726 CRNCTVIQFSC CFQPLTPLCRC CQSYHELLLQC CQIPQRTATRC CSVRQGPVQKC CSSCQNSPALC CAKQRTDPGYC CWMSPRHLGTC CHYIAGTVQGC CPLVSLRDHSC CKQSYLHHLLC 11 Phage display (common panning) 3 PMID:15466209 HPV-16 E7 oncoprotein (28-LNDSSEEEDEI-38) Not determined. Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) 727 FTGCSRLLYGWCSLN AWTCLFSTGGICQSS TLICMVKIQVKCPMQ PTWCLEFMITACIRG SAVCVSFENFMCIGP 5 Phage display (common panning) 5 PMID:15996026 PreS region of the large surface antigen (LHB) Not determined. Not determined. Not determined. X3CX7CX3 phage display library 728 QEKIRVRLSA 1 Phage display (common panning) 3 PMID:15980334 TG1 Escherichia coli cells, E.coli Not determined. Not determined. Not determined. X10 phage display library The sequence QEKIRVRLSA showed features common to a variety of antimicrobial peptides: a net positive charge (
2) and a total residue hydrophobic ratio of 40%. However, no obvious similarity to other sequences was found in the Antimicrobial Sequences Database. 729 CIVPWGRYC(6) CLIPWGRFC(4) CLVPWGRYC(3) CAVPWARYC(3) CAVPWGRLC(3) CLVPWARWC(2) CKVPWARWC(1) CLVPWGRLC(1) CNVPWGRYC(1) CDVPWRDLC(1) CVPWRDWTC(1) CIPWGRYFC(1) CAVPWGRYC(1) CIVPWARYC(1) 14 Phage display (common panning) 5 PMID:15946218 Integrin alpha-IIb-beta-3, integrin αIIbβ3 von Willebrand factor (vWF) Not determined. Not determined. CX7C phage display library A CX7C phage display library was used to search for peptides that bind to integrin αIIbβ3 in the presence of GRGDS. Sequencing of the bound phage revealed only four RGD-containing sequences (CWARGDFRC, CEPRGDWRC, CVARGDWRC, CWARGDPRC). Consistent with \r\nselection strategy the majority of sequences lacked RGD and revealed novel binders. The consensus in these sequences was the tri-amino acid motif Val-Pro-Trp (VPW). 730 VGSLR[481000] RQTND[415000] NQRSS[388000] LQRAI[367000] QRLRD[307000] PDRHM[243000] LSGGR[207000] TVDYA[134000] LSRDN[127000] RGKTN[80000] NNKLR[74000] MQVKH[34000] TTDLR[27000] RVTST[26000] AYGYK[24000] STKGI[20000] KLKET[19000] VGLYD[18000] VVMKD[15000] RVDTG[15000] GHRIN[12000] YQSLN[12000] SDKVY[9000] HETLK[9000] TSYLN[9000] MQATK[8000] EAPAK[8000] PVHLY[7000] QPNGY[6000] AYGLA[6000] YQNSS[6000] SAVRP[5000] 32 Phage display (common panning) 6 PMID:15843175 Kallikrein-14, hK14 Not determined. Not determined. Not determined. Substrate phage display library based on a modified pH0508b phagemid Fluorescence The CFP fluorescent substrate assay has been utilized to determine the kinetics of peptide substrate selection from a phage display library. The kinetic parameter kcat/Km (1/M × 1/s) was determined and shown. In fact, the target is recombinant hK14. A SwissProt database search with selected sequences identified six potential human protein substrates for hK14. Two of them, laminin α-5 and collagen IV, which are major components of the extracellular matrix, have been demonstrated to be hydrolyzed efficiently by hK14. 731 SSRFESLFAGEKESR SSKFAALWDPPKLSR SRWQALFDDGTDTSR SRWAEVWDDNSKVSR SSNTPRFKEYFMQSR SRFADFFRNEGLSGSR SSRGLLWDLLTKDSR 7 Phage display (common panning) PMID:15328534 Ligand-binding domain of androgen receptor(AR) Not determined. Not determined. Not determined. X15 phage display library Binding affinities were measured for a selected set of these peptides and their interactions with AR determined by X-ray crystallography. Structures of AR in complex with FxxLF, LxxLL, FxxLW, WxxLF, WxxVW, FxxFF, and FxxYF motifs reveal a changing surface of the AR coactivator binding interface that permits accommodation of both AR-specific aromatic-rich motifs and canonical leucine-rich motifs. 732 PLSQLTFSHLGP PLSQLTDSHLGP NLSRHTYSHPHM LSLNQSSALTRL QTSLYENIGLLR AQPNWTSLRSLP HRSPHFSRHGLL HLAHHFHNRLKL PWTQHKAMSQM YTKASIFTVQPM 10 Phage display (common panning) 3 PMID:15337767 Interferon-binding domain of human p300 Cellular tumor antigen p53 Not determined. Not determined. Ph.D.-12 phage display library (X12) Thirty clones were tested, revealing consensus sequences with over 50% homology to the conserved BOX-I motif within p53. 733 SCPGEDCHTMYPFTYKGY(14)[0.229] TCPGEDCHTMYPFTYRGY(11)[0.197] RCQFSVWSWESLRCEFPY(2)[0.861] VCHAGELPFTFRGVPFPY(2)[0.185] TCPGEDCHSMYPFTYRGY(1)[0.259] RCHQNGVCMHRNVLLTTY(1)[0.149] RCDLYPDGNLWGMPCPTY(1)[0.185] NCNPLEKWCPTVEQTPWY(1)[0.780] 8 Phage display (common panning) 3 PMID:10725425 Anti-VP2 monoclonal antibody 2F2 Outer capsid protein VP2 Not determined. Not determined. XCX15 phage display library ELISA Absorbance at 450 nm were measured. 734 YLTMPTP[0.13] WPTPPYA[0.09] TPHNTVS[0.07] SLPAHAR[0.10] HSSLQTP[0.06] YSIPKSS[0.10] ALQPRYL[0.15] 7 Phage display (subtractive panning) PMID:10747021 Kinase domain of VEGFR2 Vascular endothelial growth factor A, VEGF-A Not determined. Not determined. Ph.D.-7 phage display library (X7) ELISA Absorbance at 490 nm was measured. Data shown were reproduced from the graph. Chinese hamster ovary (CHO) cells expressing a recombinant KDR at their membrane surface were tested for their ability to bind VEGF in a variety of conditions. The last amplified eluate was absorbed twice on non-recombinant CHO cells to enrich for phage clones specifically binding KDR. At the end of the selection, 24 clones were isolated and analyzed. DNA sequencing showed that seven independent peptides had been selected, with no sequence homology. 735 ATWLPPR[1.01] NPRALNY[0.54] ANLFKAK[0.54] YHSSFQA[0.57] ILDNYKL[0.65] LPPNPTK[0.96] YAIMPLV[0.71] 7 Phage display (common panning) 3 PMID:10747021 Anti-human VEGF monoclonal antibody Vascular endothelial growth factor A, VEGF-A Not determined. Not determined. Ph.D.-7 phage display library (X7) ELISA Absorbance at 490 nm was measured. Data shown were reproduced from the graph. 736 SSNHQSSRLIELLSR GSEPKSRLLELLSAPVTDV VESGSSRLMQLLMANDLLT HPTHSSRLWELLMEATPTM QEAHGPLLWNLLSRSDTDW HVYQHPLLLSLLSSEHESG HVEMHPLLMGLLMESQWGA GHEPLTLLERLLMDDKQAV LPYEGSLLLKLLRAPVEEV SGWENSILYSLLSDRVSLD AHGESSLLAWLLSGEYSSA GVFCDSILCQLLAHDNARL HHNGHSILYGLLAGSDAPS LGERASLLDMLLRQENPAW SGWNESILYRLLQADAFDV PSGGSSVLEYLLTHSTSIL PVGEPGLLWRLLSAPVWRE S-R-L-x(2)-L(2), P-[AVLIFYW]-L-x(2)-L, [ST]-[AVLIFYW]-L-x(2)-L(2) 17 Phage display (common panning) 3 PMID:10567548 Estrogen receptor, ER Not determined. Not determined. Not determined. (X)7LXXLL(X)7 library Peptides were classified into three different classes based on sequences flanking the conserved LXXLL motif. Peptide #293 was obtained in a similar manner from random peptide libraries. 737 FHYEIWIPPHRG(6) SSPWWLVSFTST(3) SWMTTPWGFLHP(2) SHSLIWRIPLLH(2) IYVPWYYAENLP(2) YNYSWNGVVFVP(1) AQSTPLMKPQKS(1) DQTTLQRFLGSH(1) QTIKPPITVHPS(1) QYNHILGYLPFQ(1) IMDPQNSKVTVA(1) LPIQNAKRSMVS(1) IMSPWDESFWNY(1) ASESYVLFPGTR(1) SNWHGPLSYQLM(1) ALPLQDTAATLS(1) QEIYLTPRGPQQ(1) IDRTQMWRQSDL(1) INRDHPLHAGQP(1) HQTPQSLARWSL(1) HSLRAIQLITGM(1) LPSHHHHRVPAA(1) IPTYHHHHPSLR(1) QMTHHHTHRPPI(1) DLHSHHHGHMNH(1) SMHHHHRPASPT(1) WIGDAKSSLHHA(1) HNHPHTTSHVSM(1) HNSIIYHWHTLP(1) HFNHNHRGFHLI(1) AASPHYSSSHSH(1) 31 Phage display (common panning) 4 PMID:10619429 60 kDa chaperonin Not determined. Not determined. 1DKD, Ph.D.-12 phage display library (X12) The authors have determined the crystal structures of the complexes formed by the most strongly bound peptide with the isolated apical domain, and with GroEL (PDB ID: 1DKD). The peptide interacts with the groove between paired α helices in a manner similar to that of the GroES mobile loop. 738 LNTKWLRGD(10) LPNPWVRGD(9) RDCAWCRGD(6) LKNPWQRGD(3) VNNKWARGD(3) VNTKWLRGD(3) KECAWCRGF(3) DWKARREG(3) YPGWPRKDL(3) YKNPWIRGM(2) WNKAWVRGS(2) FRCSWCRGE(2) GECRWCKGD(2) RIVRGVGGT(1) LNKAWVRGS(1) NANPWSRGF(1) LTNKWMRGD(1) IGGPWRRGF(1) INKAWVRGM(1) VSSPWVRGG(1) YISPWVRGF(1) AQSSWVRGN(1) VGGSWVRGS(1) GVRWWG(1) TSHWVRDTS(1) GWIKYRLEG(1) YPGWGRNDA(1) YPGWDRADK(1) YPGWPRSDY(1) [GAVLIMP]-[NK](2)-[PK]-W(0,1)-VRG-[DE] 29 Phage display (common panning) 3 PMID:11027685 Anti-Cyt b monoclonal antibodies 7D5 Cytochrome b-245 Not determined. Not determined. J404 phage display library (X9) The antibody 7D5, secreted by the hybridoma, bound to solubilized cytochrome b of the neutrophils but not to other proteins such as emoglobin, myeloperoxidase, and pig cytochrome P-450. 739 GPLGLS[+++] GPLGLK[+++] VRPLGI[++] APLGMS[+++] PLSISG[+++] PLQFRG[+++] PLTMMG[+++] PLPMRM[++] APLAMR[+++] PLSIQD[+++] PLSFQG[+++] VLPLPM[+++] PLSLLS[+++] PAGLSD[+++] PRGLVA[+++] PKGLRA[+++] PYGMRA[+++] PVALKA[+++] PKGVYS[+++] PKGITS[+++] PSGIHV[+++] PFGFKS[+++] GPPMSL[+++] PINLHG[+++] PHPLFL[++] PSELKG[++] MAPYAL[+++] PFAFQG[+++] PSAYHS[+++] PMSYNA[+++] PAEIVA[+++] PMEMVE[++] VTPYNM[+++] PPRAIR[+++] PRPFNY[+++] PLGMRG 35 Phage display (common panning) 2-5 PMID:10906330 Collagenase 3 Not determined. Not determined. Not determined. fTC-LIB-N6 phage display library Western blot +++ strong cleavage; ++ some cleavage; + less cleavage; ND no cleavage of phage by human collagenase 3 detected by Western blotting. The selected phages were shown to be more sensitive by Western blot analysis to human collagenase 3 treatment than the positive control phage fTCol-3S (Western blotting result, [+]) with the sequences of PLGLWAR and the negative control phage fTCol-3R (NPVEPA) (Western blotting result, [ND]). Phage display screening also selected five substrate sequences that share sequence homology with a major MMP cleavage sequence in aggrecan and seven substrate sequences that share sequence homology with the primary collagenase cleavage site of human type II collagen. In addition, putative cleavage sites similar to the consensus sequence are found in human type IV collagen. 740 TLIPRSFCPTHDRDC(6)[0.37] TARVFLLGSCRSCGP(2)[0.20] VRLDHGVWGSRLSLP(2)[0.37] SSSSFVLWLLRPGFS(2)[0.65] LVWISPPPGLFASFV(2)[0.23] WTSPWLLDYPVPSGA(1)[0.09] ASLMLLGGTSGPVTH(1)[0.16] RSKGVKFNLSGVFQA(1)[0.17] L-W-L(2) 8 Phage display (common panning) 3 PMID:11058544 Human spermatozoa Zona pellucida sperm-binding protein 3 Not determined. Not determined. f3-15mer phage display library (X15) ELISA Clones M1–M12 and a random unselected clone MR2, used as a control, were added to the plates coated with paraformaldehyde-fixed sperm. After repeated washing bound phage were detected by incubating with an anti-M13 phage antibody conjugated to HRP and measurements carried out at 450 nm. The A450 value of the control phage clone MR2 was 0.05 and clones with A450 less than 0.05 represent non-binders. Data shown were reproduced from the graph. SSSSFVLWLLRPGFS displayed a high level of affinity for the sperm surface and showed sequence homology with a dominant human ZP3 epitope (hZP 25-33). 741 HWPRPDDSFWRP(10) TSNFINRMNPGL(4) TLWSTSPLTNKL(2) TLSRITVSTFTH(2) NKWPLAHSQKKR(2) L-W-L(2) 5 Phage display (common panning) 3 PMID:11058544 Human spermatozoa Zona pellucida sperm-binding protein 3 Not determined. Not determined. Ph.D.-12 phage display library (X12) 742 RINNIPWSEAMM(8)[0.0087 ± 0.0021, 0.0061 ± 0.0016, 0.0094 ± 0.0005][-8.90] CHPLTPWEC(6)[>500, >500, >500][383.90] TSPYEDWQTYLM(5)[>500, >500, >500][463.14] FWHPMHD(4)[>500, 68 ± 4, >500][94.28] SWPWDTW(3)[>130, 21, ND][74.36] DTHRWPWYISQE(1)[500, 259 ± 12, 348 ± 3][88.35] SPWYSDYTRYLW(1)[>140, >140, ND][373.94] SDPYKLWASYMY(1)[>100, >100, ND][528.60] QPASNMTLGRGL(1)[NT][NT] SSVDESTAQVNW(1)[NT][NT] 10 Phage display (competitive panning) 8 PMID:10364331 Envelope glycoprotein gp120 (SU) Anti-gp120 monoclonal antibody 17b 1G9M,1G9N,1GC1,1RZJ,1RZK,2NXY,2NXZ,2NY0,2NY1,2NY2,2NY3,2NY4,2NY5, Not determined. Ph.D.-12, Ph.D.-7 and Ph.D.-C7C phage display library pool ELISA,Surface plasmon resonance (SPR) The inhibitory capacities of the identified peptides were tested with gp120 from an additional T-tropic strain (HXB2 and SF2) and an M-tropic strain (ADA). IC50s (μm, means ± standard errors) for inhibition of the 4dCD4-gp120 interaction was measured by competition ELISA. NT, not tested. ND, not determined. Besides, surface plasmon resonance (SPR) binding assays were performed on a Biacore (Piscataway, N.J.) instrument. The MAb 17b was coupled to a CM5 sensor chip. MAb 17b was dissolved in 10 mM acetic acid-sodium acetate buffer (pH 4.9). The surface was regenerated twice with 5 ml of 4.5 M MgCl2 after gp120 binding. Sequential injections (20 μl) of HXB2-gp120 (200 nM) with peptide at increasing concentrations (0.2 to 200 μM) were made over a surface with 1,500 RU of coupled MAb 17b. The amount of gp120 bound (expressed as surface plasmon resonance units [RU]) was measured 10 s after the end of the injection and by subtracting RUs bound for the same solution on a blank mock-coupled surface. Results are given as the percentage of gp120 bound relative to gp120 bound in the absence of peptide: 100 + 100 × [(RU - RUgp120)/RUgp120]. The data shown in the second square bracket were reproduced from FIG. 4 in the reference. In the first round of selection, bound phage were eluted with glycine of BSA. In subsequent rounds of selection, phage were eluted with solution of gp160(502-516) in PBSTB. RINNIPWSEAMM inhibit the interaction between gp120 and both four-domain soluble CD4 (4dCD4) and monoclonal antibody (MAb) 17b, a neutralizing antibody that covers the chemokine receptor binding surface on gp120. 743 PCQRAIFQSICN[0.40] 1 Phage display (in vivo) 4 PMID:11687659 Mosquito salivary gland Plasmodium Not determined. Not determined. LX-8 phage display library (XCX8CX) ELISA The absorbance at 450 nm was measured. Data shown were reproduced from the graph. For selection of phages that bind to salivary glands, 10 adult Anopheles gambiae females were dissected 30 min after injecting about 1.0e11 phages into their hemocoels. After the fourth round of selection, over one-third of the phages recovered from salivary glands displayed PCQRAIFQSICN. This peptide strongly inhibited Plasmodium invasion of salivary gland and midgut epithelia. 744 PCQRAIFQSICN[0.24] 1 Phage display (in vivo) 4 PMID:11687659 Mosquito midgut lumen Plasmodium Not determined. Not determined. LX-8 phage display library (XCX8CX) ELISA The absorbance at 450 nm was measured. Data shown were reproduced from the graph. For selection of phages that bind to the midgut lumen, phages (1e15/ml) suspended in 1 mg/ml of gamma globulin/120mM NaCl/20mM NaHCO3 were fed to the mosquitoes, and midguts were dissected 30 min later. After the fourth round of selection, almost half of the phages from midguts displayed PCQRAIFQSICN. This peptide strongly inhibited Plasmodium invasion of salivary gland and midgut epithelia. 745 TDITLF(18) FHFYAF(2) 2 Phage display (common panning) 3 PMID:10967104 TrpE protein Not determined. Not determined. Not determined. f3-6mer phage display library (X6) The TrpE proteins immobilized using anti-TrpE antibodies and protein A-Sepharose beads. 746 AARNSP(14) IARIRV(6) [LI]-A-[RK]-I-R 2 Phage display (common panning) 3 PMID:10967104 p85-N-SH2 domain Serine/threonine-protein kinase A-Raf Not determined. Not determined. f3-6mer phage display library (X6) The TrpE-p85-N-SH2 fusion proteins immobilized using anti-TrpE antibodies and protein A-Sepharose beads. 747 AIARIR(11) LARIRS(7) AKIRF(2) FTHGLA(1) [LI]-A-[RK]-I-R 4 Phage display (common panning) 3 PMID:10967104 p85-C-SH2 domain Serine/threonine-protein kinase A-Raf Not determined. Not determined. f3-6mer phage display library (X6) The TrpE-p85-C-SH2 fusion proteins immobilized using anti-TrpE antibodies and protein A-Sepharose beads. 748 WANANY(10) LDSFYF(3) GDYTLF(2) TRDSFN(1) EPGLRF(1) SEDGHF(1) AVRGYR(1) GRIDYA(1) FHAFAL(1) TWASGA(1) 10 Phage display (common panning) 3 PMID:10967104 PLCγ1-N-SH2 domain Not determined. Not determined. Not determined. f3-6mer phage display library (X6) The TrpE-PLC The sequence GDYTLF is selected by each of the SH2 domains of GAP. 749 GDYTLF(9) RWYIDD(2) WLEVGK(1) SWAVNR(1) QASPIL(1) VRELVR(1) RYVFNH(1) FTASGA(1) VSDIDQ(1) ALPDTL(1) ITTHMH(1) IYYFLS(1) APARMP(1) 13 Phage display (common panning) 3 PMID:10967104 PLCγ1-C-SH2 domain Not determined. Not determined. Not determined. f3-6mer phage display library (X6) The TrpE-PLC The sequence GDYTLF is selected by each of the SH2 domains of GAP. 750 GDYTLF(4) FAQVWG(3) GSGSWG(1) SFVAYA(1) YVNADA(1) HWFLRH(1) VGWHK(1) GITPNH(1) DSWYRD(1) YPAHGL(1) FSFRFD(1) 11 Phage display (common panning) 3 PMID:10967104 GAP-N-SH2 domain Not determined. Not determined. Not determined. f3-6mer phage display library (X6) The TrpE-GAP-N-SH2 fusion proteins immobilized using anti-TrpE antibodies and protein A-Sepharose beads. The sequence GDYTLF is selected by each of the SH2 domains of PLCγ1.