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Pogodaev AA, Fernández Regueiro CL, Jakštaitė M, Hollander MJ, Huck WTS. Modular Design of Small Enzymatic Reaction Networks Based on Reversible and Cleavable Inhibitors. Angew Chem Int Ed Engl 2019; 58:14539-14543. [DOI: 10.1002/anie.201907995] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Aleksandr A. Pogodaev
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | | | - Miglė Jakštaitė
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Marijn J. Hollander
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
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2
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Pogodaev AA, Fernández Regueiro CL, Jakštaitė M, Hollander MJ, Huck WTS. Modular Design of Small Enzymatic Reaction Networks Based on Reversible and Cleavable Inhibitors. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Aleksandr A. Pogodaev
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | | | - Miglė Jakštaitė
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Marijn J. Hollander
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
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3
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Iegre J, Gaynord JS, Robertson NS, Sore HF, Hyvönen M, Spring DR. Two-Component Stapling of Biologically Active and Conformationally Constrained Peptides: Past, Present, and Future. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jessica Iegre
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | | | | | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | - Marko Hyvönen
- Department of Biochemistry; University of Cambridge; Cambridge CB2 1GA UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
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4
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Identification of peptide inhibitors of penicillinase using a phage display library. Anal Biochem 2016; 494:4-9. [DOI: 10.1016/j.ab.2015.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/18/2015] [Accepted: 10/21/2015] [Indexed: 12/20/2022]
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Selection of High-Affinity Peptidic Serine Protease Inhibitors with Increased Binding Entropy from a Back-Flip Library of Peptide-Protease Fusions. J Mol Biol 2015; 427:3110-22. [PMID: 26281711 DOI: 10.1016/j.jmb.2015.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/19/2015] [Accepted: 08/07/2015] [Indexed: 11/21/2022]
Abstract
We have developed a new concept for designing peptidic protein modulators, by recombinantly fusing the peptidic modulator, with randomized residues, directly to the target protein via a linker and screening for internal modulation of the activity of the protein. We tested the feasibility of the concept by fusing a 10-residue-long, disulfide-bond-constrained inhibitory peptide, randomized in selected positions, to the catalytic domain of the serine protease murine urokinase-type plasminogen activator. High-affinity inhibitory peptide variants were identified as those that conferred to the fusion protease the lowest activity for substrate hydrolysis. The usefulness of the strategy was demonstrated by the selection of peptidic inhibitors of murine urokinase-type plasminogen activator with a low nanomolar affinity. The high affinity could not have been predicted by rational considerations, as the high affinity was associated with a loss of polar interactions and an increased binding entropy.
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6
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Distinctive binding modes and inhibitory mechanisms of two peptidic inhibitors of urokinase-type plasminogen activator with isomeric P1 residues. Int J Biochem Cell Biol 2015; 62:88-92. [DOI: 10.1016/j.biocel.2015.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/02/2014] [Accepted: 02/23/2015] [Indexed: 01/29/2023]
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7
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The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.54] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Roodbeen R, Paaske B, Jiang L, Jensen JK, Christensen A, Nielsen JT, Huang M, Mulder FAA, Nielsen NC, Andreasen PA, Jensen KJ. Bicyclic Peptide Inhibitor of Urokinase-Type Plasminogen Activator: Mode of Action. Chembiochem 2013; 14:2179-88. [DOI: 10.1002/cbic.201300335] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Indexed: 01/24/2023]
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9
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Menegatti S, Hussain M, Naik AD, Carbonell RG, Rao BM. mRNA display selection and solid-phase synthesis of Fc-binding cyclic peptide affinity ligands. Biotechnol Bioeng 2012; 110:857-70. [DOI: 10.1002/bit.24760] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 12/25/2022]
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The Binding Mechanism of a Peptidic Cyclic Serine Protease Inhibitor. J Mol Biol 2011; 412:235-50. [DOI: 10.1016/j.jmb.2011.07.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 07/08/2011] [Accepted: 07/14/2011] [Indexed: 11/19/2022]
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11
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Hosseini M, Jiang L, Sørensen HP, Jensen JK, Christensen A, Fogh S, Yuan C, Andersen LM, Huang M, Andreasen PA, Jensen KJ. Elucidation of the Contribution of Active Site and Exosite Interactions to Affinity and Specificity of Peptidylic Serine Protease Inhibitors Using Non-Natural Arginine Analogs. Mol Pharmacol 2011; 80:585-97. [DOI: 10.1124/mol.111.072280] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Liu T, Joo SH, Voorhees JL, Brooks CL, Pei D. Synthesis and screening of a cyclic peptide library: discovery of small-molecule ligands against human prolactin receptor. Bioorg Med Chem 2008; 17:1026-33. [PMID: 18234500 DOI: 10.1016/j.bmc.2008.01.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/09/2008] [Accepted: 01/10/2008] [Indexed: 11/18/2022]
Abstract
Prolactin receptor is involved in normal lactation and reproduction; however, excessive prolactin levels can cause various reproductive disorders such as prolactinomas. Small-molecule antagonists against the human prolactin receptor (hPRLr) thus have potential clinical applications and may serve as useful molecular probes in biomedical research. In this work, we synthesized a large, support-bound cyclic peptide library (theoretical diversity of 1.2x10(7)) on 90-microm TentaGel beads and screened it against the extracellular domain of hPRLr. To facilitate hit identification, each TentaGel bead was spatially segregated into outer and inner layers, with a cyclic peptide displayed on the bead surface while the bead interior contained the corresponding linear peptide. The identity of a positive bead was revealed by sequencing the linear encoding peptide within the bead by partial Edman degradation/mass spectrometry. Screening of the library resulted in 20 hits, two of which were selected for further analysis and shown to bind to hPRLr with dissociation constants of 2-3 microM.
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Affiliation(s)
- Tao Liu
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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Farady CJ, Sun J, Darragh MR, Miller SM, Craik CS. The mechanism of inhibition of antibody-based inhibitors of membrane-type serine protease 1 (MT-SP1). J Mol Biol 2007; 369:1041-51. [PMID: 17475279 PMCID: PMC2041882 DOI: 10.1016/j.jmb.2007.03.078] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Accepted: 03/20/2007] [Indexed: 11/28/2022]
Abstract
The mechanisms of inhibition of two novel scFv antibody inhibitors of the serine protease MT-SP1/matriptase reveal the basis of their potency and specificity. Kinetic experiments characterize the inhibitors as extremely potent inhibitors with K(I) values in the low picomolar range that compete with substrate binding in the S1 site. Alanine scanning of the loops surrounding the protease active site provides a rationale for inhibitor specificity. Each antibody binds to a number of residues flanking the active site, forming a unique three-dimensional binding epitope. Interestingly, one inhibitor binds in the active site cleft in a substrate-like manner, can be processed by MT-SP1 at low pH, and is a standard mechanism inhibitor of the protease. The mechanisms of inhibition provide a rationale for the effectiveness of these inhibitors, and suggest that the development of specific antibody-based inhibitors against individual members of closely related enzyme families is feasible, and an effective way to develop tools to tease apart complex biological processes.
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Affiliation(s)
- Christopher J Farady
- Graduate Group in Biophysics, University of California, San Francisco, 600 16th St. Genentech Hall, San Francisco, CA 94143, USA
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Faraj JA, Dorati R, Schoubben A, Worthen D, Selmin F, Capan Y, Leung K, DeLuca PP. Development of a peptide-containing chewing gum as a sustained release antiplaque antimicrobial delivery system. AAPS PharmSciTech 2007; 8:26. [PMID: 17408225 PMCID: PMC2750437 DOI: 10.1208/pt0801026] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 02/02/2007] [Indexed: 11/30/2022] Open
Abstract
The objective of this study was to characterize the stability of KSL-W, an antimicrobial decapeptide shown to inhibit the growth of oral bacterial strains associated with caries development and plaque formation, and its potential as an antiplaque agent in a chewing gum formulation. KSL-W formulations with or without the commercial antibacterial agent cetylpyridinium chloride (CPC) were prepared. The release of KSL-W from the gums was assessed in vitro using a chewing gum apparatus and in vivo by a chew-out method. A reverse-phase high-performance liquid chromatography method was developed for assaying KSL-W. Raw material stability and temperature and pH effects on the stability of KSL-W solutions and interactions of KSL-W with tooth-like material, hydroxyapatite discs, were investigated. KSL-W was most stable in acidic aqueous solutions and underwent rapid hydrolysis in base. It was stable to enzymatic degradation in human saliva for 1 hour but was degraded by pancreatic serine proteases. KSL-W readily adsorbed to hydroxyapatite, suggesting that it will also adsorb to the teeth when delivered to the oral cavity. The inclusion of CPC caused a large increase in the rate and extent of KSL-W released from the gums. The gum formulations displayed promising in vitro/in vivo release profiles, wherein as much as 90% of the KSL-W was released in a sustained manner within 30 minutes in vivo. These results suggest that KSL-W possesses the stability, adsorption, and release characteristics necessary for local delivery to the oral cavity in a chewing gum formulation, thereby serving as a novel antiplaque agent.
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Affiliation(s)
- Jabar A. Faraj
- />Faculty of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY
| | - Rossella Dorati
- />Department of Medicinal Chemistry, University of Pavia, Italy
| | - Aurélie Schoubben
- />Department of Chemistry and Technology of Drugs, University of Perugia, Italy
| | - David Worthen
- />Faculty of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY
| | - Francesca Selmin
- />Institute of Medicinal Chemistry and Toxicology University of Milan, Italy
| | - Yilmaz Capan
- />Department of Pharmaceutical Technology, Faculty of Pharmacy, Hacettepe University, 06100 Ankara, Turkey
| | - Kai Leung
- />Microbiology Branch, US Army Dental and Trauma Research Detachment, Walter Reed Army Institute of Research, Great Lakes, IL
| | - Patrick P. DeLuca
- />Faculty of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY
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Hansen M, Wind T, Blouse GE, Christensen A, Petersen HH, Kjelgaard S, Mathiasen L, Holtet TL, Andreasen PA. A Urokinase-type Plasminogen Activator-inhibiting Cyclic Peptide with an Unusual P2 Residue and an Extended Protease Binding Surface Demonstrates New Modalities for Enzyme Inhibition. J Biol Chem 2005; 280:38424-37. [PMID: 16141208 DOI: 10.1074/jbc.m505933200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To find new principles for inhibiting serine proteases, we screened phage-displayed random peptide repertoires with urokinase-type plasminogen activator (uPA) as the target. The most frequent of the isolated phage clones contained the disulfide bridge-constrained sequence CSWRGLENHRMC, which we designated upain-1. When expressed recombinantly with a protein fusion partner, upain-1 inhibited the enzymatic activity of uPA competitively with a temperature and pH-dependent K(i), which at 25 degrees C and pH 7.4 was approximately 500 nm. At the same conditions, the equilibrium dissociation constant K(D), monitored by displacement of p-aminobenzamidine from the specificity pocket of uPA, was approximately 400 nm. By an inhibitory screen against other serine proteases, including trypsin, upain-1 was found to be highly selective for uPA. The cyclical structure of upain-1 was indispensable for uPA binding. Alanine-scanning mutagenesis identified Arg(4) of upain-1 as the P(1) residue and indicated an extended binding interaction including the specificity pocket and the 37-, 60-, and 97-loops of uPA and the P(1), P(2), P(3)', P(4)', and the P(5)' residues of upain-1. Substitution with alanine of the P(2) residue, Trp(3), converted upain-1 into a distinct, although poor, uPA substrate. Upain-1 represents a new type of uPA inhibitor that achieves selectivity by targeting uPA-specific surface loops. Most likely, the inhibitory activity depends on its cyclical structure and the unusual P(2) residue preventing the scissile bond from assuming a tetrahedral geometry and thus from undergoing hydrolysis. Peptide-derived inhibitors such as upain-1 may provide novel mechanistic information about enzyme-inhibitor interactions and alternative methodologies for designing effective protease inhibitors.
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Affiliation(s)
- Martin Hansen
- Department of Molecular Biology, University of Aarhus, Gustav Wied's Vej 10C, 8000 Aarhus C, Denmark
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Wu P, Leinonen J, Koivunen E, Lankinen H, Stenman UH. Identification of novel prostate-specific antigen-binding peptides modulating its enzyme activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:6212-20. [PMID: 11012675 DOI: 10.1046/j.1432-1327.2000.01696.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Prostate-specific antigen (PSA) is a serine protease with highly prostate-specific expression. Measurement of PSA in serum is widely used for diagnosis and monitoring of prostate cancer. PSA dissolves the seminal gel forming after ejaculation. It has been suggested to mediate invasion and metastasis of prostate cancer but also to exert antiangiogenic activity. We have identified peptides specific for PSA by screening cyclic phage display peptide libraries. PSA-binding peptides were isolated from four different libraries and produced as a fusion protein with glutathione S-transferase (GST). The phage and fusion proteins were shown to bind to PSA specifically as indicated by lack of binding to other serine proteinases. A peptide with four cysteines showed the highest affinity for PSA. Zn2+, an inhibitor of PSA activity, increased the affinity of the peptides to PSA. The binding specificity was characterized by cross-inhibition using monoclonal anti-PSA antibodies of known epitope specificities. The peptides bound to the same region as mAbs specific for free PSA indicating that they bind close to the active site of the enzyme. The peptides enhanced the enzyme activity of PSA against a chromogenic substrate. These results show that peptides binding to PSA and modulating its enzyme activity can be developed by phage display technique. The peptides have the potential to be used for identification of PSA variants and for imaging and targeting of prostatic tumors.
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Affiliation(s)
- P Wu
- Department of Clinical Chemistry, Helsinki University Central Hospital, Finland
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Koivunen E, Arap W, Valtanen H, Rainisalo A, Medina OP, Heikkilä P, Kantor C, Gahmberg CG, Salo T, Konttinen YT, Sorsa T, Ruoslahti E, Pasqualini R. Tumor targeting with a selective gelatinase inhibitor. Nat Biotechnol 1999; 17:768-74. [PMID: 10429241 DOI: 10.1038/11703] [Citation(s) in RCA: 397] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Several lines of evidence suggest that tumor growth, angiogenesis, and metastasis are dependent on matrix metalloproteinase (MMP) activity. However, the lack of inhibitors specific for the type IV collagenase/gelatinase family of MMPs has thus far prevented the selective targeting of MMP-2 (gelatinase A) and MMP-9 (gelatinase B) for therapeutic intervention in cancer. Here, we describe the isolation of specific gelatinase inhibitors from phage display peptide libraries. We show that cyclic peptides containing the sequence HWGF are potent and selective inhibitors of MMP-2 and MMP-9 but not of several other MMP family members. Our prototype synthetic peptide, CTTHWGFTLC, inhibits the migration of human endothelial cells and tumor cells. Moreover, it prevents tumor growth and invasion in animal models and improves survival of mice bearing human tumors. Finally, we show that CTTHWGFTLC-displaying phage specifically target angiogenic blood vessels in vivo. Selective gelatinase inhibitors may prove useful in tumor targeting and anticancer therapies.
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Affiliation(s)
- E Koivunen
- Department of Biosciences, Division of Biochemistry, Viikinkaari 5, University of Helsinki, FIN-00014, Finland
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Krook M, Mosbach K, Ramström O. Novel peptides binding to the Fc-portion of immunoglobulins obtained from a combinatorial phage display peptide library. J Immunol Methods 1998; 221:151-7. [PMID: 9894906 DOI: 10.1016/s0022-1759(98)00177-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptides interacting with the Fc portion of human IgG (IgG Fc) were selected from a phage display decapeptide library. The library was selected five times and interacting phage peptides were eluted either with Staphylococcal protein A or at low pH. Individual peptide phage clones were found to interact more strongly with IgG Fc than did either the original library or the wild-type phage. Increasing concentrations of protein A could competitively reduce the interaction of a peptide phage clone (FARLVSSIRY) eluted with protein A to the same level as the original library. Furthermore, when immunoglobulins from chicken, donkey, human, mouse, swine, rabbit, and sheep were included, peptide phage clones FGRLVSSIRY and TWKTSRISIF interacted strongly with human IgG Fc and porcine IgG and weakly with the immunoglobulins obtained from the other species.
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Affiliation(s)
- M Krook
- Pure and Applied Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Sweden.
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