The Spot Technique 67 20. Atherton, E. and Sheppard, R.C. (1989) 7.2. Activated esters of Fmoc-amino acids. In: Solid Phase <strong>Peptide</strong> Synthesis—A Practical Approach, pp.76–78. Oxford: IRL press at Oxford University Press. 21. Zander, N. (2004) New planar substrates for the in situ synthesis of peptide arrays. Mol. Divers. 8, 189–195. 22. Ast, T., Heine, N., Germeroth, L., Schneider-Mergener, J., and Wenschuh, H. (1999) Efficient assembly of peptomers on continuous surfaces. Tetrahedron Lett. 40, 4317–4318. 23. Weiler, J., Gausepohl, H., Hauser, N., Jensen, O.N., and Hoheisel, J.D. (1997) Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res. 25, 2792–2799. 24. Hilpert, K., Winkler, D.F.H., and Hancock, R.E.W. (2007) <strong>Peptide</strong> arrays on cellulose support: SPOT synthesis - a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nature Protocols 2, 1333–1349. 25. Krchnak, V., Wehland, J., Plessmann, U., Dodemont, H., Gerke, V., and Weber, W. (1988) Noninvasive continuous monitoring of solid phase peptide synthesis by acidbase indicator. Collect. Czechoslovak Chem. Commun. 53, 2542–2548. 26. Bhargava, S., Licha, K., Knaute, T., et al. (2002) A complete substitutional analysis of VIP for better tumor imaging properties. J. Mol. Recognition 15, 145–153. 27. Jung, G. and Beck-Sickinger, A.G. (1992) Multiple peptide synthesis methods and their applications. Angew. Chem. Int. Ed. (English) 31, 367–383. 28. Geysen, H.M., Meloen, R.H., and Barteling, S.J. (1984) Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc. Natl. Acad. Sci. USA 82, 3998–4002. 29. Lebl, M. (1999) Parallel personal comments on “classical” papers in combinatorial chemistry. J. Combin. Chem. 1, 3–24. 30. Maier, T., Yu, C., Külleritz, G., and Clemens, S. (2003) Localization and functional characterization of metal-binding sites in phytochelatin synthases. Planta 218, 300–308. 31. Malin, R., Steinbrecher, R., Jannsen, J., et al. (1995) Identification of Technetium- 99m binding peptides using combinatorial cellulose-bound peptide libraries. J. Am Chem. Soc. 117, 11821–11822. 32. Bialek, K., Swistowski, A., and Frank, R. (2003) Epitope-targeted proteome analysis: towards a large-scale automated protein-protein-interaction mapping utilizing synthetic peptide arrays. Anal. Bioanal. Chem. 376, 1006–1013. 33. Buss, H., Dörrie, A., Schmitz, M.L., et al. (2004) Phosphorylation of serine 468 by GSK-3� negatively regulates basal p65 NF-�B activity. J. Biol. Chem. 279, 49571–49574. 34. Schutkowski, M., Reineke, U., and Reimer, U. (2005) <strong>Peptide</strong> arrays for kinase profiling. ChemBioChem 6, 513–521. 35. Hilpert, K., Elliott, M.R., Volkmer-Engert, R., et al. (2006) Sequence requirements and an optimization strategy for short antimicrobial peptides. Chem. Biol. 13, 1101–1107.
68 Winkler and Campbell 36. Piossek, C., Thierauch, K.-H., Schneider-Mergener, J., et al. (2003) Potent inhibition of angiogenesis by D, L-peptides derived from vascular endothelial growth factor receptor 2. Thromb Haemost. 90, 501–510. 37. Grogan, J.L., Kramer, A., Nogai, A., et al. (1999) Cross-reactivity of myelin basic protein-specific T cells with multiple microbial peptides: Experimental autoimmune encephalomyelitis induction in TCR transgenic mice. J. Immunol. 163, 3764–3770. 38. Frese, S., Schubert, W.-D., Findeis, A.C., et al. (2006) The phosphotyrosine peptide binding specificity of Nck1 and Nck2 SH2 domains. J. Biol. Chem. 281, 18236–18245. 39. Jobron, L. and Hummel, G. (2000) Solid-phase synthesis of unprotected Nglycopeptide building blocks for SPOT synthesis of glycopeptides. Angew. Chem. Intl Ed. 39, 1621–1624. 40. Zimmermann, J., Kühne, R., Volkmer-Engert, R., et al. (2003) <strong>Design</strong> of Nsubstituted peptomer ligands for EVH1 domains. J. Biol. Chem. 278, 36810–36818. 41. Hahn, M., Winkler, D., Welfle, K., et al. (2001) Cross-reactive binding of cyclic peptides to an anti-TGF� antibody Fab fragment. An X-ray structural and thermodynamic analysis. J. Mol. Biol. 314, 293–309. 42. Welschof, M., Reineke, U., Kleist, C., et al. (1999) The antigen binding domain of non-idiotypic human anti-F(ab´)2 autoantibodies: Study of their interaction with IgG hinge region epitopes. Human Immunol. 60, 282–290. 43. Reineke, U., Kramer, A., and Schneider-Mergener, J. (1999) Antigen sequence- and library-based mapping of linear and discontinuous protein-protein interaction sites. Curr. Topics Microbiol. Immunol. 243, 23–36. 44. Reineke, U., Ehrhard, B., Sabat, R., Volk, H.-D., and Schneider-Mergener, J. (1998) Novel strategies for the mapping of discontinuous epitopes using cellulose-bound peptide and hybritope scans. In: <strong>Peptide</strong>s 1996: Proceedings of the 24th European <strong>Peptide</strong> Symposium, eds. R. Ramage and R. Epton, pp.751–752. Kingswinford: Mayflower Scientific Ltd. 45. Reineke, U., Sabat, R., Kramer, A., et al. (1996) Mapping protein-protein contact sites using cellulose-bound peptide scans. Mol. Divers. 1, 141–148. 46. Reineke, U., Sabat, R., Hoffmüller, U., et al. (2002) Identification of miniproteins using cellulose-bound duotope scans. In: <strong>Peptide</strong>s for the New Millenium. Proceedings of the 16th American <strong>Peptide</strong> Symposium, eds. G.B. Fields, J.P. Tam, and G. Barany, pp. 167–169. Springer Netherlands. 47. Kramer, A., Stigler, R.-D., Knaute, T., Hoffmann, B., and Schneider-Mergener, J. (1998) Stepwise transformation of a cholera toxin an a p24 (HIV-1) epitope into D-peptide analogs. Protein Eng. 11, 941–948. 48. Oggero, M., Frank, R., Etcheverrigaray, M., and Kratje, R. (2004) Defining the antigenic structure of human GM-CSF and its implications for the receptor interaction and therapeutic treatments. Mol. Divers. 8, 257–269. 49. Kramer, A., Keitel, T., Winkler, K., Stöcklein, W., Höhne, W., and Schneider- Mergener, J. (1997) Molecular basis for the binding promiscuity of an anti-p24 (HIV-1) monoclonal antibody. Cell 91, 799–809.
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Peptide-Based Drug Design
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METHODS IN MOLECULAR BIOLOGY TM Pep
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Preface Natural products chemistry
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Contents Preface...................
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Contributors Nikolinka Antcheva •
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Contributors xi Alessandro Tossi
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2 Otvos advance of computer power a
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4 Otvos see derivatives active in b
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6 Otvos was designed based on ligan
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8 Otvos 27. Borghouts, C., Kunz, C.
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10 Bulet Key Words: Invertebrate im
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12 Bulet 6. 5 �L or higher volume
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14 Bulet 2.5.2.1. MALDI-TOF-MS 1. M
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118 Copps et al. Fig. 2. Flowchart
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120 Copps et al. 10. In accordance
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122 Copps et al. Fig. 3. DSSP for g
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124 Copps et al. ingly with the sam
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126 Copps et al. 19. Essman, U., Pe
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128 Hilpert et al. Key Words: Scree
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130 Hilpert et al. Table 1 (Continu
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132 Hilpert et al. different natura
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134 Hilpert et al. wt A C D E F …
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136 Hilpert et al. methods primaril
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138 Hilpert et al. Table 2 (Continu
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140 Hilpert et al. Table 2 (Continu
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142 Hilpert et al. Table 2 (Continu
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144 Hilpert et al. Table 3 Summary
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146 Hilpert et al. Table 3 (Continu
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148 Hilpert et al. of substituting
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150 Hilpert et al. in models that c
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152 Hilpert et al. than control. Gi
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154 Hilpert et al. Table 4 Accuracy
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156 Hilpert et al. 25. Pini, A., Gi
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158 Hilpert et al. 55. Giacometti,
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9 Investigating the Mode of Action
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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Proline-Rich Antimicrobial Peptides
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10 Serum Stability of Peptides Håv
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Serum Stability of Peptides 179 2.
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Serum Stability of Peptides 181 9.
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Serum Stability of Peptides 183 �
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Serum Stability of Peptides 185 13.
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11 Preparation of Glycosylated Amin
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 1
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Glycosylated Amino Acid Synthesis 2
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Glycosylated Amino Acid Synthesis 2
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Glycosylated Amino Acid Synthesis 2
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Glycosylated Amino Acid Synthesis 2
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12 Synthesis of O-Phosphopeptides o
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Solid-Phase Synthesis of O-Phosphop
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Solid-Phase Synthesis of O-Phosphop
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Solid-Phase Synthesis of O-Phosphop
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Solid-Phase Synthesis of O-Phosphop
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Solid-Phase Synthesis of O-Phosphop
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Solid-Phase Synthesis of O-Phosphop
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13 Peptidomimetics: Fmoc Solid-Phas
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Peptidomimetics 225 O O R S N H Pep
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Peptidomimetics 227 not without its
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Peptidomimetics 229 Oxidation step:
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Peptidomimetics 231 of peptidosulfo
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Peptidomimetics 233 8. Allow the re
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Peptidomimetics 235 3.3.2. Solid-Ph
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Peptidomimetics 237 On the other ha
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Peptidomimetics 239 nitrogen (73).
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Peptidomimetics 241 3. Cover the re
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Peptidomimetics 243 efficient synth
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Peptidomimetics 245 55. Alsina, J.,
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14 Synthesis of Toll-Like Receptor-
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Lipopeptides 249 2. Materials 2.1.
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Lipopeptides 251 Fig. 1. Structural
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Lipopeptides 253 8. To enable lipid
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Lipopeptides 255 Representative res
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Lipopeptides 257 Fig. 2. Immunogeni
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Lipopeptides 259 8. A large plastic
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Lipopeptides 261 26. Nardin, E.H.,
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264 Otvos response, synthetic pepti
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266 Otvos Fig. 3. Schematic present
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268 Otvos 3. Methods The main goal
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270 Otvos 3.2.3. Purification and Q
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272 Otvos 6. Meyer, D., and Torres,
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16 Cysteine-Containing Fusion Tag f
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Targeted Therapeutic and Imaging Ag
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Index A A� peptides aggregation a
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Index 297 phosphopeptides influenci
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Index 299 for genetically synthetic
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Index 301 peptidosulfonamide, disad
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Index 303 solid phase, 180, 214 sul