Beyond helper phage: Using "helper cells" to select peptide affinity ligands

doi:10.1371/journal.pone.0160940

Title: Beyond helper phage: Using "helper cells" to select peptide affinity ligands

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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 »« less

Authors:

Phipps, Mary Lisa ^[1]; Lillo, Antoinetta M. ^[1]; Shou, Yulin ^[1]; Schmidt, Emily N. ^[1]; Paavola, Chad D. ^[2]; Naranjo, Leslie A. ^[1]; Bemdich, Sara ^[1]; Swanson, Basil I. ^[1]; Bradbury, Andrew R. M. ^[1]; Martinez, Jennifer S. ^[1]; Goldman, Ellen R. ^[3]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA (United States)
U. S. Naval Research Lab., Washington, D.C. (United States)

Publication Date:: 2016-09-14

Research Org.:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

OSTI Identifier:: 1337465

Alternate Identifier(s):: OSTI ID: 1325648

Report Number(s):: LA-UR-16-21158
Journal ID: ISSN 1932-6203

Grant/Contract Number:: AC52-06NA25396

Resource Type:: Published Article

Journal Name:: PLoS ONE

Additional Journal Information:: Journal Volume: 11; Journal Issue: 9; Journal ID: ISSN 1932-6203

Publisher:: Public Library of Science

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Biological Science; Phage display

Citation Formats


                    Phipps, Mary Lisa, Lillo, Antoinetta M., Shou, Yulin, Schmidt, Emily N., Paavola, Chad D., Naranjo, Leslie A., Bemdich, Sara, Swanson, Basil I., Bradbury, Andrew R. M., Martinez, Jennifer S., and Goldman, 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.

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                    Phipps, Mary Lisa, Lillo, Antoinetta M., Shou, Yulin, Schmidt, Emily N., Paavola, Chad D., Naranjo, Leslie A., Bemdich, Sara, Swanson, Basil I., Bradbury, Andrew R. M., Martinez, Jennifer S., & Goldman, Ellen R. Beyond helper phage: Using "helper cells" to select peptide affinity ligands.  United States.  doi:10.1371/journal.pone.0160940.

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                    Phipps, Mary Lisa, Lillo, Antoinetta M., Shou, Yulin, Schmidt, Emily N., Paavola, Chad D., Naranjo, Leslie A., Bemdich, Sara, Swanson, Basil I., Bradbury, Andrew R. M., Martinez, Jennifer S., and Goldman, Ellen R. Wed .  
        "Beyond helper phage: Using "helper cells" to select peptide affinity ligands".  United States.  doi:10.1371/journal.pone.0160940.

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@article{osti_1337465,

  title        = {Beyond helper phage: Using "helper cells" to select peptide affinity ligands},

  author       = {Phipps, Mary Lisa and Lillo, Antoinetta M. and Shou, Yulin and Schmidt, Emily N. and Paavola, Chad D. and Naranjo, Leslie A. and Bemdich, Sara and Swanson, Basil I. and Bradbury, Andrew R. M. and Martinez, Jennifer S. and Goldman, 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}

}

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