{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:04:29Z","timestamp":1785416669148,"version":"3.56.0"},"reference-count":42,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T00:00:00Z","timestamp":1785110400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","award":["R35GM139608"],"award-info":[{"award-number":["R35GM139608"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the University of Miami"},{"id":[{"id":"https:\/\/ror.org\/02dgjyy92","id-type":"ROR","asserted-by":"publisher"}]},{"name":"NSF ACCESS Allocation","award":["BIO250149"],"award-info":[{"award-number":["BIO250149"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Syntaxin-1 (Stx1), a core neuronal SNARE protein, regulates membrane docking and fusion during neurotransmitter release. Although Stx1 clustering is widely observed at presynaptic active zones and in neuroendocrine cells, how Stx1 isoforms and lipid interactions organize the plasma membrane prior to fusion remains unclear. Here, we performed MARTINI coarse-grained molecular dynamics (cgMD) simulations of 1\u201310 copies of the juxtamembrane and transmembrane domains (JMD\u2013TMDs) of Stx1A and Stx1B embedded in plasma membrane models to investigate membrane lipid disorder, Stx1 JMD\u2013TMD clustering dynamics, and regulation by Stx1 TMD palmitoylation and phosphatidylinositol 4,5-bisphosphate (PIP2). Stx1 JMD\u2013TMD regions induced local lipid disorder associated with hydrophobic mismatch, with Stx1A producing stronger and more spatially extended perturbations than Stx1B. The magnitude of local lipid disorder remained largely independent of clustering and TMD palmitoylation, whereas palmitoylation spatially restricted and PIP2 depletion broadened the radial extent of membrane perturbation. During clustering, Stx1 JMD\u2013TMDs progressively recruited and redistributed PIP2 into local membrane domains, resulting in ~7-fold local enrichment relative to the bulk membrane. Together, these findings support a model where hydrophobic mismatch primarily governs membrane disorder, whereas multivalent PIP2 recruitment and redistribution stabilize higher-order Stx1 oligomers, thereby promoting membrane environments permissive for SNARE-mediated fusion.<\/jats:p>","DOI":"10.3390\/ijms27156673","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T09:47:41Z","timestamp":1785145661000},"page":"6673","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Lipid Disorder and PIP2-Regulated Clustering of Syntaxin-1 JMD\u2013TMD Regions Govern Membrane Fusion Competence"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2506-0486","authenticated-orcid":false,"given":"Dong","family":"An","sequence":"first","affiliation":[{"name":"Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5722-9557","authenticated-orcid":false,"given":"Manfred","family":"Lindau","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"12676","DOI":"10.1002\/anie.201402380","article-title":"The principle of membrane fusion in the cell (Nobel lecture)","volume":"53","author":"Rothman","year":"2014","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"12696","DOI":"10.1002\/anie.201406359","article-title":"The Molecular Machinery of Neurotransmitter Release (Nobel Lecture)","volume":"53","year":"2014","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1146\/annurev-physiol-021113-170305","article-title":"Exocytosis and endocytosis: Modes, functions, and coupling mechanisms","volume":"76","author":"Wu","year":"2014","journal-title":"Annu. Rev. Physiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1715","DOI":"10.1042\/BST20231333","article-title":"Exploring the structural dynamics of the vesicle priming machinery","volume":"52","author":"An","year":"2024","journal-title":"Biochem. Soc. Trans."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e14","DOI":"10.1017\/S0033583525100048","article-title":"Using multiscale molecular dynamics simulations to explore the fusion machinery underlying neurotransmitter release","volume":"58","author":"An","year":"2025","journal-title":"Q. Rev. Biophys."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/s41467-018-08028-6","article-title":"Munc18 and Munc13 serve as a functional template to orchestrate neuronal SNARE complex assembly","volume":"10","author":"Wang","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Ullrich, A., B\u00f6hme, M.A., Sch\u00f6neberg, J., Depner, H., Sigrist, S.J., and No\u00e9, F. (2015). Dynamical organization of syntaxin-1A at the presynaptic active zone. PLoS Comput. Biol., 11.","DOI":"10.1371\/journal.pcbi.1004407"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1146\/annurev-biophys-111821-104732","article-title":"Molecular Mechanisms Underlying Neurotransmitter Release","volume":"51","author":"Rizo","year":"2022","journal-title":"Annu. Rev. Biophys."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1146\/annurev-biochem-081820-103615","article-title":"Chaperoning SNARE Folding and Assembly","volume":"90","author":"Zhang","year":"2021","journal-title":"Annu. Rev. Biochem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1111\/jnc.12722","article-title":"HPC-1\/syntaxin 1A and syntaxin 1B play distinct roles in neuronal survival","volume":"130","author":"Kofuji","year":"2014","journal-title":"J. Neurochem."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Mishima, T., Fujiwara, T., Sanada, M., Kofuji, T., Kanai-Azuma, M., and Akagawa, K. (2014). Syntaxin 1B, but not syntaxin 1A, is necessary for the regulation of synaptic vesicle exocytosis and of the readily releasable pool at central synapses. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0090004"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"16698","DOI":"10.1523\/JNEUROSCI.0187-13.2013","article-title":"Titration of Syntaxin1 in Mammalian Synapses Reveals Multiple Roles in Vesicle Docking, Priming, and Release Probability","volume":"33","author":"Arancillo","year":"2013","journal-title":"J. Neurosci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2404","DOI":"10.1152\/jn.00577.2015","article-title":"Syntaxin 1B is important for mouse postnatal survival and proper synaptic function at the mouse neuromuscular junctions","volume":"114","author":"Wu","year":"2015","journal-title":"J. Neurophysiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"7911","DOI":"10.1523\/JNEUROSCI.1314-16.2016","article-title":"Distinct Functions of Syntaxin-1 in Neuronal Maintenance, Synaptic Vesicle Docking, and Fusion in Mouse Neurons","volume":"36","author":"Vardar","year":"2016","journal-title":"J. Neurosci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41593-025-02140-9","article-title":"Munc18 modulates syntaxin phase separation to promote exocytosis","volume":"29","author":"Pei","year":"2025","journal-title":"Nat. Neurosci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3914","DOI":"10.1038\/ncomms4914","article-title":"Contact-induced clustering of syntaxin and munc18 docks secretory granules at the exocytosis site","volume":"5","author":"Gandasi","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"20804","DOI":"10.1073\/pnas.1014823107","article-title":"Syntaxin clusters assemble reversibly at sites of secretory granules in live cells","volume":"107","author":"Barg","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/S0092-8674(01)00229-X","article-title":"SNARE complex oligomerization by synaphin\/complexin is essential for synaptic vesicle exocytosis","volume":"104","author":"Tokumaru","year":"2001","journal-title":"Cell"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/nsmb.2570","article-title":"Phosphatidylinositol 4, 5-bisphosphate clusters act as molecular beacons for vesicle recruitment","volume":"20","author":"Honigmann","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nature10545","article-title":"Membrane protein sequestering by ionic protein-lipid interactions","volume":"479","author":"Meyenberg","year":"2011","journal-title":"Nature"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"18440","DOI":"10.1021\/jacs.7b10677","article-title":"t-SNARE Transmembrane Domain Clustering Modulates Lipid Organization and Membrane Curvature","volume":"139","author":"Sharma","year":"2017","journal-title":"J. Am. Chem. Soc."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e2523347123","DOI":"10.1073\/pnas.2523347123","article-title":"Synaptic transmission: Munc13 assembles onto PI(4,5)P2-rich domains into trimers that cooperate to capture vesicles","volume":"123","author":"Li","year":"2026","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"4773","DOI":"10.1016\/j.jmb.2020.07.005","article-title":"Syntaxin clustering and optogenetic control for synaptic membrane fusion","volume":"432","author":"Li","year":"2020","journal-title":"J. Mol. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"jcs264344","DOI":"10.1242\/jcs.264344","article-title":"The local detergent model of SNARE-mediated membrane fusion","volume":"139","author":"Rizo","year":"2026","journal-title":"J. Cell Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e2321447121","DOI":"10.1073\/pnas.2321447121","article-title":"Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations","volume":"121","author":"Rizo","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5984","DOI":"10.1038\/ncomms6984","article-title":"Hydrophobic mismatch sorts SNARE proteins into distinct membrane domains","volume":"6","author":"Milovanovic","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2571","DOI":"10.1073\/pnas.1818200116","article-title":"Thermodynamically reversible paths of the first fusion intermediate reveal an important role for membrane anchors of fusion proteins","volume":"116","author":"Smirnova","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e78182","DOI":"10.7554\/eLife.78182","article-title":"Syntaxin-1A modulates vesicle fusion in mammalian neurons via juxtamembrane domain dependent palmitoylation of its transmembrane domain","volume":"11","author":"Vardar","year":"2022","journal-title":"eLife"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1111\/tra.12562","article-title":"PtdIns(4,5)P2 is not required for secretory granule docking","volume":"19","author":"Gandasi","year":"2018","journal-title":"Traffic"},{"key":"ref_30","unstructured":"Deserno, M. (2026, June 30). Fluid Lipid Membranes\u2013A Primer. Available online: http:\/\/www.cmu.edu\/biolphys\/deserno\/pdf\/membrane_theory.pdf."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/S0022-5193(87)80021-8","article-title":"Membrane fusion: Overcoming of the hydration barrier and local restructuring","volume":"129","author":"Leikin","year":"1987","journal-title":"J. Theor. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s41580-023-00668-x","article-title":"Mechanisms of SNARE proteins in membrane fusion","volume":"25","author":"Jahn","year":"2024","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1002\/jnr.24154","article-title":"The role of spontaneous neurotransmission in synapse and circuit development","volume":"96","author":"Andreae","year":"2018","journal-title":"J. Neurosci. Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/nrn3875","article-title":"The mechanisms and functions of spontaneous neurotransmitter release","volume":"16","author":"Kavalali","year":"2015","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"41301","DOI":"10.1074\/jbc.M106853200","article-title":"Crystal structure and biophysical properties of a complex between the N-terminal SNARE region of SNAP25 and syntaxin 1a","volume":"276","author":"Misura","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3948","DOI":"10.1016\/j.bpj.2025.05.022","article-title":"Syntaxin 1A transmembrane domain palmitoylation induces a fusogenic conformation","volume":"124","author":"An","year":"2025","journal-title":"Biophys. J."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"12751","DOI":"10.1073\/pnas.1816495115","article-title":"Molecular mechanism of fusion pore formation driven by the neuronal SNARE complex","volume":"115","author":"Sharma","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","first-page":"82","article-title":"Pymol: An open-source molecular graphics tool","volume":"40","author":"DeLano","year":"2002","journal-title":"CCP4 Newsl. Protein Crystallogr."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Sharma, S., Kim, B.N., Stansfeld, P.J., Sansom, M.S.P., and Lindau, M. (2015). A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0144814"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"9418","DOI":"10.1021\/acs.jpcb.4c04901","article-title":"Introductory Tutorials for Simulating Protein Dynamics with GROMACS","volume":"128","author":"Lemkul","year":"2024","journal-title":"J. Phys. Chem. B"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Brown, S.T., Buitrago, P., Hanna, E., Sanielevici, S., Scibek, R., and Nystrom, N.A. (2021). Bridges-2: A Platform for Rapidly-Evolving and Data Intensive Research. Practice and Experience in Advanced Research Computing 2021, ACM.","DOI":"10.1145\/3437359.3465593"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1016\/j.bpj.2015.08.015","article-title":"MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories","volume":"109","author":"McGibbon","year":"2015","journal-title":"Biophys. J."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6673\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T09:55:43Z","timestamp":1785146143000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6673"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,27]]},"references-count":42,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ijms27156673"],"URL":"https:\/\/doi.org\/10.3390\/ijms27156673","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,27]]}}}