Cargando…

De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries

The α-helix is one of the most common protein surface recognition motifs found in nature, and its unique amide-cloaking properties also enable α-helical polypeptide motifs to exist in membranes. Together, these properties have inspired the development of α-helically constrained (Helicon) therapeutic...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Kunhua, Tokareva, Olena S., Thomson, Ty M., Wahl, Sebastian C. T., Travaline, Tara L., Ramirez, Jessica D., Choudary, Santosh K., Agarwal, Sorabh, Walkup, Ward G., Olsen, Tivoli J., Brennan, Matthew J., Verdine, Gregory L., McGee, John H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9907135/
https://www.ncbi.nlm.nih.gov/pubmed/36534810
http://dx.doi.org/10.1073/pnas.2210435119
_version_ 1784884111936061440
author Li, Kunhua
Tokareva, Olena S.
Thomson, Ty M.
Wahl, Sebastian C. T.
Travaline, Tara L.
Ramirez, Jessica D.
Choudary, Santosh K.
Agarwal, Sorabh
Walkup, Ward G.
Olsen, Tivoli J.
Brennan, Matthew J.
Verdine, Gregory L.
McGee, John H.
author_facet Li, Kunhua
Tokareva, Olena S.
Thomson, Ty M.
Wahl, Sebastian C. T.
Travaline, Tara L.
Ramirez, Jessica D.
Choudary, Santosh K.
Agarwal, Sorabh
Walkup, Ward G.
Olsen, Tivoli J.
Brennan, Matthew J.
Verdine, Gregory L.
McGee, John H.
author_sort Li, Kunhua
collection PubMed
description The α-helix is one of the most common protein surface recognition motifs found in nature, and its unique amide-cloaking properties also enable α-helical polypeptide motifs to exist in membranes. Together, these properties have inspired the development of α-helically constrained (Helicon) therapeutics that can enter cells and bind targets that have been considered “undruggable”, such as protein–protein interactions. To date, no general method for discovering α-helical binders to proteins has been reported, limiting Helicon drug discovery to only those proteins with previously characterized α-helix recognition sites, and restricting the starting chemical matter to those known α-helical binders. Here, we report a general and rapid screening method to empirically map the α-helix binding sites on a broad range of target proteins in parallel using large, unbiased Helicon phage display libraries and next-generation sequencing. We apply this method to screen six structurally diverse protein domains, only one of which had been previously reported to bind isolated α-helical peptides, discovering 20 families that collectively comprise several hundred individual Helicons. Analysis of 14 X-ray cocrystal structures reveals at least nine distinct α-helix recognition sites across these six proteins, and biochemical and biophysical studies show that these Helicons can block protein–protein interactions, inhibit enzymatic activity, induce conformational rearrangements, and cause protein dimerization. We anticipate that this method will prove broadly useful for the study of protein recognition and for the development of both biochemical tools and therapeutics for traditionally challenging protein targets.
format Online
Article
Text
id pubmed-9907135
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher National Academy of Sciences
record_format MEDLINE/PubMed
spelling pubmed-99071352023-02-08 De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries Li, Kunhua Tokareva, Olena S. Thomson, Ty M. Wahl, Sebastian C. T. Travaline, Tara L. Ramirez, Jessica D. Choudary, Santosh K. Agarwal, Sorabh Walkup, Ward G. Olsen, Tivoli J. Brennan, Matthew J. Verdine, Gregory L. McGee, John H. Proc Natl Acad Sci U S A Biological Sciences The α-helix is one of the most common protein surface recognition motifs found in nature, and its unique amide-cloaking properties also enable α-helical polypeptide motifs to exist in membranes. Together, these properties have inspired the development of α-helically constrained (Helicon) therapeutics that can enter cells and bind targets that have been considered “undruggable”, such as protein–protein interactions. To date, no general method for discovering α-helical binders to proteins has been reported, limiting Helicon drug discovery to only those proteins with previously characterized α-helix recognition sites, and restricting the starting chemical matter to those known α-helical binders. Here, we report a general and rapid screening method to empirically map the α-helix binding sites on a broad range of target proteins in parallel using large, unbiased Helicon phage display libraries and next-generation sequencing. We apply this method to screen six structurally diverse protein domains, only one of which had been previously reported to bind isolated α-helical peptides, discovering 20 families that collectively comprise several hundred individual Helicons. Analysis of 14 X-ray cocrystal structures reveals at least nine distinct α-helix recognition sites across these six proteins, and biochemical and biophysical studies show that these Helicons can block protein–protein interactions, inhibit enzymatic activity, induce conformational rearrangements, and cause protein dimerization. We anticipate that this method will prove broadly useful for the study of protein recognition and for the development of both biochemical tools and therapeutics for traditionally challenging protein targets. National Academy of Sciences 2022-12-19 2022-12-27 /pmc/articles/PMC9907135/ /pubmed/36534810 http://dx.doi.org/10.1073/pnas.2210435119 Text en Copyright © 2022 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Biological Sciences
Li, Kunhua
Tokareva, Olena S.
Thomson, Ty M.
Wahl, Sebastian C. T.
Travaline, Tara L.
Ramirez, Jessica D.
Choudary, Santosh K.
Agarwal, Sorabh
Walkup, Ward G.
Olsen, Tivoli J.
Brennan, Matthew J.
Verdine, Gregory L.
McGee, John H.
De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries
title De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries
title_full De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries
title_fullStr De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries
title_full_unstemmed De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries
title_short De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries
title_sort de novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9907135/
https://www.ncbi.nlm.nih.gov/pubmed/36534810
http://dx.doi.org/10.1073/pnas.2210435119
work_keys_str_mv AT likunhua denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT tokarevaolenas denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT thomsontym denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT wahlsebastianct denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT travalinetaral denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT ramirezjessicad denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT choudarysantoshk denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT agarwalsorabh denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT walkupwardg denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT olsentivolij denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT brennanmatthewj denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT verdinegregoryl denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries
AT mcgeejohnh denovomappingofahelixrecognitionsitesonproteinsurfacesusingunbiasedlibraries