Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands
Abstract
Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combinationmore »
- Authors:
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1337465
- Alternate Identifier(s):
- OSTI ID: 1325648
- Report Number(s):
- LA-UR-16-21158
Journal ID: ISSN 1932-6203; 10.1371/journal.pone.0160940
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Published Article
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Name: PLoS ONE Journal Volume: 11 Journal Issue: 9; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science (PLoS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological Science; Phage display
Citation Formats
Phipps, M. Lisa, Lillo, Antoinetta M., Shou, Yulin, Schmidt, Emily N., Paavola, Chad D., Naranjo, Leslie, Bemdich, Sara, Swanson, Basil I., Bradbury, Andrew R. M., Martinez, Jennifer S., and Goldman, ed., Ellen R. Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands. United States: N. p., 2016.
Web. doi:10.1371/journal.pone.0160940.
Phipps, M. Lisa, Lillo, Antoinetta M., Shou, Yulin, Schmidt, Emily N., Paavola, Chad D., Naranjo, Leslie, Bemdich, Sara, Swanson, Basil I., Bradbury, Andrew R. M., Martinez, Jennifer S., & Goldman, ed., Ellen R. Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands. United States. https://doi.org/10.1371/journal.pone.0160940
Phipps, M. Lisa, Lillo, Antoinetta M., Shou, Yulin, Schmidt, Emily N., Paavola, Chad D., Naranjo, Leslie, Bemdich, Sara, Swanson, Basil I., Bradbury, Andrew R. M., Martinez, Jennifer S., and Goldman, ed., Ellen R. Wed .
"Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands". United States. https://doi.org/10.1371/journal.pone.0160940.
@article{osti_1337465,
title = {Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands},
author = {Phipps, M. Lisa and Lillo, Antoinetta M. and Shou, Yulin and Schmidt, Emily N. and Paavola, Chad D. and Naranjo, Leslie and Bemdich, Sara and Swanson, Basil I. and Bradbury, Andrew R. M. and Martinez, Jennifer S. and Goldman, ed., Ellen R.},
abstractNote = {Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Here, based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.},
doi = {10.1371/journal.pone.0160940},
journal = {PLoS ONE},
number = 9,
volume = 11,
place = {United States},
year = {2016},
month = {9}
}
https://doi.org/10.1371/journal.pone.0160940
Works referenced in this record:
Factors promoting acute and chronic diseases caused by yersiniae.
journal, July 1991
- Brubaker, R. R.
- Clinical Microbiology Reviews, Vol. 4, Issue 3
Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface
journal, June 1985
- Smith, G.
- Science, Vol. 228, Issue 4705
The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p
journal, February 1998
- Lubkowski, Jacek; Hennecke, Frank; Plückthun, Andreas
- Nature Structural Biology, Vol. 5, Issue 2
Complete DNA Sequence and Detailed Analysis of the Yersinia pestis KIM5 Plasmid Encoding Murine Toxin and Capsular Antigen
journal, December 1998
- Lindler, Luther E.; Plano, Gregory V.; Burland, Valerie
- Infection and Immunity, Vol. 66, Issue 12
Site-selective dual modification of periplasmic binding proteins for sensing applications
journal, September 2010
- Crochet, Amanda P.; Kabir, Mohiuddin M.; Francis, Matthew B.
- Biosensors and Bioelectronics, Vol. 26, Issue 1
Eliminating helper phage from phage display
journal, November 2006
- Chasteen, L.; Ayriss, J.; Pavlik, P.
- Nucleic Acids Research, Vol. 34, Issue 21
The antibody mining toolbox: An open source tool for the rapid analysis of antibody repertoires
journal, November 2013
- D'Angelo, Sara; Glanville, Jacob; Ferrara, Fortunato
- mAbs, Vol. 6, Issue 1
Fraction 1 capsular antigen (F1) purification from Yersinia pestis CO92 and from an Escherichia coli recombinant strain and efficacy against lethal plague challenge.
journal, January 1996
- Andrews, G. P.; Heath, D. G.; Anderson, G. W.
- Infection and immunity, Vol. 64, Issue 6
Recombinatorial Cloning Using Heterologous Lox Sites
journal, May 2004
- Siegel, R. W.
- Genome Research, Vol. 14, Issue 6
Yeast surface display for screening combinatorial polypeptide libraries
journal, June 1997
- Boder, Eric T.; Wittrup, K. Dane
- Nature Biotechnology, Vol. 15, Issue 6
Antibody as a surrogate receptor in the screening of a phage display library
journal, June 1993
- Roberts, Doug; Guegler, Karl; Winter, Jill
- Gene, Vol. 128, Issue 1
Development of Phage-Based Single Chain Fv Antibody Reagents for Detection of Yersinia pestis
journal, December 2011
- Lillo, Antonietta M.; Ayriss, Joanne E.; Shou, Yulin
- PLoS ONE, Vol. 6, Issue 12
Isolating and engineering human antibodies using yeast surface display
journal, July 2006
- Chao, Ginger; Lau, Wai L.; Hackel, Benjamin J.
- Nature Protocols, Vol. 1, Issue 2
A general strategy to identify mimotopes of pathological antigens using only random peptide libraries and human sera.
journal, May 1994
- Folgori, A.; Tafi, R.; Meola, A.
- The EMBO Journal, Vol. 13, Issue 9
Filamentous Phage Display in the New Millennium
journal, November 2005
- Kehoe, John W.; Kay, Brian K.
- Chemical Reviews, Vol. 105, Issue 11
Dissection of functional domains in phage fd adsorption protein
journal, March 1990
- Stengele, Irina; Bross, Peter; Garces, Xaver
- Journal of Molecular Biology, Vol. 212, Issue 1
Phage-displayed peptide libraries
journal, August 1998
- Zwick, Michael B.; Shen, Juqun; Scott, Jamie K.
- Current Opinion in Biotechnology, Vol. 9, Issue 4
Phage Anti-Immune Complex Assay: General Strategy for Noncompetitive Immunodetection of Small Molecules
journal, October 2007
- González-Techera, A.; Vanrell, L.; Last, J. A.
- Analytical Chemistry, Vol. 79, Issue 20
Exploiting recombination in single bacteria to make large phage antibody libraries
journal, January 2000
- Sblattero, Daniele; Bradbury, Andrew
- Nature Biotechnology, Vol. 18, Issue 1
Works referencing / citing this record:
Selection of phage-displayed accessible recombinant targeted antibodies (SPARTA): methodology and applications
journal, May 2018
- D’Angelo, Sara; Staquicini, Fernanda I.; Ferrara, Fortunato
- JCI Insight, Vol. 3, Issue 9