1676 PRILMR(0.2) PRLLAP(0.075) PRILLP(0.0375) PRLLQP(0.0375) PRVLAL(0.0375) PRVLAP(0.025) PRLLVL(0.025) PRLLHL(0.025) PRLVQR(0.025) PKLLAP(0.0125) P-R-x-L-x(2) 10 Phage display (subtractive panning) 5 PMID:12203838 Cationic trypsin Trypsin inhibitor 2 Not determined. Not determined. EETI-II mRNA display library (X6) Potential column binders were removed from the reverse transcribed EETI-II fusion library (1 pmol in 700μl) by incubating the library with 100μl CL-sepharose beads (Sigma) for 15 min at room temperature. The cDNA pool from the fifth round of selection was cloned and 108 clones were sequenced. The sequence analysis revealed that wild-type EETI-II represented 20% of the clones. The binding efficiency of each clone was determined and, unexpectedly, a lower percentage of wild-type bound than any of the other screened clones; despite the fact that the wild-type clone bound the tightest, followed closely by the P(1)-lysine variant. 1677 CASVISEREC(1) EEYLVSEYVM(1) RQYLISEYEH(1) LQRLISEQMF(1) IVRLLSEYHM(1) EEYLLSEYVM(1) MQNLISEHEL(1) TMDLIPEHYM(1) EQKLISEEDL(1) DMMLISEKEL(1) FQALIAEEEL(1) QRVLISEFWL(1) x-[QE]-x-L-I-S-E-x(2)-[LM] 12 mRNA display (common panning) 5-6 PMID:12203838 Anti-c-myc monoclonal antibody 9E10 Myc proto-oncogene protein Not determined. Not determined. c-myc mRNA display library (X27) The cDNA pools from the fifth and sixth rounds were cloned and 116 colonies were sequenced. As presented in Table 3, two selected clones contained the sequence of the wild-type c-Myc epitope (EQKLISEEDL). A third clone differed from the wild-type by two point mutations in the nucleotide sequence, only one of which altered an amino acid (Ile to Val). The consensus sequence selected [X(Q,E)XLISEXX(L,M)] included the full length 10 amino acid wild-type sequence; identical or homologous sequences to the four of the core residues, LISE, were conserved in 86% of the 116 clones examined. Experiments confirmed the specific binding of the RNA-peptide fusions to the antigen-binding site of the anti-c-Myc monoclonal antibody. The selected sequences bound the c-Myc antibody with an affinity similar to that of the wild-type Myc fusion. 1678 LYDIDRNWVGHPQG(5) NYDADLAWDTHPQD(4) MHSDLDNMWETHPQ(1) ITDWLSHPQGPRSN(1) MYSADDTFRHMHPQ(1) CFNGQEDRINHPQG(1) DVGSWSGNEFIHPQ(1) DLSSPWLVGHPQAT(1) YWNSNDMAMHPQVN(1) SINLMDRFASHPQA(1) VEAWLDERVPLVET(3) VEAWLADRSQVSPN(1) VCAWLEVESHPVRE(1) VLSWLESNSVRITR(1) VEAWIADPAVHFTT(2) VEAWISYQSPLPDQ(1) VEAWIMHPCPLCSC(1) VESWVEQYSVPIVP(1) VNAWVSNMDCKECR(1) LYKVPSHCHPMMPC(2) EYLSGVQFATWQCP(1) TWTVGCSCMMACVH(1) CLAVLQNEVHPVYD(1) GMTEWWYGLRCVVA(1) SFNGFQNEGHPLDD(1) HPQ, DVEAW, D-V-x(2)-W 25 Ribosome display (common panning) 7 PMID:12758084 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. [VGAED]-X(14) ribosome display library The 37 randomly chosen clones were sequenced: 26 different sequences were observed and 46% of the sequenced clones contained the HPQ motif. Of the clones sequenced, 32% carried the unknown DVEAW or DVXXW motif. The remaining 22% of the sequenced clones revealed no further motif. 1679 RQERSSLSKPVV(12) 1 Ribosome display (common panning) PMID:16269342 Prepilin Not determined. Not determined. Not determined. X12 ribosome display library The random ribosome display system was used, and mRNA-attached peptide products bound to prePilS-GST-Sepharose 4B beads. An unmeasureably small fraction of total mRNA product was bead-associated. A 12-mer peptide (RQERSSLSKPVV), binding to the structural protein PilS of the type IVB pili of S. Typhi, was isolated with a ribosome display system. This peptide was designated as peptide R. Authors found that peptide R inhibited adhesion to/invasion of human monocytic THP-1 cells by piliated S. Typhi bacteria, but had no effects on nonpiliated S. Typhi bacteria. 1680 VWAWVFGASTRERARVGWQGY(1) CFVLPGVRPCSSHILTLSFSY(1) EGVRDMFRRCLWISLRSWCVH(1) GGVYASCASYLLALRSRVGGN(1) SDSASVSRVGGLWPTCCPH(1) WGRVDNSGSWGRVGAPWRYLH(1) CAAVYLVTSLFGIVTGVREDH(1) DSRGVRAFACDYVLFVLWVPY(1) DLAPVRVGFYNALRELRVFRY(1) RVGALRYFMVWYLMWFFLLFH(1) PVLDAGSVYLGYLGVRFLSY(1) VRNRVIARVGGVPYVGGPCYN(1) ACCLVRFYSHGRGKRVGFLWY(1) LRYSGLLGFPLWVGRIFVCVD(1) RMRCVSLELVVYGGGVRMWEN(1) FMGYGRSVWVVSSSLVLCIYD(1) ARMLWGRGTTLLLIRRRVSAY(1) VDLSWYASCRVSICVFVVVY(1) WPNYQSREHMALRSRMYYYFY(1) CVVALRNVKAAALIPGVVSRH(1) WWCLLGYWALGGNHSAALRSY(1) YGSYLEALRWGTSACWALRY(1) GVAVDCAVVGWALRVLGVHSY(1) RCLEAGKIWWGALRSHLAVYD(1) GSGSAVGWALRSYASGLAIAY(1) HAWARWMGWGHGGVLSWALRY(1) FVSWALRYSRCLVWLCWFPNY(1) VKGNPVFDHRHFSLWGALREY(1) FVQHWSFTAGSRSDRAPYPGH(1) AGWVNALRMWSLMPLMWLWSY(1) DRTTGRWFYIRRTAEVLGWTY(1) RFINPTSHCFGSLSLWRQLSY(1) VGCLVSVGSVWGCSSVVVRVY(1) RMESGAPLAAYGKMRLRPGTH(1) VWNRVIARVGGVLYVGGPCTN(1) SGHMHSYWPTTWILVLIRRTY(1) LEVLVWYSLWSYWLDVAAASH(1) SWGGGFYDWSYVGGGAYWAY(1) MGLFRSYKYRFVHDSESSFN(1) MALYLAWYGCSDSAVVMLADD(1) MYCWRMLANSCALRMVLAMRN(1) VIVNVAVLYRRCWPCAEFWPY(1) RLGSFYPLLWRLVSHEYSLWH(1) RYWFGRWRCFYGPFVSSYFLY(1) VCCCRCLPWSYMCEWGSMRLY(1) VLKIHSWHNWVYGVMLYDMEY(1) MGYAWDLALRMGPYFLMDLIN(1) SDKCAPVCYVMDRLCLANWD(1) ALR, RVG 48 Ribosome display (common panning) 5 PMID:16878349 Model membranes Not determined. Not determined. Not determined. X20-[YHND] ribosome display library Following stabilization of the peptide-ribosome-mRNA complex by addition of 50 mM Mg(2+), it was incubated with the model membrane immobilized on magnetic beads via streptavidin. mRNA was eluted from the bound complex in buffer containing EDTA. Of the resultant colonies, 50 clones were sequenced, 48 of which encoded 21 amino acids without a deletion. Authors obtained a high frequency of motifs consisting of several specific amino acids (e.g. ALR, RVG) in the peptides obtained from the random peptide library. These motifs consisted of a basic amino acid, K or R, and several hydrophobic amino acids, and may represent the minimum units essential for interaction with the bacterial membrane. 1681 RPVFRTYRSVVKSG(1) NRACLKRPRYLRKH(1) KACVRFSKSTSKRY(1) RFRPKAVRYRIKFN(1) RSHFRRVKRHSKTP(1) KDVLRNHKHSDRVG(1) KSARKVLKLYRKIT(1) KKNSCRDGRFSRKC(1) KGYFRGRRSYLRAF(1) KGCAKVLKRITRHI(1) KGRHRHCRYILRGN(1) KCTFRRRVLIIKPS(1) KTDWFKVLMTFLMD(1) RGFVRLIKPYAEAS(1) RNLCRSLRSHLEA(1) KIPGRFTRAGRKTT(1) KSDHKVLKNLPKTI(1) RRTGRIDKVSVKAY(1) KVLIKLAKCCIRIS(1) RAACRDSKLCSRYY(1) KHFVRCPKCAVRSS(1) KISDRNSKHHCRSS(1) KVGLIVDKASVKTA(1) RDVCKSSRHSHKGS(1) RFVSKGTDAINRRS(1) KGNCRLYRLRCKVV(1) RLLLKAVRFCCKCF(1) KGGGKVGKHTRSR(2) RHFRKNCKFCHRHC(1) KRCTKVLRAYTKLT(1) KSYGKAPKFVGRIC(1) RAAIRHFRSATKRP(1) KYSARFCKYGGRSH(1) RFTARVRKSVFRSC(1) KVYSRSSKSAHKCF(1) KRAYKDARHIYLCS(1) KIFVRTIRAAHKRD(1) KSLTKCCKVLRLSC(1) RCDIKSVKHILRCS(1) KASVRNSKVLPRFC(1) KGAFRLAKVLIRHY(1) RHVPKANKGADRSC(1) KTSWVRAAALVVVH(1) KSVNKDVRISLRD(1) KCIARRGRLPVKRY(1) KVLFRHARSSCKHY(1) KVL 46 Ribosome display (common panning) PMID:16878349 Model membranes Not determined. Not determined. Not determined. ZXXXZXXZXXXZXX ribosome display library Following stabilization of the peptide-ribosome-mRNA complex by addition of 50 mM Mg(2+), it was incubated with the model membrane immobilized on magnetic beads via streptavidin. mRNA was eluted from the bound complex in buffer containing EDTA. Of the resultant colonies, 50 clones were subjected to sequencing, of which 47 encoded a full-length peptide without a deletion. Sequences such as KVZ and RVZ were present in several of the peptides, and K/R was often followed by a hydrophobic amino acid in most of these, and rarely by a hydrophilic but nonpolar amino acid, but never by a basic or acidic amino acid. 1682 HHCRGHTVHSHHRCIG(6)[94] HHCRGHTVHSHHHCIR(2)[70] HHCRGHTVHSHHRCII(2)[NT] 3 Ribosome display (subtractive panning) 6 PMID:18613123 Cobalt(II) complex, Co(II) Not determined. Not determined. Not determined. X(2)-C-X(10)-C-X(2) ribosome display library ELISA,Surface plasmon resonance (SPR) SPR measurements were performed on a Biacore 2000 instrument with CM5 sensor chip. The dissociation constants KD (μM) were shown. NT denotes not tested. In vitro selection was carried out for the cobalt(II) complex immobilized on resin (Co-IR). The ribosomal conjugates displaying peptides with specific affinities to Co-IR were eluted and dissociated by adding imidazole and EDTA solutions to recover the corresponding mRNAs. Before the fourth, fifth, and sixth rounds of selection, the translation solution was incubated with bare resins for 40 min to exclude mRNAs of peptides that bound nonspecifically to bare resins. After six rounds of selection, 20 clones were chosen from the selected library and the sequences were analyzed. Table shows the peptide sequences that were found in more than two clones. The sequences were histidine-rich and similar to each other. In the major group of peptides, six histidines were found in 14 amino acid sequences except for the cysteines for cyclization. 1683 DYKGLDRGVI DYKFEDNLEC DYKFLDEVQN DYKWEDKVCI ARILDCKMDDD DYKMMDRRDF DYKCHDTGTD ALRSDYKWTD VDYQLRGAGY DYKSTDKWGY DYKPSVNEGG AYAIDYKRTD ISRDYKVDDA GDYKFADDMA TSHWDYKCWE SYKDFDLRKG DYKFMGYVAS FDDYKMTDIY D-Y-K-x(2)-D 18 Ribosome display (competitive panning) 2 PMID:19228777 Anti-FLAG M2 monoclonal antibody FLAG fusion protein Not determined. Not determined. X10 ribosome display library Dynabeads M-280 Streptavidin (Invitrogen, Carlsbad, CA, USA) was used for the immobilization of biotinylated anti-FLAG M2 antibody. To eliminate non-specific ternary complexes, the library was then incubated with 50ml magnetic beads without ligands for 30 min at room temperature. Remained supernatant was incubated with monoclonal antibody-immobilized magnetic beads for 1 h at room temperature. Elution of the ternary complex was carried out by the addition of Wash buffer with 100 mg/ml FLAG peptide in the case of competitive elution. The library after the second round of selection was cloned and sequenced. Out of 19 randomly picked clones, 12 clones possessed the consensus epitope equence for the anti-FLAG M2 antibody (DYKXXD), six possessed a partial epitope sequence and only one did not possess any consensus sequence. 1684 STKFDSVFGV(12) YLDSCCRSPW(9) STKFDALCSG(3) 3 Ribosome display (competitive panning) 3 PMID:19228777 Anti-β-cat monoclonal antibody 36a Catenin beta-1 Not determined. Not determined. X10 ribosome display library Dynabeads Protein G (Invitrogen, Carlsbad, CA, USA) was used for the immobilization of anti-b-Cat mAbs. To eliminate non-specific ternary complexes, the library was then incubated with 50ml magnetic beads without ligands for 30 min at room temperature. Remained supernatant was incubated with monoclonal antibody-immobilized magnetic beads for 1 h at room temperature. Elution of the ternary complex was carried out by the addition of Wash buffer with 20 nM β-Cat in the case of competitive elution. Irrespective of the selection round, obtained sequences contained putative epitope motifs that were found in the sequence of the original antigen, β-Cat. STKFD sequence, which has a homology for the β-Cat(111-115) (STQFD; amino acid residues 111-115 of β-Cat), was observed in the selected peptides. The YLDS sequence that is identical to the β-Cat(29-32) (YLDS; amino acid residues 29-32 of β-Cat) was also found. 1685 TLVMDLNAIE(7) TLVVGLDAID(1) 2 Ribosome display (competitive panning) 3 PMID:19228777 Anti-β-cat monoclonal antibody 48a Catenin beta-1 Not determined. Not determined. X10 ribosome display library Dynabeads Protein G (Invitrogen, Carlsbad, CA, USA) was used for the immobilization of anti-b-Cat mAbs. To eliminate non-specific ternary complexes, the library was then incubated with 50ml magnetic beads without ligands for 30 min at room temperature. Remained supernatant was incubated with monoclonal antibody-immobilized magnetic beads for 1 h at room temperature. Elution of the ternary complex was carried out by the addition of Wash buffer with 20 nM β-Cat in the case of competitive elution. Irrespective of the selection round, obtained sequences contained putative epitope motifs that were found in the sequence of the original antigen, β-Cat. TLVMDLNAIE sequence and a related sequence (TLVVGLDAID), which have a homology for the β-Cat(3-15) (TQADLMELDMAME; amino acid residues 3-15 of β-Cat), were found to be enriched. 1686 GFGRYRRHGSPW(1)[50] MAIGPYPACGSG(1)[43] LSVLVISMFNAV(1)[NB] MARHRNWPLVMV(1)[19] 4 Ribosome display (subtractive panning) 12 PMID:20479194 Envelope glycoprotein E2 Not determined. Not determined. Not determined. X12 ribosome display library Surface plasmon resonance (SPR) SPR measurements were performed using a Biacore 1000 biosensor. The dissociation constants KD (nM) were shown. NB denotes no binding. E2-GST-Sepharose 4B was utilized as a selection target. GST-Sepharose 4B was utilized as a counterselection target. Thirty individual clones were selected for DNA sequencing and then translated into 12-mer amino acid sequences. The results of an NCBI BLAST analysis showed that the four selected 12-mer peptides have protein-binding potentials. The selected peptide MARHRNWPLVMV demonstrated the highest specificity and affinity to the HCV E2 protein. Furthermore, amino acids 489 to 508 (YPPRPCGIVPAKSVCGPVYC) of E2 were identified as crucial for binding to PE2D. The selected peptides, especially MARHRNWPLVMV, not only dramatically blocked E2 protein binding to hepatocytes but also dramatically inhibited HCV cell culture (HCVcc) entry into hepatocytes. HCVcc and HCV particles from HCV patient serum samples could also be specifically captured using peptide MARHRNWPLVMV. 1687 RSDRGKAHPSRRS(1) RSSGYMTDTGPRSKHHPRNRETRS(1) RSVHASHHHIMRS(1) RSRLGHPVNHHRSRLAEQISQRRS(1) RSHARAERHHQRS(1) RSESRVDPAADRSHARAERHHQRS(1) RSFSVTSYSNGRSVGQVEPAGRRSQPPDVTRPRRS(1) RSVLRHLHLRRRSGDDLHETAARS(1) RSKLGHSPTIHRSEDQSAQAHARS(1) RSLQLRTGPGLRSHPIGRRTKHRS(1) RSGVHRNRIHKRS(1) RSHELHTHARSRS(1) RSQLARHHKHIRS(1) RSTGIHVIHHMRS(1) RSMNPRTHATTRSNMHHAAGASRS(1) 15 Bacterial display (common panning) 3 PMID:11722894 Zinc ion, Zn(2+) Not determined. Not determined. Not determined. X9 E. coli bacterial display library Bacterial cells were bound to zinc ions by use of stripped Ni(2+)-nitrilotriacetic acid (NTA) solid matrix (Qiagen) recoated with Zn(2+) by a standard method. Of the 20 clones, 15 displayed a Zn(2+)-binding phenotype. None of the isolated sequences showed similarity to known Zn(2+)-binding proteins, indicating that completely novel Zn(2+)-binding peptide sequences had been isolated. By changing the protein scaffold system, we demonstrated that the Zn(2+)-binding seems to be uniquely mediated by the peptide insert and to be independent of the sequence of the carrier protein. 1688 EWACNDRGFNCQLQR(1)[1] FPIYNQRGFITLASP(1)[3] MIFNSRGFLSLMSSG(1)[8] YPPRFQYYRFYYRGP(1)[5] HMRWNTRGFLYPAMS(1)[NT] RYIMNHRGFYIFVPR(1)[NT] VRTWNDRGFQQSVDR(1)[NT] LMNWRGFMVPRESPK(1)[NT] WTKLKNSRGFELQLD(1)[NT] PYLNARGFSVTREQI(1)[NT] TDFLSYYRVYRTPLQ(1)[NT] TFMPSYYRSWGPPPT(1)[NT] TTCKYYLSCRWRKDL(1)[NT] I-x-N-x-R-G-F, SYYRSY 13 Bacterial display (subtractive panning) PMID:15531628 C-reactive protein Not determined. Not determined. Not determined. X15 E. coli bacterial display library Flow Cytometry The apparent binding affinities of a subset of the selected peptides were determined using flow cytometric analysis. KDs (nM) measured by flow cytometry were shown. NT denotes not tested. For negative selection, 150ml of streptavidin-coated magnetic beads (QIAgen) were incubated with cells. For positive selection, biotinylated antigen (typically 1-100 nM) was added to the supernatant fraction and incubated on ice for 30-60 min. Cells were centrifuged as above and resuspended in 7.5 ml of cold PBS with 150ml of streptavidin-coated magnetic particles (QIAgen or Miltenyi). Consensus sequences were readily apparent for the target protein after two to three rounds of magnetic selection and one or two rounds of FACS. 1689 RLEICQNVCYYLGTL(1)[10] ICSYVMYTTCFLRVY(1)[8] TVLICMNICWTGETQ(1)[4] VTSLCMNVCYSLTTY(1)[NT] YWVCMNVCMYYTARQ(1)[NT] LPVWCVMHVCLTSSR(1)[NT] NEWYCQNVCERMPHS(1)[NT] IMMECFYVCTIANTQ(1)[NT] TWVQCTMVCYGMSTT(1)[NT] SITICWYTCMVQKTA(1)[NT] ADTICWYVCTISVHA(1)[NT] ICMNVC 11 Bacterial display (common panning) PMID:15531628 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. X15 E. coli bacterial display library Surface plasmon resonance (SPR),Flow Cytometry The apparent binding affinities of a subset of the selected peptides were determined using flow cytometric analysis. KDs (nM) measured by flow cytometry were shown. Besides, the YFP-SA-1(RLEICQNVCYYLGTL) insertional fusion exhibited an equilibrium dissociation constant of ~50 μM, as determined using surface plasmon resonance with 200 RU of immobilized streptavidin. NT denotes not tested. Consensus sequences were readily apparent for the target protein after two to three rounds of magnetic selection and one or two rounds of FACS. 1690 NPFCSWYRWRNWCTK(1) RHLYCWTWRWCHFKD(1) SYISTWLNFLFCGQS(1) NNYSAWLRCLLRAYS(1) C-x-W-x(2)-W-R-x-W, S-x-W-L-x(2)-L-x(4)-S 4 Bacterial display (common panning) PMID:15531628 Human serum albumin Not determined. Not determined. Not determined. X15 E. coli bacterial display library For negative selection, 150ml of streptavidin-coated magnetic beads (QIAgen) were incubated with cells. For positive selection, biotinylated antigen (typically 1-100 nM) was added to the supernatant fraction and incubated on ice for 30-60 min. Cells were centrifuged as above and resuspended in 7.5 ml of cold PBS with 150ml of streptavidin-coated magnetic particles (QIAgen or Miltenyi). Consensus sequences were readily apparent for the target protein after two to three rounds of magnetic selection and one or two rounds of FACS. 1691 GDTWVWYCWYWTRSI(1) WVCTWNYWTRVTWCL(1) PWCWMWTKGRWYYVA(1) QIQWCWVNHRWSPVV(1) WVAGYWWCWSVMYRS(1) TWTWCWRNYIWQLST(1) QEWRQLTRWCWVQIK(1) QTATVSYWCYWWWKV(1) W-V-x(4)-Y-W-T-R, W-C-W-x(3)-K 8 Bacterial display (common panning) PMID:15531628 Surface protein gp120, SU Not determined. Not determined. Not determined. X15 E. coli bacterial display library For negative selection, 150ml of streptavidin-coated magnetic beads (QIAgen) were incubated with cells. For positive selection, biotinylated antigen (typically 1-100 nM) was added to the supernatant fraction and incubated on ice for 30-60 min. Cells were centrifuged as above and resuspended in 7.5 ml of cold PBS with 150ml of streptavidin-coated magnetic particles (QIAgen or Miltenyi). Consensus sequences were readily apparent for the target protein after two to three rounds of magnetic selection and one or two rounds of FACS. 1692 QGRVMGPQQLYVMMR(1) NSLSMAPQQGWVQTG(1) TNKLMGPQQSKMFYW(1) GEGVMSPTQQRGPAR(1) AIVVSMTPFQQWSLS(1) AVHARHYTPWQQLYS(1) ERTGTYSPWQQLRVE(1) QQLSYGPQQQHAHMG(1) PMAIIGPQQMHLVLH(1) VYKSMAPQQTNAWQH(1) LQYSTAMGPQQMTSW(1) GSTSMGPQQFAWGTL(1) QKSTMTGWQQMGVMG(1) 13 Bacterial display (common panning) PMID:15531628 Anti-T7·Tag monoclonal antibody T7·Tag peptide MASMTGGQQMG Not determined. Not determined. X15 E. coli bacterial display library For negative selection, 150ml of streptavidin-coated magnetic beads (QIAgen) were incubated with cells. For positive selection, biotinylated antigen (typically 1-100 nM) was added to the supernatant fraction and incubated on ice for 30-60 min. Cells were centrifuged as above and resuspended in 7.5 ml of cold PBS with 150ml of streptavidin-coated magnetic particles (QIAgen or Miltenyi). Consensus sequences were readily apparent for the target protein after two to three rounds of magnetic selection and one or two rounds of FACS. 1693 AGFEG(1) SMWAHSSRDDAV(1) AKSSAKGKASGV(1) 3 Bacterial display (competitive panning) 5 PMID:16258189 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. FliTrx bacterial display library (X12) In-lab coated microtiter plates were blocked using bovine serum albumin or powdered skimmed milk in phosphate-buffered saline (PBS) buffer. Bound clones were eluted by displacing with excess biotin or mechanical shearing of flagella. Eight contained a stop codon in the region coding for the displayed random peptide. Given that the bacterial strain has no ability to suppress any stop codon, stop codon in this region is expected to stop the translation of functional flagellin. One of the bacterial clones selected expressed a pentapeptide instead of the expected dodecapeptide, most probably the result of an error in the process of library construction or a later mutation. 1694 YNCCHPMNNLCKE(1) EMCHPMWYVLCYH(1) SCCHPMSGVWCSM(1) KLCHPQAWYACTY(1) PSCHPQWYIVCWG(1) RSCHPMWWYLCES(1) FVCENVCYWVCDN(1) H-P-[QM] 7 Bacterial display (competitive panning) 4 PMID:16600968 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. OmpX7C bacterial display library ( X(2)-C-X(7)-C-X(2) ) Streptavidin binding peptides were enriched using two cycles of magnetic selection (MACS) with streptavidin-coated magnetic beads. Subsequently, the enriched population was screened using two cycles of FACS. In the final round of FACS, biotin was used as a competitor to favor the detection and sorting of clones with slow dissociation kinetics. 1695 QSLVCQNVCWMRE(1) CMIICQNVCYRKC(1) SKWICQNVCYPGL(1) KALVCQNVCYTMS(1) PTLICMNVCFYDQ(1) GTLVCMNFCYLSK(1) TRLICANLCWYAE(1) TYSWCANVCMHYS(1) SILRCENACYMVR(1) SHWFCVNVCFRIQ(1) LAWKCENVCYLEA(1) GAWSCWYVCERTT(1) L-[IV]-C-Q-N-V-C-Y 12 Bacterial display (competitive panning) 4 PMID:16600968 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. OmpX3C bacterial display library ( X(4)-C-X(3)-C-X(4) ) Streptavidin binding peptides were enriched using two cycles of magnetic selection (MACS) with streptavidin-coated magnetic beads. Subsequently, the enriched population was screened using two cycles of FACS. In the final round of FACS, biotin was used as a competitor to favor the detection and sorting of clones with slow dissociation kinetics. 1696 ERCWYVMHWPCNA(1) VNCGWMYYGPCTN(1) LRCHPQGGWSCIQ(1) H-P-[QM], C-G-W-M-Y-[FY]-x-E-C 3 Bacterial display (competitive panning) 4 PMID:16600968 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. CX7(1)C bacterial display library ( X(2)-C-X(7)-C-X(2) ) Streptavidin binding peptides were enriched using two cycles of magnetic selection (MACS) with streptavidin-coated magnetic beads. Subsequently, the enriched population was screened using two cycles of FACS. In the final round of FACS, biotin was used as a competitor to favor the detection and sorting of clones with slow dissociation kinetics. 1697 PKCGWMYYPECKV(1) LRCGWMYFEECKE(1) LICGWMYFEECDS(1) IYCGWMYYVECAY(1) MRCGWMYFPECLN(1) WVCHPMWEVMCLR(1) LVCHPQGPTWCIE(1) SWCHPQGMRECDW(1) VGCHPMAPLWCED(1) LWCHPQFLTTCHV(1) NQCHPQFQGWCGM(1) EWCHPQFNFLCGA(1) GTCWDHPQVGCNW(1) H-P-[QM], C-G-W-M-Y-[FY]-x-E-C 13 Bacterial display (competitive panning) 4 PMID:16600968 Streptavidin Biotin 1DF8,1LUQ,1MEP,1MK5,1N43,1N9M,1NDJ,1NQM,1STP,1SWD,1SWE,1SWG,1SWK,1SWN,1SWP,1SWR,1SWT,2F01,2GH7,2IZF,2IZG,2IZH,2IZI,2IZJ,2RTD,2RTE,2RTF,2RTG,2Y3F,3MG5, Not determined. CX7(2)C bacterial display library ( X(2)-C-X(7)-C-X(2) ) Streptavidin binding peptides were enriched using two cycles of magnetic selection (MACS) with streptavidin-coated magnetic beads. Subsequently, the enriched population was screened using two cycles of FACS. In the final round of FACS, biotin was used as a competitor to favor the detection and sorting of clones with slow dissociation kinetics. 1698 VCRLMRGRCLLYSVF(1) TCVLHRQRCLMFTLR(2) ICVNIKKSLWACEIR(1) NCVRILMTFLDCTID(1) GCLQILPTLSECFGR(3) KQRGATMVLRTYTLR(1) YERRPTLVLRTWRPW(1) SVLVWVKDRGWRPAR(3) LYAHYDESRGWRWIR(1) WKFVWIINSRLREQA(1) WARVLLIEGRLIVCE(1) GNVLGKDYRLVKHVN(1) ARWIWYRNTATLNSV(1) CWILPYNTRTRCPLR(2) NQGLIGECHAYWCHG(2) NLIIGFCWLKKCPIR(1) LKVCGRYPGICDGIR(1) WWDMVSDRYIWKPVK(3) TQWIIPSKLAIKTPS(1) 19 Bacterial display (common panning) 3 PMID:16448666 Human breast ductal carcinoma cell line, ZR-75-1 Not determined. Not determined. Not determined. X15 E. coli bacterial display library Binding peptides were enriched after two rounds of co-sedimentation and one round of FACS. Of 70 isolated clones, 48 contained unique sequences. After screening, 36 of 48 of these exhibited binding to tumor cells as measured using flow cytometry. Within these 36 binding clones, phylogenetic analysis identified 19 clones sharing differing degrees of similarity. Isolated peptides could be categorized into several distinct groups possessing strong consensus sequences with as many as six identities. 1699 SSWCMRGQYNKICMW(2) 1 Bacterial display (subtractive panning) 3 PMID:16448666 Human breast ductal carcinoma cell line, ZR-75-1 Not determined. Not determined. Not determined. X15 CPX bacterial display library Binding peptides were enriched after two rounds of co-sedimentation and one round of FACS. Prior to the second round, a negative selection was performed by panning 5.0e7 bacteria against 1.0e7 adhered normal cells containing a mixture of immortalized human mammary cell line (MCF-10A) and Clonetics human mammary epithelial cells (HMEC). Bacteria not bound to normal cells in the supernatant were removed and immediately incubated with 1.0e7 suspended ZR-75-1 cells for a second round of positive selection using cosedimentation. Following an additional round of similar negative panning and positive coincubation with 10-fold fewer cells, tumor cells with fluorescent bacteria bound were immediately sorted using a FACSAria (Becton Dickinson, San Jose, CA). 1700 VPCQKRPGWVCLW(1) KWCVIWSKEGCLF(1) VECYLIRDNLCIY(1) WWCLGERVVRCAH(1) FYCVIERLGVCLY(1) RVCFLWQDGRCVF(1) 6 Bacterial display (subtractive panning) 3 PMID:16448666 Human breast ductal carcinoma cell line, ZR-75-1 Not determined. Not determined. Not determined. CX7(1)C bacterial display library ( X(2)-C-X(7)-C-X(2) ) Binding peptides were enriched after two rounds of co-sedimentation and one round of FACS. Prior to the second round, a negative selection was performed by panning 5.0e7 bacteria against 1.0e7 adhered normal cells containing a mixture of immortalized human mammary cell line (MCF-10A) and Clonetics human mammary epithelial cells (HMEC). Bacteria not bound to normal cells in the supernatant were removed and immediately incubated with 1.0e7 suspended ZR-75-1 cells for a second round of positive selection using cosedimentation. Following an additional round of similar negative panning and positive coincubation with 10-fold fewer cells, tumor cells with fluorescent bacteria bound were immediately sorted using a FACSAria (Becton Dickinson, San Jose, CA).