Loading…
Structure-based prediction of protein-protein interaction network in rice
Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark s...
Saved in:
Published in: | Genetics and molecular biology 2024-01, Vol.47 (1), p.e20230068-e20230068 |
---|---|
Main Authors: | , , , , , , |
Format: | Article |
Language: | English |
Subjects: | |
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-c497t-2b62ffcc7a8709dc220b9be48cb253e6061734349c9a25d03ccfd0265c82fc9d3 |
container_end_page | e20230068 |
container_issue | 1 |
container_start_page | e20230068 |
container_title | Genetics and molecular biology |
container_volume | 47 |
creator | Sun, Fangnan Deng, Yaxin Ma, Xiaosong Liu, Yuan Zhao, Lingxia Yu, Shunwu Zhang, Lida |
description | Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice. |
doi_str_mv | 10.1590/1678-4685-GMB-2023-0068 |
format | article |
fullrecord | <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_59a748e5eaf142658f8c7074a6e36d9f</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><scielo_id>S1415_47572024000100801</scielo_id><doaj_id>oai_doaj_org_article_59a748e5eaf142658f8c7074a6e36d9f</doaj_id><sourcerecordid>2922952543</sourcerecordid><originalsourceid>FETCH-LOGICAL-c497t-2b62ffcc7a8709dc220b9be48cb253e6061734349c9a25d03ccfd0265c82fc9d3</originalsourceid><addsrcrecordid>eNpdUk1v1DAQjRCIlsJfgJW4cHEZf9snRCsoKxVxKJwtxxkvXrLx4iQg_j0Ou6wop7Fn3nt6M3pN84LCJZUWXlOlDRHKSHLz8YowYJwAKPOgOT9NHta3oJIILfVZ82QctwBMc8keN2fccCqM4efN-m4qc5jmgqT1I3arfcEuhSnlYZVj_eUJ00COdZWGCYs_jAecfubyrfZWJQV82jyKvh_x2bFeNF_ev_t8_YHcfrpZX7-9JUFYPRHWKhZjCNobDbYLjEFrWxQmtExyVKCo5oILG6xnsgMeQuyAKRkMi8F2_KJZH3S77LduX9LOl18u--T-NHLZOF-mFHp00notDEr0kYoqYaIJGrTwCrnqbKxalwetMSTss9vmuQzVvLtbTueW09XbCgCgAAZoJbw5EPZzu8Mu4DAV399zcX8ypK9uk384CkZY4LwqvDoqlPx9xnFyuzQG7Hs_YJ5HxyxjVjIpFujL_6Anf8xyRq2xSlWUPqBCyeNYMJ7cUHBLWNwSCbdEwm12rVvC4pawVObzf5c58f6mg_8GcfK5Ng</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2932198966</pqid></control><display><type>article</type><title>Structure-based prediction of protein-protein interaction network in rice</title><source>SciELO Brazil</source><source>DOAJ Directory of Open Access Journals</source><creator>Sun, Fangnan ; Deng, Yaxin ; Ma, Xiaosong ; Liu, Yuan ; Zhao, Lingxia ; Yu, Shunwu ; Zhang, Lida</creator><creatorcontrib>Sun, Fangnan ; Deng, Yaxin ; Ma, Xiaosong ; Liu, Yuan ; Zhao, Lingxia ; Yu, Shunwu ; Zhang, Lida</creatorcontrib><description>Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.</description><identifier>ISSN: 1415-4757</identifier><identifier>ISSN: 1678-4685</identifier><identifier>EISSN: 1678-4685</identifier><identifier>DOI: 10.1590/1678-4685-GMB-2023-0068</identifier><identifier>PMID: 38314883</identifier><language>eng</language><publisher>Brazil: Sociedade Brasileira de Genetica</publisher><subject>BIOCHEMISTRY & MOLECULAR BIOLOGY ; Docking ; Functional morphology ; GENETICS & HEREDITY ; Genomics and Bioinformatics ; interactome ; Nucleotides ; protein docking ; Protein interaction ; Protein structure ; protein-protein interaction ; Proteins ; Proteomes ; Rice ; Single-nucleotide polymorphism</subject><ispartof>Genetics and molecular biology, 2024-01, Vol.47 (1), p.e20230068-e20230068</ispartof><rights>Copyright Sociedade Brasileira de Genetica 2024</rights><rights>This work is licensed under a Creative Commons Attribution 4.0 International License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c497t-2b62ffcc7a8709dc220b9be48cb253e6061734349c9a25d03ccfd0265c82fc9d3</cites><orcidid>0000-0001-9483-0563 ; 0000-0002-5207-2458</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,864,885,2102,24150,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38314883$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Fangnan</creatorcontrib><creatorcontrib>Deng, Yaxin</creatorcontrib><creatorcontrib>Ma, Xiaosong</creatorcontrib><creatorcontrib>Liu, Yuan</creatorcontrib><creatorcontrib>Zhao, Lingxia</creatorcontrib><creatorcontrib>Yu, Shunwu</creatorcontrib><creatorcontrib>Zhang, Lida</creatorcontrib><title>Structure-based prediction of protein-protein interaction network in rice</title><title>Genetics and molecular biology</title><addtitle>Genet Mol Biol</addtitle><description>Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.</description><subject>BIOCHEMISTRY & MOLECULAR BIOLOGY</subject><subject>Docking</subject><subject>Functional morphology</subject><subject>GENETICS & HEREDITY</subject><subject>Genomics and Bioinformatics</subject><subject>interactome</subject><subject>Nucleotides</subject><subject>protein docking</subject><subject>Protein interaction</subject><subject>Protein structure</subject><subject>protein-protein interaction</subject><subject>Proteins</subject><subject>Proteomes</subject><subject>Rice</subject><subject>Single-nucleotide polymorphism</subject><issn>1415-4757</issn><issn>1678-4685</issn><issn>1678-4685</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNpdUk1v1DAQjRCIlsJfgJW4cHEZf9snRCsoKxVxKJwtxxkvXrLx4iQg_j0Ou6wop7Fn3nt6M3pN84LCJZUWXlOlDRHKSHLz8YowYJwAKPOgOT9NHta3oJIILfVZ82QctwBMc8keN2fccCqM4efN-m4qc5jmgqT1I3arfcEuhSnlYZVj_eUJ00COdZWGCYs_jAecfubyrfZWJQV82jyKvh_x2bFeNF_ev_t8_YHcfrpZX7-9JUFYPRHWKhZjCNobDbYLjEFrWxQmtExyVKCo5oILG6xnsgMeQuyAKRkMi8F2_KJZH3S77LduX9LOl18u--T-NHLZOF-mFHp00notDEr0kYoqYaIJGrTwCrnqbKxalwetMSTss9vmuQzVvLtbTueW09XbCgCgAAZoJbw5EPZzu8Mu4DAV399zcX8ypK9uk384CkZY4LwqvDoqlPx9xnFyuzQG7Hs_YJ5HxyxjVjIpFujL_6Anf8xyRq2xSlWUPqBCyeNYMJ7cUHBLWNwSCbdEwm12rVvC4pawVObzf5c58f6mg_8GcfK5Ng</recordid><startdate>20240101</startdate><enddate>20240101</enddate><creator>Sun, Fangnan</creator><creator>Deng, Yaxin</creator><creator>Ma, Xiaosong</creator><creator>Liu, Yuan</creator><creator>Zhao, Lingxia</creator><creator>Yu, Shunwu</creator><creator>Zhang, Lida</creator><general>Sociedade Brasileira de Genetica</general><general>Sociedade Brasileira de Genética</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>GPN</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-9483-0563</orcidid><orcidid>https://orcid.org/0000-0002-5207-2458</orcidid></search><sort><creationdate>20240101</creationdate><title>Structure-based prediction of protein-protein interaction network in rice</title><author>Sun, Fangnan ; Deng, Yaxin ; Ma, Xiaosong ; Liu, Yuan ; Zhao, Lingxia ; Yu, Shunwu ; Zhang, Lida</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c497t-2b62ffcc7a8709dc220b9be48cb253e6061734349c9a25d03ccfd0265c82fc9d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>BIOCHEMISTRY & MOLECULAR BIOLOGY</topic><topic>Docking</topic><topic>Functional morphology</topic><topic>GENETICS & HEREDITY</topic><topic>Genomics and Bioinformatics</topic><topic>interactome</topic><topic>Nucleotides</topic><topic>protein docking</topic><topic>Protein interaction</topic><topic>Protein structure</topic><topic>protein-protein interaction</topic><topic>Proteins</topic><topic>Proteomes</topic><topic>Rice</topic><topic>Single-nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sun, Fangnan</creatorcontrib><creatorcontrib>Deng, Yaxin</creatorcontrib><creatorcontrib>Ma, Xiaosong</creatorcontrib><creatorcontrib>Liu, Yuan</creatorcontrib><creatorcontrib>Zhao, Lingxia</creatorcontrib><creatorcontrib>Yu, Shunwu</creatorcontrib><creatorcontrib>Zhang, Lida</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SciELO</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Genetics and molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Fangnan</au><au>Deng, Yaxin</au><au>Ma, Xiaosong</au><au>Liu, Yuan</au><au>Zhao, Lingxia</au><au>Yu, Shunwu</au><au>Zhang, Lida</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structure-based prediction of protein-protein interaction network in rice</atitle><jtitle>Genetics and molecular biology</jtitle><addtitle>Genet Mol Biol</addtitle><date>2024-01-01</date><risdate>2024</risdate><volume>47</volume><issue>1</issue><spage>e20230068</spage><epage>e20230068</epage><pages>e20230068-e20230068</pages><issn>1415-4757</issn><issn>1678-4685</issn><eissn>1678-4685</eissn><abstract>Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.</abstract><cop>Brazil</cop><pub>Sociedade Brasileira de Genetica</pub><pmid>38314883</pmid><doi>10.1590/1678-4685-GMB-2023-0068</doi><orcidid>https://orcid.org/0000-0001-9483-0563</orcidid><orcidid>https://orcid.org/0000-0002-5207-2458</orcidid><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1415-4757 |
ispartof | Genetics and molecular biology, 2024-01, Vol.47 (1), p.e20230068-e20230068 |
issn | 1415-4757 1678-4685 1678-4685 |
language | eng |
recordid | cdi_doaj_primary_oai_doaj_org_article_59a748e5eaf142658f8c7074a6e36d9f |
source | SciELO Brazil; DOAJ Directory of Open Access Journals |
subjects | BIOCHEMISTRY & MOLECULAR BIOLOGY Docking Functional morphology GENETICS & HEREDITY Genomics and Bioinformatics interactome Nucleotides protein docking Protein interaction Protein structure protein-protein interaction Proteins Proteomes Rice Single-nucleotide polymorphism |
title | Structure-based prediction of protein-protein interaction network in rice |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-29T00%3A25%3A31IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Structure-based%20prediction%20of%20protein-protein%20interaction%20network%20in%20rice&rft.jtitle=Genetics%20and%20molecular%20biology&rft.au=Sun,%20Fangnan&rft.date=2024-01-01&rft.volume=47&rft.issue=1&rft.spage=e20230068&rft.epage=e20230068&rft.pages=e20230068-e20230068&rft.issn=1415-4757&rft.eissn=1678-4685&rft_id=info:doi/10.1590/1678-4685-GMB-2023-0068&rft_dat=%3Cproquest_doaj_%3E2922952543%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c497t-2b62ffcc7a8709dc220b9be48cb253e6061734349c9a25d03ccfd0265c82fc9d3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2932198966&rft_id=info:pmid/38314883&rft_scielo_id=S1415_47572024000100801&rfr_iscdi=true |