https://m2.mtmt.hu/ eng 2026-05-30 19:10 JournalArticle 34410484 VALIDATED true Export Date: 10 January 2024; Cited By: 0; Correspondence Address: A. Szilágyi; Systems Biology of Reproduction Research Group, Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, 1117, Hungary; email: szilagyi.andras@ttk.hu 0 false 2026-05-23T10:10:13.676+0000 2024-02-13T10:57:52.195+0000 2023-12-01T12:51:12.776+0000 true 10071503 Szabó Regina /api/admin/10071503 Admin Regina Szabó (ELTE TTK admin 5) true 2024-04-03T10:45:31.748+0000 2024-04-03T10:45:31.748+0000 2024-02-13T10:57:52.386+0000 true 10058019 Serf András /api/admin/10058019 Admin András Serf (PPKE ITK admin 5) true 10058019 2024-02-16T21:58:42.254+0000 true 521 Szuper Admin /api/admin/521 Admin Admin Szuper (admin) true Admin 10014568 /api/admin/10014568 Andrea Vándor (VA, admin) Vándor Andrea true 10014568 true 2024-04-04T10:42:31.810+0000 true false true 24 24 /api/publicationtype/24 PublicationType Journal Article 1 true 24 JournalArticle true 10000059 Article true 24 24 /api/publicationtype/24 PublicationType Journal Article 1 true 24 JournalArticle /api/subtype/10000059 Szakcikk SubType Article (Journal Article) 101 true 10000059 true 1 /api/category/1 Category Scientific true 1 Györffy, Dániel true true /api/journal/10018879 REVIEWED BIOMOLECULES 2218-273X 2218-273X true false 10018879 false 10018879 true 2218-273X 2218-273X Journal FOREIGN 13 12 1708 1708 2023 Protein homodimers have been classified as three-state or two-state dimers depending on whether a folded monomer forms before association, but the details of the folding–binding mechanisms are poorly understood. Kinetic transition networks of conformational states have provided insight into the folding mechanisms of monomeric proteins, but extending such a network to two protein chains is challenging as all the relative positions and orientations of the chains need to be included, greatly increasing the number of degrees of freedom. Here, we present a simplification of the problem by grouping all states of the two chains into two layers: a dissociated and an associated layer. We combined our two-layer approach with the Wako–Saito–Muñoz–Eaton method and used Transition Path Theory to investigate the dimer formation kinetics of eight homodimers. The analysis reveals a remarkable diversity of dimer formation mechanisms. Induced folding, conformational selection, and rigid docking are often simultaneously at work, and their contribution depends on the protein concentration. Pre-folded structural elements are always present at the moment of association, and asymmetric binding mechanisms are common. Our two-layer network approach can be combined with various methods that generate discrete states, yielding new insights into the kinetics and pathways of flexible binding processes. true 2023 true true true false false GOLD 2026-05-23 false http://www.mdpi.com/journal/biomolecules 1 0 1 1 0 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0 2 2 Folyóiratcikk Journal Article 24 1 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 2024 0 1 1 1 1 Q1 false 10010376 false false false 2024-02-12T10:57:52.022+0000 Enzimológiai Intézet (TTK); Információs Technológiai és Bionikai Kar (PPKE); Lendület Reprodukció Rendszerbiológiája Kutatóc... (HRN TTK / MÉI) 3 20 3 3 0 true 10014568 Language 10002 /api/language/10002 English Angol English true 2 true PersonAuthorship 112759491 /api/authorship/112759491 Györffy, Dániel [Györffy, Dániel (Bioinformatika), author] Institute of Enzymology (RCNS); Információs Technológiai és Bionikai Kar (PPCU) 1 0.333 true false false Author 10019484 /api/author/10019484 Dániel Györffy (Bioinformatika) Györffy Dániel true 10019484 true Györffy Dániel true false false AuthorshipType 1 /api/authorshiptype/1 Author 0 true 0 true false true PersonAuthorship 112759492 /api/authorship/112759492 Závodszky, Péter [Závodszky, Péter (Molekuláris immun...), author] Institute of Enzymology (RCNS) 2 0.333 false false false Author 10000346 /api/author/10000346 Péter Závodszky (Molekuláris immunológia, biokémia) Závodszky Péter true 10000346 true Závodszky Péter true false false AuthorshipType 1 /api/authorshiptype/1 Author 0 true 0 true false true PersonAuthorship 112759493 /api/authorship/112759493 Szilágyi, András [Szilágyi, András (Bioinformatika), author] Institute of Enzymology (RCNS); Enzim_416 (IMLS) 3 0.333 false true false Author 10010376 /api/author/10010376 András Szilágyi (Bioinformatika) Szilágyi András true 10010376 true Szilágyi András true false false AuthorshipType 1 /api/authorshiptype/1 Author 0 true 0 true false true PublicationIdentifier 25051597 /api/publicationidentifier/25051597 DOI: 10.3390/biom13121708 PlainSource 6 /api/publicationsource/6 DOI PublicationSourceType 10001 /api/publicationsourcetype/10001 DOI true true true DOI DOI https://doi.org/@@@ true true 6 true IDENTICAL 10.3390/biom13121708 https://doi.org/10.3390/biom13121708 false true PublicationIdentifier 25265355 /api/publicationidentifier/25265355 WoS: 001131139200001 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 001131139200001 https://www.webofscience.com/wos/woscc/full-record/001131139200001 false true PublicationIdentifier 25265354 /api/publicationidentifier/25265354 Scopus: 85180480247 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 85180480247 http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85180480247 false true PublicationIdentifier 25333461 /api/publicationidentifier/25333461 PubMed: 38136580 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 38136580 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=38136580&dopt=Abstract false true PublicationIdentifier 25051598 /api/publicationidentifier/25051598 Other URL: https://www.mdpi.com/2218-273X/13/12/1708 PlainSource 40 /api/publicationsource/40 Other URL PublicationSourceType 10006 /api/publicationsourcetype/10006 Link true true true Egyéb URL Other URL @@@ true true 40 true https://www.mdpi.com/2218-273X/13/12/1708 https://www.mdpi.com/2218-273X/13/12/1708 false true SjrRating 11357702 /api/sjrrating/11357702 sjr:Q1 (2023) Scopus - Biochemistry BIOMOLECULES 2218-273X 2218-273X 88 0.24 journal RatingType 10002 /api/ratingtype/10002 sjr sjr true true ClassificationExternal 1303 /api/classificationexternal/1303 Scopus - Biochemistry true 1303 true Q1 DIRECT true true Reference 47550185 /api/reference/47550185 1. 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(2023) BIOMOLECULES 2218-273X 2218-273X 13 12<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="10019484"><a href="/gui2/?type=authors&mode=browse&sel=10019484" target="_blank">Györffy Dániel (<span class="authorship-author-name">Györffy Dániel</span> <span class="authorAux-mtmt"> Bioinformatika</span>) </a> </span> <span class="author-affil"><span title="Research Centre for Natural Sciences">RCNS</span>/Institute of Enzymology; <span title="Pázmány Péter Catholic University">PPCU</span>/Információs Technológiai és Bionikai Kar</span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="10000346"><a href="/gui2/?type=authors&mode=browse&sel=10000346" target="_blank">Závodszky Péter (<span class="authorship-author-name">Závodszky Péter</span> <span class="authorAux-mtmt"> Molekuláris immunológia, biokémia</span>) </a> </span> <span class="author-affil"><span title="Research Centre for Natural Sciences">RCNS</span>/Institute of Enzymology</span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="10010376"><a href="/gui2/?type=authors&mode=browse&sel=10010376" target="_blank">Szilágyi András (<span class="authorship-author-name">Szilágyi András</span> <span class="authorAux-mtmt"> Bioinformatika</span>) </a> </span> <span class="author-affil"><span title="Research Centre for Natural Sciences">RCNS</span>/Institute of Enzymology; <span title="Research Centre for Natural Sciences">RCNS</span>/<span title="Institute of Molecular Life Sciences">IMLS</span>/Enzim_416</span> </div> </div> <div class="title"><a href="/gui2/?mode=browse&params=publication;34410484" target="_blank">A Kinetic Transition Network Model Reveals the Diversity of Protein Dimer Formation Mechanisms</a></div> <div> <span class="journal-title">BIOMOLECULES</span> <span class="journal-issn">(<a target="_blank" href="https://portal.issn.org/resource/ISSN/2218-273X">2218-273X</a> <a target="_blank" href="https://portal.issn.org/resource/ISSN/2218-273X">2218-273X</a>)</span>: <span class="journal-volume">13</span> <span class="journal-issue">12</span> <span class="page"> Paper 1708. </span> <span class="year">(2023)</span> </div> <div class="pub-footer"> <span class="language" xmlns="http://www.w3.org/1999/html">Language: English | </span> <span class="identifiers"> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="10.3390/biom13121708" target="_blank" href="https://doi.org/10.3390/biom13121708"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="001131139200001" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/001131139200001"> WoS </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="85180480247" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85180480247"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="38136580" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=38136580&dopt=Abstract"> PubMed </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:black" title="https://www.mdpi.com/2218-273X/13/12/1708" target="_blank" href="https://www.mdpi.com/2218-273X/13/12/1708"> Other URL </a> </span> </span> <OnlyViewableByAuthor><div class="ratings"> <div class="journal-subject">Journal subject: Scopus - Biochemistry&nbsp;&nbsp;&nbsp;Rank:&nbsp;Q1</div> <div class="journal-subject">Journal subject: Scopus - Molecular Biology&nbsp;&nbsp;&nbsp;Rank:&nbsp;Q2</div> </div></OnlyViewableByAuthor> <div class="publication-citation" style="margin-left: 0.5cm;"> <span title="" class="citingPub-count">Citing papers: 1</span> | Independent citation: 1 | Self citation: 0 | Unknown citation: 0 | Number of citations in WoS: 1 | Number of citations in Scopus:&nbsp;1 | WoS/Scopus assigned:&nbsp;1 | Number of citations with DOI:&nbsp;1 </div> <div class="publication-citation"> <a target="_blank" href="/api/publication?cond=citations.related;eq;34410484&sort=publishedYear,desc&sort=title"> Number of cited publications: 2 </a> </div> <div class="mtid"><span class="long-pub-mtid">Publication: 34410484</span> | <span class="status-data status-VALIDATED"> Validated </span> Core Citing | <span class="type-subtype">Journal Article ( Article ) </span> | <span class="pub-category">Scientific</span> | <span class="publication-sourceOfData">kézi felvitel</span> </div> <div class="lastModified">Last Modified: 2024.02.13. 11:57 András Serf (PPKE ITK admin 5) </div> <div class="lockedBy">Centrally managed 2024.04.04. 12:42 Andrea Vándor (VA, admin) </div> <pre class="comment" style="margin-top: 0; margin-bottom: 0;"><u>Comments</u>: Export Date: 10 January 2024; Cited By: 0; Correspondence Address: A. Szilágyi; Systems Biology of Reproduction Research Group, Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, 1117, Hungary; email: szilagyi.andras@ttk.hu</pre> </div></div>