The role of non-native interactions in the folding of knotted proteins
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an...
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| Veröffentlicht in: | PLoS computational biology 2012-06, Vol.8 (6), p.e1002504-e1002504 |
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| creator | Skrbić, Tatjana Micheletti, Cristian Faccioli, Pietro |
| description | Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein shows a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavouring early knotting events. |
| doi_str_mv | 10.1371/journal.pcbi.1002504 |
| format | Article |
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The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein shows a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavouring early knotting events.</description><identifier>ISSN: 1553-7358</identifier><identifier>ISSN: 1553-734X</identifier><identifier>EISSN: 1553-7358</identifier><identifier>DOI: 10.1371/journal.pcbi.1002504</identifier><identifier>PMID: 22719235</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biomathematics ; Carboxyl and Carbamoyl Transferases - chemistry ; Computational Biology ; Computer Simulation ; Experiments ; Kinetics ; Learning models (Stochastic processes) ; Models, Molecular ; Monte Carlo Method ; Ornithine Carbamoyltransferase - chemistry ; Physics ; Protein Conformation ; Protein Folding ; Static Electricity ; Stochastic Processes ; Studies</subject><ispartof>PLoS computational biology, 2012-06, Vol.8 (6), p.e1002504-e1002504</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Skrbic´ et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Skrbi? T, Micheletti C, Faccioli P (2012) The Role of Non-Native Interactions in the Folding of Knotted Proteins. 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The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein shows a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavouring early knotting events.</description><subject>Biomathematics</subject><subject>Carboxyl and Carbamoyl Transferases - chemistry</subject><subject>Computational Biology</subject><subject>Computer Simulation</subject><subject>Experiments</subject><subject>Kinetics</subject><subject>Learning models (Stochastic processes)</subject><subject>Models, Molecular</subject><subject>Monte Carlo Method</subject><subject>Ornithine Carbamoyltransferase - chemistry</subject><subject>Physics</subject><subject>Protein Conformation</subject><subject>Protein Folding</subject><subject>Static Electricity</subject><subject>Stochastic Processes</subject><subject>Studies</subject><issn>1553-7358</issn><issn>1553-734X</issn><issn>1553-7358</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqVkk1v1DAQhiMEoqXwDxBE4kIPWfwRJ84FqapoWakCCcrZmjjjrZesvdhOBf8eL5tWXcQFzcFfz_uOZzRF8ZKSBeUtfbf2U3AwLra6twtKCBOkflQcUyF41XIhHz_YHxXPYlwTkrdd87Q4YqylHePiuLi4vsEy-BFLb0rnXeUg2VssrUsYQCfrXcyHMmXM-HGwbrUjvzufEg7lNviE1sXnxRMDY8QX83pSfLv4cH3-sbr6fLk8P7uqdMN5qkDWLSKV2HPRUACme0CuqQYhjMG-6QkOzSAp76Fm2Nf5WXaYi6slF7zjJ8Xrve929FHNLYiK8hxS5B5kYrknBg9rtQ12A-GX8mDVnwsfVgpCsnpENSDTojFSgIC6k0YSg4azvid1g2KA7PV-zjb1Gxw0uhRgPDA9fHH2Rq38reK8FYzKbPB2Ngj-x4QxqY2NGscRHPop_5sw2knOapLRN3-h_65usadWkAuwzvicV-cYcGO1d2hsvj9jnWjbltY7wemBIDMJf6YVTDGq5dcv_8F-OmTrPauDjzGgue8KJWo3n3ffV7v5VPN8Ztmrhx29F90NJP8NxzjiPg</recordid><startdate>20120601</startdate><enddate>20120601</enddate><creator>Skrbić, Tatjana</creator><creator>Micheletti, Cristian</creator><creator>Faccioli, Pietro</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>ISN</scope><scope>ISR</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AL</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>LK8</scope><scope>M0N</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20120601</creationdate><title>The role of non-native interactions in the folding of knotted proteins</title><author>Skrbić, Tatjana ; Micheletti, Cristian ; Faccioli, Pietro</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c633t-a847ee18eb3561aa2cbae3c1ca55ffeb6b0ed6d813ba42eb4bae89e0024835393</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Biomathematics</topic><topic>Carboxyl and Carbamoyl Transferases - chemistry</topic><topic>Computational Biology</topic><topic>Computer Simulation</topic><topic>Experiments</topic><topic>Kinetics</topic><topic>Learning models (Stochastic processes)</topic><topic>Models, Molecular</topic><topic>Monte Carlo Method</topic><topic>Ornithine Carbamoyltransferase - chemistry</topic><topic>Physics</topic><topic>Protein Conformation</topic><topic>Protein Folding</topic><topic>Static Electricity</topic><topic>Stochastic Processes</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Skrbić, Tatjana</creatorcontrib><creatorcontrib>Micheletti, Cristian</creatorcontrib><creatorcontrib>Faccioli, Pietro</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Computing Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Computer Science Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Computing Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS computational biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Skrbić, Tatjana</au><au>Micheletti, Cristian</au><au>Faccioli, Pietro</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The role of non-native interactions in the folding of knotted proteins</atitle><jtitle>PLoS computational biology</jtitle><addtitle>PLoS Comput Biol</addtitle><date>2012-06-01</date><risdate>2012</risdate><volume>8</volume><issue>6</issue><spage>e1002504</spage><epage>e1002504</epage><pages>e1002504-e1002504</pages><issn>1553-7358</issn><issn>1553-734X</issn><eissn>1553-7358</eissn><abstract>Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein shows a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavouring early knotting events.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22719235</pmid><doi>10.1371/journal.pcbi.1002504</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Biomathematics Carboxyl and Carbamoyl Transferases - chemistry Computational Biology Computer Simulation Experiments Kinetics Learning models (Stochastic processes) Models, Molecular Monte Carlo Method Ornithine Carbamoyltransferase - chemistry Physics Protein Conformation Protein Folding Static Electricity Stochastic Processes Studies |
| title | The role of non-native interactions in the folding of knotted proteins |
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