2401 VTQESCCWWEDMVGMECGRLE 1 Phage display (common panning) 3 PMID:11075354 Bovine insulin-Like growth factor-binding protein 2, bIGFbp-2 Insulin-like growth factor I, IGF-I Not determined. Not determined. X5CX9CX4 phage display library BlGFbp-2 was coated directly onto immunosorbant plates. The library was subjected to three rounds of selection, using 100 mM HC1 elution, followed by neutralization. Phage from round 1 were amplified in E. coli before use in round 2. The eluted phage from round 2 were not amplified before use in round 3. 2402 RDCDTSCGH 1 Phage display (common panning) 3 PMID:11075354 Bovine insulin-Like growth factor-binding protein 2, bIGFbp-2 Insulin-like growth factor I, IGF-I Not determined. Not determined. X2CX3CX2 phage display library BlGFbp-2 was coated directly onto immunosorbant plates. The library was subjected to three rounds of selection, using 100 mM HC1 elution, followed by neutralization. Phage from round 1 were amplified in E. coli before use in round 2. The eluted phage from round 2 were not amplified before use in round 3. 2403 SNCFWDGATVVCAQ TDCTGPWVWVWCPQV 2 Phage display (common panning) 3 PMID:11075354 Bovine insulin-Like growth factor-binding protein 2, bIGFbp-2 Insulin-like growth factor I, IGF-I Not determined. Not determined. X2CX8CX2 phage display library BlGFbp-2 was coated directly onto immunosorbant plates. The library was subjected to three rounds of selection, using 100 mM HC1 elution, followed by neutralization. Phage from round 1 were amplified in E. coli before use in round 2. The eluted phage from round 2 were not amplified before use in round 3. 2404 DGCAWDGVQMVDCTG 1 Phage display (common panning) 3 PMID:11075354 Bovine insulin-Like growth factor-binding protein 2, bIGFbp-2 Insulin-like growth factor I, IGF-I Not determined. Not determined. X2CX10CX2 phage display library BlGFbp-2 was coated directly onto immunosorbant plates. The library was subjected to three rounds of selection, using 100 mM HC1 elution, followed by neutralization. Phage from round 1 were amplified in E. coli before use in round 2. The eluted phage from round 2 were not amplified before use in round 3. 2405 DALRRTRGGAAAGFAVHGSL GNARLHVVARDHTGFAVLGT LTTDLMHCSGFALSPGCPQI MNGKVGWAIHAREAVGTREG DDSSHTGWAVLDLGLRQPVF GDTHIGPDSGQREHVGFAIL DALRRTRGGAAAGFAVHGSL GNARLHVVARDHTGFAVLGT LTTDLMHCSGFALSPGCPQI MNGKVGWAIHAREAVGTREG DDSSHTGWAVLDLGLRQPVF GDTHIGPDSGQREHVGFAIL G-[FW]-A 12 Phage display (common panning) PMID:19653209 Anti-gp120 monoclonal antibody GV4H3 Surface protein gp120, SU Not determined. Not determined. X20 FUSE5-based phage display library No particular motif can be identified for the first six sequences. However, the common GFA (GWA) tripeptide can be recognized for the last six sequences. In this case, homologies with the sequence 221-226 (AGFAIL) of HIV-1 gp120 can be identified. 2406 TLPSPLALLTVH(2) SPPSNLIPPTLR(2) ATWSHHLSSAGL(1) QTRPHHLRSATQ(1) 4 Phage display (common panning) 3 PMID:18195017 Death-associated protein kinase 1 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) For each round of panning, the bound phage particles were eluted by ATP incubation and neutralized with 15 μl of 1 M Tris-HCl (pH 9.1). 2407 LPFEEHLRRPVG(1)[0.452 ± 0.071] SNLPQSWPPHQW(1)[NT] QGAWHPSRTHFL(1)[NT] TQPPIPPSRTLH(1)[NT] TFGLWQPGVQST(1)[NT] WHWSWFSHFPSA(1)[NT] 6 Phage display (common panning) 3 PMID:18195017 Death-associated protein kinase 1 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA The ability of purified DAPK-1 to bind isolated phage 12-mers was further assessed using synthesized biotinylated peptide. Synthetic peptide Φ (LPFEEHLRRPVG), the naturally occurring peptide sequence in MAP1B itself (1B, IVTEEHLRRAIG), or control peptides (NR) were added to the wells with DAPK-1. Peptide binding activity (RLU, relative light units) were reproduced from the graph and shown. The values of the peptide 1B and NR were 0.939 ± 0.168 and 0.018, respectively. NT denotes not tested. For each round of panning, the bound phage particles were eluted by acid incubation and neutralized with 15 μl of 1 M Tris-HCl (pH 9.1). 2408 CPNNTISLC[1.246 ± 0.024] CPLTTKTLC[1.448 ± 0.054] 2 Phage display (competitive panning) 3 PMID:24447276 Globotriaosylceramide, Gb3 Shiga toxin, Shiga toxin subunit A and Shiga toxin subunit B Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) ELISA Phage ELISA Gb3-binding assay was performed. The absorbance of the end product was measured at a wavelength of 492 nm using an ELISA microplate reader. Raw absorbance data were corrected by subtraction of the values obtained from an OPD-containing blank. This assay was performed in triplicate. The absorbance values were determined. Data were reproduced from the graph and shown as means ± the standard deviations. The panning procedure was repeated for a total of three rounds for the Ph.D.-C7C library. For each round of panning, bound phages were eluted with Gb3. The highest competition percentages for binding to Gb3 between the toxins and peptides (CPNNTISLC and CPLTTKTLC) were observed at peptide concentrations ranging from 25 to 100 μg. The Stx cytotoxic activity neutralization assay indicated that when Escherichia coli O157 : H7 cell-free filtrate was applied to Vero cells, the inhibition of cell death was similar for the two peptides at the different concentrations assayed. Besides, the inhibition of lethality assay by using peptides CPNNTISLC and CPLTTKTLC was performed. The peptide CPNNTISLC partially inhibited the lethality caused by Stx1 in mice, whereas peptide CPLTTKTLC abolished the lethality induced by Stx1. In contrast, none of the peptides assayed inhibited the lethality caused by the Stx2 toxin in mice. Moreover, none of the peptides themselves induced lethality in mice. 2409 DGYYRSNNAGTP[0.504 ± 0.039] DNYTRYDYMDIP[0.137 ± 0.005] SAPRHNVPDNPR[2.093 ± 0.029] SSQPHTVFDPSK[0.429 ± 0.021] 4 Phage display (competitive panning) 3 PMID:24447276 Globotriaosylceramide, Gb3 Shiga toxin, Shiga toxin subunit A and Shiga toxin subunit B Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Phage ELISA Gb3-binding assay was performed. The absorbance of the end product was measured at a wavelength of 492 nm using an ELISA microplate reader. Raw absorbance data were corrected by subtraction of the values obtained from an OPD-containing blank. This assay was performed in triplicate. The absorbance values were determined. Data were reproduced from the graph and shown as means ± the standard deviations. The panning procedure was repeated for a total of three rounds for the Ph.D.-12 library. For each round of panning, bound phages were eluted with Gb3. The highest competition percentages for binding to Gb3 between the toxins and the peptide SAPRHNVPDNPR were observed at peptide concentrations ranging from 25 to 100 μg. The Stx cytotoxic activity neutralization assay indicated that when Escherichia coli O157 : H7 cell-free filtrate was applied to Vero cells, the inhibition of cell death was similar for the three peptides at the different concentrations assayed. The only exception was the inhibition caused by the peptide SAPRHNVPDNPR, which was higher than the inhibition caused by peptides CPNNTISLC and CPLTTKTLC at the concentration of 50 μg per well. Besides, the inhibition of lethality assay by using the peptide SAPRHNVPDNPR was performed. The peptide partially inhibited the lethality caused by Stx1 in mice. In contrast, it didn't inhibit the lethality caused by the Stx2 toxin in mice. Moreover, it didn't induce lethality in mice. 2410 TEPSTRGSWKFW(13) SVPQESTIRATK(5) SGHTHYYPAETN(4) LCNTYLPLARST(3) VPILAHPSTGHS(2) SENRKVPFYSHS 5 Phage display (common panning) 5 PMID:24468276 The Domain III of the Japan Encephalitis Virus Envelope Protein, E DIII Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The homologous alignment of peptides displayed by frequently encountered phages was analyzed, resulting in the identification of a highly conserved 12 amino acid peptide sequence that was also synthesized and named P3 (SENRKVPFYSHS). The inhibitory ability of the peptides against JEV infection were determined by plaque assays, qRT-PCR and WB. The plaque assay results showed that P3 significantly inhibited JEV infection in a concentration-dependent manner, whereas P1 (TEPSTRGSWKFW) inhibited JEV infection only at high concentrations. P2 (SVPQESTIRATK) did not show any inhibitory effect. Besides, P3 bound to E DIII with a Kd of 6.06 × 10 (-6) M, indicating that P3 has a higher affinity for E DIII. Also P3 interfered with JEV binding to the cell receptor. Eventually A model of the E DIII/P3 complex was developed by molecular modeling based on the available E DIII structure. 2411 IPTLPSS(3) SSPSTSR(3) TRAPWPP(2) YRAPWPP(2) LPSL*NI(1) SSPATSR(1) FSESTQAS(1) STYTSVS(1) APQPPEP(1) TPSPHRV(1) WAPTPSR(1) STPSWWA(1) AITRSPA(1) FSPPRFY(1) YMTPLRP(1) TPWHPLA(1) 16 Phage display (subtractive panning) 4 PMID:24480037 BCR/ABL-expressing NIH3T3 mouse fibroblast cells Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The phage-display linear heptapeptide library Ph.D 7.0 was used to pan NIH3T3 clones, using a combination of negative/positive panning in each round. All planning stages were performed at RT in PBS/3% BSA. Phages were preincubated in 10 volumes PBS/3% prior to each round of panning and then used to first pan the control cells (3T3C.pCVT). The supernatant was removed and used to negatively pan a second set of 3T3C.pCVT cells. This phage-depleted supernatant was used to positively pan against the BCR/ABL+ cells (3T3B.pGD210). This panning strategy was performed in two independent experiments, with 10 phages initially sequenced following three rounds of panning in each experiment. Although no dominant motif was observed, the combined analysis showed a predominance of ligands containing proline, serine and threonine residues, with 71% containing at least one proline residue and 57% containing serine or threonine residues. Round 4 panning was performed and 20/27 phages were sequenced respectively. No significant difference was observed between the two experiments in terms of sequence dominance and thus the 47 sequences were analysed collectively to look for predominant motifs. Again, a similar enrichment of phage peptides containing serine, threonine and proline residues was observed. 2412 TNLTLAS(8) GALPNNL(6) SLAVSRS(4) SEIVDNH(1) NVNSTSF(1) SPDTVQK(1) GNRLSAD(1) LGFREKE(1) TQVYHPM(1) ANHQSAN(1) TNSSFHK(1) NTVIYQK(1) HVQYWQF(1) VSVNSRT(1) RLLNPWI(1) 15 Phage display (common panning) 5 PMID:24512376 Amorphous Ni3B Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) 2413 LEQTPMF(1) ELTQISS(1) SDPQTHT(1) TPPLLSP(1) MNHAESY(1) VPSLTPT(1) VPIPYLP(1) DPYNRIN(1) RTFDAIS(1) YELVLPK(1) ETFPARG(1) GPVNHQL(1) LNHVLPA(1) HAMRTEP(1) ATSTAHA(1) ANHQSAN(1) SYTKLHL(1) SPPKSNA(1) SASKVHN(1) SPSTHWK(1) WNAKYTL(1) YQVVPAR(1) GDPKAAR(1) GDHSRHK(1) AGLPKHQ(1) STFNSRV(1) VHTNPSR(1) GASATRT(1) 28 Phage display (common panning) 5 PMID:24512376 Crystalline Ni3B Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) 2414 AGNWTPI(7)[0.623 ± 0.034] RPTSHQL(1)[0.486 ± 0.021] QWTPSHP(1)[0.589 ± 0.017] APDTKTQ(1)[0.561 ± 0.048] 4 Phage display (common panning) 4 PMID:24530908 Fibroblast growth factor 1, FGF-1 FGFR-1, FGFR-2, FGFR-3 and FGFR-4 1DJS,1E0O,3CU1,3OJ2,3OJM,4J23,1EVT,3OJV,1RY7, Not determined. Ph.D.-7 phage display library (X7) ELISA Binding abilities of phage clones to aFGF were determined by ELISA. The absorbance at 370 nm was measured. Data were reproduced from the graph and expressed as means ± S.D. The AP8 peptide (AGNWTPI), with amino acids identical to FGFR1, may bind aFGF via electrostatic interactions and may interrupt aFGF binding to FGFR1. Results of competitive inhibition assay indicated that the synthetic peptide AP8 and the corresponding phage clone A8 thus compete for the same binding site, and the binding of phage A8 to aFGF was mediated by the peptide AP8. Besides, the proliferation of MDA-MB-231, MCF-7 and HUVEC cells stimulated with aFGF could be inhibited by AP8 in a dose-dependent manner, while AP8 had little inhibitory effect on Cos-7 cells that do not express aFGF receptors. AP8 arrests aFGF-induced cells at the G0/G1 phase via Cyclin D1. aFGF significantly stimulated the phosphorylation of Erk1/2 and Akt signal molecules, while the pretreatment of cells with AP8 for 30 min prior to aFGF stimulation resulted in significant blockage of the activation of the both signal molecules in a dose-dependent manner. AP8 counteracts the regulatory effect of aFGF on PA2G4 and PCNA expression. 2415 ERNSVSPS DRNPPLPS EPFQVGDQ VHNTTSSS [DE]-R-N-x(3)-P-S 4 Phage display (common panning) 3 PMID:24533565 Prostate-specific antigen Not determined. Not determined. Not determined. f8-8mer phage display library (X8) 2416 KPPKRKADRWVP LGADRTRDRRHN TERRGSSKYPKR SHLPKVRSPTQK NKWPLAHSQKKR LKPNKPRMHLDI GGSGTSRTPILG SRSSGLKKQYHK 8 Phage display (common panning) 4 PMID:24535972 Calcium silicate hydrate 0.66, C-S-H 0.66 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The pH during the panning experiment was 8.9. 2417 YHPNGMNPYTKA LPGRAHDPWKVP SATNGSLTRPVH GTTTLNHNYSAK DGNTAARMATLK VPRSMAATHSTF ANHLSGNNYGIS DSASTQFTRADS 8 Phage display (common panning) 4 PMID:24535972 Calcium silicate hydrate 1.0, C-S-H 1.0 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The pH during the panning experiment was 11.6. 2418 LPNHLGAILRAD SSLHSSHHEMNK GTTTLNHNYSAK KFNPGNSEWQRT SKHDTPTYINTV IDRVTSRDPAMN VDTVKHELATYR SATNGSLTRPVH YHPNGMNPYTKA VPRSMAATHSTF GGSIAASELEYY IFAALDYNLGRH 12 Phage display (common panning) 4 PMID:24535972 Calcium silicate hydrate 1.5, C-S-H 1.5 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The pH during the panning experiment was 12.5. 2419 LPNHLGAILRAD YHPNGMNPYTKA GGSIAASELEYY SATNGSLTRPVH TLRVPPNPNMNV VPRSMAATHSTF IEAQYNHSNRFP MTFDTVSNIYKM HAAGIRDNQRLG DGNTAARMATLK TCAKATSTPPLS 11 Phage display (common panning) 4 PMID:24535972 Calcium silicate hydrate 1.7, C-S-H 1.7 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The pH during the panning experiment was 12.5. 2420 TLHDLTRGQRTT(2)[12.748 ± 0.187] ANPYSSTAKPAG(2)[6.660 ± 0.062] RPLTISSAADHF(1)[14.448 ± 0.152] EAHVMHKVAPRP(1)[6.847 ± 0.124] SEPPKAHGVLSS(1)[4.256] LPSPPRIPGHKL(1)[9.473 ± 0.187] NSAAVRAYSPPS(1)[13.522 ± 0.428] QHANHQAWNNLR(1)[8.208 ± 0.028] SHNNSPLSYKPS(1)[9.998 ± 0.097] NFMESLPRLGMH(1)[12.347 ± 0.553] 10 Phage display (competitive panning) 3 PMID:24607635 Salivary pellicle Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Binding assay All the 10 novel salivary pellicle-binding peptides were analyzed for binding to saliva-coated HA. The amount of bound peptide (μg) to saliva-coated HA was reproduced from the graph and shown as means ± S.D (N = 3). In total three rounds of panning were performed. In the first round of panning the pellet, washing was done with 1 ml saliva buffer containing 0.1% Tween-20. In the second and third round of panning the pellet, containing phages bound to saliva-coated HA, was washed ten times with saliva buffer containing 0.5% Tween-20. Binding of SPBP10 (NSAAVRAYSPPS) to HA was evaluated in saliva buffer, containing 1 mM CaCl2. To determine whether SPBP 10 exerts antifouling activity, the effect of treatment of HA with SPBP 10 on the adherence of S. gordonii was evaluated in an in vitro adherence model. In the absence of SPBP10, approximately 7.7e5 CFU/ml S gordonii adhered to the surface of the HA discs. After treatment of HA discs with SPBP 10, the number of adhered bacteria decreased significantly to approximately 3.8e5 CFU/ml ( p ≤ 0.05). Considerably fewer bacteria adhered to saliva-coated discs than to HA discs. After treatment with SPBP 10 the number of adhered bacteria was even lower, but no statistical significance was reached. 2421 AARPVAL ASRPPAP SAGHPKY 3 Phage display (competitive panning) PMID:20412822 Lipopolysaccharide, LPS Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The wells of a microtiter plate were coated with LPS or lipid A by treating with 50 μl of 100 μg/ml LPS or lipid A in phosphate-buffered saline. After washing with 0.05% Tween-20 in PBS (PBST), the wells were blocked with 200 μl of 1% skim milk at 25 °C for 2 h and washed with PBST. Then, 0.1 ml of M13 phagee expressing 7- or 12-residue peptides encoded by random sequences of nucleotides fused with DNA for phage coat protein was added to the wells. After washing off free phage particles, the wells were treated with 0.1 ml of PBS containing 100μg/ml of LPS or lipid A to elute the phages bound to the ligand. Using a 7 residues library, 3 ELISA positive clones from 18 clones were obtained. Among the 7-residue peptides, Li1 (AARPVAL) and Li2 (ASRPPAP) have a common motif, AXRPXA, but this sequence was not found in Li3 (SAGHPKY). Among these 3 peptides, we synthesized AARPVALGGSC by adding 3-residue spacer peptide (GGS) and cysteine at the C-terminus of Li1 . Its binding affinity to LPS, as measured by Biacore, was very weak. 2422 MGHRPPSPSLSG(4) 1 Phage display (competitive panning) PMID:20412822 Lipopolysaccharide, LPS Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The wells of a microtiter plate were coated with LPS or lipid A by treating with 50 μl of 100 μg/ml LPS or lipid A in phosphate-buffered saline. After washing with 0.05% Tween-20 in PBS (PBST), the wells were blocked with 200 μl of 1% skim milk at 25 °C for 2 h and washed with PBST. Then, 0.1 ml of M13 phagee expressing 7- or 12-residue peptides encoded by random sequences of nucleotides fused with DNA for phage coat protein was added to the wells. After washing off free phage particles, the wells were treated with 0.1 ml of PBS containing 100μg/ml of LPS or lipid A to elute the phages bound to the ligand. Four ELISA positive clones were obtained from 18 clones and these 4 clones had the same sequence. 2423 KNYSSSISSIRA 1 Phage display (competitive panning) PMID:20412822 Lipopolysaccharide, LPS Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The wells of a microtiter plate were coated with LPS or lipid A by treating with 50 μl of 100 μg/ml LPS or lipid A in phosphate-buffered saline. After washing with 0.05% Tween-20 in PBS (PBST), the wells were blocked with 200 μl of 1% skim milk at 25 °C for 2 h and washed with PBST. Then, 0.1 ml of M13 phagee expressing 7- or 12-residue peptides encoded by random sequences of nucleotides fused with DNA for phage coat protein was added to the wells. After washing off free phage particles, the wells were treated with 0.1 ml of PBS containing 100μg/ml of LPS or lipid A to elute the phages bound to the ligand. In a 12-residue library, one positive clone (displaying KNYSSSISSIRA) was obtained from 12 clones. 2424 WPHFHHLRVPPV[370] DQRVLPSTFAAD[ND] DRLHHHRHSWKY[ND] HIHKHTVFLNSP[ND] HLKWLPHHRQPM[ND] HYFTWWPHRNPH[ND] KPISHHPHHRAW[ND] QYKTQHIYGYGP[ND] TFTHHRHYPKVV[ND] TPHLHMWHAHKR[ND] WHRHTLAPHSHP[ND] WHRIQIPPAPIL[ND] WPHNWWPHFKVK[ND] WPYHPHRHPEPL[ND] 14 Phage display (common panning) 3 PMID:12659965 Calcium silicate hydrate 1.7, C-S-H 1.7 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The apparent variation in the association and dissociation rates of individual phage-displayed peptides on the LA chip suggests the potential of strategically using SPR technology to rapidly rank the LPS/LA binding affinities of phage-displayed peptides with high throughput. The calculated apparent KD (nM) is 370 nM for LA/11 (WPHFHHLRVPPV). ND denotes not determined. 2425 KSLSRHDHIHHH[0.0055] HFKHKHPEPPGR[ND] YPFHHKHWQRPD[ND] LGRHTHHFWHYP[ND] YPWHSRHAPRVL[ND] YPWTHHHSRWDL[ND] FTRHHHPGFWWN[ND] WGFHYPRYHTLK[ND] WWTPWRLHGGPH[ND] WHKSPKLPLSPV[ND] HLKMFHWSVPPN[ND] APMHKYHSWHKR[ND] WPHQKLHLMRHS[ND] HTYSVYPPRDFK[ND] HILNQRPIYLGT[ND] 15 Phage display (common panning) 3 PMID:12659965 Lipopolysaccharide, LPS Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Surface plasmon resonance (SPR) The apparent variation in the association and dissociation rates of individual phage-displayed peptides on the LA chip suggests the potential of strategically using SPR technology to rapidly rank the LPS/LA binding affinities of phage-displayed peptides with high throughput. The calculated apparent KD (nM) is 0.0055 nM for LPS/10 (KSLSRHDHIHHH). ND denotes not determined.