Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
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Four different proteases were screened for their capability of selectively digesting murine monoclonal IgGl to obtain active F(ab)2. For the screening, a series of five different mouse monoclonal antibodies (IgGl, k) was used, recognizing different tumor-associated antigens and currently used for radioimmunoimaging studies. The enzymes (pepsin, bromelain, ficin and elastase) showed different fragmentation capability and the fragments obtained showed different stability and immunoreactivity. No digestion was noticed using elastase. Pepsin gave discontinuous results, in that its activity ranged from reduction of IgG to small inactive fragments to an inability to digest the immunoglobulin. Pepsin activity was strongly pH-dependent and immunoreactivity of the obtained fragments was not always conserved. Bromelain and, in particular, ficin gave excellent results. Digestion was always rapid and stable, all five MAbs were reduced to F(ab)2 in a comparable time range and with high yields. Moreover, ficin-obtained F(ab)2 showed a highly conserved immunoreactivity. Therefore, ficin was selected as the murine monoclonal IgGl digestion enzyme to obtain active bivalent antibody fragments. The digestion procedure gave a uniform result for all five different MAbs and was easily scaled up to produce hundreds of milligrams of F(ab)2.
Mol Immunol
PMID:A new enzymatic method to obtain high-yield F(ab)2 suitable for clinical use from mouse IgGl. 201 Nov 30

The molecular structure of porcine pepsinogen at 1.8 A resolution has been determined by a combination of molecular replacement and multiple isomorphous phasing techniques. The resulting structure was refined by restrained-parameter least-squares methods. The final R factor [formula: see text] is 0.164 for 32,264 reflections with I greater than or equal to sigma (I) in the resolution range of 8.0 to 1.8 A. The model consists of 2785 protein atoms in 370 residues, a phosphoryl group on Ser68 and 238 ordered water molecules. The resulting molecular stereochemistry is consistent with a well-refined crystal structure with co-ordinate accuracy in the range of 0.10 to 0.15 A for the well-ordered regions of the molecule (B less than 15 A2). For the enzyme portion of the zymogen, the root-mean-square difference in C alpha atom co-ordinates with the refined porcine pepsin structure is 0.90 A (284 common atoms) and with the C alpha atoms of penicillopepsin it is 1.63 A (275 common atoms). The additional 44 N-terminal amino acids of the prosegment (Leu1p to Leu44p, using the letter p after the residue number to distinguish the residues of the prosegment) adopt a relatively compact structure consisting of a long beta-strand followed by two approximately orthogonal alpha-helices and a short 3(10)-helix. Intimate contacts, both electrostatic and hydrophobic interactions, are made with residues in the pepsin active site. The N-terminal beta-strand, Leu1p to Leu6p, forms part of the six-stranded beta-sheet common to the aspartic proteinases. In the zymogen the first 13 residues of pepsin, Ile1 to Glu13, adopt a completely different conformation from that of the mature enzyme. The C alpha atom of Ile1 must move approximately 44 A in going from its position in the inactive zymogen to its observed position in active pepsin. Electrostatic interactions of Lys36pN and hydrogen-bonding interactions of Tyr37pOH, and Tyr90H with the two catalytic aspartate groups, Asp32 and Asp215, prevent substrate access to the active site of the zymogen. We have made a detailed comparison of the mammalian pepsinogen fold with the fungal aspartic proteinase fold of penicillopepsin, used for the molecular replacement solution. A structurally derived alignment of the two sequences is presented.
J Mol Biol 1991 Jun 20
PMID:Refined structure of porcine pepsinogen at 1.8 A resolution. 205 34

The molecular structure of the archetypal aspartic proteinase, porcine pepsin (EC 3.4.23.1), has been refined using data collected from a single monoclinic crystal on a twin multiwire detector system to 1.8 A resolution. The current crystallographic R-factor (= sigma parallel to Fo/-/Fc parallel to/sigma/Fo/) is 0.174 for the 20,519 reflections with /Fo/ greater than or equal to 3 sigma (Fo) in the range 8.0 to 1.8 A (/Fo/ and /Fc/ are the observed and calculated structure factor amplitudes respectively). The refinement has shown conclusively that there are only 326 amino acid residues in porcine pepsin. Ile230 is not present in the molecule. The two catalytic residues Asp32 and Asp215 have dispositions in porcine pepsin very similar to the dispositions of the equivalent residues in the other aspartic proteinases of known structure. A bound solvent molecule is associated with both carboxyl groups at the active site. No bound ethanol molecule could be identified conclusively in the structure. The average thermal motion parameter of the residues that comprise the C-terminal domain of pepsin is approximately twice that of the residues in the N-terminal domain. Comparisons of the tertiary structure of pepsin with porcine pepsinogen, penicillopepsin, rhizopus pepsin and endothia pepsin reveal that the N-terminal domains are topographically more similar than the conformationally flexible C-terminal domains. The conformational differences may be modeled as rigid-body movements of "reduced" C-terminal domains (residues 193 to 212 and 223 to 298 in pepsin numbering). A similar movement of the C-terminal domain of endothia pepsin has been observed upon inhibitor binding. A phosphoryl group covalently attached to Ser68 O gamma has been identified in the electron density map of porcine pepsin. The low pKa1 value for this group, coupled with unusual microenvironments for several of the aspartyl carboxylate groups, ensures a net negative charge on porcine pepsin in a strongly acid medium. Thus, there is a structural explanation for the very early observations of "anodic migration" of porcine pepsin at pH 1. In the crystals, the molecules are packed tightly into a monoclinic unit cell. There are 190 direct contacts (less than or equal to 4.0 A) between a central pepsin molecule and the five unique symmetry-related molecules surrounding it in the crystalline lattice. The tight packing in this cell makes pepsin's active site and binding cleft relatively inaccessible to substrate analogs or inhibitors.
J Mol Biol 1990 Jul 05
PMID:Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution. 211 87

The molecular structure of the hexagonal crystal form of porcine pepsin (EC 3.4.23.1), an aspartic proteinase from the gastric mucosa, has been determined by molecular replacement using the fungal enzyme, penicillopepsin (EC 3.4.23.6), as the search model. This defined the space group as P6522 and refinement led to an R-factor of 0.190 at 2.3 A resolution. The positions of 2425 non-hydrogen protein atoms in 326 residues have been determined and the model contains 371 water molecules. The structure is bilobal, consisting of two predominantly beta-sheet lobes which, as in other aspartic proteinases, are related by a pseudo 2-fold axis. The strands of the mixed beta-sheets (1N and 1C) of each lobe are related by an intra-lobe topological 2-fold symmetry. Two further beta-sheets, 2N and 2C, are each composed of two topologically related beta-hairpins folded below the 1N and 1C sheets. A further six-stranded sheet (3) spans the two lobes and forms a structure resembling an arch upon which the four other sheets reside. The interface between sheets 1N and 1C forms the catalytic centre consisting of absolutely conserved aspartate residues 32 and 215, which are shielded from solvent by a beta-hairpin loop (75 to 78). The crystal structure of a mammalian aspartic proteinase indicates that interactions with substrate may be more extensive on the prime side of the active site cleft than in the fungal enzymes and involve Tyr189 and the loop 290 to 295, perhaps contributing to the transpeptidase activity of pepsin and the specificity of the renins. Comparison with the high-resolution structure of pepsinogen gives a root-mean-square deviation of 0.9 A and reveals that, in addition to local rearrangement at the active site, there appears to be a rigid group movement of part of the C-terminal lobe of pepsin towards the cleft on activation. A large proportion of the absolutely conserved residues in aspartic proteinases are polar and buried. An examination of the pepsin structure reveals that these side-chains are involved in hydrogen-bond interactions with either the main chain of the protein or other conserved side-chains of the enzyme or propart.
J Mol Biol 1990 Jul 05
PMID:X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution. 211 88

Macrophages are thought to participate in tissue repair following injury by releasing growth factors into the local environment. To evaluate whether pulmonary macrophages can mediate airway epithelial repair, we attempted to determine if pulmonary macrophages can stimulate growth of bovine bronchial epithelial cells in vitro. Bronchial epithelial cells isolated by protease digestion of the bovine bronchi were plated into tissue culture dishes with and without macrophage-conditioned medium. Bronchial epithelial cells cultured with macrophage-conditioned medium showed a significantly greater cell growth than those without macrophage-conditioned medium when assessed by direct enumeration of the cell numbers and by clonal growth assay. Stimulation of proliferation was confirmed by autoradiography using [3H]thymidine uptake into cell nuclei. Co-culture of pulmonary macrophages with bronchial epithelial cells also led to an increase in cell number. Immunohistochemical staining of the proliferating cells showed that these cells were positively stained by anti-keratin antibodies confirming that they were bronchial epithelial cells. Partial characterization of the activity in macrophage-conditioned medium showed that it was nondialyzable, pepsin- and acid-labile, and lipid-inextractable. Sephadex G-75 column fractionation indicated this activity existed in a high molecular fraction, thus suggesting a peptide. DEAE ion exchange chromatography revealed 3 peaks of stimulating activity. One peak resulted in a decrease in cell number, suggesting a possible inhibitory activity. The DEAE results thus suggest that macrophages may release several factors that can affect bronchial epithelial cell proliferation. In conclusion, pulmonary macrophages stimulate cell proliferation of bronchial epithelial cells in vitro. The stimulatory activity that may be heterogeneous appears to have the properties of a peptide.
Am J Respir Cell Mol Biol 1990 Mar
PMID:Pulmonary macrophages can stimulate cell growth of bovine bronchial epithelial cells. 217 48

Chemically and enzymatically modified kappa chains were tested by inhibition radioimmunoassay for their ability to block the binding of antibody K-1-21 with native kappa chains. Complete reduction and carboxymethylation of intrachain disulphide bonds destroyed the free kappa-chain epitope, a result confirmed by Western blotting of unreduced and reduced kappa monomers and dimers. Purified V kappa fragments failed to block the homologous interaction while inhibition was obtained with a pepsin digest yielding predominantly the C kappa region. Dimeric kappa chains were less effective than monomers in the inhibition assay, although HPLC analysis of immune complexes demonstrated the binding of two antibody molecules per molecule of dimer. Thus, the epitope on free kappa chains recognized by K-1-21 is dependent upon conformational integrity of the C kappa domain, the decreased binding activity of dimeric chains possibly being due to minor conformational changes induced by C-domain interactions.
Mol Immunol 1985 Dec
PMID:Conformation dependence of a monoclonal antibody defined epitope on free human kappa chains. 242 Nov 54

Monoclonal antibodies were made against a truncated form of human laminin isolated from placenta. 12 antibodies were isolated and characterized. All antibodies stained basement membranes in placenta and immunoprecipitated laminin from media of cultured choriocarcinoma cells. Three antibodies, 3E5, 4C7, and 4E10, partially blocked the neurite-promoting activity of laminin. Addition of a second antibody, goat anti-mouse IgG, caused more complete blocking of the activity. Two of the blocking antibodies, 4C7 and 4E10, reacted with epitopes within the globular domain at the end of the long arm of laminin, and the third one, 3E5, reacted at the end of the rod-like portion of the long arm adjacent to the globular domain, as shown by electron microscopy after rotary shadowing. Five nonblocking antibodies used in the same test reacted with epitopes in other domains of the molecule. Blocking antibodies 3E5 and 4E10 could be used in immunoblotting and both antibodies reacted with the same polypeptides in pepsin fragments of human laminin, the predominant polypeptides being approximately 400 kD. When a crude extract of human amnion was used as a source of intact laminin, the 4E10 antibody detected a single polypeptide of approximately 400 kD. A nonblocking antibody, 2E8, which reacted at the center of the laminin cross, reacted predominantly with a 200-kD polypeptide in human laminin fragments and exclusively with a 200-kD polypeptide in amnion extract and in rat laminin. Our results with human laminin match the results by Edgar, D., R. Timpl, and H. Thoenen, 1984, EMBO (Eur. Mol. Biol. Organ.) J., 3:1463-1468, in which the neurite-promoting activity of mouse laminin resides at the end of the long arm, which is also the site for heparin binding. However, since the active fragments of human laminin did not bind to heparin, the neurite-promoting site should be different from the heparin-binding site. Our results further suggest that the neurite-promoting site may be contained in or close to the 400-kD component of laminin.
 ...
PMID:Mapping of domains in human laminin using monoclonal antibodies: localization of the neurite-promoting site. 243 Sep 84

The characterization of the major antigenic determinants present in human protamine P1 has been carried out by the use of specific rabbit polyclonal and mouse monoclonal antisera raised against protamine P1. This basic protein, the full amino acid sequence of which has been determined here, has been cleaved by cyanogen bromide and/or by pepsin to generate a discrete number of peptides. These have been purified, characterized by partial amino acid sequencing and used for the determination of their antigenic reactivities with antisera to native protamine P1. Both rabbit polyclonal and mouse monoclonal antibodies were able to recognize the NH2-terminal CNBr peptide encompassing residues 1-36 to the same extent as the intact protamine. A minor epitope present on the COOH-terminal peptide 37-50 could be detected only with the polyclonal rabbit antisera. Attempts to further cleave the P1 molecule in order to isolate peptides shorter than fragments 1-36 whilst retaining full antigenic reactivities, were unsuccessful. This suggests that the epitopes in P1 are conformation-dependent and located for the most part on the amino-terminal half of the molecule, which comprises the characteristic central arginine cluster. The implication of these findings for the studies of the specificities of autoantibodies in sera from infertile and vasectomized individuals is discussed.
Mol Immunol 1988 Apr
PMID:Detection of the major epitopes of human protamine P1 recognized by rabbit and mouse antibodies. 245 55

By sequencing lysozymes c from deer and pig stomachs and comparing them to the known amino acid sequences of other lysozymes c, it was possible to examine the rate of sequence change during and after the period in which this enzyme acquired a new function. Evolutionary tree analysis suggests that the rate went up while lysozyme was being recruited to function as a digestive enzyme in the stomach of early ruminants. Later, presumably after lysozyme was well adapted for functioning in the new environment, which contains acid, pepsin, and fermentation products, the rate of amino acid replacement became subnormal.
J Mol Evol 1989 Jun
PMID:Episodic evolution in the stomach lysozymes of ruminants. 250 28

The interaction between the epithelial cells and the subjacent mesenchymal cells in the airway is thought to play a major role during tissue repair after airway injury and lung morphogenesis. To evaluate this interaction, we cultured human lung fibroblasts, and bovine and human bronchial epithelial cells, and determined that bronchial epithelial cell-conditioned medium has a chemotactic activity for lung fibroblasts. This activity had the characteristics of protein: it was nondialyzable, heat-labile, pepsin-labile, acid-stable, and lipid-inextractable. Molecular sieve chromatography on Sephadex G-150 and affinity chromatography on gelatin-Sepharose revealed that there was one peak of chemotactic activity in high molecular weight range, which bound to gelatin, thus suggesting that the chemotactic factor might be fibronectin. Production and secretion of fibronectin into the culture media were demonstrated by biosynthetic incorporation of radioactive amino acid into fibronectin followed by immunoprecipitation on SDS-PAGE and autoradiography. Release into the culture medium was confirmed by ELISA. The identity of fibronectin as the chemotactic activity was confirmed by the addition of antifibronectin antibody to the conditioned medium, which inhibited chemotaxis in dose-dependent manner. Thus, bronchial epithelial cells produce fibronectin which can function as a chemotactic factor for lung fibroblasts. This production of fibronectin by bronchial epithelial cells may play an important role in regulating interaction between the bronchial epithelial cells that line the lumenal surface of the bronchial epithelial wall and the mesenchymal fibroblasts that underlie the bronchial epithelial basement membrane.
Am J Respir Cell Mol Biol 1989 Jul
PMID:Bronchial epithelial cells produce lung fibroblast chemotactic factor: fibronectin. 262 56


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