Applications of the Ph.D. Phage Display Peptide Libraries
| General methods |
| Antimicrobial peptides |
| Antiviral peptides |
| Cell-targeting peptides |
| Computer analysis |
| Construction of custom libraries in M13KE |
| Epitope mapping/Vaccine development |
| In vivo panning |
| Inhibitors of protein folding |
| Inhibitors/modulators of enzyme activity/specificity |
| Material-specific peptides |
| Mirror image phage display |
| Peptide ligands for affinity chromatography |
| Peptide mimics of non-peptide ligands |
| Protein modification-specific peptides |
| Receptor-specific peptides (purified receptor panning) |
| Receptor-specific peptides (whole cell panning) |
| Small molecule-binding peptides |
General methods
Kay, B.K. et al. (2001) "Screening phage-displayed combinatorial peptide libraries."Methods24, 240-246. Messmer, B.T. et al. (2000) "Sequential determination of ligands binding to discrete components in heterogeneous mixtures by iterative panning and blocking (IPAB)." J. Mol. Biol.296, 821-832. Messmer, B.T. and D.S. Thaler (2001) "Specific blocking to improve biopanning in biological samples such as serum and hybridoma supernatants." Biotechniques30, 798-802. Noren, K.A. and C.J. Noren (2001) "Construction of high-complexity combinatorial phage display peptide libraries." Methods23, 169-178. Noren, K.A. et al. (2000) "Construction and use of pIII-displayed peptide libraries." Phage Display: A Laboratory Manual. Cold Spring Harbor Laboratory Press, 19.1-19.41. Rahim, A. et al. (2003) "High-throughput Pyrosequencing of a phage display library for the identification of enriched target-specific peptides." Biotechniques35, 317-324. Receptor-specific peptides (purified receptor panning)
An, P. et al. (2004) "Suppression of tumor growth and metastasis by a VEGFR-1 antagonizing peptide identified from a phage display library." Int J Cancer111, 165-173. Biorn, A.C. et al. (2004) "Mode of action for linear peptide inhibitors of HIV-1 gp120 interactions." Biochemistry43, 1928-1938. Ferrer, M. and S. C. Harrison (1999) "Peptide ligands to human immunodeficiency virus type 1 gp120 identified from phage display libraries." J Virol73, 5795-5802. Guo, H.P. et al. (2002) "Screening of tumor necrosis factor-alpha-binding peptides by phage display peptide library." Di Yi Jun Yi Da Xue Xue Bao22, 597-599. Hessling, J. et al. (2003) "Peptide G protein agonists from a phage display library." Biochem Pharmacol65, 961-7. Hetian, L. et al. (2002) "A Novel Peptide Isolated from a Phage Display Library Inhibits Tumor Growth and Metastasis by Blocking the Binding of Vascular Endothelial Growth Factor to Its Kinase Domain Receptor." J Biol Chem277, 43137-43142. Hsu, C.L. et al. (2003) "The use of phage display technique for the isolation of androgen receptor interacting peptides with (F/W)XXL(F/W) and FXXLY new signature motifs." J Biol Chem278, 23691-23698. Koolpe, M. et al. (2002) "An ephrin mimetic peptide that selectively targets the EphA2 receptor." J Biol Chem277, 46974-46979. Kraft, S. et al. (1999) "Definition of an unexpected ligand recognition motif for alphav beta6 integrin." J Biol Chem274, 1979-1985. Luo, X. et al. (2002) "The Mad2 spindle checkpoint protein undergoes similar major conformational changes upon binding to either Mad1 or Cdc20." Mol Cell9, 59-71. Pillutla, R.C. et al. (2002) "Peptides identify the critical hotspots involved in the biological activation of the insulin receptor." J Biol Chem277, 22590-22594. Tournaire, R. et al. (2004) "A short synthetic peptide inhibits signal transduction, migration and angiogenesis mediated by Tie2 receptor." EMBO Rep5, 262-267. Receptor-specific peptides (whole cell panning)
Binetruy-Tournaire, R. et al. (2000) "Identification of a peptide blocking vascular endothelial growth factor (VEGF)-mediated angiogenesis." EMBO J.19, 1525-1533. Gazouli, M. et al. (2002) "Identification of a peptide antagonist to the peripheral-type benzodiazepine receptor that inhibits hormone-stimulated leydig cell steroid formation." J Pharmacol Exp Ther303, 627-632. Kragler, F. et al. (2000) "Peptide antagonists of the plasmodesmal macromolecular trafficking pathway." EMBO J.19, 2856-2868. Lee, J. H., J. A. Engler, et al. (2001) "Receptor mediated uptake of peptides that bind the human transferrin receptor." Eur J Biochem268(7): 2004-2012. Maruta, F. et al. (2002) "Identification of FGF receptor-binding peptides for cancer gene therapy." Cancer Gene Ther9, 543-552. Messmer, B.T. et al. (2000) "Sequential determination of ligands binding to discrete components in heterogeneous mixtures by iterative panning and blocking (IPAB)." J. Mol. Biol.296, 821-832. Rao, W.H. and R.D. Camp (2003) "Novel cyclic and linear oligopeptides that bind to integrin beta1 chain and either inhibit or costimulate T lymphocytes." Int Immunopharmacol3, 435-443. White, S.J. et al. (2001) "Identification of peptides that target the endothelial cell-specific LOX-1 receptor." Hypertension37, 449-455. Cell-targeting peptides
Curiel, T.J. et al. (2004) "Peptides identified through phage display direct immunogenic antigen to dendritic cells." J Immunol172, 7425-7431. Eidne, K.A. et al. (2000) "Selection of peptides targeting the human sperm surface using random peptide phage display identify ligands homologous to ZP3." Biol Reprod63, 1396-1402. Jost, P.J. et al. (2001) "A novel peptide, THALWHT, for the targeting of human airway epithelia." FEBS Lett489, 263-269. Maruta, F. et al. (2003) "Use of a phage display library to identify oligopeptides binding to the lumenal surface of polarized endothelium by ex vivo perfusion of human umbilical veins." J Drug Target11, 53-59. Mi, Z. et al. (2003) "Identification of a synovial fibroblast-specific protein transduction domain for delivery of apoptotic agents to hyperplastic synovium." Mol Ther8, 295-305. Mummert, D.I. et al. (2003) "Involvement of hyaluronan in epidermal Langerhans cell maturation and migration in vivo." J Dermatol Sci33, 91-97. Mummert, M.E. et al. (2000) "Development of a peptide inhibitor of hyaluronan-mediated leukocyte trafficking." J Exp Med192, 769-779. Mummert, M.E. et al. (2002) "Synthesis and surface expression of hyaluronan by dendritic cells and its potential role in antigen presentation." J Immunol169, 4322-4331. Mummert, M.E. et al. (2003) "Functional roles of hyaluronan in B16-F10 melanoma growth and experimental metastasis in mice." Mol Cancer Ther2, 295-300. Nicklin, S.A. et al. (2001) "Efficient and selective AAV2-mediated gene transfer directed to human vascular endothelial cells." Mol Ther4, 174-181. Nicklin, S.A. et al. (2001) "Ablating adenovirus type 5 fiber-CAR binding and HI loop insertion of the SIGYPLP peptide generate an endothelial cell-selective adenovirus." Mol Ther4, 534-542. Nicklin, S.A. et al. (2004) "In vitro and in vivo characterisation of endothelial cell selective adenoviral vectors." J Gene Med6, 300-308. Nicklin, S.A. et al. (2000) "Selective targeting of gene transfer to vascular endothelial cells by use of peptides isolated by phage display." Circulation102, 231-237. Rasmussen, U.B. et al. (2002) "Tumor cell-targeting by phage-displayed peptides." Cancer Gene Ther9, 606-612. Romanczuk, H. et al. (1999) "Modification of an adenoviral vector with biologically selected peptides: a novel strategy for gene delivery to cells of choice." Hum Gene Ther10, 2615-2626. Samoylov, A.M. et al. (2002) "Recognition of cell-specific binding of phage display derived peptides using an acoustic wave sensor." Biomol Eng18, 269-272. Samoylov, A.M. et al. (2002) "Peptide biosensor for recognition of cross-species cell surface markers." J Mol Recognit15, 197-203. Samoylova, T.I. et al. (2002) "Targeting peptides for microglia identified via phage display." J Neuroimmunol127, 13-21. Samoylova, T.I. and B.F. Smith (1999) "Elucidation of muscle-binding peptides by phage display screening." Muscle Nerve22, 460-466. Shadidi, M. and M. Sioud (2003) "Identification of novel carrier peptides for the specific delivery of therapeutics into cancer cells." Faseb J17, 256-258. Shadidi, M. and M. Sioud (2004) "Selection of peptides for specific delivery of oligonucleotides into cancer cells." Methods Mol Biol252, 569-580. Takashima, A. et al. (2000) "New technologies to prevent and treat contact hypersensitivity responses." Ann N Y Acad Sci919, 205-213. Work, L.M. et al. (2004) "Development of efficient viral vectors selective for vascular smooth muscle cells." Mol Ther9, 198-208. In vivo panning
Duerr, D.M. et al. (2004) "Identification of peptide sequences that induce the transport of phage across the gastrointestinal mucosal barrier." J Virol Methods116, 177-180. Higgins, L.M. et al. (2004) "In vivo phage display to identify M cell-targeting ligands." Pharm Res21, 695-705. Lee, L. et al. (2002) "Identification of synovium-specific homing peptides by in vivo phage display selection." Arthritis Rheum46, 2109-2120. Liu, C. et al. (2003) "In vivo interrogation of the molecular display of atherosclerotic lesion surfaces." Am J Pathol163, 1859-1871. Antimicrobial peptides
da Silva, A. et al. (2002) "Avian anticoccidial activity of a novel membrane-interactive peptide selected from phage display libraries." Mol Biochem Parasitol120, 53-60. Ide, T. et al. (2003) "Identification by the phage-display technique of peptides that bind to H7 flagellin of Escherichia coli." Biosci Biotechnol Biochem67, 1335-1341. Knurr, J. et al. (2003) "Peptide ligands that bind selectively to spores of Bacillus subtilis and closely related species." Appl Environ Microbiol69, 6841-6847. Mourez, M. et al. (2001) "Designing a polyvalent inhibitor of anthrax toxin." Nat Biotechnol19, 958-961. Stratmann, J. et al. (2004) "A 38-kilobase pathogenicity island specific for Mycobacterium avium subsp. paratuberculosis encodes cell surface proteins expressed in the host." Infect Immun72, 1265-1274. Stratmann, J. et al. (2002) "Development of a Peptide-Mediated Capture PCR for Detection of Mycobacterium avium subsp. paratuberculosis in Milk." J Clin Microbiol40, 4244-4250. Tao, J. et al. (2000) "Drug target validation: lethal infection blocked by inducible peptide." Proc Natl Acad Sci U S A97, 783-786. Tinoco, L.W. et al. (2002) "NMR structure of PW2 bound to SDS micelles. A tryptophan-rich anticoccidial peptide selected from phage display libraries." J Biol Chem277, 36351-36356. Turnbough, C.L., Jr. (2003) "Discovery of phage display peptide ligands for species-specific detection of Bacillus spores." J Microbiol Methods53, 263-271. Williams, D.D. et al. (2003) "Species-specific peptide ligands for the detection of Bacillus anthracis spores." Appl Environ Microbiol69, 6288-6293. Antiviral peptides
Biorn, A.C. et al. (2004) "Mode of action for linear peptide inhibitors of HIV-1 gp120 interactions." Biochemistry43, 1928-1938. Ferrer, M. and S. C. Harrison (1999) "Peptide ligands to human immunodeficiency virus type 1 gp120 identified from phage display libraries." J Virol73, 5795-5802. Ho, K. L. et al. (2003) "Selection of high affinity ligands to hepatitis B core antigen from a phage-displayed cyclic peptide library." J Med Virol69, 27-32. Ramanujam, P. et al. (2002) "Novel peptides that inhibit the propagation of Newcastle disease virus." Arch Virol147, 981-993. Ramanujam, P. et al. (2004) "Pathotyping of Newcastle disease virus with a filamentous bacteriophage." Biotechniques36, 296-302. Yang, B. et al. (2003) "Potent suppression of viral infectivity by the peptides that inhibit multimerization of human immunodeficiency Virus type I (HIV-1) Vif proteins." J Biol Chem278, 6596-6602. Protein modification-specific peptides
Anni, H. et al. (2001) "Selection of phage-display library peptides recognizing ethanol targets on proteins." Alcohol25, 201-209. Inhibitors/modulators of enzyme activity/specificity
Amin, A. et al. (2003) "Identification of constrained peptides that bind to and preferentially inhibit the activity of the hepatitis C viral RNA-dependent RNA polymerase." Virology313, 158-169. Chaudhary, J. et al. (2001) "Caloxin: a novel plasma membrane Ca2+ pump inhibitor." Am J Physiol Cell Physiol280, C1027-1030. El Zoeiby, A. et al. (2003) "Identification of novel inhibitors of Pseudomonas aeruginosa MurC enzyme derived from phage-displayed peptide libraries." J Antimicrob Chemother51, 531-543. Giannattasio, R. B. and B. Weisblum (2000) "Modulation of erm methyltransferase activity by peptides derived from phage display." Antimicrob Agents Chemother44, 1961-1963. Huang, W. et al. (2003) "A broad-spectrum peptide inhibitor of beta-lactamase identified using phage display and peptide arrays." Protein Eng, 853-860. Sheu, T.J. et al. (2002) "Use of a phage display technique to identify potential osteoblast binding sites within osteoclast lacunae." J Bone Miner Res17, 915-922. Tao, J. et al. (2000) "Drug target validation: lethal infection blocked by inducible peptide." Proc Natl Acad Sci U S A97, 783-786. Yoshida, H. et al. (2003) "Improved substrate specificity of water-soluble pyrroloquinoline quinone glucose dehydrogenase by a peptide ligand." Biotechnol Lett25, 301-305. Mirror image phage display
Wiesehan, K. et al. (2003) "Selection of D-amino-acid peptides that bind to Alzheimer’s disease amyloid peptide abeta1-42 by mirror image phage display." Chembiochem4, 748-753. Computer analysis
Davies, J.M. et al. (1999) "Multiple alignment and sorting of peptides derived from phage-displayed random peptide libraries with polyclonal sera allows discrimination of relevant phagotopes." Mol Immunol36, 659-667. Gazarian, K.G. et al. (2001) "Post-Panning Computer-Aided Analysis of Phagotope Collections Selected with Neurocysticercosis Patient Polyclonal Antibodies: Separation of Disease-Relevant and Irrelevant Peptide Sequences." Comb Chem High Throughput Screen4, 221-235. Makowski, L. and A. Soares (2003) "Estimating the diversity of peptide populations from limited sequence data." Bioinformatics19, 483-489. Rodi, D.J. et al. (2002) "Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries." J Mol Biol322(5): 1039-1052. Construction of custom libraries in M13KE
Noren, K.A. and C.J. Noren (2001) "Construction of high-complexity combinatorial phage display peptide libraries." Methods23, 169-178. Oleksiewicz, M.B. et al. (2001) "Epitope mapping porcine reproductive and respiratory syndrome virus by phage display: the nsp2 fragment of the replicase polyprotein contains a cluster of B-cell epitopes." J Virol75, 3277-3290. Oleksiewicz, M.B. et al. (2002) "Porcine B-cells recognize epitopes that are conserved between the structural proteins of American- and European-type porcine reproductive and respiratory syndrome virus." J Gen Virol83, 1407-1418. Oleksiewicz, M.B. et al. (2004). "Phage display of the Equine arteritis virus nsp1 ZF domain and examination of its metal interactions." J Virol Methods119, 159-169. Sandman, K.E. et al. (2000). "Phage display of selenopeptides." J. Am. Chem. Soc.122, 960-961. Sandman, K.E. and C.J. Noren (2000) "The efficiency of Escherichia coli selenocysteine insertion is influenced by the immediate downstream nucleotide." Nucleic Acids Res28, 755-761. Sandman, K.E. et al. (2003) "Revised Escherichia coli selenocysteine insertion requirements determined by in vivo screening of combinatorial libraries of SECIS variants." Nucleic Acids Res31, 2234-2241. Material-specific peptides
Matsubara, T. et al. (2003) "Selection of novel structural zinc sites from a random peptide library." FEBS Lett555, 317-321. Whaley, S.R. et al. (2000) "Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly." Nature405, 665-668. Wolcke, J. and E. Weinhold (2001) "A DNA-binding peptide from a phage display library." Nucleosides Nucleotides Nucleic Acids20, 1239-1241. Small molecule-binding peptides
Janssen, G.G. et al. (2004) "Selective targeting of a laccase from Stachybotrys chartarum covalently linked to a carotenoid-binding peptide." J Pept Res64, 10-24. Miura, Y. et al. (2004) "Peptides binding to a Gb3 mimic selected from a phage library." Biochim Biophys Acta1673, 131-138. Rodi, D. J. et al. (1999) "Screening of a library of phage-displayed peptides identifies human bcl- 2 as a taxol-binding protein." J Mol Biol285, 197-203. Rozinov, M.N. and G.P. Nolan (1998) "Evolution of peptides that modulate the spectral qualities of bound, small-molecule fluorophores." Chem Biol5, 713-728. Inhibitors of protein folding
Kundu, B. et al. (2002) "Manipulation of unfolding-induced protein aggregation by peptides selected for aggregate-binding ability through phage display library screening." Biochem Biophys Res Commun291, 903-907. Peptide mimics of non-peptide ligands
Hou, Y. and X.X. Gu (2003) "Development of peptide mimotopes of lipooligosaccharide from nontypeable Haemophilus influenzae as vaccine candidates." J Immunol170, 4373-4379. Jouault, T. et al. (2001) "Peptides that mimic Candida albicans-derived beta-1,2-linked mannosides." Glycobiology11, 693-701. Peptide ligands for affinity chromatography
Ehrlich, G.K. and P. Bailon (2001) "Identification of model peptides as affinity ligands for the purification of humanized monoclonal antibodies by means of phage display." J Biochem Biophys Methods49, 443-454. Gaskin, D.J. et al. (2001) "Phage display combinatorial libraries of short peptides: ligand selection for protein purification." Enzyme Microb Technol28, 766-772. Jensen, L.B. et al. (2004) "Efficient purification of unique antibodies using peptide affinity-matrix columns." J Immunol Methods284, 45-54. Mapping protein-protein contacts (two-hybrid alternative)
Baltrusch, S. et al. (2001) "Characterization of Glucokinase-binding Protein Epitopes by a Phage- displayed Peptide Library. Identification of 6-phosphofructo-2- kinase/fructose-2,6-bisphosphatase as a novel interaction partner." J Biol Chem276, 43915-43923. Berggard, T. et al. (2002) "myo-Inositol Monophosphatase Is an Activated Target of Calbindin D28k." J Biol Chem277, 41954-41959. Bitto, E. and D. B. McKay (2003) "The periplasmic molecular chaperone protein SurA binds a peptide motif that is characteristic of integral outer membrane proteins." J Biol Chem278, 49316-49322. BouHamdan, M. et al. (1998) "Diversity of HIV-1 Vpr interactions involves usage of the WXXF motif of host cell proteins." J Biol Chem273, 8009-8016. Burch, L. et al. (2004) "Expansion of protein interaction maps by phage peptide display using MDM2 as a prototypical conformationally flexible target protein." J Mol Biol337, 129-45. Burch, L.R. et al. (2004) "Phage-peptide display identifies the interferon-responsive, death-activated protein kinase family as a novel modifier of MDM2 and p21WAF1." J Mol Biol337, 115-128. Chen, L. and P. B. Sigler (1999) "The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity." Cell99, 757-768. Dintilhac, A. and J. Bernues (2002) "HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences." J Biol Chem277, 7021-7028. Dornan, D. et al. (2003) "The proline repeat domain of p53 binds directly to the transcriptional coactivator p300 and allosterically controls DNA-dependent acetylation of p53." Mol Cell Biol23, 8846-8861. Hoff, K.G. et al. (2002) "Hsc66 substrate specificity is directed toward a discrete region of the iron-sulfur cluster template protein IscU." J Biol Chem277, 27353-27359. Kenny, C.H. et al. (2003) "Development of a fluorescence polarization assay to screen for inhibitors of the FtsZ/ZipA interaction." Anal Biochem323, 224-233. MacDonald, N. J. et al. (2001) "Endostatin binds tropomyosin: A potential modulator of the anti-tumor activity of endostatin." J Biol Chem276, 25190-25196. Petersen, G. et al. (2001) "Dissection of the ATP binding domain of the chaperone hsc70 for interaction with the cofactor Hap46." J. Biol. Chem.276, 10178-10184. Sarnowski, T.J. et al. (2002) "AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time." Nucleic Acids Res30, 3412-3421. Sheu, T.J. et al. (2002) "Use of a phage display technique to identify potential osteoblast binding sites within osteoclast lacunae." J Bone Miner Res17, 915-922. Shimizu, H., L. Burch, et al. (2002). "The conformationally-flexible S9-S10 linker region in the core domain of p53 contains a novel MDM2-binding site whose mutation increases ubiquitination of p53 in vivo." J Biol Chem277: 28446-28458. Wang, X.G. et al. (2004) "Analysis of differences in the functional properties of the substrate binding proteins of the Borrelia burgdorferi oligopeptide permease (Opp) operon." J Bacteriol186, 51-60. Epitope mapping/Vaccine development
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Appl Environ Microbiol67, 3201-3207. Youn, J.H. et al. (2004) "Production and characterization of peptide mimotopes of phenolic glycolipid-I of Mycobacterium leprae." FEMS Immunol Med Microbiol41, 51-57. Updated August 13, 2004. |