LBP, which contains the TEDWS repeats, is involved in cell adhesion to laminin-1, and we specifically implicate the repeat sequence in that activity.

NMR studies on the conformation of the CD4 36-59 peptide bound to HIV-1 gp120.

A peptide containing residues 36-59 of the human CD4 receptor includes most of the residues thought to be involved in binding the HIV surface glycoprotein, gp120. This peptide was synthesized and inhibited the binding of gp120 to soluble CD4. NMR relaxation experiments indicated that the peptide was in fast exchange between the free and gp120-bound states. Transferred NOESY NMR showed a number of long-range NOEs, from the gp120-bound state, between residues 38, 40, 45, 48, and 49 of the peptide. NMR evidence also suggested that the Phe43 in the peptide, which corresponds to a critical residue in CD4 for the binding of gp120, makes intimate contact with gp120. The Tr-NOESY cross-peak intensities provided proton-proton distance constraints on the conformation of the gp120-bound peptide. The distance constraints were used in simulated annealing, and a set of 20 very similar structures was obtained for the central region of the gp120-bound peptide. Residues 42-49 of the peptide formed a loop with the side chain of Phe43 pointing away from the rest of the peptide. This Phe43 ring points away from the protein surface in two structures of the amino-terminal domain of CD4 found by X-ray crystallography. Differences in the conformation of CD4 in the two crystal forms suggest that the 36-59 region might be flexible. The NMR data on the 36-59 CD4 peptide predicts a gp120-bound conformation different from either of the CD4 crystal forms in the absence of gp120.

In vitro effects of anti-HIV immunotoxins directed against multiple epitopes on HIV type 1 envelope glycoprotein 160.

We have used a panel of anti-gp160 MAbs to construct anti-HIV immunotoxins by coupling antibodies to ricin A chain (RAC). The ability of the immunotoxins to kill HIV-1-infected cells and halt the spread of infection was tested in tissue culture on persistently and acutely infected cell lines and primary lymphocyte cultures stimulated with phytohemagglutinin (PHA blasts). Laboratory strains and clinical isolates of HIV both were tested. The constitution and antigen-binding capacity of the immunotoxins were confirmed by ELISA and indirect immunofluorescence. Immunotoxins that bind epitopes exposed on the cell surface effectively killed persistently infected cells, although killing was not directly proportional to binding of immunotoxin to cell. The activity of anti-gp41, but not anti-gp120, immunotoxins was markedly enhanced in the presence of soluble CD4 or peptides corresponding to the CDR3 region of CD4. CD4-mediated enhancement of anti-gp41 immunotoxin activity was observed for laboratory strains neutralized by sCD4 and for clinical isolates that were resistant to neutralization by sCD4. Immunotoxin action was potentiated by brefeldin A, bafilomycin A1, cortisone, and an amphipathic fusion peptide, but not by cytochalasin D, nocodazol, monodansyl cadaverine, or trans-retinoic acid. Anti-HIV immunotoxins are useful tool with which to study the functional expression of gp120/gp41 antigens on the surface of HIV-infected cells, as well as potential AIDS therapeutics. Because these studies relate to the accessibility of viral antigens to antibody-mediated attack, these studies also have relevance for vaccine development.

The role of the leader sequence coding region in expression and assembly of bacteriorhodopsin.

Bacterio-opsin is made as a precursor in Halobacterium halobium, which has 13 additional residues at the amino terminus. The codons for these residues have been proposed to form a hairpin structure in the mRNA and play a role in ribosome binding; the leader peptide sequence also has been proposed to have a role in membrane insertion of bacteriorhodopsin (BR). We have made mutations in the bop gene region coding for the leader sequence and expressed the mutant genes in an H. halobium mutant lacking wild-type BR. The leader sequence coding region was found to be important for the stability of the mRNA and for its efficient translation. Single base substitutions in this region that did not affect the amino acid sequence caused significant reductions in protein expression. Deletion of the leader region resulted in unstable mRNA and almost no BR production. Introduction of a new ribosome-binding sequence within the coding region of the mature protein restored mRNA stability and some protein expression. Protein made without the leader peptide was properly assembled in the membrane.

RecA-assisted rapid enrichment of specific clones from model DNA libraries.

An approach to library screening is being developed, in which the desired clone is "fished" out of a mixture of all the recombinants in a library with a RecA-coated probe. In the current embodiment of this method, we used as a probe the (+) strand of an M13 phage containing a fragment of the human albumin gene and a (dA)49 stretch. We screened a library of two plasmids, one containing the same albumin fragment as the probe, and one heterologous to the probe in 50-100 fold molar excess. The plasmids were linearized. Probe and library were reacted in the presence of RecA, the mixture was loaded onto an oligo(dT) column, which retained the probe-target complex by base-pairing to the dAs of the probe, the uncaptured plasmids were washed, and the probe-target complex was released from the column, religated and propagated into E. coli. Recovery of the homologous target was 15-28%, and enrichment for the homologous plasmid was 200 to 400-fold. This approach may provide a general method for expedited DNA library screening.

Characterization of calcium-binding sites in development-specific protein S of Myxococcus xanthus using site-specific mutagenesis.

Protein S, the most abundant protein synthesized during development of the Gram-negative bacterium Myxococcus xanthus, assembles on the surface of the spores. It can be dissociated from the spores using divalent metal chelators and will reassemble on the spores in the presence of calcium. The amino acid sequence of protein S contains regions which have homology to the calcium-binding sites of calmodulin. Protein S was found to bind 2 mol of calcium/mol of protein with Kd values of 27 and 76 microM. Using oligonucleotide-directed site-specific mutagenesis, the gene coding for protein S was changed in each of two regions of homology to calmodulin (Ser40----Arg,Ser129----Arg), and a double mutant was also constructed. Each mutant gene was then transduced into the genome of a M. xanthus strain from which the wild-type genes had been deleted. All three mutants produced protein S normally during development. One of the mutants (Ser129----Arg) had normal amounts of protein S on its spores, whereas the other (Ser40----Arg) bound much less and the double mutant had virtually none. Analysis of the calcium binding affinities of the purified proteins showed that [Arg40]protein S and [Arg40, Arg129]protein S did not bind detectable quantities of calcium, whereas [Arg129]protein S bound less calcium than the wild-type protein and with a reduced affinity.

Two homologous genes coding for spore-specific proteins are expressed at different times during development of Myxococcus xanthus.

The ops and tps genes of Myxococcus xanthus have ca. 90% DNA and amino acid sequence homology and are in the same orientation separated by a spacer region of only 1.4 kilobases. The products of the two genes were found to cross-react immunologically, and both were capable of Ca2+-dependent self-assembly on the surface of myxospores. However, the ops and tps genes were expressed very differently during the developmental cycle of M. xanthus. The tps gene is induced early during fruiting body formation on a solid surface, and its product, protein S, is made in large quantities (up to 15% of total protein synthesis). When the cells turn into myxospores, protein S is assembled on the outer surface of the spore. We have now also found it in much smaller quantities inside the spores. The ops gene, on the other hand, appears to be induced later in development, after the cells have sporulated, since the ops gene product was found only inside the spores. When an ops gene under the control of a tps gene promoter was inserted into a wild-type strain, the ops gene product was synthesized at the same time as protein S and assembled onto the spore surface.

Effects of deletion of the gene for the development-specific protein S on differentiation in Myxococcus xanthus.

A deletion mutation of the gene for protein S (tps), a development-specific protein of Myxococcus xanthus, was constructed. No significant differences in the process of fruiting body formation or the yield of myxospores were observed between mutant and wild-type cells. On the other hand, when the tps gene was deleted together with a 2.0-kilobase sequence including the ops gene immediately upstream of the tps gene, fruiting body formation was substantially delayed, and the yield of myxospores was reduced. These results indicate that protein S is not essential for differentiation of M. xanthus, whereas a gene product(s) coded from the sequence upstream of the tps gene appears to be required for normal fruiting body formation.

Biogenesis of mitochondrial ubiquinol:cytochrome c reductase (cytochrome bc1 complex). Precursor proteins and their transfer into mitochondria.

The precursor proteins to the subunits of ubiquinol:cytochrome c reductase (cytochrome bc1 complex) of Neurospora crassa were synthesized in a reticulocyte lysate. These precursors were immunoprecipitated with antibodies prepared against the individual subunits and compared to the mature subunits immunoprecipitated or isolated from mitochondria. Most subunits were synthesized as precursors with larger apparent molecular weights (subunits I, 51,500 versus 50,000; subunit II, 47,500 versus 45,000; subunit IV (cytochrome c1), 38,000 versus 31,000; subunit V (Fe-S protein), 28,000 versus 25,000; subunit VII, 12,000 versus 11,500; subunit VIII, 11,600 versus 11,200). Subunit VI (14,000) was synthesized with the same apparent molecular weight. The post-translational transfer of subunits I, IV, V, and VII was studied in an in vitro system employing reticulocyte lysate and isolated mitochondria. The transfer and proteolytic processing of these precursors was found to be dependent on the mitochondrial membrane potential. In the transfer of cytochrome c1, the proteolytic processing appears to take place in two separate steps via an intermediate both in vivo and in vitro. In vivo, the intermediate form accumulated when cells were kept at 8 degrees C and was chased into mature cytochrome c1 at 25 degrees C. Both processing steps were energy-dependent.

Structure of ferric pseudobactin, a siderophore from a plant growth promoting Pseudomonas.

Both plant growth promoting Pseudomonas B10 and its yellow-green, fluorescent iron transfer agent (siderophore) pseudobactin enhance the growth of the potato and control certain phytopathogenic microorganisms. The structure of the little compound has been determined by single-crystal X-ray diffraction methods using counter data. The structure consisted of a linear hexapeptide, L-Lys-D-threo-beta-OH-Asp-L-Ala-D-allo-Thr-L-Ala-D-N delta-OH-Orn, in which the N delta-OH nitrogen of the ornithine was cyclized with the C-terminal carboxyl group, and the N epsilon-amino group of the lysine was linked via an amide bond to a fluorescent quinoline derivative. The iron-chelating groups consisted of a hydroxamate group derived from N delta-hydroxyornithine, an alpha-hydroxy acid derived from beta-hydroxyaspartic acid, and an o-dihydroxy aromatic group derived from the quinoline moiety. The combination of metal-chelating ligands and the alternating L- and D-amino acids was unusual. The little compound crystallized as a single coordination isomer with the lambda absolute configuration. The present study is the first structural determination of a fluorescent siderophore. In the crystal structure, ferric pseudobactin formed a dimer, which constituted the asymmetric unit. The asymmetric unit also contained 26 water molecules. The molecules in the dimer were related by a pseudo-2-fold symmetry axis. Red-brown crystals of ferric pseudobactin (C42H57N12O16Fe . 13H2O), obtained from pyridine-acetic acid buffer solution equilibrated with water, conformed to space group I2 with a = 29.006 (23) A, b = 14.511 (13) A, c = 28.791 (21) A, and beta = 96.06 (5) degrees at -135 (2) degrees C. For eight molecules per unit cell, the calculated density was 1.38 g/cm3; the observed density was 1.40 g/cm3. The structure was refined by least-squares methods with anisotropic thermal parameters for all nonhydrogen atoms to a final R factor of 0.08 (8989 observed reflections).

Structure of pseudobactin A, a second siderophore from plant growth promoting Pseudomonas B10.

The structure of nonfluorescent pseudobactin A, one of two extracellular siderophores (microbial iron transport agents) produced by the plant growth promoting bacterium Pseudomonas B10, was determined by comparison of its 1H and 13C NMR spectra with those of yellow-green, fluorescent pseudobactin, the other siderophore. The molecular and crystal structure of ferric pseudobactin is reported in the preceding paper in this issue [Teintze, M., Hossain, M. B., Barnes, C. L., Leong J., & van der Helm, D. (1981) Biochemistry (preceding paper in this issue)]. The only structural difference between pseudobactin and pseudobactin A was that the latter was saturated at carbons 3 and 4 of the quinoline derivative, whereas pseudobactin is unsaturated at these positions. A mechanism is proposed for the observed conversion of pseudobactin A into pseudobactin in aqueous solution.

Spectroscopic studies of the nature of ligand bonding in carbonmonoxyhemoglobins: evidence of a specific function for histidine-E7 from infrared and nuclear magnetic resonance intensities.

Infrared spectra of carbon monoxide ligated hemoglobins from human, horse, and rabbit donors have been examined. A single vibrational frequency at 1951 cm-1 is observed for CO bound to the heme in horse and human hemoglobins. Studies of the isolated alpha-CO and beta-CO subunits of human hemoglobin reveal that the observation of a single frequency in the intact tetramer is the result of a superposition of the alpha-CO and beta-CO vibrational frequencies. The apparent integrated absorption intensities of these CO vibrations are shown both to have values of 1.0 X 10(5)M-1cm-2 within experimental error. For rabbit CO-Hb two vibrational frequencies appear (Caughey, W. S., et al. (1973) Fed. Proc., Fed. Am. Soc. Exp. Biol. 32, 552) and are assigned to CO bound to the beta (1951 cm-1) and alpha(1928 cm-1) subunits within the intact tetramer. The beta-CO subunit exhibits both frequency and intensity similarities with horse and human hemoglobins. The rabbit alpha-CO subunit, however, exhibits a markedly lower frequency and much smaller intensity compared with the other CO-hemoglobins. These data are interpreted in terms of a specific role for the distal histidine (E7) in rabbit alpha subunits, in which this histidine functions as a nucleophilic donor to coordinated CO.