2426 QTHQELQTLTTS[0.98] HLNQRNQPPDGA[0.139] VPTHNKGLPEPV[0.301] 3 Phage display (common panning) 4 PMID:24759178 IGVH1 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The SPR assay of the peptides binding to the human Fv templates was performed. The binding affinity (KD, μM) between ligand peptides and human FV templates was shown. The value shows the representative data of two-time experiments. 2427 WSEYDIPTPQIP[6.29] HIPWLHAMSVMK[0.0605] IAFNTPPHHPLR[0.00803] GAMHLPWHMGTL[ND] NRPDSAQFWLHH[ND] HFAYWWNGVRGP[ND] SWMPHPRWSPQH[ND] HGWTLWHMALTS[ND] HLWLPNGAFRSW[ND] 9 Phage display (common panning) 4 PMID:24759178 IGVH3 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The SPR assay of the peptides binding to the human Fv templates was performed. The binding affinity (KD, μM) between ligand peptides and human FV templates was shown. The value shows the representative data of two-time experiments. ND denotes not determined. 2428 HFAYWWNGVRGP 1 Phage display (common panning) 4 PMID:24759178 IGVH4 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) 2429 HFPWLDRSAVDM[0.0587] QTHQELQTLTTS[ND] 2 Phage display (common panning) 4 PMID:24759178 IGVH6 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The SPR assay of the peptides binding to the human Fv templates was performed. The binding affinity (KD, μM) between ligand peptides and human FV templates was shown. The value shows the representative data of two-time experiments. ND denotes not determined. 2430 HFWFVPALQGAP[0.047] TPTKSSFYLPPN[0.0141] HFAYWWNGVRGP[ND] HIRWDVNHNSMS[ND] SHPWYIGPHPNA[ND] HSQSLLRLWQVY[ND] 6 Phage display (common panning) 4 PMID:24759178 IGVK1 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The SPR assay of the peptides binding to the human Fv templates was performed. The binding affinity (KD, μM) between ligand peptides and human FV templates was shown. The value shows the representative data of two-time experiments. ND denotes not determined. 2431 HFAYWWNGVRGP WHWSWNPRFAPS 2 Phage display (common panning) 4 PMID:24759178 IGVK2 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) 2432 NIYRDTHLEKFA VHYEDPTQLFTS 2 Phage display (common panning) 4 PMID:24759178 IGVK3 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) 2433 WHWNWMRLDPMT[2.48] 1 Phage display (common panning) 4 PMID:24759178 IGVK4 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The SPR assay of the peptides binding to the human Fv templates was performed. The binding affinity (KD, μM) between ligand peptides and human FV templates was shown. The value shows the representative data of two-time experiments. 2434 WHWNWMRLDPMT 1 Phage display (common panning) 4 PMID:24759178 IGVK5 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) 2435 HSWGWVAMNTQT[0.646] HFAYWWNGVRGP[ND] 2 Phage display (common panning) 4 PMID:24759178 IGVK6 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The SPR assay of the peptides binding to the human Fv templates was performed. The binding affinity (KD, μM) between ligand peptides and human FV templates was shown. The value shows the representative data of two-time experiments. ND denotes not determined. 2436 SLMVPSHSEPIR[0.782 ± 0.010] HYNAWNGWRFWT[0.628 ± 0.031] FHWTWQFPYTST[0.683 ± 0.031] SEFHRSWDMETN[0.366 ± 0.124] QAMYSKYPMINV[0.202 ± 0.011] FHRSHWYQTWVP[0.989 ± 0.010] HLWSNWQFWNMA[1.222 ± 0.015] 7 Phage display (common panning) 4 PMID:24759178 IGVK3 template protein Receptor tyrosine-protein kinase erbB-2 Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Phage ELISA was performed for measuring peptide binding to the IGVK template. Absorbance at 405 nm was determined, reproduced from the graph and expressed as means ± S.D. The data shows the representative data of two-time experiments. 2437 WLAYPGAVSYR(19/20)[0.916][678 ± 23] 1 Phage display (common panning) 3 PMID:12351647 Ephrin type-A receptor 2 Type A ephrins Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA,Surface plasmon resonance (SPR) Phage ELISA was performed to measure the affinity of phage to EphA2. Absorbance at 405 nm was determined, reproduced from the graph and shown. Besides, equilibrium binding data obtained by surface plasmon resonance indicate that the SWLAYPGAVSYR peptide binds to EphA2 with certain affinity (KD = 678 nM ± 23). Nineteen of 20 individual phage clones from the pool eluted with low pH bind specifically to EphA2 Fc. All 19 clones display the same peptide: SWLAYPGAVSYR (SWL peptide). 2438 SWLAYPGAVSYR(7/10)[0.916][678 ± 23] YSAYPDSVPMMS(2/10)[0.856][186 ± 7] 2 Phage display (competitive panning) 3 PMID:12351647 Ephrin type-A receptor 2 Type A ephrins Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA,Surface plasmon resonance (SPR) Phage ELISA was performed to measure the affinity of phage to EphA2. Absorbance at 405 nm was determined, reproduced from the graph and shown. Besides, equilibrium binding data obtained by surface plasmon resonance indicate that the YSAYPDSVPMMS peptide binds to EphA2 with higher affinity (KD = 186 nM ± 7) than the SWLAYPGAVSYR peptide (KD = 678 nM ± 23). For each round of biopanning, phages remaining bound after washing were eluted with ephrin-A1 Fc. Nine of 10 phage clones from the pool eluted with ephrin-A1 bind specifically to EphA2 (data not shown). Seven of these clones display the SWLAYPGAVSYR peptide (SWL peptide) and two display the peptide YSAYPDSVPMMS (YSA peptide). The YSA peptide targets EphA2 on the cell surface and stimulates activation of the receptor. Thus, the YSA peptide is an agonist for EphA2. Besides, the YSA and SWL peptides inhibit ephrin-A binding to EphA2. To further characterize the binding site of the YSA and SWL peptides, competition experiments with phage displayed peptides were performed. Synthetic SWL peptide competes with YSA phage bound to immobilized EphA2, and conversely YSA peptide competes with SWL phage. This indicates that the YSA and SWL peptides bind to the same or overlapping sites on EphA2. 2439 HAIYPRH[1.10 ± 0.08] AKPGYLS[>1.9] ALTPTPP[>1.9] ANYPREP[>1.9] ATTVPAS[>1.9] LTTHYKL[>1.9] NLVNLLP[>1.9] KCCFPAQ[NT] 8 Phage display (in vivo) 3 PMID:22463021 Colonic adenomas Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Flow Cytometry Binding to isolated colonic epithelial cells from adenomas for each phage clone was analyzed using flow cytometry. A common 7-mer phage that expresses the sequence HAIYPRH is a known contaminant and was run to ensure the validity of the assay. The T/B ratio for clone HAIYPRH was found to be 1.10 ± 0.08, indicating minimal binding from a nonspecific clone, as expected. Six phage clones with a T/B ratio (target to wild-type phage) >1.9 were identified as ALTPTPP, NLVNLLP, ANYPREP, ATTVPAS, LTTHYKL, and AKPGYLS. ND denotes not determined. A seven-month old CPC, Apc mouse, was injected via tail vein with the phage display library. A total of three rounds of phage biopanning were performed, with amplification of the recovered eluate after each biopanning round. After three rounds of in vivo phage biopanning, 42 individual phage clones were sequenced from the third round of biopanning and were individually amplified and conjugated to 5'-FITC. 2440 SLDSTHTHAPWP(3)[1.687 ± 0.075] TLADTHTHRPWT(2)[1.523 ± 0.117] LALDTPSHRPWT(2)[1.486 ± 0.078] FWGVTPHGELRS(1)[1.491 ± 0.103] 4 Phage display (subtractive panning) 4 PMID:24478253 Hepatocellular carcinoma cell line HepG2 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Phage ELISA was performed to evaluate the affinity of eight phage clones to HepG2 cells. Plates were read at 450 nm. Phage clones displaying IRPs and PBS treatments were used as negative controls. Triplicate determinations were performed. Absorbance at 450 nm was reproduced from the graph and expressed as means ± S.D. The absorbances of phage clones displaying IRPs and PBS treatments were 0.031 and 0.025 ± 0.006, respectively. HepG2 cells and HEK293 cells were separately seeded into six-well. The phage library was incubated with HEK293 cells. After incubation, culture medium containing the unbound phages was transferred to HepG2 cell monolayer cultures and incubated. Four rounds of biopanning were performed. In phage ELISA, the PC28 clone (displaying SLDSTHTHAPWP) appeared to bind most effectively to HepG2 cells than the other clones. Immunofluorescence assay further evaluated the affinity of the PC28 phage clone binding to HepG2 cells. Besides, the synthetic peptide HCSP4, SLDSTHTHAPWP, can compete with the binding of the PC28 phage clone to HepG2 cells in competitive inhibition assay, which indicated that the binding of phage PC28 to target cells was mediated by the peptide HCSP4. The binding specificity of the FITC-conjugated HCSP4 to HepG2 cells was further validated by flow cytometry analysis. 2441 HPWIPKR[0.330 ± 0.017] WPWQHHR[0.493 ± 0.031] WPWHHVR[0.417 ± 0.029] WPWHNHR[0.514 ± 0.050] VLRSDFK[0.048 ± 0.035] W-P-W-x(3)-R 5 Phage display (common panning) 3 PMID:24573486 Envelope glycoprotein E2 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) ELISA In phage ELISA, the absorbance values were measured at 490 nm (A490). The values shown were reproduced from the graph and expressed as means ± S.D. Twenty-five plaques were randomly selected from the third round phages, and their binding reactivity to the HCV E2661 protein was determined individually using an ELISA. Clone no. 3 (displaying VLRSDFK) had the lowest affinity to E2661 protein. Four clones with the highest affinities (nos. 7, 11, 17 and 18 displaying HPWIPKR, WPWQHHR, WPWHHVR and WPWHNHR, respectively) were selected for subsequent analysis. Peptide C18, WPWHNHR, significantly inhibited HCVpp from entering Huh7.5 cells detected by flow cytometry. The HCVpp entry was notably inhibited in the presence of peptide C18, compared to the group of HCVpp and the group of the unrelated peptide. Furthermore, quantitative real-time RT-PCR demonstrated that the level of HCV RNA in HCVcc-infected Huh7.5 cells was significantly lower in the presence of peptide C18, compared to Huh7.5 cells incubated with HCVcc and the unrelated peptide. 2442 GWWYKGRARPVSAVA(2) WHWRHRIPLQLAAGR(2) GIGGVWYSSIVGPGR(2) SSPPRYTRSWHWHVR(1) RLLGAGRWWNVHPRV(1) SRWRGWHHSWLVVAN(1) FRWVPKFFSAAALPR(1) WRRWFYQFPTPLAAA(1) 8 Phage display (common panning) 3-4 PMID:17237992 The anticodon stem and loop of human tRNA(Lys3), ASL(Lys3) Not determined. Not determined. Not determined. f5-15mer phage display library (X15) Biotinylated unmodified ASL(Lys3) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. Bound phages were eluted with acid elution buffer. 2443 APTTCSKPQWYCDNYV(2) 1 Phage display (common panning) 3-4 PMID:17237992 The anticodon stem and loop of human tRNA(Lys3), ASL(Lys3) Not determined. Not determined. Not determined. f88-4/Cys6 phage display library (X4CX6CX4) Biotinylated unmodified ASL(Lys3) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. Bound phages were eluted with acid elution buffer. 2444 GIGGVWYSSIVGPGR(4) RVPPRYHAKISPMVK(2) GWWYKGRARPVSAVA(1) 3 Phage display (common panning) 3-4 PMID:17237992 The anticodon stem and loop of human tRNA(Lys3), ASL(Lys3) Not determined. Not determined. Not determined. f5-15mer phage display library (X15) Biotinylated unmodified ASL(Lys3) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. Bound phages were eluted with alkaline elution buffer. 2445 WRRWFYQFPTPLAAA(16) RVPPRYHAKISPMVK(3) VRVYFGFGPPPYFGG(2) GLYLPLPSSMSVRAV(1) GRAIDGFPYFRTALL(1) 5 Phage display (common panning) 3-4 PMID:17237992 ASL(Lys3) (s2U34;Ψ39) Not determined. Not determined. Not determined. f5-15mer phage display library (X15) Biotinylated ASL(Lys3) (s2U34;Ψ39) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. Bound phages were eluted with acid elution buffer. 2446 TRQQCQKWTLWCRTVL(2) TQEYCNAHNEKCFQRT(1) APTTCSKPQWYCDNYV(1) 3 Phage display (common panning) 3-4 PMID:17237992 ASL(Lys3) (s2U34;Ψ39) Not determined. Not determined. Not determined. f88-4/Cys6 phage display library (X4CX6CX4) Biotinylated ASL(Lys3) (s2U34;Ψ39) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. Bound phages were eluted with acid elution buffer. 2447 RVPPRYHAKISPMLK(16) GIGGVWYSSIVGPGR(3) GWWYKGRARPVSAVA(1) VSVDGVTSVWHRLSG(1) PPKFPRTSSWRLSSL(1) WRRWFYQFPTPLAAA(1) 6 Phage display (common panning) 3-4 PMID:17237992 ASL(Lys3) (s2U34;Ψ39) Not determined. Not determined. Not determined. f5-15mer phage display library (X15) Biotinylated ASL(Lys3) (s2U34;Ψ39) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. Bound phages were eluted with alkaline elution buffer. 2448 RVPPRYHAKISPMVK(11) WRRWFYQFPTPLAAA(6) RYASQLSDQILFTLP(2) GWWYKGRARPVSAVA(1) SSPPRYTRSWHWHVR(1) SRQTGHSRNSYTRLP(1) WPVPLAPYWSDLSPS(1) GSFALLRSAQASARP(1) 8 Phage display (common panning) 3-4 PMID:17237992 The anticodon stem and loop of human tRNA(Lys3), ASL(Lys3) Not determined. Not determined. Not determined. f5-15mer phage display library (X15) Biotinylated unmodified ASL(Lys3) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. With Zn2+ present, bound phages were eluted with acid elution buffer. 2449 RVPPRYHAKISPMVK(3) WRRWFYQFPTPLAAA(3) 2 Phage display (common panning) 3-4 PMID:17237992 ASL(Lys3) (s2U34;Ψ39) Not determined. Not determined. Not determined. f5-15mer phage display library (X15) Biotinylated ASL(Lys3) (s2U34;Ψ39) was attached to streptavidin selection plates. Three or four rounds of selection were conducted. With Zn2+ present, bound phages were eluted with acid elution buffer. 2450 RERIHSPGSTQILF(2) PLLSLASHAQRTVGR(2) RSLWSDFYASASRGP(2) GWWYKGRARPVSAVA(1) GRAIDGFPYFRTALL(1) GEQGTNSRVSRLHTW(1) RGVFSHPHTAVPSHN(1) GWRFLVSSARVMRSD(1) GSRGGTLRGAEAGLP(1) WASHYMFHGYSVASD(1) LAVRRYALGQGYDWS(1) GVVAGASRPYVWWVS(1) AREYGTRFSLIGGYR(1) HSDVPACTSGDGCLA(1) GWRFLVSSARVMRSD(1) 15 Phage display (subtractive panning) 3-4 PMID:17237992 ASL(Lys3) (s2U34;Ψ39) Not determined. Not determined. Not determined. f5-15mer phage display library (X15) Biotinylated unmodified ASL(Lys3) and ASL(Lys3) (s2U34;Ψ39) were immobilized on the surface of streptavidin-coated microplates. The phage dsiplay library was pre-incubated with unmodified ASL(Lys3). The phages that were easily washed from the plate were subjected to selection on ASL(Lys3) (s2U34;Ψ39). Bound phages were eluted with acid elution buffer.