1 NHNYPPLSLLTF(1)[2.871] SHDWRLMLSHLQ(1)[2.779] QHDRLLMLSYLV(1)[2.666] HHILPPKALLFG(1)[2.623] SHTFPPSWLLVR(1)[2.509] YSVKPPLPYLPP(1)[2.536] H-x(2)-P(2)-x(2)-L(2) 6 Phage display (common panning) 3/4 PMID:17881351 Anti-Ogawa O-antigen monoclonal antibody S-20-4 O-specific polysaccharide of LPS Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Absorbance was measured at 450 nm with a kinetic microplate reader (Molecular Devices). Phage were incubated with the selection Ab in solution, followed by affinity capture of the Ab-phage complexes onto protein A/G-agarose. In panning, phage bound to resin were eluted with of glycine HCl (pH 2.2) and rapidly neutralized with Tris-HCl (pH 9.1). Each of the six phage clones that could bind to both monoclonal antibodies also competed with LPS for binding to S-20-4, suggesting that the peptides bind close to the paratope of the Ab. In order to predict how these peptide mimics interact with S-20-4 compared with its carbohydrate counterpart, one peptide mimic, 4P-8 (NHNYPPLSLLTF), which is one of the highest affinity binders and shares motifs with several other peptide mimics, was selected for further studies using computer modeling methods and site-directed mutagenesis. These studies suggest that 4P-8 is recognized as a hairpin structure that mimics some O-SP interactions with S-20-4 and also makes unique ligand interactions with S-20-4. In addition, 4P-8-KLH was able to elicit anti-LPS Abs in mice, but the immune response was not vibriocidal or protective. However, boosting with 4P-8-KLH after immunizing with LPS prolonged the LPS-reactive IgG and IgM Ab responses as well as vibriocidal titers and provided a much greater degree of protection than priming with LPS alone. 2 NHNYPPLSLLTF(1)[2.871] SHKIHPFQTTPY(1)[0.851] HSPRYHSEPQFG(1)[2.118] HAPRYHTIYGWP(1)[1.976] H-x(2)-P(2)-x(2)-L(2), S-H-[KR]-[LI], H-x-P-R-x-H 4 Phage display (common panning) 3/4 PMID:17881351 Anti-Ogawa O-antigen monoclonal antibody S-20-4 O-specific polysaccharide of LPS Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Absorbance was measured at 450 nm with a kinetic microplate reader (Molecular Devices). Phage were incubated with the selection Ab in solution, followed by affinity capture of the Ab-phage complexes onto protein A/G-agarose. In panning, phage bound to resin were (nonelution) directly added to a culture of E. coli strain ER2738 for amplification. Amplified phage were purified by precipitating the phage with polyethylene glycol/NaCl. In order to predict how these peptide mimics interact with S-20-4 compared with its carbohydrate counterpart, one peptide mimic, 4P-8(NHNYPPLSLLTF), which is one of the highest affinity binders and shares motifs with several other peptide mimics,was selected for further studies using computer modeling methods and site-directed mutagenesis. These studies suggest that 4P-8 is recognized as a hairpin structure that mimics some O-SP interactions with S-20-4 and also makes unique ligand interactions with S-20-4. In addition, 4P-8-KLH was able to elicit anti-LPS Abs in mice, but the immune response was not vibriocidal or protective. However, boosting with 4P-8-KLH after immunizing with LPS prolonged the LPS-reactive IgG and IgM Ab responses as well as vibriocidal titers and provided a much greater degree of protection than priming with LPS alone. 3 SHKLHKV(1)[0.526] SHRLPLK(1)[1.350] SHRLPAK(1)[1.075] SHRLPVK(1)[1.115] S-H-[KR]-[LI] 4 Phage display (common panning) 3/4 PMID:17881351 Anti-Ogawa O-antigen monoclonal antibody S-20-4 O-specific polysaccharide of LPS Not determined. Not determined. Ph.D.-7 phage display library (X7) ELISA Absorbance was measured at 450 nm with a kinetic microplate reader (Molecular Devices). Phage were incubated with the selection Ab in solution, followed by affinity capture of the Ab-phage complexes onto protein A/G-agarose. In panning, phage bound to resin were eluted with of glycine HCl (pH 2.2) and rapidly neutralized with Tris-HCl (pH 9.1). 4 HAPRWHL(2)[1.935/2.274] HAPRWHW(1)[1.421] HAPRYHY(1)[1.656] HSPRWHL(1)[2.177] HSPRYHM(1)[1.288] H-x-P-R-x-H 5 Phage display (common panning) 3/4 PMID:17881351 Anti-Ogawa O-antigen monoclonal antibody S-20-4 O-specific polysaccharide of LPS Not determined. Not determined. Ph.D.-7 phage display library (X7) ELISA Absorbance was measured at 450 nm with a kinetic microplate reader (Molecular Devices). Phage were incubated with the selection Ab in solution, followed by affinity capture of the Ab-phage complexes onto protein A/G-agarose. In panning, phage bound to resin were (nonelution) directly added to a culture of E. coli strain ER2738 for amplification. Amplified phage were purified by precipitating the phage with polyethylene glycol/NaCl. 5 NPEDCFKTGCNSPT(6) LMEPCYAWGCTGPK(3) IMEQCFEIGCPATN(2) NDSQCWKLGCIAEK(1) SNVECDGLNCDWII(1) N-x-E-x(2)-[FYW]-x(2)-G 5 Phage display (subtractive panning) 3 PMID:15034020 Anti-IA-2 monoclonal antibody 96/3 Receptor-type tyrosine-protein phosphatase-like N (R-PTP-N) Not determined. Not determined. f88-4/15mer and f88-4/Cys4 phage display library pool The two libraries were mixed and phage reactive to bovine IgG was removed by incubation in tubes coated with purified bovine IgG. The predicted surface on a three-dimensional homology model of the tyrosine phosphatase domain of IA-2 was analyzed for clusters of Asn, Glu, and aromatic residues and amino acids contributing to the epitope investigated using site-directed mutagenesis. Mutation of each of amino acids Asn(858), Glu(836), and Trp(799) reduced 96/3 Ab binding by >45%. Mutations of these residues also inhibited binding of serum autoantibodies from IA-2 Ab-positive type 1 diabetic patients. This study identifies a region commonly recognized by autoantibodies in type 1 diabetes that overlaps with dominant T cell determinants. 6 EIDAPRVFDARFSRHYSVQL[0.47 ± 0.07] LAVFRPWKARNNGTNEYRSR[0.81 ± 0.07] GAEASTSLFHFRIPRSYFLR[0.73 ± 0.02] FCSLTSLATSCGAAVFIPFR[0.72 ± 0.02] 4 Phage display (subtractive panning) 4 PMID:14742560 Anti-AMA1 monoclonal antibody 4G2dc1 Apical membrane antigen 1, AMA1 Not determined. Not determined. X20 fUSE5 phage display library ELISA The absorbance value was measured at 490 nm. All ELISAs were performed in duplicate. Data shown were reproduced from the graph and expressed as the means ± individual values. 4G2dc1-coated wells were blocked with 5% BLOTTO (milk powder diluted in phosphate-buffered saline [PBS]), and the 20-mer phage peptide library was preincubated in 1% BLOTTO for 15 min to remove any milk-binding phage before being added to the 4G2dc1-coated wells. 7 WGILSRAATNSGWVGLIPHK[0.81 ± 0.28] 1 Phage display (subtractive panning) 5 PMID:14742560 Anti-AMA1 monoclonal antibody 4G2dc1 Apical membrane antigen 1, AMA1 Not determined. Not determined. X20 fUSE5 phage display library ELISA The absorbance value was measured at 490 nm. All ELISAs were performed in duplicate. Data shown were reproduced from the graph and expressed as the means ± individual values. 4G2dc1-coated wells were blocked with 5% BLOTTO (milk powder diluted in phosphate-buffered saline [PBS]), and the 20-mer phage peptide library was preincubated in 1% BLOTTO for 15 min to remove any milk-binding phage before being added to the 4G2dc1-coated wells. 8 IPSTAFTDIAWVRLPNHY[1.07 ± 0.02] LASLRKAFADTVPVRPPSNY[0.90 ± 0.01] FGGVSNEDVPSVHFKPPSSR[0.89 ± 0.04] A-F-x-D-x(3)-V-R-x-P-x(2)-Y 3 Phage display (subtractive panning) 6 PMID:14742560 Anti-AMA1 monoclonal antibody 4G2dc1 Apical membrane antigen 1, AMA1 Not determined. Not determined. X20 fUSE5 phage display library ELISA The absorbance value was measured at 490 nm. All ELISAs were performed in duplicate. Data shown were reproduced from the graph and expressed as the means ± individual values. 4G2dc1-coated wells were blocked with 5% BLOTTO (milk powder diluted in phosphate-buffered saline [PBS]), and the 20-mer phage peptide library was preincubated in 1% BLOTTO for 15 min to remove any milk-binding phage before being added to the 4G2dc1-coated wells. The three peptides elicited antibody responses in rabbits that recognized the peptide immunogen and both recombinant and parasite AMA1. Human antibodies in plasma samples from individuals exposed to chronic malaria reacted with J1 (IPSTAFTDIAWVRLPNHY) and J7 (LASLRKAFADTVPVRPPSNY) peptides and were isolated using immobilized peptide immunoadsorbents. Both rabbit and human antibodies specific for J1 and J7 peptides were able to inhibit the invasion of erythrocytes by P. falciparum merozoites. 9 AFDWTFVPSLIL(17) SLDWSHVPLLVL(3) GPFINKSLGSSP(2) LDVRPWYVTPLP(2) LEPPQLWWPWEH(2) WSSNLRVLPWSP(1) SLYVAPWWDDPP(1) QLVIFPWNVTVP(1) MLTVEPWTISNT(1) 9 Phage display (subtractive panning) 4 PMID:16960395 C-C chemokine receptor type 5, CCR5 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) In this study, CCR5-expressing CHO cells (CHO/CCR5 cells) were used to select CCR5-binding peptides from a phage-displayed 12-mers peptide library. According to the paper, the peptide AFDWTFVPSLIL was specific for CCR5 and that it might become a CCR5 antagonist. 10 CLSLMPRLC[1.795 ± 0.192] CNPMMRPLC[1.922 ± 0.105] CQMRTTIRC[1.662 ± 0.125] CRLMMLQQC[1.629 ± 0.218] CMLLQNRQC[0.997 ± 0.157] CTLQASILC[1.011 ± 0.176] CLSLITRLC[0.585 ± 0.088] 7 Phage display (subtractive panning) 4 PMID:15930303 Interleukin-6 receptor subunit alpha Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) ELISA Individual sIL-6Rα-binding phage clones were tested for their ability to compete with IL-6 protein for binding to immobilized sIL-6Rα. Phages were added to sIL-6Rα-coated wells in a 96-well plate at a concentration of e12 pfu/mL. After 1 hour of incubation with phage, IL-6 protein was added to the wells, and bound IL-6 was then measured using biotin-conjugated anti-IL-6 mAb, HRP-conjugated streptavidin, and TMB substrate. Optical density was quantified at 405 nm. Data were reproduced from the graph and shown as mean of three independent experiments ± SD. The phage library was added to non-bait-coated dishes (those coated with human IL-6Rβ proteins) for preabsorption. According to paper, peptide LSLITRL substantially inhibits IL-6-induced vascular endothelial growth factor-A expression and angiogenesis in different cancer cell lines. 11 YTPPPLIEAFAT 1 Phage display (common panning) 3 PMID:16740692 EWS-Fli1 protein RNA helicase A, RHA Not determined. Not determined. Ph.D.-12 phage display library (X12) Panning was performed on the surface of a well from a 96-well microtiter plate (Costar, Cambridge, MA). By screening, twenty-eight novel peptides that differentially bind to EWS-FLI1 were identified from phage sequencing. Peptide YTPPPLIEAFAT showed significant homology to human RHA (GenBank accession number A47363) at the amino acid 822 to 831 region. 12 CWWEWTATC(11) CWWEWTIGC(3) CWWEWTGAC(2) CQFTVWEWC(1) CCLGRWCWC(1) CWEWSGNGC(1) CSWTSLPFC(1) CHAWMGLRC(1) CFKRSGSLC(1) CWRRGYGGC(1) CKPWFPELC(1) CALMIANSC(1) CRLTANLPC(1) W(2)-E-W-[ST] 13 Phage display (subtractive panning) 4 PMID:16705086 Anti-CD20 monoclonal antibody rituximab B-lymphocyte antigen CD20 2OSL, Not determined. CX7C fUSE5 phage display library In the third and fourth rounds of selection, the library was precleared on the antibody cetuximab (Merck, Darmstadt, Germany). According to the paper, rituximab binds a discontinuous epitope in CD20, comprised of (170)ANPS(173) and (182)YCYSI(185), with both strings brought in steric proximity by a disulfide bridge between C(167) and C(183). 13 CTRGFEWLC(10) CVFYYNWVC(3) CVYLYEWVC(2) CVYHYRWLC(1) CRDRYWPWC(1) CEWIYHYWC(1) [FY]-[EH]-W-[LV] 6 Phage display (subtractive panning) 4 PMID:17440057 Anti-CD25 monoclonal antibody basiliximab Interleukin-2 receptor subunit alpha 3IU3, Not determined. CX7C fUSE5 phage display library In the third and fourth round of selection, the library was precleared on rituximab. A striking amino acid sequence motif was enriched. This motif is homologous to the peptide ERIYHFV comprising amino acid positions 116 to 122 within the extracellular domain of CD25, suggesting that this is the basiliximab epitope. 14 CEFAQC(2) CDWVFC(1) CDFKAC(1) CDFVGC(1) CEYKEC(1) CEENLC(1) CEFLFC(1) CEFFFC(1) CEKFPC(1) CEHYPC(1) CEFESC(1) CPFIRC(1) CPFTEC(1) CPFDRC(1) CPYRHC(1) CPFMAC(1) CPFKEC(1) CPFHTC(1) CPYKQC(1) CPFKQC(1) CPFAAC(1) CPYHEC(1) CPYRRC(1) CPYRFC(1) C-[DEP]-[FYW]-[DEHKR]-x-C 24 Phage display (common panning) 3 PMID:12538646 Baculoviral IAP repeat-containing protein 4 Not determined. Not determined. Not determined. CX4C and X6 phage display library pool Recombinant full-length human XIAP are used to select peptides from phage display peptide libraries. The DNA inserts of 36 randomly chosen phage clones (18 from the X6 library and 18 from the CX4C library) recovered from the third round of biopanning on XIAP were sequenced. A total of 32 phage clones derived from both libraries displayed the consensus motif C-(D/E/P)-(aromatic)-(charged)-xC. Protein-protein interaction assays revealed that caspase-3 and caspase-7 (but not caspase-8) blocked the binding of the CEFESC phage to XIAP, indicating that this peptide targets a domain within XIAP that is related to the caspase-binding site. In fact, the sequence EFES is homologous to a loop unique to the executioner caspase-3 and caspase-7 that are targeted by XIAP. 15 HLANHQGKWRLH(11) LPLFNANGTWQF(6) VELRNLGGTWRP(1) 3 Phage display (common panning) 3 PMID:16496330 Anti-glycoprotein E2 monoclonal antibody AP33 Envelope glycoprotein E2 Not determined. Not determined. Ph.D.-12 phage display library (X12) Nineteen selected by AP33, were analyzed, and of these 17 were reactive to the selecting antibody. Phage selected by MAb AP33 could be divided into three groups based on the amino acid sequence of the random peptide insert. Multiple alignment of the phage sequences showed absolute conservation of four amino acids, namely L413 (Leucine corresponding to position 413 of the H77 E1E2 sequence), N415, G418, and W420. 16 SRVPQHSYWHSN(3) SKSILNSQGSWH(3) TEPWLPSNPSWA(1) STLPTFPRWMTD(1) YEPGPAWRFHRE(1) RNTHINVDGQYH(1) VHSPNPYWGPTL(1) HKTLNMASYWHN(1) GRPIFNEQAEYL(1) DARPIVGPFLLH(1) SIPTGSSWYALA(1) SPTTFGQAWHTV(1) THPIISTEASWH(1) YTQTGWLNWHER(1) NPHNNNYWGPRI(1) VYPQNKHHTWYS(1) NIWPKQSPYYTS(1) QYRANESSRWHV(1) SFPNQSIHRSTW(1) 19 Phage display (common panning) 3 PMID:16496330 Anti-glycoprotein E2 monoclonal antibody 3/11 Envelope glycoprotein E2 Not determined. Not determined. Ph.D.-12 phage display library (X12) 17 GRYFPDSPAWNH(3) NPHNNNYWGPRI(2) NTGWLPKFPAWT(1) SQVWNTNPEYLT(1) SYTFWPDSYYSS(1) IPNAWNPRAPWQ(1) SKSILNSQGSWH(1) 7 Phage display (common panning) 4 PMID:16496330 Anti-glycoprotein E2 monoclonal antibody 3/11 Envelope glycoprotein E2 Not determined. Not determined. Ph.D.-12 phage display library (X12) 18 WGQQPIDPALWM(2) FQQPLDPWTSPI(2) WQHPLHDWFDLV(2) SNGNWQFPVDPS(1) HVWQGPVDPATF(1) QSWWQQPFDPMD(1) SPWQQWQMPVDV(1) LQTPIDWDEPWF(1) HQAPLDLDWWVD(1) SQLPLDLWMFPD(1) MWQKPLVVHWPT(1) WQMPLTTELDSP(1) NTHQYPIYYPWR(1) HQHPLNNWPNIT(1) SPQVPLTTWNYH(1) WHSQTPVYYWHT(1) TQSPMWWDDFFF(1) IQPQQYWDPFRY(1) FNPQKFWDPYLD(1) NQQAAWDPWMLM(1) HQSYVDPWMLDH(1) WQFHMDPWSLHQ(1) REQLYLDYNVFS(1) QQSRTDPWLPVP(1) WQLHYEPFSVNP(1) NGGQVALSPDWL(1) THMYQSIYVPDI(1) YPYQHHLTYNMW(1) NIPQEHMKFFMA(1) VPQEVWSFFSIP(1) SQQELMLWFNTQ(1) VPTWQQSVPYDL(1) HQIETLLHWFKP(1) GPQQYVNALLFY(1) THQQALPWADMF(1) YQQHINWHSWDT(1) Q-x-P-[AVLIFYW]-D-P(0,1), Q-x-P-[AVLIFYW], Q-x(2)-[AVLIFYW]-D-P 36 Phage display (common panning) 4 PMID:16636049 Protein-glutamine gamma-glutamyltransferase 2 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) This study further confirmed that the sequences were favored for transamidation using modified glutathione S-transferase (GST) for recombinant peptide-GST fusion proteins. Most of the fusion proteins exhibited a considerable increase in incorporation of primary amines over that of modified GST alone. 19 EQYQLAWPAMQS(3) DQMMLPWPAVKL(2) SQHPLPWPVLML(2) WQHKIDLRYNGA(2) WHYPPPYDLMRT(2) LDQIVIPWPTPR(1) DQWMMAWPSLTL(1) SEQHLLKWPPWH(1) EQQQLSWPPFLP(1) SQIPMAWPLLSL(1) TQYTMTWPFSWR(1) WQQQMKWPSFTY(1) WQIPVDWPPLPP(1) WQMQLPWPPRLS(1) GQMILPWPSPRA(1) EQFPIAFPRYSI(1) HQMVLTYPWVPT(1) DQYVLTFPWTPR(1) WQMPVNLPIRYP(1) WQLKYPWISPVG(1) HQIPIQIHSFAM(1) DQSKVWLLPSWK(1) WHYQVPQWLYRH(1) WYHPLQLTPAPI(1) WSHMLYLPGSAP(1) WSHPMYLGPSAL(1) YNAPSSFIPLVM(1) NHPIYPHMLLSY(1) WDSHILTYHVPY(1) Q-x(2)-[AVLIFYW]-x-W-P 29 Phage display (common panning) 4 PMID:16636049 Coagulation factor XIII A chain Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) This study further confirmed that the sequences were favored for transamidation using modified glutathione S-transferase (GST) for recombinant peptide-GST fusion proteins. Most of the fusion proteins exhibited a considerable increase in incorporation of primary amines over that of modified GST alone. 20 CSNSDKPKC(2) CYNSDKPKC(1) CRNSDKPKC(1) CSDSDKPKC(1) CWESDKPKC(1) CKWSDKPKC(1) 6 Phage display (common panning) 3 PMID:16988228 Anti-AMA1 monoclonal antibody 45B1 Apical membrane antigen-1 Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The MAb 45B1 epitope is conserved and located within the AMA1 domain II loop. 21 CFYEMPTRC(5) CDHFGMHRC(3) CTPTFRANC(1) CTSLWALQC(1) 4 Phage display (common panning) 5 PMID:16988228 Anti-P235 rhoptry protein monoclonal antibody 25.77 P235 rhoptry protein Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) The epitope recognized by 25.77 could not be assigned. 22 HMSEYPW(4) CMTCLVK(3) IRPMVYS(3) IRPMVDP(3) IVPMVTL(3) IRPMVST(2) IRPMVYV(1) IRPMLPG(1) IRPMLPA(1) IVPMMPE(1) MPHWWYP(1) IRPMV 11 Phage display (common panning) 4 PMID:16229273 Anti-ochratoxin A monoclonal antibody 10G7 Ochratoxin A Not determined. Not determined. Ph.D.-7 phage display library (X7) 23 QLIMIRH(2) ITPRNRS(2) LQQKHLL(1) 3 Phage display (common panning) 3 PMID:16276928 Vibrio cholerae El Tor Typing Phage VP1 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) 24 RHKIQLRQNII(5) 1 Phage display (common panning) 3 PMID:16520318 Tumor necrosis factor ligand superfamily member 13B Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISAs were used to identify positive phages 25 WHWTYGWRPPAM(2) STYWSHYGQQPY(1) HWRYWHYPSETF(1) WHYSWFSPYRTY(1) TWWPHYHSLPRV(1) W-[SP]-H-Y 5 Phage display (common panning) 3 PMID:16864112 Acetylcholinesterase Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12)