Phage display technology is undoubtedly a powerful tool for affinity selection of target-specific peptide. Commercially available premade phage libraries allow us to take screening in the easiest way. On the other hand, construction of a custom phage library seems to be inaccessible, because several practical tips are absent in instructions. This paper focuses on what should be born in mind for beginners using commercially available cloning kits (Ph.D. with type 3 vector and T7Select systems for M13 and T7 phage, respectively). In the M13 system, Pro or a basic amino acid (especially, Arg) should be avoided at the N-terminus of peptide fused to gp3. In both systems, peptides containing odd number(s) of Cys should be designed with caution. Also, DNA sequencing of a constructed library before biopanning is highly recommended for finding unexpected bias. 1. Introduction Phage display technology was born in 1985 when George Smith reported that foreign peptide could be displayed on the surface of filamentous bacteriophage [3]. Today, the phage display is a versatile tool for finding specific interactions between randomized library peptides/proteins on phage and target proteins, peptides, or other molecules. For example, it is applicable for generation of therapeutic peptides against cancer [4], microbe [5], novel functional protein [6], or fully humanized monoclonal antibody [7]. The advantages of the phage display technology over other selection methods are as follows. (1) Cost of a routine is cheap. (2) Time required for selection/amplification is fast. (3) Extreme care for handling, such as RNA isolation/selection, is not necessary. The phage is a DNA-containing virus that infects bacteria and makes many copies of the library within a very short time [8]. A phage that specifically binds a target can be selected from mixtures of billions of phages, propagated by in vivo amplification, and then subjected to additional rounds of affinity selection (Figure 1). This whole process is so-called “biopanning” [9]. After multiple rounds of the biopanning, enrichment of target-binding phage can be assessed by phage titering and enzyme-linked immunosorbent assay (ELISA). Finally, the peptide displayed on the phage can be analyzed by DNA sequencing. Figure 1: A typical procedure of the biopanning. (a) Incubation of phage library with an immobilized target. (b) Washing of unbound phage. (c) Elution of target-bound phage. (d) Amplification of the eluted phage for subsequent rounds of the biopanning. 1.1. Categorization of Phage Display Systems Based on vector systems,
References
[1]
C. Heinis, T. Rutherford, S. Freund, and G. Winter, “Phage-encoded combinatorial chemical libraries based on bicyclic peptides,” Nature Chemical Biology, vol. 5, no. 7, pp. 502–507, 2009.
[2]
X. Fan, R. Venegas, R. Fey et al., “An in vivo approach to structure activity relationship analysis of peptide ligands,” Pharmaceutical Research, vol. 24, no. 5, pp. 868–879, 2007.
[3]
G. P. Smith, “Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface,” Science, vol. 228, no. 4705, pp. 1315–1317, 1985, Features of M13 phage, as well as basic strategies for insert DNA construction, are well described therein.
[4]
R. Brissette, J. K. A. Prendergast, and N. I. Goldstein, “Identification of cancer targets and therapeutics using phage display,” Current Opinion in Drug Discovery and Development, vol. 9, no. 3, pp. 363–369, 2006.
[5]
T. K. Lu and M. S. Koeris, “The next generation of bacteriophage therapy,” Current Opinion in Microbiology, vol. 14, no. 5, pp. 524–531, 2011.
[6]
A. Skerra, “Alternative binding proteins: anticalins—Harnessing the structural plasticity of the lipocalin ligand pocket to engineer novel binding activities,” FEBS Journal, vol. 275, no. 11, pp. 2677–2683, 2008.
[7]
N. Lonberg, “Fully human antibodies from transgenic mouse and phage display platforms,” Current Opinion in Immunology, vol. 20, no. 4, pp. 450–459, 2008.
[8]
L. R. H. Krumpe and T. Mori, “The use of phage-displayed peptide libraries to develop tumor-targeting drugs,” International Journal of Peptide Research and Therapeutics, vol. 12, no. 1, pp. 79–91, 2006.
[9]
E. Koivunen, W. Arap, D. Rajotte, J. Lahdenranta, and R. Pasqualini, “Identification of receptor ligands with phage display peptide libraries,” Journal of Nuclear Medicine, vol. 40, no. 5, pp. 883–888, 1999.
[10]
M. Russel, “Moving through the membrane with filamentous phages,” Trends in Microbiology, vol. 3, no. 6, pp. 223–228, 1995.
[11]
T. Haaparanta and W. D. Huse, “A combinatorial method for constructing libraries of long peptides displayed by filamentous phage,” Molecular Diversity, vol. 1, no. 1, pp. 39–52, 1995.
[12]
T. Bratkovi？, “Progress in phage display: evolution of the technique and its applications,” Cellular and Molecular Life Sciences, vol. 67, no. 5, pp. 749–767, 2010.
[13]
M. Russel, H. B. Lowman, and T. Clackson, “Introduction to phage biology and phage display,” in Phage Display—A Practical Approach, vol. 266, pp. 1–26, Oxford University Press, 2004.
[14]
G. P. Smith and V. A. Petrenko, “Phage display,” Chemical Reviews, vol. 97, no. 2, pp. 391–410, 1997.
[15]
V. A. Petrenko and G. P. Smith, “Vectors and modes of display,” in Phage Display in Biotechnology and Drug Discovery, pp. 63–98, CRC Press, 2005.
[16]
X. Agirrezabala, J. Martín-Benito, J. R. Castón, R. Miranda, J. M. Valpuesta, and J. L. Carrascosa, “Maturation of phage T7 involves structural modification of both shell and inner core components,” EMBO Journal, vol. 24, no. 21, pp. 3820–3829, 2005.
[17]
B. G. Condron, J. F. Atkins, and R. F. Gesteland, “Frameshifting in gene 10 of bacteriophage T7,” Journal of Bacteriology, vol. 173, no. 21, pp. 6998–7003, 1991.
[18]
A. Rosenberg, K. Griffin, F.W. Studier, et al., “T7 Select Phage Display System: a powerful new protein display system based on bacteriophage T7,” inNovations, vol. 6, pp. 1–6, 1998.
[19]
K. A. Noren and C. J. Noren, “Construction of high-complexity combinatorial phage display peptide libraries,” Methods, vol. 23, no. 2, pp. 169–178, 2001.
[20]
G. A. Barkocy-Gallagher, J. G. Cannon, and P. J. Bassford Jr., “β-Turn formation in the processing region is important for efficient maturation of Escherichia coli maltose-binding protein by signal peptidase I in vivo,” Journal of Biological Chemistry, vol. 269, no. 18, pp. 13609–13613, 1994.
[21]
E. H. Manting and A. J. M. Driessen, “Escherichia coli translocase: the unravelling of a molecular machine,” Molecular Microbiology, vol. 37, no. 2, pp. 226–238, 2000.
[22]
E. A. Peters, P. J. Schatz, S. S. Johnson, and W. J. Dower, “Membrane insertion defects caused by positive charges in the early mature region of protein pIII of filamentous phage fd can be corrected by prlA suppressors,” Journal of Bacteriology, vol. 176, no. 14, pp. 4296–4305, 1994.
[23]
H. Andersson and G. Von Heijne, “A 30-residue-long “export initiation domain” adjacent to the signal sequence is critical for protein translocation across the inner membrane of Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 88, no. 21, pp. 9751–9754, 1991.
[24]
D. J. Rodi, A. S. Soares, and L. Makowski, “Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries,” Journal of Molecular Biology, vol. 322, no. 5, pp. 1039–1052, 2002.
[25]
I. Nilsson and G. Von Heijne, “A signal peptide with a proline next to the cleavage site inhibits leader peptidase when present in a sec-independent protein,” FEBS Letters, vol. 299, no. 3, pp. 243–246, 1992.
[26]
A. Plückthun and J. R. Knowles, “The consequences of stepwise deletions from the signal-processing site of beta-lactamase,” Journal of Biological Chemistry, vol. 262, no. 9, pp. 3951–3957, 1987.
[27]
T. N. Petersen, S. Brunak, G. Von Heijne, and H. Nielsen, “SignalP 4.0: discriminating signal peptides from transmembrane regions,” Nature Methods, vol. 8, no. 10, pp. 785–786, 2011.
[28]
S. J. McConnell, A. J. Uveges, D. M. Fowlkes, and D. G. Spinella, “Construction and screening of M13 phage libraries displaying long random peptides,” Molecular Diversity, vol. 1, no. 3, pp. 165–176, 1996.
[29]
L. R. H. Krumpe, A. J. Atkinson, G. W. Smythers et al., “T7 lytic phage-displayed peptide libraries exhibit less sequence bias than M13 filamentous phage-displayed peptide libraries,” Proteomics, vol. 6, no. 15, pp. 4210–4222, 2006.
[30]
B. K. Kay, N. B. Adey, Y. S. He, J. P. Manfredi, A. H. Mataragnon, and D. M. Fowlkes, “An M13 phage library displaying random 38-amino-acid peptides as a source of novel sequences with affinity to selected targets,” Gene, vol. 128, no. 1, pp. 59–65, 1993.
[31]
I. Kather, C. A. Bippes, and F. X. Schmid, “A stable disulfide-free gene-3-protein of phage fd generated by in vitro evolution,” Journal of Molecular Biology, vol. 354, no. 3, pp. 666–678, 2005.
[32]
R. E. Herman, D. Badders, M. Fuller et al., “The Trp cage motif as a scaffold for the display of a randomized peptide library on bacteriophage T7,” Journal of Biological Chemistry, vol. 282, no. 13, pp. 9813–9824, 2007.
[33]
X. Wu, H. J？rnvall, K. D. Berndt, and U. Oppermann, “Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance,” Biochemical and Biophysical Research Communications, vol. 313, no. 1, pp. 89–96, 2004.
[34]
A. Hilterbrand, J. Saelens, and C. Putonti, “CBDB: the codon bias database,” BMC Bioinformatics, vol. 13, no. 1, p. 62, 2012.
[35]
J. J. Steven and B. L. Trus, “The structure of bacteriophage T7,” Electron Microscopy of Proteins, vol. 5, pp. 1–35, 1991.
[36]
X. Agirrezabala, J. A. Velázquez-Muriel, P. Gómez-Puertas, S. H. W. Scheres, J. M. Carazo, and J. L. Carrascosa, “Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold,” Structure, vol. 15, no. 4, pp. 461–472, 2007.
[37]
M. A. McLafferty, R. B. Kent, R. C. Ladner, and W. Markland, “M13 bacteriophage displaying disulfide-constrained microproteins,” Gene, vol. 128, no. 1, pp. 29–36, 1993.
[38]
R. C. Ladner, “Constrained peptides as binding entities,” Trends in Biotechnology, vol. 13, no. 10, pp. 426–430, 1995.
[39]
K. Tanaka, M. Nishimura, Y. Yamaguchi et al., “A mimotope peptide of Aβ42 fibril-specific antibodies with Aβ42 fibrillation inhibitory activity induces anti-Aβ42 conformer antibody response by a displayed form on an M13 phage in mice,” Journal of Neuroimmunology, vol. 236, no. 1-2, pp. 27–38, 2011.
[40]
H. B. Lowman, “Bacteriophage display and discovery of peptide leads for drug development,” Annual Review of Biophysics and Biomolecular Structure, vol. 26, pp. 401–424, 1997.
[41]
F. Uchiyama, Y. Tanaka, Y. Minari, and N. Tokui, “Designing scaffolds of peptides for phage display libraries,” Journal of Bioscience and Bioengineering, vol. 99, no. 5, pp. 448–456, 2005.
[42]
K. Sakamoto, Y. Ito, T. Hatanaka, P. B. Soni, T. Mori, and K. Sugimura, “Discovery and characterization of a peptide motif that specifically recognizes a non-native conformation of human IgG induced by acidic pH conditions,” Journal of Biological Chemistry, vol. 284, no. 15, pp. 9986–9993, 2009.
[43]
P. Laakkonen, K. Porkka, J. A. Hoffman, and E. Ruoslahti, “A tumor-homing peptide with a targeting specificity related to lymphatic vessels,” Nature Medicine, vol. 8, no. 7, pp. 751–755, 2002.
[44]
M. Essler and E. Ruoslahti, “Molecular specialization of breast vasculature: a breast-homing phage-displayed peptide binds to aminopeptidase P in breast vasculature,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 4, pp. 2252–2257, 2002.
[45]
H. Witt, K. Hajdin, K. Iljin et al., “Identification of a rhabdomyosarcoma targeting peptide by phage display with sequence similarities to the tumour lymphatic-homing peptide LyP-1,” International Journal of Cancer, vol. 124, no. 9, pp. 2026–2032, 2009.
[46]
Y. G. Mikawa, I. N. Maruyama, and S. Brenner, “Surface display of proteins on bacteriophage λ heads,” Journal of Molecular Biology, vol. 262, no. 1, pp. 21–30, 1996.
[47]
B. A. Katz, “Streptavidin-binding and -dimerizing ligands discovered by phage display, topochemistry, and structure-based design,” Biomolecular Engineering, vol. 16, no. 1–4, pp. 57–65, 1999.
[48]
P. A. C. 't Hoen, S. M. G. Jirka, B. R. ten Broeke et al., “Phage display screening without repetitious selection rounds,” Analytical Biochemistry, vol. 421, no. 2, pp. 622–631, 2012.
[49]
L. A. Brammer, B. Bolduc, J. L. Kass, K. M. Felice, C. J. Noren, and M. F. Hall, “A target-unrelated peptide in an M13 phage display library traced to an advantageous mutation in the gene II ribosome-binding site,” Analytical Biochemistry, vol. 373, no. 1, pp. 88–98, 2008.
[50]
M. Vodnik, U. Zager, B. Strukelj, and M. Lunder, “Phage display: selecting straws instead of a needle from a haystack,” Molecules, vol. 16, no. 1, pp. 790–817, 2011.
[51]
J. Huang, B. Ru, S. Li, H. Lin, and F. B. Guo, “SAROTUP: scanner and reporter of target-unrelated peptides,” Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 101932, 7 pages, 2010.
[52]
T. Duchrow, T. Shtatland, D. Guettler, M. Pivovarov, S. Kramer, and R. Weissleder, “Enhancing navigation in biomedical databases by community voting and database-driven text classification,” BMC Bioinformatics, vol. 10, article 1471, p. 317, 2009.
