Nonnatural Protein-Protein Interaction-Pair Design by Key Residues Grafting

Protein-protein interface design is one of the most exciting fields in protein science; however, designing nonnatural protein-protein interaction pairs remains difficult. In this article we report a de novo design of a nonnatural protein-protein interaction pair by scanning the Protein Data Bank for...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Proceedings of the National Academy of Sciences - PNAS 2007-03, Vol.104 (13), p.5330-5335
Hauptverfasser: Liu, Sen, Liu, Shiyong, Zhu, Xiaolei, Liang, Huanhuan, Cao, Aoneng, Chang, Zhijie, Lai, Luhua
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 5335
container_issue 13
container_start_page 5330
container_title Proceedings of the National Academy of Sciences - PNAS
container_volume 104
creator Liu, Sen
Liu, Shiyong
Zhu, Xiaolei
Liang, Huanhuan
Cao, Aoneng
Chang, Zhijie
Lai, Luhua
description Protein-protein interface design is one of the most exciting fields in protein science; however, designing nonnatural protein-protein interaction pairs remains difficult. In this article we report a de novo design of a nonnatural protein-protein interaction pair by scanning the Protein Data Bank for suitable scaffold proteins that can be used for grafting key interaction residues and can form stable complexes with the target protein after additional mutations. Using our design algorithm, an unrelated protein, rat ${\rm PLC}\delta _{1}-{\rm PH}$ (pleckstrin homology domain of phospholipase C-δ1), was successfully designed to bind the human erythropoietin receptor (EPOR) after grafting the key interaction residues of human erythropoietin binding to EPOR. The designed mutants of rat ${\rm PLC}\delta _{1}-{\rm PH}$ were expressed and purified to test their binding affinities with EPOR. A designed triple mutation of ${\rm PLC}\delta _{1}-{\rm PH}$ (ERPH1) was found to bind EPOR with high affinity $K_{D}$ of 24 nM and an ${\rm IC}_{50}$ of 5.7 μM) both in vitro and in a cell-based assay, respectively, although the WT ${\rm PLC}\delta _{1}-{\rm PH}$ did not show any detectable binding under the assay conditions. The in vitro binding affinities of the ${\rm PLC}\delta _{1}-{\rm PH}$ mutants correlate qualitatively to the computational binding affinities, validating the design and the protein-protein interaction model. The successful practice of finding a proper protein scaffold and making it bind with EPOR demonstrates a prospective application in protein engineering targeting protein- protein interfaces.
doi_str_mv 10.1073/pnas.0606198104
format Article
fullrecord <record><control><sourceid>jstor_proqu</sourceid><recordid>TN_cdi_proquest_journals_201359389</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><jstor_id>25427195</jstor_id><sourcerecordid>25427195</sourcerecordid><originalsourceid>FETCH-LOGICAL-c594t-8df2267db3470d0d9f530597795e2dd107eac1e1f05bf8f339ae24fe64ff01903</originalsourceid><addsrcrecordid>eNp9kc1vEzEQxS0EoqFw5gSsOCAu246_1vYFCRUoVStACM6Ws2sHRxs7tb2I_Pc4yqoBDpxGM_7N8zw9hJ5iOMMg6Pk2mHwGHXRYSQzsHlpgULjtmIL7aAFARCsZYSfoUc5rAFBcwkN0ggUVhBC5QNefYgimTMmMzZcUi_WhnWtzFYpNpi8-1pnxqXlns1-FZrlrru2u-Vq7YbK5uUzGFR9Wj9EDZ8Zsn8z1FH3_8P7bxcf25vPl1cXbm7bnipVWDo6QTgxLygQMMCjHKXAlhOKWDEP1ZU2PLXbAl046SpWxhDnbMecAK6Cn6M1BdzstN3bobSj1fL1NfmPSTkfj9d8vwf_Qq_hTY0kl63gVeDULpHhbHRS98bm342iCjVPWWFWoo_ufXv4DruOUQjWnCWDKFZWqQucHqE8x52Td3SUY9D4lvU9JH1OqG8__NHDk51gq8HoG9ptHOaYx1ZxS0G4ax2J_lYq--D9aiWcHYp1LTHcI4YwIrDj9DWpOsBQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>201359389</pqid></control><display><type>article</type><title>Nonnatural Protein-Protein Interaction-Pair Design by Key Residues Grafting</title><source>MEDLINE</source><source>JSTOR Archive Collection A-Z Listing</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><source>Free Full-Text Journals in Chemistry</source><creator>Liu, Sen ; Liu, Shiyong ; Zhu, Xiaolei ; Liang, Huanhuan ; Cao, Aoneng ; Chang, Zhijie ; Lai, Luhua</creator><creatorcontrib>Liu, Sen ; Liu, Shiyong ; Zhu, Xiaolei ; Liang, Huanhuan ; Cao, Aoneng ; Chang, Zhijie ; Lai, Luhua</creatorcontrib><description>Protein-protein interface design is one of the most exciting fields in protein science; however, designing nonnatural protein-protein interaction pairs remains difficult. In this article we report a de novo design of a nonnatural protein-protein interaction pair by scanning the Protein Data Bank for suitable scaffold proteins that can be used for grafting key interaction residues and can form stable complexes with the target protein after additional mutations. Using our design algorithm, an unrelated protein, rat ${\rm PLC}\delta _{1}-{\rm PH}$ (pleckstrin homology domain of phospholipase C-δ1), was successfully designed to bind the human erythropoietin receptor (EPOR) after grafting the key interaction residues of human erythropoietin binding to EPOR. The designed mutants of rat ${\rm PLC}\delta _{1}-{\rm PH}$ were expressed and purified to test their binding affinities with EPOR. A designed triple mutation of ${\rm PLC}\delta _{1}-{\rm PH}$ (ERPH1) was found to bind EPOR with high affinity $K_{D}$ of 24 nM and an ${\rm IC}_{50}$ of 5.7 μM) both in vitro and in a cell-based assay, respectively, although the WT ${\rm PLC}\delta _{1}-{\rm PH}$ did not show any detectable binding under the assay conditions. The in vitro binding affinities of the ${\rm PLC}\delta _{1}-{\rm PH}$ mutants correlate qualitatively to the computational binding affinities, validating the design and the protein-protein interaction model. The successful practice of finding a proper protein scaffold and making it bind with EPOR demonstrates a prospective application in protein engineering targeting protein- protein interfaces.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0606198104</identifier><identifier>PMID: 17372228</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Algorithms ; Animals ; Atoms ; Binding sites ; Biochemistry ; Biological Sciences ; Blotting, Western ; Cells ; Databases, Protein ; Epics ; Epitopes ; Gene expression ; Genetic engineering ; Humans ; Inhibitory Concentration 50 ; Kinetics ; Models, Molecular ; Mutation ; Packing density ; Protein Conformation ; Protein Interaction Mapping ; Protein Structure, Secondary ; Proteins ; Proteins - chemistry ; Rats ; Receptors ; Scaffolds ; Surface areas ; Surface Plasmon Resonance</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2007-03, Vol.104 (13), p.5330-5335</ispartof><rights>Copyright 2007 The National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Mar 27, 2007</rights><rights>2007 by The National Academy of Sciences of the USA 2007</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c594t-8df2267db3470d0d9f530597795e2dd107eac1e1f05bf8f339ae24fe64ff01903</citedby><cites>FETCH-LOGICAL-c594t-8df2267db3470d0d9f530597795e2dd107eac1e1f05bf8f339ae24fe64ff01903</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/104/13.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/25427195$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/25427195$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,727,780,784,803,885,27923,27924,53790,53792,58016,58249</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17372228$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Sen</creatorcontrib><creatorcontrib>Liu, Shiyong</creatorcontrib><creatorcontrib>Zhu, Xiaolei</creatorcontrib><creatorcontrib>Liang, Huanhuan</creatorcontrib><creatorcontrib>Cao, Aoneng</creatorcontrib><creatorcontrib>Chang, Zhijie</creatorcontrib><creatorcontrib>Lai, Luhua</creatorcontrib><title>Nonnatural Protein-Protein Interaction-Pair Design by Key Residues Grafting</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>Protein-protein interface design is one of the most exciting fields in protein science; however, designing nonnatural protein-protein interaction pairs remains difficult. In this article we report a de novo design of a nonnatural protein-protein interaction pair by scanning the Protein Data Bank for suitable scaffold proteins that can be used for grafting key interaction residues and can form stable complexes with the target protein after additional mutations. Using our design algorithm, an unrelated protein, rat ${\rm PLC}\delta _{1}-{\rm PH}$ (pleckstrin homology domain of phospholipase C-δ1), was successfully designed to bind the human erythropoietin receptor (EPOR) after grafting the key interaction residues of human erythropoietin binding to EPOR. The designed mutants of rat ${\rm PLC}\delta _{1}-{\rm PH}$ were expressed and purified to test their binding affinities with EPOR. A designed triple mutation of ${\rm PLC}\delta _{1}-{\rm PH}$ (ERPH1) was found to bind EPOR with high affinity $K_{D}$ of 24 nM and an ${\rm IC}_{50}$ of 5.7 μM) both in vitro and in a cell-based assay, respectively, although the WT ${\rm PLC}\delta _{1}-{\rm PH}$ did not show any detectable binding under the assay conditions. The in vitro binding affinities of the ${\rm PLC}\delta _{1}-{\rm PH}$ mutants correlate qualitatively to the computational binding affinities, validating the design and the protein-protein interaction model. The successful practice of finding a proper protein scaffold and making it bind with EPOR demonstrates a prospective application in protein engineering targeting protein- protein interfaces.</description><subject>Algorithms</subject><subject>Animals</subject><subject>Atoms</subject><subject>Binding sites</subject><subject>Biochemistry</subject><subject>Biological Sciences</subject><subject>Blotting, Western</subject><subject>Cells</subject><subject>Databases, Protein</subject><subject>Epics</subject><subject>Epitopes</subject><subject>Gene expression</subject><subject>Genetic engineering</subject><subject>Humans</subject><subject>Inhibitory Concentration 50</subject><subject>Kinetics</subject><subject>Models, Molecular</subject><subject>Mutation</subject><subject>Packing density</subject><subject>Protein Conformation</subject><subject>Protein Interaction Mapping</subject><subject>Protein Structure, Secondary</subject><subject>Proteins</subject><subject>Proteins - chemistry</subject><subject>Rats</subject><subject>Receptors</subject><subject>Scaffolds</subject><subject>Surface areas</subject><subject>Surface Plasmon Resonance</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kc1vEzEQxS0EoqFw5gSsOCAu246_1vYFCRUoVStACM6Ws2sHRxs7tb2I_Pc4yqoBDpxGM_7N8zw9hJ5iOMMg6Pk2mHwGHXRYSQzsHlpgULjtmIL7aAFARCsZYSfoUc5rAFBcwkN0ggUVhBC5QNefYgimTMmMzZcUi_WhnWtzFYpNpi8-1pnxqXlns1-FZrlrru2u-Vq7YbK5uUzGFR9Wj9EDZ8Zsn8z1FH3_8P7bxcf25vPl1cXbm7bnipVWDo6QTgxLygQMMCjHKXAlhOKWDEP1ZU2PLXbAl046SpWxhDnbMecAK6Cn6M1BdzstN3bobSj1fL1NfmPSTkfj9d8vwf_Qq_hTY0kl63gVeDULpHhbHRS98bm342iCjVPWWFWoo_ufXv4DruOUQjWnCWDKFZWqQucHqE8x52Td3SUY9D4lvU9JH1OqG8__NHDk51gq8HoG9ptHOaYx1ZxS0G4ax2J_lYq--D9aiWcHYp1LTHcI4YwIrDj9DWpOsBQ</recordid><startdate>20070327</startdate><enddate>20070327</enddate><creator>Liu, Sen</creator><creator>Liu, Shiyong</creator><creator>Zhu, Xiaolei</creator><creator>Liang, Huanhuan</creator><creator>Cao, Aoneng</creator><creator>Chang, Zhijie</creator><creator>Lai, Luhua</creator><general>National Academy of Sciences</general><general>National Acad Sciences</general><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>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7QO</scope><scope>5PM</scope></search><sort><creationdate>20070327</creationdate><title>Nonnatural Protein-Protein Interaction-Pair Design by Key Residues Grafting</title><author>Liu, Sen ; Liu, Shiyong ; Zhu, Xiaolei ; Liang, Huanhuan ; Cao, Aoneng ; Chang, Zhijie ; Lai, Luhua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c594t-8df2267db3470d0d9f530597795e2dd107eac1e1f05bf8f339ae24fe64ff01903</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Atoms</topic><topic>Binding sites</topic><topic>Biochemistry</topic><topic>Biological Sciences</topic><topic>Blotting, Western</topic><topic>Cells</topic><topic>Databases, Protein</topic><topic>Epics</topic><topic>Epitopes</topic><topic>Gene expression</topic><topic>Genetic engineering</topic><topic>Humans</topic><topic>Inhibitory Concentration 50</topic><topic>Kinetics</topic><topic>Models, Molecular</topic><topic>Mutation</topic><topic>Packing density</topic><topic>Protein Conformation</topic><topic>Protein Interaction Mapping</topic><topic>Protein Structure, Secondary</topic><topic>Proteins</topic><topic>Proteins - chemistry</topic><topic>Rats</topic><topic>Receptors</topic><topic>Scaffolds</topic><topic>Surface areas</topic><topic>Surface Plasmon Resonance</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Sen</creatorcontrib><creatorcontrib>Liu, Shiyong</creatorcontrib><creatorcontrib>Zhu, Xiaolei</creatorcontrib><creatorcontrib>Liang, Huanhuan</creatorcontrib><creatorcontrib>Cao, Aoneng</creatorcontrib><creatorcontrib>Chang, Zhijie</creatorcontrib><creatorcontrib>Lai, Luhua</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium &amp; Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Sen</au><au>Liu, Shiyong</au><au>Zhu, Xiaolei</au><au>Liang, Huanhuan</au><au>Cao, Aoneng</au><au>Chang, Zhijie</au><au>Lai, Luhua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Nonnatural Protein-Protein Interaction-Pair Design by Key Residues Grafting</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>2007-03-27</date><risdate>2007</risdate><volume>104</volume><issue>13</issue><spage>5330</spage><epage>5335</epage><pages>5330-5335</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><abstract>Protein-protein interface design is one of the most exciting fields in protein science; however, designing nonnatural protein-protein interaction pairs remains difficult. In this article we report a de novo design of a nonnatural protein-protein interaction pair by scanning the Protein Data Bank for suitable scaffold proteins that can be used for grafting key interaction residues and can form stable complexes with the target protein after additional mutations. Using our design algorithm, an unrelated protein, rat ${\rm PLC}\delta _{1}-{\rm PH}$ (pleckstrin homology domain of phospholipase C-δ1), was successfully designed to bind the human erythropoietin receptor (EPOR) after grafting the key interaction residues of human erythropoietin binding to EPOR. The designed mutants of rat ${\rm PLC}\delta _{1}-{\rm PH}$ were expressed and purified to test their binding affinities with EPOR. A designed triple mutation of ${\rm PLC}\delta _{1}-{\rm PH}$ (ERPH1) was found to bind EPOR with high affinity $K_{D}$ of 24 nM and an ${\rm IC}_{50}$ of 5.7 μM) both in vitro and in a cell-based assay, respectively, although the WT ${\rm PLC}\delta _{1}-{\rm PH}$ did not show any detectable binding under the assay conditions. The in vitro binding affinities of the ${\rm PLC}\delta _{1}-{\rm PH}$ mutants correlate qualitatively to the computational binding affinities, validating the design and the protein-protein interaction model. The successful practice of finding a proper protein scaffold and making it bind with EPOR demonstrates a prospective application in protein engineering targeting protein- protein interfaces.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>17372228</pmid><doi>10.1073/pnas.0606198104</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0027-8424
ispartof Proceedings of the National Academy of Sciences - PNAS, 2007-03, Vol.104 (13), p.5330-5335
issn 0027-8424
1091-6490
language eng
recordid cdi_proquest_journals_201359389
source MEDLINE; JSTOR Archive Collection A-Z Listing; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry
subjects Algorithms
Animals
Atoms
Binding sites
Biochemistry
Biological Sciences
Blotting, Western
Cells
Databases, Protein
Epics
Epitopes
Gene expression
Genetic engineering
Humans
Inhibitory Concentration 50
Kinetics
Models, Molecular
Mutation
Packing density
Protein Conformation
Protein Interaction Mapping
Protein Structure, Secondary
Proteins
Proteins - chemistry
Rats
Receptors
Scaffolds
Surface areas
Surface Plasmon Resonance
title Nonnatural Protein-Protein Interaction-Pair Design by Key Residues Grafting
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-12T20%3A15%3A42IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-jstor_proqu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Nonnatural%20Protein-Protein%20Interaction-Pair%20Design%20by%20Key%20Residues%20Grafting&rft.jtitle=Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20-%20PNAS&rft.au=Liu,%20Sen&rft.date=2007-03-27&rft.volume=104&rft.issue=13&rft.spage=5330&rft.epage=5335&rft.pages=5330-5335&rft.issn=0027-8424&rft.eissn=1091-6490&rft_id=info:doi/10.1073/pnas.0606198104&rft_dat=%3Cjstor_proqu%3E25427195%3C/jstor_proqu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=201359389&rft_id=info:pmid/17372228&rft_jstor_id=25427195&rfr_iscdi=true