Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes

The atomic‐resolution structural information that X‐ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the en...

Full description

Saved in:
Bibliographic Details
Published in:Protein science 2024-01, Vol.33 (1), p.e4824-n/a
Main Authors: Bruce, Heather A., Singer, Alexander U., Filippova, Ekaterina V., Blazer, Levi L., Adams, Jarrett J., Enderle, Leonie, Ben‐David, Moshe, Radley, Elizabeth H., Mao, Daniel Y. L., Pau, Victor, Orlicky, Stephen, Sicheri, Frank, Kurinov, Igor, Atwell, Shane, Kossiakoff, Anthony A., Sidhu, Sachdev S.
Format: Article
Language:English
Subjects:
Antibodies
antibody fragments
antibody library
Antigen-Antibody Complex - chemistry
Antigens
Antigens - chemistry
Binding
crystal lattice contacts
Crystallization
Crystallization - methods
crystallization platform
Crystallography
Crystallography, X-Ray
Display devices
Elbow
Fab
Humans
Immunoglobulin Fab Fragments - chemistry
Immunoglobulin Fab Fragments - genetics
Protein Conformation
protein engineering
surface entropy reduction
Citations: Items that this one cites
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by
cites cdi_FETCH-LOGICAL-c4004-b3dc8c4c5906cf5e6c83ae265b642f4f13482742bc992587fd04c4b0974dff63
container_end_page n/a
container_issue 1
container_start_page e4824
container_title Protein science
container_volume 33
creator Bruce, Heather A.
Singer, Alexander U.
Filippova, Ekaterina V.
Blazer, Levi L.
Adams, Jarrett J.
Enderle, Leonie
Ben‐David, Moshe
Radley, Elizabeth H.
Mao, Daniel Y. L.
Pau, Victor
Orlicky, Stephen
Sicheri, Frank
Kurinov, Igor
Atwell, Shane
Kossiakoff, Anthony A.
Sidhu, Sachdev S.
description The atomic‐resolution structural information that X‐ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the endeavor a considerable effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallization by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage‐display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallize. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in an extraordinary improvement in Fab and Fab:antigen complex crystallizability, revealing a strong synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallization screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallization and how they complement each other in the process.
doi_str_mv 10.1002/pro.4824
format article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10731619</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2906183633</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4004-b3dc8c4c5906cf5e6c83ae265b642f4f13482742bc992587fd04c4b0974dff63</originalsourceid><addsrcrecordid>eNp1kc1KHTEYhoO06Kkt9ApkoJtuxuZvMombImJ_QLAUF92FTObLGJlJjskc7XHlJfQaeyWNemproasQ8uTh_b4XodcE7xOM6btlivtcUr6FFoQLVUslvj1DC6wEqSUTcge9yPkCY8wJZdtoh7WKNw1jC2SOw-ADQIK-MmH2A4Sftz86H3ofhsolM0wQ5ly5mCoI5ybYAtq0zrMZR39jZh9DFd393y7264ONpLJxWo7wHfJL9NyZMcOrzbmLzj4cnx19qk9OP34-OjypLS-56o71VlpuG4WFdQ0IK5kBKppOcOq4I6wM2HLaWaVoI1vXY255h1XLe-cE20XvH7TLVTdBb0vqZEa9TH4yaa2j8frpS_DneohXmuCWEUFUMbzdGFK8XEGe9eSzhXE0AeIqayqlopwy1RT0zT_oRVylUMbTtOQnZeeM_RHaFHNO4B7TEKzveiv3qO96K-je3-kfwd9FFaB-AK79COv_ivSXr6f3wl-KHKUJ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2906183633</pqid></control><display><type>article</type><title>Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes</title><source>Wiley</source><source>PubMed Central</source><creator>Bruce, Heather A. ; Singer, Alexander U. ; Filippova, Ekaterina V. ; Blazer, Levi L. ; Adams, Jarrett J. ; Enderle, Leonie ; Ben‐David, Moshe ; Radley, Elizabeth H. ; Mao, Daniel Y. L. ; Pau, Victor ; Orlicky, Stephen ; Sicheri, Frank ; Kurinov, Igor ; Atwell, Shane ; Kossiakoff, Anthony A. ; Sidhu, Sachdev S.</creator><creatorcontrib>Bruce, Heather A. ; Singer, Alexander U. ; Filippova, Ekaterina V. ; Blazer, Levi L. ; Adams, Jarrett J. ; Enderle, Leonie ; Ben‐David, Moshe ; Radley, Elizabeth H. ; Mao, Daniel Y. L. ; Pau, Victor ; Orlicky, Stephen ; Sicheri, Frank ; Kurinov, Igor ; Atwell, Shane ; Kossiakoff, Anthony A. ; Sidhu, Sachdev S.</creatorcontrib><description>The atomic‐resolution structural information that X‐ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the endeavor a considerable effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallization by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage‐display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallize. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in an extraordinary improvement in Fab and Fab:antigen complex crystallizability, revealing a strong synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallization screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallization and how they complement each other in the process.</description><identifier>ISSN: 0961-8368</identifier><identifier>ISSN: 1469-896X</identifier><identifier>EISSN: 1469-896X</identifier><identifier>DOI: 10.1002/pro.4824</identifier><identifier>PMID: 37945533</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley &amp; Sons, Inc</publisher><subject>Antibodies ; antibody fragments ; antibody library ; Antigen-Antibody Complex - chemistry ; Antigens ; Antigens - chemistry ; Binding ; crystal lattice contacts ; Crystallization ; Crystallization - methods ; crystallization platform ; Crystallography ; Crystallography, X-Ray ; Display devices ; Elbow ; Fab ; Humans ; Immunoglobulin Fab Fragments - chemistry ; Immunoglobulin Fab Fragments - genetics ; Protein Conformation ; protein engineering ; surface entropy reduction</subject><ispartof>Protein science, 2024-01, Vol.33 (1), p.e4824-n/a</ispartof><rights>2023 The Authors. published by Wiley Periodicals LLC on behalf of The Protein Society.</rights><rights>2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.</rights><rights>2023. This article is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c4004-b3dc8c4c5906cf5e6c83ae265b642f4f13482742bc992587fd04c4b0974dff63</cites><orcidid>0000-0003-3174-9359</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10731619/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10731619/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37945533$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bruce, Heather A.</creatorcontrib><creatorcontrib>Singer, Alexander U.</creatorcontrib><creatorcontrib>Filippova, Ekaterina V.</creatorcontrib><creatorcontrib>Blazer, Levi L.</creatorcontrib><creatorcontrib>Adams, Jarrett J.</creatorcontrib><creatorcontrib>Enderle, Leonie</creatorcontrib><creatorcontrib>Ben‐David, Moshe</creatorcontrib><creatorcontrib>Radley, Elizabeth H.</creatorcontrib><creatorcontrib>Mao, Daniel Y. L.</creatorcontrib><creatorcontrib>Pau, Victor</creatorcontrib><creatorcontrib>Orlicky, Stephen</creatorcontrib><creatorcontrib>Sicheri, Frank</creatorcontrib><creatorcontrib>Kurinov, Igor</creatorcontrib><creatorcontrib>Atwell, Shane</creatorcontrib><creatorcontrib>Kossiakoff, Anthony A.</creatorcontrib><creatorcontrib>Sidhu, Sachdev S.</creatorcontrib><title>Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes</title><title>Protein science</title><addtitle>Protein Sci</addtitle><description>The atomic‐resolution structural information that X‐ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the endeavor a considerable effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallization by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage‐display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallize. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in an extraordinary improvement in Fab and Fab:antigen complex crystallizability, revealing a strong synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallization screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallization and how they complement each other in the process.</description><subject>Antibodies</subject><subject>antibody fragments</subject><subject>antibody library</subject><subject>Antigen-Antibody Complex - chemistry</subject><subject>Antigens</subject><subject>Antigens - chemistry</subject><subject>Binding</subject><subject>crystal lattice contacts</subject><subject>Crystallization</subject><subject>Crystallization - methods</subject><subject>crystallization platform</subject><subject>Crystallography</subject><subject>Crystallography, X-Ray</subject><subject>Display devices</subject><subject>Elbow</subject><subject>Fab</subject><subject>Humans</subject><subject>Immunoglobulin Fab Fragments - chemistry</subject><subject>Immunoglobulin Fab Fragments - genetics</subject><subject>Protein Conformation</subject><subject>protein engineering</subject><subject>surface entropy reduction</subject><issn>0961-8368</issn><issn>1469-896X</issn><issn>1469-896X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><recordid>eNp1kc1KHTEYhoO06Kkt9ApkoJtuxuZvMombImJ_QLAUF92FTObLGJlJjskc7XHlJfQaeyWNemproasQ8uTh_b4XodcE7xOM6btlivtcUr6FFoQLVUslvj1DC6wEqSUTcge9yPkCY8wJZdtoh7WKNw1jC2SOw-ADQIK-MmH2A4Sftz86H3ofhsolM0wQ5ly5mCoI5ybYAtq0zrMZR39jZh9DFd393y7264ONpLJxWo7wHfJL9NyZMcOrzbmLzj4cnx19qk9OP34-OjypLS-56o71VlpuG4WFdQ0IK5kBKppOcOq4I6wM2HLaWaVoI1vXY255h1XLe-cE20XvH7TLVTdBb0vqZEa9TH4yaa2j8frpS_DneohXmuCWEUFUMbzdGFK8XEGe9eSzhXE0AeIqayqlopwy1RT0zT_oRVylUMbTtOQnZeeM_RHaFHNO4B7TEKzveiv3qO96K-je3-kfwd9FFaB-AK79COv_ivSXr6f3wl-KHKUJ</recordid><startdate>202401</startdate><enddate>202401</enddate><creator>Bruce, Heather A.</creator><creator>Singer, Alexander U.</creator><creator>Filippova, Ekaterina V.</creator><creator>Blazer, Levi L.</creator><creator>Adams, Jarrett J.</creator><creator>Enderle, Leonie</creator><creator>Ben‐David, Moshe</creator><creator>Radley, Elizabeth H.</creator><creator>Mao, Daniel Y. L.</creator><creator>Pau, Victor</creator><creator>Orlicky, Stephen</creator><creator>Sicheri, Frank</creator><creator>Kurinov, Igor</creator><creator>Atwell, Shane</creator><creator>Kossiakoff, Anthony A.</creator><creator>Sidhu, Sachdev S.</creator><general>John Wiley &amp; Sons, Inc</general><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7T5</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-3174-9359</orcidid></search><sort><creationdate>202401</creationdate><title>Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes</title><author>Bruce, Heather A. ; Singer, Alexander U. ; Filippova, Ekaterina V. ; Blazer, Levi L. ; Adams, Jarrett J. ; Enderle, Leonie ; Ben‐David, Moshe ; Radley, Elizabeth H. ; Mao, Daniel Y. L. ; Pau, Victor ; Orlicky, Stephen ; Sicheri, Frank ; Kurinov, Igor ; Atwell, Shane ; Kossiakoff, Anthony A. ; Sidhu, Sachdev S.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4004-b3dc8c4c5906cf5e6c83ae265b642f4f13482742bc992587fd04c4b0974dff63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Antibodies</topic><topic>antibody fragments</topic><topic>antibody library</topic><topic>Antigen-Antibody Complex - chemistry</topic><topic>Antigens</topic><topic>Antigens - chemistry</topic><topic>Binding</topic><topic>crystal lattice contacts</topic><topic>Crystallization</topic><topic>Crystallization - methods</topic><topic>crystallization platform</topic><topic>Crystallography</topic><topic>Crystallography, X-Ray</topic><topic>Display devices</topic><topic>Elbow</topic><topic>Fab</topic><topic>Humans</topic><topic>Immunoglobulin Fab Fragments - chemistry</topic><topic>Immunoglobulin Fab Fragments - genetics</topic><topic>Protein Conformation</topic><topic>protein engineering</topic><topic>surface entropy reduction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bruce, Heather A.</creatorcontrib><creatorcontrib>Singer, Alexander U.</creatorcontrib><creatorcontrib>Filippova, Ekaterina V.</creatorcontrib><creatorcontrib>Blazer, Levi L.</creatorcontrib><creatorcontrib>Adams, Jarrett J.</creatorcontrib><creatorcontrib>Enderle, Leonie</creatorcontrib><creatorcontrib>Ben‐David, Moshe</creatorcontrib><creatorcontrib>Radley, Elizabeth H.</creatorcontrib><creatorcontrib>Mao, Daniel Y. L.</creatorcontrib><creatorcontrib>Pau, Victor</creatorcontrib><creatorcontrib>Orlicky, Stephen</creatorcontrib><creatorcontrib>Sicheri, Frank</creatorcontrib><creatorcontrib>Kurinov, Igor</creatorcontrib><creatorcontrib>Atwell, Shane</creatorcontrib><creatorcontrib>Kossiakoff, Anthony A.</creatorcontrib><creatorcontrib>Sidhu, Sachdev S.</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Wiley Online Library Free Content</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Immunology Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Protein science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bruce, Heather A.</au><au>Singer, Alexander U.</au><au>Filippova, Ekaterina V.</au><au>Blazer, Levi L.</au><au>Adams, Jarrett J.</au><au>Enderle, Leonie</au><au>Ben‐David, Moshe</au><au>Radley, Elizabeth H.</au><au>Mao, Daniel Y. L.</au><au>Pau, Victor</au><au>Orlicky, Stephen</au><au>Sicheri, Frank</au><au>Kurinov, Igor</au><au>Atwell, Shane</au><au>Kossiakoff, Anthony A.</au><au>Sidhu, Sachdev S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes</atitle><jtitle>Protein science</jtitle><addtitle>Protein Sci</addtitle><date>2024-01</date><risdate>2024</risdate><volume>33</volume><issue>1</issue><spage>e4824</spage><epage>n/a</epage><pages>e4824-n/a</pages><issn>0961-8368</issn><issn>1469-896X</issn><eissn>1469-896X</eissn><abstract>The atomic‐resolution structural information that X‐ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the endeavor a considerable effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallization by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage‐display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallize. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in an extraordinary improvement in Fab and Fab:antigen complex crystallizability, revealing a strong synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallization screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallization and how they complement each other in the process.</abstract><cop>Hoboken, USA</cop><pub>John Wiley &amp; Sons, Inc</pub><pmid>37945533</pmid><doi>10.1002/pro.4824</doi><tpages>21</tpages><orcidid>https://orcid.org/0000-0003-3174-9359</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0961-8368
ispartof Protein science, 2024-01, Vol.33 (1), p.e4824-n/a
issn 0961-8368
1469-896X
1469-896X
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10731619
source Wiley; PubMed Central
subjects Antibodies
antibody fragments
antibody library
Antigen-Antibody Complex - chemistry
Antigens
Antigens - chemistry
Binding
crystal lattice contacts
Crystallization
Crystallization - methods
crystallization platform
Crystallography
Crystallography, X-Ray
Display devices
Elbow
Fab
Humans
Immunoglobulin Fab Fragments - chemistry
Immunoglobulin Fab Fragments - genetics
Protein Conformation
protein engineering
surface entropy reduction
title Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-11T12%3A37%3A34IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Engineered%20antigen%E2%80%90binding%20fragments%20for%20enhanced%20crystallization%20of%20antibody:antigen%20complexes&rft.jtitle=Protein%20science&rft.au=Bruce,%20Heather%20A.&rft.date=2024-01&rft.volume=33&rft.issue=1&rft.spage=e4824&rft.epage=n/a&rft.pages=e4824-n/a&rft.issn=0961-8368&rft.eissn=1469-896X&rft_id=info:doi/10.1002/pro.4824&rft_dat=%3Cproquest_pubme%3E2906183633%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c4004-b3dc8c4c5906cf5e6c83ae265b642f4f13482742bc992587fd04c4b0974dff63%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2906183633&rft_id=info:pmid/37945533&rfr_iscdi=true