Domain‐Swapping Design by Polyproline Rod Insertion
During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. Engineering this process by design is important for creating a higher order protein assembly with minimal modification. Herein, a simple design strategy is shown for domain‐swapping formation by loop d...
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| Veröffentlicht in: | Chembiochem : a European journal of chemical biology 2019-10, Vol.20 (19), p.2454-2457 |
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| container_title | Chembiochem : a European journal of chemical biology |
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| creator | Shiga, Shota Yamanaka, Masaru Fujiwara, Wataru Hirota, Shun Goda, Shuichiro Makabe, Koki |
| description | During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. Engineering this process by design is important for creating a higher order protein assembly with minimal modification. Herein, a simple design strategy is shown for domain‐swapping formation by loop deletion and insertion of a polyproline rod. Crystal structures revealed the formation of the domain‐swapped dimers and polyproline portion formed a polyproline II (PPII) structure. Small‐angle X‐ray scattering demonstrated that an extended orientation of domain‐swapped dimer was retained in solution. It is found that a multiple of three of inserting proline residue is favored for domain swapping because of the helical nature of PPII. The rigid nature of the polyproline rod enables precise control of the interdomain distance and orientation.
Straighten up! During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. To achieve domain swapping by design, insertion of a rigid polyproline rod has been investigated. Crystal structure and small‐angle X‐ray scattering analyses confirm the extended orientation of the two subunits. |
| doi_str_mv | 10.1002/cbic.201900179 |
| format | Article |
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Straighten up! During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. To achieve domain swapping by design, insertion of a rigid polyproline rod has been investigated. Crystal structure and small‐angle X‐ray scattering analyses confirm the extended orientation of the two subunits.</description><identifier>ISSN: 1439-4227</identifier><identifier>EISSN: 1439-7633</identifier><identifier>DOI: 10.1002/cbic.201900179</identifier><identifier>PMID: 31094059</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>biophysics ; Control rods ; Crystal structure ; Design ; Design modifications ; Dimers ; domain swapping ; Insertion ; Molecular structure ; Polyproline ; Proline ; protein design ; protein folding ; Proteins ; Structural members</subject><ispartof>Chembiochem : a European journal of chemical biology, 2019-10, Vol.20 (19), p.2454-2457</ispartof><rights>2019 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim</rights><rights>2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4769-c1b76c228ecfdc6f9a6c9cd353c6a5a4025e23f010914379bf815839295e93413</citedby><cites>FETCH-LOGICAL-c4769-c1b76c228ecfdc6f9a6c9cd353c6a5a4025e23f010914379bf815839295e93413</cites><orcidid>0000-0003-3168-8445</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fcbic.201900179$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fcbic.201900179$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27922,27923,45572,45573</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31094059$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shiga, Shota</creatorcontrib><creatorcontrib>Yamanaka, Masaru</creatorcontrib><creatorcontrib>Fujiwara, Wataru</creatorcontrib><creatorcontrib>Hirota, Shun</creatorcontrib><creatorcontrib>Goda, Shuichiro</creatorcontrib><creatorcontrib>Makabe, Koki</creatorcontrib><title>Domain‐Swapping Design by Polyproline Rod Insertion</title><title>Chembiochem : a European journal of chemical biology</title><addtitle>Chembiochem</addtitle><description>During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. Engineering this process by design is important for creating a higher order protein assembly with minimal modification. Herein, a simple design strategy is shown for domain‐swapping formation by loop deletion and insertion of a polyproline rod. Crystal structures revealed the formation of the domain‐swapped dimers and polyproline portion formed a polyproline II (PPII) structure. Small‐angle X‐ray scattering demonstrated that an extended orientation of domain‐swapped dimer was retained in solution. It is found that a multiple of three of inserting proline residue is favored for domain swapping because of the helical nature of PPII. The rigid nature of the polyproline rod enables precise control of the interdomain distance and orientation.
Straighten up! During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. To achieve domain swapping by design, insertion of a rigid polyproline rod has been investigated. Crystal structure and small‐angle X‐ray scattering analyses confirm the extended orientation of the two subunits.</description><subject>biophysics</subject><subject>Control rods</subject><subject>Crystal structure</subject><subject>Design</subject><subject>Design modifications</subject><subject>Dimers</subject><subject>domain swapping</subject><subject>Insertion</subject><subject>Molecular structure</subject><subject>Polyproline</subject><subject>Proline</subject><subject>protein design</subject><subject>protein folding</subject><subject>Proteins</subject><subject>Structural members</subject><issn>1439-4227</issn><issn>1439-7633</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNqFkLtOwzAUhi0EoqWwMqJILCwpvsROPELLpVIlEJfZchyncpXYIW5UZeMReEaeBFctILEwnTN85z-ffgBOERwjCPGlyo0aY4g4hCjle2CIEsLjlBGyv9sTjNMBOPJ-CSHkjKBDMCAI8gRSPgR06mpp7Of7x_NaNo2xi2iqvVnYKO-jR1f1TesqY3X05IpoZr1uV8bZY3BQysrrk90cgdfbm5fJfTx_uJtNruaxSlLGY4XylCmMM63KQrGSS6a4KgglikkqE4ipxqSEwSaopjwvM0QzwjGnmpMEkRG42OYGi7dO-5WojVe6qqTVrvMCY4JheEU36PkfdOm61ga7QHFOaEoyFqjxllKt877VpWhaU8u2FwiKTaFiU6j4KTQcnO1iu7zWxQ_-3WAA-BZYm0r3_8SJyfVs8hv-BWdDgEQ</recordid><startdate>20191001</startdate><enddate>20191001</enddate><creator>Shiga, Shota</creator><creator>Yamanaka, Masaru</creator><creator>Fujiwara, Wataru</creator><creator>Hirota, Shun</creator><creator>Goda, Shuichiro</creator><creator>Makabe, Koki</creator><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-3168-8445</orcidid></search><sort><creationdate>20191001</creationdate><title>Domain‐Swapping Design by Polyproline Rod Insertion</title><author>Shiga, Shota ; Yamanaka, Masaru ; Fujiwara, Wataru ; Hirota, Shun ; Goda, Shuichiro ; Makabe, Koki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4769-c1b76c228ecfdc6f9a6c9cd353c6a5a4025e23f010914379bf815839295e93413</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>biophysics</topic><topic>Control rods</topic><topic>Crystal structure</topic><topic>Design</topic><topic>Design modifications</topic><topic>Dimers</topic><topic>domain swapping</topic><topic>Insertion</topic><topic>Molecular structure</topic><topic>Polyproline</topic><topic>Proline</topic><topic>protein design</topic><topic>protein folding</topic><topic>Proteins</topic><topic>Structural members</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shiga, Shota</creatorcontrib><creatorcontrib>Yamanaka, Masaru</creatorcontrib><creatorcontrib>Fujiwara, Wataru</creatorcontrib><creatorcontrib>Hirota, Shun</creatorcontrib><creatorcontrib>Goda, Shuichiro</creatorcontrib><creatorcontrib>Makabe, Koki</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids 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>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Chembiochem : a European journal of chemical biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shiga, Shota</au><au>Yamanaka, Masaru</au><au>Fujiwara, Wataru</au><au>Hirota, Shun</au><au>Goda, Shuichiro</au><au>Makabe, Koki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Domain‐Swapping Design by Polyproline Rod Insertion</atitle><jtitle>Chembiochem : a European journal of chemical biology</jtitle><addtitle>Chembiochem</addtitle><date>2019-10-01</date><risdate>2019</risdate><volume>20</volume><issue>19</issue><spage>2454</spage><epage>2457</epage><pages>2454-2457</pages><issn>1439-4227</issn><eissn>1439-7633</eissn><abstract>During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. Engineering this process by design is important for creating a higher order protein assembly with minimal modification. Herein, a simple design strategy is shown for domain‐swapping formation by loop deletion and insertion of a polyproline rod. Crystal structures revealed the formation of the domain‐swapped dimers and polyproline portion formed a polyproline II (PPII) structure. Small‐angle X‐ray scattering demonstrated that an extended orientation of domain‐swapped dimer was retained in solution. It is found that a multiple of three of inserting proline residue is favored for domain swapping because of the helical nature of PPII. The rigid nature of the polyproline rod enables precise control of the interdomain distance and orientation.
Straighten up! During domain swapping, proteins mutually interconvert structural elements to form a di‐/oligomer. To achieve domain swapping by design, insertion of a rigid polyproline rod has been investigated. Crystal structure and small‐angle X‐ray scattering analyses confirm the extended orientation of the two subunits.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>31094059</pmid><doi>10.1002/cbic.201900179</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0003-3168-8445</orcidid></addata></record> |
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| subjects | biophysics Control rods Crystal structure Design Design modifications Dimers domain swapping Insertion Molecular structure Polyproline Proline protein design protein folding Proteins Structural members |
| title | Domain‐Swapping Design by Polyproline Rod Insertion |
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