{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T17:09:50Z","timestamp":1785431390897,"version":"3.56.0"},"posted":{"date-parts":[[2025,5,23]]},"group-title":"Biophysics","reference-count":84,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T00:00:00Z","timestamp":1747958400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["R35GM153388"],"award-info":[{"award-number":["R35GM153388"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>Protein aggregation, which is implicated in aging and neurodegenerative diseases, typically involves a transition from soluble monomers and oligomers to insoluble fibrils. Polyglutamine (polyQ) tracts in proteins can form amyloid fibrils, which are linked to polyQ diseases, including Huntington\u2019s disease (HD), where the length of the polyQ tract inversely correlates with the age of onset. Despite significant research on the mechanisms of Httex1 aggregation, atomistic information regarding the intermediate stages of its fibrillation and the morphological characteristics of the end-state amyloid fibrils remains limited. Recently, molecular dynamics (MD) simulations based on a hybrid multistate structure-based model, Multi-eGO, have shown promise in capturing the kinetics and mechanism of amyloid fibrillation with high computational efficiency while achieving qualitative agreement with experiments. Here, we utilize the multi-eGO simulation methodology to study the mechanism and kinetics of polyQ fibrillation and the effect of the N17 flanking domain of Huntingtin protein. Aggregation simulations of polyQ produced highly heterogeneous amyloid fibrils with variable-width branched morphologies by incorporating combinations of \u03b2-turn, \u03b2-arc, and \u03b2-strand structures, while the presence of the N17 flanking domain reduces amyloid fibril heterogeneity by favoring \u03b2-strand conformations. Our simulations reveal that the presence of N17 domain enhanced aggregation kinetics by promoting the formation of large, structurally stable oligomers. Furthermore, the early-stage aggregation process involves two distinct mechanisms: backbone interactions driving \u03b2-sheet formation and side-chain interdigitation. Overall, our study provides detailed insights into fibrillation kinetics, mechanisms, and end-state polymorphism associated with Httex1 amyloid aggregation.<\/jats:p>\n                <jats:sec>\n                  <jats:title>SIGNIFICANCE STATEMENT<\/jats:title>\n                  <jats:p>Polyglutamine (polyQ) aggregation is central to Huntington\u2019s disease and related neurodegenerative disorders. Despite extensive experimental efforts, a complete molecular understanding of this process\u2014from early aggregation events to the origins of fibril polymorphism\u2014has remained elusive, with varied interpretations of complex fibril architectures. Through multiscale simulations, we reveal how polyQ fibrils adopt diverse tertiary and quaternary structures and demonstrate how the N-terminal flanking domain (N17) modulates fibril architecture and accelerates aggregation. Our hybrid multi-eGO simulations capture early-stage fibrillation kinetics and identify distinct structural polymorphs that align with experimental observations. This work provides a molecular framework for understanding amyloid polymorphism and illuminates the role of flanking domains in shaping aggregation pathways\u2014 offering valuable insights for therapeutic strategies targeting early toxic intermediates.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.05.19.654960","type":"posted-content","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T14:40:11Z","timestamp":1748011211000},"source":"Crossref","is-referenced-by-count":0,"title":["Multiscale simulations elucidate the mechanism of polyglutamine aggregation and the role of flanking domains in fibril polymorphism"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4542-8372","authenticated-orcid":false,"given":"Avijeet","family":"Kulshrestha","sequence":"first","affiliation":[{"name":"Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8608-7359","authenticated-orcid":false,"given":"Tien Minh","family":"Phan","sequence":"additional","affiliation":[{"name":"Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3590-0829","authenticated-orcid":false,"given":"Azamat","family":"Rizuan","sequence":"additional","affiliation":[{"name":"Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3919-3527","authenticated-orcid":false,"given":"Priyesh","family":"Mohanty","sequence":"additional","affiliation":[{"name":"Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9725-6402","authenticated-orcid":false,"given":"Jeetain","family":"Mittal","sequence":"additional","affiliation":[{"name":"Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843"},{"name":"Department of Chemistry, Texas A&M University, College Station, TX, 77843"},{"name":"Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041123024060000_2025.05.19.654960v1.1","doi-asserted-by":"publisher","DOI":"10.3389\/fnins.2017.00616"},{"key":"2026041123024060000_2025.05.19.654960v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2016.02.003"},{"key":"2026041123024060000_2025.05.19.654960v1.3","first-page":"1","article-title":"Huntington disease","volume":"1","year":"2015","journal-title":"Nat Rev Dis Primers"},{"key":"2026041123024060000_2025.05.19.654960v1.4","doi-asserted-by":"publisher","DOI":"10.1021\/ja110715f"},{"key":"2026041123024060000_2025.05.19.654960v1.5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1521933113"},{"key":"2026041123024060000_2025.05.19.654960v1.6","doi-asserted-by":"publisher","DOI":"10.1097\/nen.0b013e318040b2c8"},{"key":"2026041123024060000_2025.05.19.654960v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-016-0009-6"},{"key":"2026041123024060000_2025.05.19.654960v1.8","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M209852200"},{"key":"2026041123024060000_2025.05.19.654960v1.9","doi-asserted-by":"publisher","DOI":"10.1177\/1535370219856620"},{"key":"2026041123024060000_2025.05.19.654960v1.10","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.00247"},{"key":"2026041123024060000_2025.05.19.654960v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.nano.2004.11.004"},{"key":"2026041123024060000_2025.05.19.654960v1.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.08.009"},{"key":"2026041123024060000_2025.05.19.654960v1.13","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.2c00509"},{"key":"2026041123024060000_2025.05.19.654960v1.14","doi-asserted-by":"publisher","DOI":"10.1042\/BST20230731"},{"key":"2026041123024060000_2025.05.19.654960v1.15","doi-asserted-by":"crossref","unstructured":"M. B. Helabad , et al., Integrative determination of the atomic structure of mutant huntingtin exon 1 fibrils from Huntington\u2019s disease. Nat Commun 15, 10793 (2024).","DOI":"10.1038\/s41467-024-55062-8"},{"key":"2026041123024060000_2025.05.19.654960v1.16","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0812083106"},{"key":"2026041123024060000_2025.05.19.654960v1.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20241-w"},{"key":"2026041123024060000_2025.05.19.654960v1.18","doi-asserted-by":"publisher","DOI":"10.1002\/ADVS.202501462"},{"key":"2026041123024060000_2025.05.19.654960v1.19","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.7b00838"},{"key":"2026041123024060000_2025.05.19.654960v1.20","doi-asserted-by":"crossref","first-page":"11597","DOI":"10.1021\/jp206373g","article-title":"Secondary structures of native and pathogenic huntingtin N-terminal fragments","volume":"115","year":"2011","journal-title":"Journal of Physical Chemistry B"},{"key":"2026041123024060000_2025.05.19.654960v1.21","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.6b08665"},{"key":"2026041123024060000_2025.05.19.654960v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2020.05.013"},{"key":"2026041123024060000_2025.05.19.654960v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2022.06.031"},{"key":"2026041123024060000_2025.05.19.654960v1.24","doi-asserted-by":"crossref","unstructured":"E. Scalone , et al., Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution. Proceedings of the National Academy of Sciences 119 (2022).","DOI":"10.1073\/pnas.2203181119"},{"key":"2026041123024060000_2025.05.19.654960v1.25","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.3c01182"},{"key":"2026041123024060000_2025.05.19.654960v1.26","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2110877119"},{"key":"2026041123024060000_2025.05.19.654960v1.27","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.3c01182"},{"key":"2026041123024060000_2025.05.19.654960v1.28","doi-asserted-by":"crossref","unstructured":"T. Kandola , et al., Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. Elife 12 (2023).","DOI":"10.7554\/eLife.86939.3"},{"key":"2026041123024060000_2025.05.19.654960v1.29","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.05.028"},{"key":"2026041123024060000_2025.05.19.654960v1.30","doi-asserted-by":"publisher","DOI":"10.1111\/j.1399-3011.1997.tb00622.x"},{"key":"2026041123024060000_2025.05.19.654960v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2020.04.008"},{"key":"2026041123024060000_2025.05.19.654960v1.32","doi-asserted-by":"publisher","DOI":"10.1002\/anie.201711530"},{"key":"2026041123024060000_2025.05.19.654960v1.33","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1521933113"},{"key":"2026041123024060000_2025.05.19.654960v1.34","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1401587111"},{"key":"2026041123024060000_2025.05.19.654960v1.35","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2005.08.066"},{"key":"2026041123024060000_2025.05.19.654960v1.36","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.106.100404"},{"key":"2026041123024060000_2025.05.19.654960v1.37","doi-asserted-by":"publisher","DOI":"10.1021\/ja110715f"},{"key":"2026041123024060000_2025.05.19.654960v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-016-0009-6"},{"key":"2026041123024060000_2025.05.19.654960v1.39","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2011.06.045"},{"key":"2026041123024060000_2025.05.19.654960v1.40","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.6b08665"},{"key":"2026041123024060000_2025.05.19.654960v1.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2021.167222"},{"key":"2026041123024060000_2025.05.19.654960v1.42","doi-asserted-by":"crossref","unstructured":"K. Shen , et al., Control of the structural landscape and neuronal proteotoxicity of mutant Huntingtin by domains flanking the polyQ tract. Elife 5 (2016).","DOI":"10.7554\/eLife.18065"},{"key":"2026041123024060000_2025.05.19.654960v1.43","doi-asserted-by":"crossref","unstructured":"T. Kandola , et al., Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. Elife 12 (2023).","DOI":"10.7554\/eLife.86939.3"},{"key":"2026041123024060000_2025.05.19.654960v1.44","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2011.06.045"},{"key":"2026041123024060000_2025.05.19.654960v1.45","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.5b00281"},{"key":"2026041123024060000_2025.05.19.654960v1.46","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1821216116"},{"key":"2026041123024060000_2025.05.19.654960v1.47","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2011.12.010"},{"key":"2026041123024060000_2025.05.19.654960v1.48","doi-asserted-by":"publisher","DOI":"10.1039\/d2sm00888b"},{"key":"2026041123024060000_2025.05.19.654960v1.49","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2023.09.005"},{"key":"2026041123024060000_2025.05.19.654960v1.50","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1021\/acs.jpcb.2c05785","article-title":"Conformational Flexibility Is a Key Determinant for the Lytic Activity of the Pore-Forming Protein, Cytolysin A","volume":"127","year":"2023","journal-title":"Journal of Physical Chemistry B"},{"key":"2026041123024060000_2025.05.19.654960v1.51","unstructured":"A. Kulshrestha , Computational study of membrane driven secondary structural changes in proteins. (2023)."},{"key":"2026041123024060000_2025.05.19.654960v1.52","doi-asserted-by":"crossref","unstructured":"R. Wetzel , Physical chemistry of polyglutamine: Intriguing tales of a monotonous sequence. 421, 466\u2013490 (2013).","DOI":"10.1016\/j.jmb.2012.01.030"},{"key":"2026041123024060000_2025.05.19.654960v1.53","doi-asserted-by":"publisher","DOI":"10.1101\/2025.03.06.641960"},{"key":"2026041123024060000_2025.05.19.654960v1.54","doi-asserted-by":"publisher","DOI":"10.1177\/1535370219856620"},{"key":"2026041123024060000_2025.05.19.654960v1.55","doi-asserted-by":"publisher","DOI":"10.1101\/2023.07.21.549993"},{"key":"2026041123024060000_2025.05.19.654960v1.56","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb1215"},{"key":"2026041123024060000_2025.05.19.654960v1.57","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.694"},{"key":"2026041123024060000_2025.05.19.654960v1.58","doi-asserted-by":"crossref","unstructured":"A. Rizuan , J. Shenoy , P. Mohanty , P. M. S. Passos , F. Jos\u00e9 , Structural details of helix-mediated TDP-43 C-terminal domain multimerization. (2024).","DOI":"10.1101\/2024.07.05.602258"},{"key":"2026041123024060000_2025.05.19.654960v1.59","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2015.06.074.miR-302"},{"key":"2026041123024060000_2025.05.19.654960v1.60","doi-asserted-by":"crossref","first-page":"9507","DOI":"10.1021\/acs.jpcb.8b09213","article-title":"Dynamics of the Proline-Rich C-Terminus of Huntingtin Exon-1 Fibrils","volume":"122","year":"2018","journal-title":"Journal of Physical Chemistry B"},{"key":"2026041123024060000_2025.05.19.654960v1.61","doi-asserted-by":"publisher","DOI":"10.3844\/ajbsp.2016.1.9"},{"key":"2026041123024060000_2025.05.19.654960v1.62","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1401587111"},{"key":"2026041123024060000_2025.05.19.654960v1.63","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2005.08.066"},{"key":"2026041123024060000_2025.05.19.654960v1.64","doi-asserted-by":"crossref","first-page":"11671","DOI":"10.1021\/acs.jpcb.0c10489","article-title":"Molecular details of protein condensates probed by microsecond long atomistic simulations","volume":"124","year":"2020","journal-title":"Journal of Physical Chemistry B"},{"key":"2026041123024060000_2025.05.19.654960v1.65","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c00450"},{"key":"2026041123024060000_2025.05.19.654960v1.66","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.10349"},{"key":"2026041123024060000_2025.05.19.654960v1.67","doi-asserted-by":"crossref","first-page":"3712","DOI":"10.1021\/jp994072s","article-title":"Modification of the Generalized Born Model Suitable for Macromolecules","volume":"104","year":"2000","journal-title":"Journal of Physical Chemistry B"},{"key":"2026041123024060000_2025.05.19.654960v1.68","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1021\/acs.jpcb.3c06662","article-title":"OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials","volume":"128","year":"2024","journal-title":"Journal of Physical Chemistry B"},{"key":"2026041123024060000_2025.05.19.654960v1.69","doi-asserted-by":"publisher","DOI":"10.1021\/ct500569b"},{"key":"2026041123024060000_2025.05.19.654960v1.70","doi-asserted-by":"crossref","unstructured":"J. L. F. Abascal , C. Vega , A general purpose model for the condensed phases of water: TIP4P\/2005. Journal of Chemical Physics 123 (2005).","DOI":"10.1063\/1.2121687"},{"key":"2026041123024060000_2025.05.19.654960v1.71","doi-asserted-by":"publisher","DOI":"10.1021\/jz900079w"},{"key":"2026041123024060000_2025.05.19.654960v1.72","doi-asserted-by":"publisher","DOI":"10.1063\/1.447334"},{"key":"2026041123024060000_2025.05.19.654960v1.73","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"2026041123024060000_2025.05.19.654960v1.74","unstructured":"J Comput Chem - 1999 - Feenstra - Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich.pdf."},{"key":"2026041123024060000_2025.05.19.654960v1.75","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"2026041123024060000_2025.05.19.654960v1.76","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90098-5"},{"key":"2026041123024060000_2025.05.19.654960v1.77","doi-asserted-by":"crossref","unstructured":"E. Scalone , et al., Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution. Proc Natl Acad Sci U S A 119 (2022).","DOI":"10.1073\/pnas.2203181119"},{"key":"2026041123024060000_2025.05.19.654960v1.78","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360221211"},{"key":"2026041123024060000_2025.05.19.654960v1.79","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq1105"},{"key":"2026041123024060000_2025.05.19.654960v1.80","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21787"},{"key":"2026041123024060000_2025.05.19.654960v1.81","doi-asserted-by":"crossref","first-page":"11671","DOI":"10.1021\/acs.jpcb.0c10489","article-title":"Molecular details of protein condensates probed by microsecond long atomistic simulations","volume":"124","year":"2020","journal-title":"Journal of Physical Chemistry B"},{"key":"2026041123024060000_2025.05.19.654960v1.82","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"2026041123024060000_2025.05.19.654960v1.83","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3235"},{"key":"2026041123024060000_2025.05.19.654960v1.84","doi-asserted-by":"publisher","DOI":"10.1002\/PRO.4792"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.05.19.654960","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:10:18Z","timestamp":1782277818000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.19.654960"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,23]]},"references-count":84,"URL":"https:\/\/doi.org\/10.1101\/2025.05.19.654960","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1021\/acs.jpcb.5c06627","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2025,5,23]]},"subtype":"preprint"}}