Amino‐acid composition after loop deletion drives domain swapping
Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain‐swapped oligomer over the monomer. While it is known that the deletion of loops between β‐strands can promote domain swapping, the spliced seq...
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Veröffentlicht in: | Protein science 2017-10, Vol.26 (10), p.1994-2002 |
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container_end_page | 2002 |
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container_issue | 10 |
container_start_page | 1994 |
container_title | Protein science |
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creator | Nandwani, Neha Surana, Parag Udgaonkar, Jayant B. Das, Ranabir Gosavi, Shachi |
description | Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain‐swapped oligomer over the monomer. While it is known that the deletion of loops between β‐strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop‐deletion mutants of the non‐domain‐swapping protein monellin, frame‐shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping.
PDB Code(s): 5XFU |
doi_str_mv | 10.1002/pro.3237 |
format | Article |
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PDB Code(s): 5XFU</description><identifier>ISSN: 0961-8368</identifier><identifier>EISSN: 1469-896X</identifier><identifier>DOI: 10.1002/pro.3237</identifier><identifier>PMID: 28710790</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Amino acids ; Amino Acids - chemistry ; Amino Acids - genetics ; Crystallography, X-Ray ; Deletion mutant ; domain swapping ; hinge loop composition ; hinge loop length ; Models, Molecular ; Protein Domains ; Protein engineering ; Protein Engineering - methods ; Proteins - chemistry ; Proteins - genetics ; Proteins - metabolism ; Recombinant Proteins ; Sequence Deletion ; single‐chain monellin ; X‐ray crystallography</subject><ispartof>Protein science, 2017-10, Vol.26 (10), p.1994-2002</ispartof><rights>2017 The Protein Society</rights><rights>2017 The Protein Society.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5047-5455ac48706e951fb73b5b0f6e9409bcddfbf5829af7af749465413da142561e3</citedby><cites>FETCH-LOGICAL-c5047-5455ac48706e951fb73b5b0f6e9409bcddfbf5829af7af749465413da142561e3</cites><orcidid>0000-0001-5114-6817</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/PMC5606538/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5606538/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,1417,1433,27924,27925,45574,45575,46409,46833,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28710790$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nandwani, Neha</creatorcontrib><creatorcontrib>Surana, Parag</creatorcontrib><creatorcontrib>Udgaonkar, Jayant B.</creatorcontrib><creatorcontrib>Das, Ranabir</creatorcontrib><creatorcontrib>Gosavi, Shachi</creatorcontrib><title>Amino‐acid composition after loop deletion drives domain swapping</title><title>Protein science</title><addtitle>Protein Sci</addtitle><description>Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain‐swapped oligomer over the monomer. While it is known that the deletion of loops between β‐strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop‐deletion mutants of the non‐domain‐swapping protein monellin, frame‐shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping.
PDB Code(s): 5XFU</description><subject>Amino acids</subject><subject>Amino Acids - chemistry</subject><subject>Amino Acids - genetics</subject><subject>Crystallography, X-Ray</subject><subject>Deletion mutant</subject><subject>domain swapping</subject><subject>hinge loop composition</subject><subject>hinge loop length</subject><subject>Models, Molecular</subject><subject>Protein Domains</subject><subject>Protein engineering</subject><subject>Protein Engineering - methods</subject><subject>Proteins - chemistry</subject><subject>Proteins - genetics</subject><subject>Proteins - metabolism</subject><subject>Recombinant Proteins</subject><subject>Sequence Deletion</subject><subject>single‐chain monellin</subject><subject>X‐ray crystallography</subject><issn>0961-8368</issn><issn>1469-896X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kdlKxTAQhoMoelzAJ5CCN95UJ23WG0EObiAcEQXvQtqmGmmbmpyFc-cj-Iw-iXE7LiAEwsx8fMzwI7SNYR8DZAe9d_t5lvMlNMCEyVRIdruMBiAZTkXOxBpaD-EBAAjO8lW0lgmOgUsYoOFRazv38vSsS1slpWt7F-zYui7R9dj4pHGuTyrTmPde5e3UhKRyrbZdEma67213t4lWat0Es_X5b6Cbk-Pr4Vl6MTo9Hx5dpCUFwlNKKNUlERyYkRTXBc8LWkAdKwKyKKuqLmoqMqlrHh-RhFGC80pjklGGTb6BDj-8_aRoTVWabux1o3pvW-3nymmrfk86e6_u3FRRBozmIgr2PgXePU5MGKvWhtI0je6MmwSFZQZYciAkort_0Ac38V08L1IEqOCCy29h6V0I3tSLZTCot2Ri7dRbMhHd-bn8AvyKIgLpBzCzjZn_K1KXV6N34SuZR5kE</recordid><startdate>201710</startdate><enddate>201710</enddate><creator>Nandwani, Neha</creator><creator>Surana, Parag</creator><creator>Udgaonkar, Jayant B.</creator><creator>Das, Ranabir</creator><creator>Gosavi, Shachi</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</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>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/0000-0001-5114-6817</orcidid></search><sort><creationdate>201710</creationdate><title>Amino‐acid composition after loop deletion drives domain swapping</title><author>Nandwani, Neha ; Surana, Parag ; Udgaonkar, Jayant B. ; Das, Ranabir ; Gosavi, Shachi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5047-5455ac48706e951fb73b5b0f6e9409bcddfbf5829af7af749465413da142561e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Amino acids</topic><topic>Amino Acids - chemistry</topic><topic>Amino Acids - genetics</topic><topic>Crystallography, X-Ray</topic><topic>Deletion mutant</topic><topic>domain swapping</topic><topic>hinge loop composition</topic><topic>hinge loop length</topic><topic>Models, Molecular</topic><topic>Protein Domains</topic><topic>Protein engineering</topic><topic>Protein Engineering - methods</topic><topic>Proteins - chemistry</topic><topic>Proteins - genetics</topic><topic>Proteins - metabolism</topic><topic>Recombinant Proteins</topic><topic>Sequence Deletion</topic><topic>single‐chain monellin</topic><topic>X‐ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nandwani, Neha</creatorcontrib><creatorcontrib>Surana, Parag</creatorcontrib><creatorcontrib>Udgaonkar, Jayant B.</creatorcontrib><creatorcontrib>Das, Ranabir</creatorcontrib><creatorcontrib>Gosavi, Shachi</creatorcontrib><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 & 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>Nandwani, Neha</au><au>Surana, Parag</au><au>Udgaonkar, Jayant B.</au><au>Das, Ranabir</au><au>Gosavi, Shachi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Amino‐acid composition after loop deletion drives domain swapping</atitle><jtitle>Protein science</jtitle><addtitle>Protein Sci</addtitle><date>2017-10</date><risdate>2017</risdate><volume>26</volume><issue>10</issue><spage>1994</spage><epage>2002</epage><pages>1994-2002</pages><issn>0961-8368</issn><eissn>1469-896X</eissn><abstract>Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain‐swapped oligomer over the monomer. While it is known that the deletion of loops between β‐strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop‐deletion mutants of the non‐domain‐swapping protein monellin, frame‐shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping.
PDB Code(s): 5XFU</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>28710790</pmid><doi>10.1002/pro.3237</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0001-5114-6817</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Amino acids Amino Acids - chemistry Amino Acids - genetics Crystallography, X-Ray Deletion mutant domain swapping hinge loop composition hinge loop length Models, Molecular Protein Domains Protein engineering Protein Engineering - methods Proteins - chemistry Proteins - genetics Proteins - metabolism Recombinant Proteins Sequence Deletion single‐chain monellin X‐ray crystallography |
title | Amino‐acid composition after loop deletion drives domain swapping |
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