{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T22:55:20Z","timestamp":1789685720072,"version":"4.0.1"},"reference-count":60,"publisher":"IOP Publishing","issue":"13","license":[{"start":{"date-parts":[[2024,1,9]],"date-time":"2024-01-09T00:00:00Z","timestamp":1704758400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/iopscience.iop.org\/page\/copyright"},{"start":{"date-parts":[[2024,1,9]],"date-time":"2024-01-09T00:00:00Z","timestamp":1704758400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/iopscience.iop.org\/info\/page\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"crossref","award":["2242021R41168"],"award-info":[{"award-number":["2242021R41168"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100010905","name":"Major Research Plan","doi-asserted-by":"crossref","award":["52275558"],"award-info":[{"award-number":["52275558"]}],"id":[{"id":"10.13039\/501100010905","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Science and Technology Program of Nanjing","award":["202110014 and 202205052"],"award-info":[{"award-number":["202110014 and 202205052"]}]},{"DOI":"10.13039\/501100010035","name":"Outstanding Youth Foundation of Jiangsu Province","doi-asserted-by":"crossref","award":["BK20230084"],"award-info":[{"award-number":["BK20230084"]}],"id":[{"id":"10.13039\/501100010035","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["iopscience.iop.org"],"crossmark-restriction":false},"short-container-title":["Nanotechnology"],"published-print":{"date-parts":[[2024,3,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Protein sequencing is crucial for understanding the complex mechanisms driving biological functions. However, proteins are usually folded in their native state and the mechanism of fast protein conformation transitions still remains unclear, which make protein sequencing challenging. Molecular dynamics simulations with accurate force field are now able to observe the entire folding\/unfolding process, providing valuable insights into protein folding mechanisms. Given that proteins can be unfolded, nanopore technology shows great potential for protein sequencing. In this study, we proposed to use MoS<jats:sub>2<\/jats:sub>\/SnS<jats:sub>2<\/jats:sub> heterostructures to firstly unfold proteins and then detect them by a nanopore in the heterostructural membrane. All-atom molecular dynamics simulations performed in this work provided rich atomic-level information for a comprehensive understanding of protein unfolding process and mechanism on the MoS<jats:sub>2<\/jats:sub>\/SnS<jats:sub>2<\/jats:sub> heterostructure, it was found that the strong binding of protein to SnS<jats:sub>2<\/jats:sub> nanostripe and hydrogen bond breaking were the main reasons for unfolding the protein on the heterostructure. After the protein was fully unfolded, it was restrained on the nanostripe because of the affinity of protein to the SnS<jats:sub>2<\/jats:sub> nanostripe. Thus by integrating the proposed unfolding technique with nanopore technology, detection of linear unfolded peptide was realized in this work, allowing for the identification of protein components, which is essential for sequencing proteins in the near future.<\/jats:p>","DOI":"10.1088\/1361-6528\/ad177f","type":"journal-article","created":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T22:29:07Z","timestamp":1703111347000},"page":"135501","update-policy":"https:\/\/doi.org\/10.1088\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Unfolding of protein using MoS<sub>2<\/sub>\/SnS<sub>2<\/sub> heterostructure for nanopore-based sequencing"],"prefix":"10.1088","volume":"35","author":[{"given":"Runyi","family":"Yuan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gensheng","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingjie","family":"Sha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunfei","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7285-058X","authenticated-orcid":false,"given":"Wei","family":"Si","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"266","published-online":{"date-parts":[[2024,1,9]]},"reference":[{"key":"nanoad177fbib1","doi-asserted-by":"publisher","first-page":"1042","DOI":"10.1126\/science.1219021","volume":"338","author":"Dill","year":"2012","journal-title":"Science"},{"key":"nanoad177fbib2","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1038\/nature02261","volume":"426","author":"Dobson","year":"2003","journal-title":"Nature"},{"key":"nanoad177fbib3","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1038\/ncb1104-1054","volume":"6","author":"Selkoe","year":"2004","journal-title":"Nat. Cell Biol."},{"key":"nanoad177fbib4","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1038\/nature10317","volume":"475","author":"Hartl","year":"2011","journal-title":"Nature"},{"key":"nanoad177fbib5","doi-asserted-by":"publisher","first-page":"3518","DOI":"10.1021\/cr500638n","volume":"115","author":"Nasica-Labouze","year":"2015","journal-title":"Chem. Rev."},{"key":"nanoad177fbib6","doi-asserted-by":"publisher","first-page":"3607","DOI":"10.1021\/cr030403s","volume":"104","author":"Dyson","year":"2004","journal-title":"Chem. Rev."},{"key":"nanoad177fbib7","doi-asserted-by":"publisher","first-page":"3271","DOI":"10.1016\/S0006-3495(03)74745-6","volume":"85","author":"Kolinski","year":"2003","journal-title":"Biophys. J."},{"key":"nanoad177fbib8","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1126\/science.282.5389.740","volume":"282","author":"Duan","year":"1998","journal-title":"Science"},{"key":"nanoad177fbib9","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/S1359-0278(97)00004-7","volume":"2","author":"Demchuk","year":"1997","journal-title":"Fold Des."},{"key":"nanoad177fbib10","doi-asserted-by":"publisher","first-page":"8926","DOI":"10.1073\/pnas.92.19.8926","volume":"92","author":"Oliveberg","year":"1995","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"nanoad177fbib11","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1146\/annurev.physchem.52.1.499","volume":"52","author":"Shea","year":"2001","journal-title":"Annu. Rev. Phys. Chem."},{"key":"nanoad177fbib12","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1021\/ar9700825","volume":"31","author":"Eaton","year":"1998","journal-title":"Acc. Chem. Res."},{"key":"nanoad177fbib13","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1006\/jmbi.1998.2145","volume":"284","author":"Lacroix","year":"1998","journal-title":"J. Mol. Biol."},{"key":"nanoad177fbib14","doi-asserted-by":"publisher","first-page":"13518","DOI":"10.1073\/pnas.250473497","volume":"97","author":"Mayor","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"nanoad177fbib15","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1002\/prot.10409","volume":"52","author":"Nikiforovich","year":"2003","journal-title":"Proteins"},{"key":"nanoad177fbib16","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/nsb0197-10","volume":"4","author":"Dill","year":"1997","journal-title":"Nat. Struct. Mol. Biol."},{"key":"nanoad177fbib17","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1038\/nsb0994-584","volume":"1","author":"Blanco","year":"1994","journal-title":"Nat. Struct. Mol. Biol."},{"key":"nanoad177fbib18","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1002\/prot.10576","volume":"55","author":"Lee","year":"2004","journal-title":"Proteins"},{"key":"nanoad177fbib19","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1042\/BST20130055","volume":"42","author":"Baker","year":"2014","journal-title":"Biochem. Soc. Trans."},{"key":"nanoad177fbib20","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1002\/pmic.201300288","volume":"14","author":"Verheggen","year":"2014","journal-title":"Proteomics"},{"key":"nanoad177fbib21","doi-asserted-by":"publisher","first-page":"9078","DOI":"10.1073\/pnas.1105682108","volume":"108","author":"Meinhold","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"nanoad177fbib22","doi-asserted-by":"publisher","first-page":"11175","DOI":"10.1073\/pnas.162268099","volume":"99","author":"Shimada","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"nanoad177fbib23","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1016\/0003-2697(84)90359-2","volume":"137","author":"Brauer","year":"1984","journal-title":"Anal. Biochem."},{"key":"nanoad177fbib24","doi-asserted-by":"publisher","first-page":"283","DOI":"10.3891\/acta.chem.scand.04-0283","volume":"4","author":"Edman","year":"1950","journal-title":"Acta Chem. Scand."},{"key":"nanoad177fbib25","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1126\/science.1133987","volume":"314","author":"Chait","year":"2006","journal-title":"Science"},{"key":"nanoad177fbib26","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1002\/mas.21400","volume":"33","author":"Chapman","year":"2014","journal-title":"Mass Spectrom. Rev."},{"key":"nanoad177fbib27","doi-asserted-by":"publisher","first-page":"1629","DOI":"10.1021\/ja3094313","volume":"135","author":"Yates","year":"2013","journal-title":"J. Am. Chem. Soc."},{"key":"nanoad177fbib28","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1038\/s41565-018-0236-6","volume":"13","author":"Restrepo-Perez","year":"2018","journal-title":"Nat. Nanotechnol."},{"key":"nanoad177fbib29","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/j.carbon.2017.01.012","volume":"115","author":"Yang","year":"2017","journal-title":"Carbon"},{"key":"nanoad177fbib30","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1126\/science.276.5315.1109","volume":"276","author":"Rief","year":"1997","journal-title":"Science"},{"key":"nanoad177fbib31","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1038\/387308a0","volume":"387","author":"Tskhovrebova","year":"1997","journal-title":"Nature"},{"key":"nanoad177fbib32","doi-asserted-by":"publisher","first-page":"1676","DOI":"10.1126\/science.283.5408.1676","volume":"283","author":"Weiss","year":"1999","journal-title":"Science"},{"key":"nanoad177fbib33","doi-asserted-by":"publisher","first-page":"1769","DOI":"10.1021\/cr0404390","volume":"106","author":"Royer","year":"2006","journal-title":"Chem. Rev."},{"key":"nanoad177fbib34","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1016\/j.bpj.2013.12.025","volume":"106","author":"Larkin","year":"2014","journal-title":"Biophys. J."},{"key":"nanoad177fbib35","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1021\/nl3042678","volume":"13","author":"Plesa","year":"2013","journal-title":"Nano Lett."},{"key":"nanoad177fbib36","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1002\/smll.201201423","volume":"9","author":"Freedman","year":"2013","journal-title":"Small"},{"key":"nanoad177fbib37","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1038\/nnano.2011.12","volume":"6","author":"Yusko","year":"2011","journal-title":"Nat. Nanotechnol."},{"key":"nanoad177fbib38","doi-asserted-by":"publisher","first-page":"9287","DOI":"10.1021\/ja901088b","volume":"131","author":"Talaga","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"nanoad177fbib39","doi-asserted-by":"publisher","first-page":"4081","DOI":"10.1021\/ja710787a","volume":"130","author":"Mohammad","year":"2008","journal-title":"J. Am. Chem. Soc."},{"key":"nanoad177fbib40","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/80295","volume":"18","author":"Movileanu","year":"2000","journal-title":"Nat. Biotechnol."},{"key":"nanoad177fbib41","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/nbt.2799","volume":"32","author":"Rosen","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"nanoad177fbib42","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1038\/nnano.2014.54","volume":"9","author":"Zhao","year":"2014","journal-title":"Nat. Nanotechnol."},{"key":"nanoad177fbib43","doi-asserted-by":"publisher","first-page":"2923","DOI":"10.1021\/ja1073245","volume":"133","author":"Pastoriza-Gallego","year":"2011","journal-title":"J. Am. Chem. Soc."},{"key":"nanoad177fbib44","doi-asserted-by":"publisher","first-page":"3371","DOI":"10.1016\/j.febslet.2007.06.036","volume":"581","author":"Pastoriza-Gallego","year":"2007","journal-title":"FEBS Lett."},{"key":"nanoad177fbib45","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1016\/j.bbamem.2009.03.011","volume":"1788","author":"Pastoriza-Gallego","year":"2009","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"nanoad177fbib46","doi-asserted-by":"publisher","first-page":"4071","DOI":"10.1021\/ac300129e","volume":"84","author":"Payet","year":"2012","journal-title":"Anal. Chem."},{"key":"nanoad177fbib47","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1038\/s41586-021-03338-0","volume":"591","author":"Zhao","year":"2021","journal-title":"Nature"},{"key":"nanoad177fbib48","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1109\/3M-NANO56083.2022.9941518","author":"Yuan","year":"2022"},{"key":"nanoad177fbib49","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"Phillips","year":"2005","journal-title":"J. Comput. Chem."},{"key":"nanoad177fbib50","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1002\/jcc.21367","volume":"31","author":"Vanommeslaeghe","year":"2010","journal-title":"J. Comput. Chem."},{"key":"nanoad177fbib51","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1016\/0021-9991(83)90014-1","volume":"52","author":"Andersen","year":"1983","journal-title":"J. Comput. Phys."},{"key":"nanoad177fbib52","doi-asserted-by":"publisher","first-page":"952","DOI":"10.1002\/jcc.540130805","volume":"13","author":"Miyamoto","year":"1992","journal-title":"J. Comput. Phys."},{"key":"nanoad177fbib53","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"nanoad177fbib54","doi-asserted-by":"publisher","DOI":"10.1063\/5.0014475","volume":"153","author":"Phillips","year":"2020","journal-title":"J. Chem. Phys."},{"key":"nanoad177fbib55","doi-asserted-by":"publisher","DOI":"10.1063\/1.2408420","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"key":"nanoad177fbib56","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"nanoad177fbib57","doi-asserted-by":"publisher","first-page":"7091","DOI":"10.1021\/acsnano.7b02718","volume":"11","author":"Si","year":"2017","journal-title":"ACS Nano"},{"key":"nanoad177fbib58","doi-asserted-by":"publisher","first-page":"3863","DOI":"10.1021\/acs.jpclett.2c00533","volume":"13","author":"Si","year":"2022","journal-title":"J. Phys. Chem. Lett."},{"key":"nanoad177fbib59","doi-asserted-by":"publisher","first-page":"9132","DOI":"10.1021\/acs.jpclett.1c02414","volume":"12","author":"Yu","year":"2021","journal-title":"J. Phys. Chem. Lett."},{"key":"nanoad177fbib60","doi-asserted-by":"publisher","DOI":"10.1002\/smll.201900036","volume":"15","author":"Si","year":"2019","journal-title":"Small"}],"container-title":["Nanotechnology"],"original-title":[],"link":[{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f","content-type":"text\/html","content-version":"am","intended-application":"text-mining"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f\/pdf","content-type":"application\/pdf","content-version":"am","intended-application":"text-mining"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f\/pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f\/pdf","content-type":"application\/pdf","content-version":"am","intended-application":"similarity-checking"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,14]],"date-time":"2025-06-14T14:47:17Z","timestamp":1749912437000},"score":1,"resource":{"primary":{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1361-6528\/ad177f"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,9]]},"references-count":60,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2024,1,9]]},"published-print":{"date-parts":[[2024,3,25]]}},"URL":"https:\/\/doi.org\/10.1088\/1361-6528\/ad177f","relation":{},"ISSN":["0957-4484","1361-6528"],"issn-type":[{"value":"0957-4484","type":"print"},{"value":"1361-6528","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,9]]},"assertion":[{"value":"Unfolding of protein using MoS2\/SnS2 heterostructure for nanopore-based sequencing","name":"article_title","label":"Article Title"},{"value":"Nanotechnology","name":"journal_title","label":"Journal Title"},{"value":"paper","name":"article_type","label":"Article Type"},{"value":"\u00a9 2024 IOP Publishing Ltd. All rights, including for text and data mining, AI training, and similar technologies, are reserved.","name":"copyright_information","label":"Copyright Information"},{"value":"2023-10-16","name":"date_received","label":"Date Received","group":{"name":"publication_dates","label":"Publication dates"}},{"value":"2023-12-20","name":"date_accepted","label":"Date Accepted","group":{"name":"publication_dates","label":"Publication dates"}},{"value":"2024-01-09","name":"date_epub","label":"Online publication date","group":{"name":"publication_dates","label":"Publication dates"}}]}}