Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins

https://m2.mtmt.hu/ hun 2026-10-24 12:57 JournalArticle 33585703 APPROVED true Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, 1117, Hungary Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, 1094, Hungary Export Date: 4 July 2023 Correspondence Address: Magyar, C.; Institute of Enzymology, Hungary; email: magyar.csaba@ttk.hu Chemicals/CAS: protein, 67254-75-5; Proteins 0 false 2026-10-23T06:39:07.363+0000 2025-07-01T19:16:13.047+0000 2023-01-23T09:44:21.752+0000 true 10035718 Sonnevend Kinga /api/admin/10035718 Admin Sonnevend Kinga (SE_AOK_Adm5_Élet_kutcsop, admin) true 10035718 2026-09-25T14:01:03.249+0000 Admin 10014568 /api/admin/10014568 Vándor Andrea (VA, admin) Vándor Andrea true 10014568 true 2024-04-04T10:40:50.359+0000 true false true 24 24 /api/publicationtype/24 PublicationType Folyóiratcikk 1 true 24 JournalArticle true 10000059 Article true 24 24 /api/publicationtype/24 PublicationType Folyóiratcikk 1 true 24 JournalArticle /api/subtype/10000059 Szakcikk SubType Szakcikk (Folyóiratcikk) 101 true 10000059 true 1 /api/category/1 Category Tudományos true 1 Magyar, C Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins true true /api/journal/10003252 REVIEWED INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 1661-6596 1422-0067 true false 10003252 false 10003252 true 1661-6596 1422-0067 Journal FOREIGN 24 2 1790 1790 8 2023 Mutual synergistic folding (MSF) proteins belong to a recently emerged subclass of disordered proteins, which are disordered in their monomeric forms but become ordered in their oligomeric forms. They can be identified by experimental methods following their unfolding, which happens in a single-step cooperative process, without the presence of stable monomeric intermediates. Only a limited number of experimentally validated MSF proteins are accessible. The amino acid composition of MSF proteins shows high similarity to globular ordered proteins, rather than to disordered ones. However, they have some special structural features, which makes it possible to distinguish them from globular proteins. Even in the possession of their oligomeric three-dimensional structure, classification can only be performed based on unfolding experiments, which are frequently absent. In this work, we demonstrate a simple protocol using molecular dynamics simulations, which is able to indicate that a protein structure belongs to the MSF subclass. The presumption of the known atomic resolution quaternary structure is an obvious limitation of the method, and because of its high computational time requirements, it is not suitable for screening large databases; still, it is a valuable in silico tool for identification of MSF proteins. true 2023 true true true false true false GOLD 2026-10-23 true https://doi.org/10.3390/ijms24021790 2 0 2 2 0 2 2 2 2 2 2 2 2 2 0 0 2 2 2 2 0 9 9 Folyóiratcikk Journal Article 24 2 Könyvrészlet Chapter in Book 25 0 Könyv Book 23 0 Egyéb konferenciaközlemény Conference paper 31 0 Egyéb konferenciakötet Conference proceedings 32 0 Oltalmi formák Protection forms 26 0 Disszertáció Thesis 28 0 Egyéb Miscellaneous 29 0 Alkotás Achievement 22 0 Kutatási adat Research data 33 0 Folyóiratcikk Journal Article 24 0 0 0 Könyvrészlet Chapter in Book 25 0 0 0 Könyv Book 23 0 0 0 Egyéb konferenciaközlemény Conference paper 31 0 0 0 Egyéb konferenciakötet Conference proceedings 32 0 0 0 Oltalmi formák Protection forms 26 0 0 0 Disszertáció Thesis 28 0 0 0 Egyéb Miscellaneous 29 0 0 0 Alkotás Achievement 22 0 0 0 Kutatási adat Research data 33 0 0 0 2025 0 2 2 2 2 D1 false 10000064,10000249 false false false 2023-02-08T10:00:03.596+0000 Akadémikus bibliográfia; Enzimológiai Intézet (TTK); Élettani Intézet (SE / AOK / I) 4 22 3 4 0 true 10014568 Language 10002 /api/language/10002 Angol Angol English true 2 true PersonAuthorship 106401014 /api/authorship/106401014 Magyar, C ✉ [Magyar, Csaba (Fehérjék szerkeze...), szerző] Enzimológiai Intézet (TTK) 1 0.25 true false true Author 10000064 /api/author/10000064 Magyar Csaba (Fehérjék szerkezeti stabilitása, szerkezet alapú hatóanyag tervezés) Magyar Csaba true 10000064 true Magyar C true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 106401015 /api/authorship/106401015 Németh, B.Z. [Németh, Zoltán Bálint (molekuláris biológia), szerző] Enzimológiai Intézet (TTK) 2 0.25 false false false Author 10073845 /api/author/10073845 Németh Zoltán Bálint (molekuláris biológia) Németh Zoltán Bálint true true Németh B.Z. true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 106401016 /api/authorship/106401016 Cserző, M [Cserző, Miklós (Fehérjék molekulá...), szerző] Enzimológiai Intézet (TTK); Élettani Intézet (SE / AOK / I) 3 0.25 false false false Author 10015497 /api/author/10015497 Cserző Miklós (Fehérjék molekuláris modellezése) Cserző Miklós true 10015497 true Cserző M true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 106401017 /api/authorship/106401017 Simon, I [Simon, István (biofizika, biokém...), szerző] Enzimológiai Intézet (TTK) 4 0.25 false true false Author 10000249 /api/author/10000249 Simon István (biofizika, biokémia, bioinformatika) Simon István true 10000249 true Simon I true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true Institute 19040 /api/institute/19040 Akadémikus bibliográfia [2016-] 0 false false true Akadémikus bibliográfia Bibliografy of Hungarian of Academy of Sciences' academicians true 19040 true PublicationIdentifier 22917658 /api/publicationidentifier/22917658 DOI: 10.3390/ijms24021790 PlainSource 6 /api/publicationsource/6 DOI PublicationSourceType 10001 /api/publicationsourcetype/10001 DOI true true true DOI DOI https://doi.org/@@@ true true 6 true GOLD true IDENTICAL 10.3390/ijms24021790 https://doi.org/10.3390/ijms24021790 false true PublicationIdentifier 23136591 /api/publicationidentifier/23136591 WoS: 000917764600001 PlainSource 1 /api/publicationsource/1 WoS PublicationSourceType 10003 /api/publicationsourcetype/10003 Indexelő adatbázis false true true WoS WoS https://www.webofscience.com/wos/woscc/full-record/@@@ true true 1 true IDENTICAL 000917764600001 https://www.webofscience.com/wos/woscc/full-record/000917764600001 false true PublicationIdentifier 22994879 /api/publicationidentifier/22994879 Scopus: 85146667204 PlainSource 3 /api/publicationsource/3 Scopus PublicationSourceType 10003 /api/publicationsourcetype/10003 Indexelő adatbázis false true true Scopus Scopus http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-@@@ true true 3 true IDENTICAL 85146667204 http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85146667204 false true PublicationIdentifier 23052440 /api/publicationidentifier/23052440 PubMed: 36675304 PlainSource 17 /api/publicationsource/17 PubMed PublicationSourceType 10003 /api/publicationsourcetype/10003 Indexelő adatbázis false true true PubMed PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=@@@&dopt=Abstract true true 17 true IDENTICAL 36675304 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=36675304&dopt=Abstract false true PublicationIdentifier 29941720 /api/publicationidentifier/29941720 Egyéb URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146667204&doi=10.3390%2Fijms24021790&partnerID=40&md5=593d24691d44283d1f7fcd714c14914c PlainSource 40 /api/publicationsource/40 Egyéb URL PublicationSourceType 10006 /api/publicationsourcetype/10006 Link true true true Egyéb URL Other URL @@@ true true 40 true NONE IDENTICAL https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146667204&doi=10.3390%2Fijms24021790&partnerID=40&md5=593d24691d44283d1f7fcd714c14914c https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146667204&doi=10.3390%2Fijms24021790&partnerID=40&md5=593d24691d44283d1f7fcd714c14914c false true Classification 10578 /api/classification/10578 Enzimológia true true SjrRating 11388415 /api/sjrrating/11388415 sjr:D1 (2023) Scopus - Inorganic Chemistry INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 1661-6596 1422-0067 7 0.1 journal RatingType 10002 /api/ratingtype/10002 sjr sjr true true ClassificationExternal 1604 /api/classificationexternal/1604 Scopus - Inorganic Chemistry true 1604 true D1 DIRECT true true Reference 37644179 /api/reference/37644179 1. 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(2023) INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 1661-6596 1422-0067 24 2<div class="JournalArticle Publication long-list"> <div class="authors"> <img title="Forrásközlemény" style="float: left" src="/frontend/resources/grid/publication-core-icon.png"> <img title="Idézőközlemény" style="float: left" src="/frontend/resources/grid/publication-citation-icon.png"> <div class="autype autype0"> <span class="author-name" mtid="10000064"><a href="/gui2/?type=authors&mode=browse&sel=10000064" target="_blank">Magyar C ✉ (<span class="authorship-author-name">Magyar Csaba</span> <span class="authorAux-mtmt"> Fehérjék szerkezeti stabilitása, szerkezet alap...</span>) </a> </span> <span class="author-affil"><span title="Természettudományi Kutatóközpont">TTK</span>/Enzimológiai Intézet</span> ;    <span class="author-name" mtid="10073845"><a href="/gui2/?type=authors&mode=browse&sel=10073845" target="_blank">Németh B.Z. (<span class="authorship-author-name">Németh Zoltán Bálint</span> <span class="authorAux-mtmt"> molekuláris biológia</span>) </a> </span> <span class="author-affil"><span title="Természettudományi Kutatóközpont">TTK</span>/Enzimológiai Intézet</span> ;    <span class="author-name" mtid="10015497"><a href="/gui2/?type=authors&mode=browse&sel=10015497" target="_blank">Cserző M (<span class="authorship-author-name">Cserző Miklós</span> <span class="authorAux-mtmt"> Fehérjék molekuláris modellezése</span>) </a> </span> <span class="author-affil"><span title="Természettudományi Kutatóközpont">TTK</span>/Enzimológiai Intézet; <span title="Semmelweis Egyetem">SE</span>/<span title="Általános Orvostudományi Kar">AOK</span>/<span title="Intézet">I</span>/Élettani Intézet</span> ;    <span class="author-name" mtid="10000249"><a href="/gui2/?type=authors&mode=browse&sel=10000249" target="_blank">Simon I (<span class="authorship-author-name">Simon István</span> <span class="authorAux-mtmt"> biofizika, biokémia, bioinformatika</span>) </a> </span> <span class="author-affil"><span title="Természettudományi Kutatóközpont">TTK</span>/Enzimológiai Intézet</span> </div> </div> <div class="title"><a href="/gui2/?mode=browse&params=publication;33585703" target="_blank">Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins</a></div> <div> <span class="journal-title">INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES</span> <span class="journal-issn">(<a target="_blank" href="https://portal.issn.org/resource/ISSN/1661-6596">1661-6596</a> <a target="_blank" href="https://portal.issn.org/resource/ISSN/1422-0067">1422-0067</a>)</span>: <span class="journal-volume">24</span> <span class="journal-issue">2</span> <span class="page"> Paper 1790. 8 p. </span> <span class="year">(2023)</span> </div> <div class="pub-footer"> <span class="language" xmlns="http://www.w3.org/1999/html">Nyelv: Angol | </span> <span class="identifiers"> <span class="id identifier oa_GOLD" title=" Gold "> <a style="color:blue" title="10.3390/ijms24021790" target="_blank" href="https://doi.org/10.3390/ijms24021790"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="000917764600001" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000917764600001"> WoS </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="85146667204" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85146667204"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="36675304" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=36675304&dopt=Abstract"> PubMed </a> </span> <span class="id identifier oa_NONE" title=" Nincs "> <a style="color:blue" title="https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146667204&doi=10.3390%2Fijms24021790&partnerID=40&md5=593d24691d44283d1f7fcd714c14914c" target="_blank" href="https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146667204&doi=10.3390%2Fijms24021790&partnerID=40&md5=593d24691d44283d1f7fcd714c14914c"> Egyéb URL </a> </span> </span> <OnlyViewableByAuthor><div class="ratings"> <div class="journal-subject">Folyóirat szakterülete: Scopus - 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