Random peptide library

Phage display of random peptide libraries identified agonists of erythropoietin receptor... 

EMPl, selected by phage display from random peptide libraries, demonstrates that a dimer of a 20-residue peptide can mimic the function of a monomeric 166-residue protein. In contrast to the minimized Z domain, this selected peptide shares neither the sequence nor the structure of the natural hormone. Thus, there can be a number of ways to solve a molecular recognition problem, and combinatorial methods such as phage display allow us to sort through a multitude of structural scaffolds to discover novel solutions. 

Folgori, A., Taft, R., Meola, A., Felici, F., Galfre, G., Cortese, R., Monaci, P., and Nicosia, A. (1994). A general strategy to identify mimotopes of pathological antigens using only random peptide libraries and human sera. EMBO J. 13, 2236-2243. 

Yao, Z.-J., Kao, M. C. C., and Chung, M. C. M. (1995). Epitope identification by polyclonal antibody from phage-displayed random peptide library. J. Protein Chem. 14, 161-166. 

We have previously developed an in vivo selection method in which peptides that home to specific vascular beds are selected after intravenous administration of a phage display random peptide library [5]. This strategy revealed a vascular address system that allows tissue-specific targeting of normal blood vessels [6-8] and angiogenesis-related targeting of tumor blood vessels [3, 6, 9-12]. While the biologi-... 

Barry MA, Dower WJ, Johnston SA. Toward cell-targeting gene therapy vectors selection of cell-binding peptides from random peptide-presenting phage libraries. Nat Med 1996 2(3) 299-305. 

A variation on the theme has been to map out protease specificity.28 A library of fusion proteins was constructed in a modular manner. The synthetic protein had an N-terminal domain that binds very tightly to an affinity column. This domain was connected to the C-terminal domain of M13 gene III by a randomized peptide sequence. The phages were then bound to the affinity support and treated with a protease. Phages that had a protease-susceptible site were cleaved from the support and eluted. This procedure was subsequently used to map out the specificity of furin,29 which is described in the next chapter. 

Schmidt, T G. M. and Skerra, A. (1993) The random peptide library-assisted engineering of a C-terminal affinity peptide, useful for the detection and purification of a functional Ig Fv fragment. Protein Eng 6, 109—122. 

Peptide libraries made up of millions of randomized peptide sequences have proven useful for the identification of novel ligands that may be of interest for the development of medicinally active compounds.[123,124] However, due to the short length of the individual peptides in linear peptide libraries, they possess considerable conformational flexibility and can populate multiple random-like conformations. This flexibility does not allow one to determine the precise three-dimensional orientation of the side chains, which greatly impedes structure-based design. These facts have greatly accelerated studies into conformationally restricted libraries, where constraints have been introduced to decrease peptide flexibility. However, what is really required is the design of conformationally defined and constrained templates for library display. These templates present the side chains of selected residues in a defined three-dimensional space. Thus, as an alternative to linear peptide libraries, the well-char-... 

Another form of displayed peptide library is the FliTrx Random Peptide Display Library (Invitrogen, Paisley, UK), which uses the bacterial flagellum to display random peptide libraries on the E. coli cell surface (14). This library was constructed in the pFliTrx vector, which positions the random peptides in a flagellin (Fli) thioredoxin (Trx) fusion protein. Biopanning with bacteria works surprisingly well in our experience (15) and screening on nitrocellulose is similar to the Smith method. 

Lu, Z., Murray, K. S., Van Cleave, V., LaVallie, E. R., Stahl, M. L., and McCoy, J. M. (1995) Expression of thioredoxin random peptide libraries on the Escherichia coli cell surface as functional fusions to flagellin a system designed for exploring protein-protein interactions. Biotechnology 13, 366-372. 

This is far more than the number of atoms that make up the Earth. It is also the reason why directing the evolution of an existing enzyme is much likelier to succeed than searching for catalytically active amino add sequences in random peptide libraries. 

Another possibility to screen for active peptides without prior knowledge of a starting sequence is use of a random peptide library. This array contains randomized peptide sequences (61). Compared with the combinatorial peptide... 

Xie, Q Matsunaga, S Wen, Z., et al. (2006) In vitro system for high-throughput screening of random peptide libraries for antimicrobial peptides that recognize bacterial membranes. J. Pept. Sci. 12, 643-652. 

However, the majority of positive leads identified so far have been isolated from the natural reservoir of peptides. A possible explanation for this may be that these peptides have undergone natural selection over billions of years, resulting in enhanced in vivo stability. Another explanation may be that the majority of random peptide sequences from chemical and recombinant libraries do not fold into stable structures (12) however, this may not nessesarily render these peptides more susceptible to proteolytic degradation. 

In a model enrichment, the DNA encoding a peptide with the myc-epitope was diluted in different ratios in a DNA pool encoding random peptide sequences. The myc-epitope peptide was enriched by immuno-precipitation with an anti-c-myc antibody by a factor of twenty to forty per cycle of mRNA-peptide fusion (Roberts and Szostak, 1997). More recently, the mRNA-peptide fusion approach has been used to select peptides for binding to this anti-c-myc antibody from a library of 2 X 1013 molecules (Roberts andja, 1999). In these experiments, the enrichment factor was reported to be 200 per round and is therefore similar to the enrichment factors observed with ribosome display. 

Fig. 7. STABLE. A biotinylated DNA library encoding streptavidin-random peptide fusions is dispersed together with the reaction mixture for in vitro transcription and translation in water in oil compartments. The dilution is chosen such that each compartment contains a single DNA molecule on average, which is transcribed and translated. The encoded streptavidin-peptide fusion is synthesized in the compartment and can bind to its encoding biotinylated DNA. The DNA-protein complexes are subsequently recovered from the emulsion and used for affinity selection. The DNA of the bound complexes is then eluted and amplified by PCR.

The first successful application of ribosome display system was demonstrated for the display of a library of random peptide decamers... 

Devlin JJ, Panganiban LC, Devlin PE, Random peptide libraries A source of specific protein binding molecules, Science, 249 404-406, 1990. 

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