{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T19:13:18Z","timestamp":1722885198503},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Single-molecule force spectroscopy has facilitated the experimental investigation of biomolecular force-coupled kinetics, from which the kinetics at zero force can be extrapolated via explicit theoretical models. The atomic force microscope (AFM) in particular is routinely used to study protein unfolding kinetics, but only rarely protein folding kinetics. The discrepancy arises because mechanical protein refolding studies are more technically challenging.<\/jats:p>\n               <jats:p>Results: We developed software that can drive and analyse mechanical refolding experiments when used with the commercial AFM setup \u2018Picoforce AFM\u2019, Bruker (previously Digital Instruments). We expect the software to be easily adaptable to other AFM setups. We also developed an improved method for the statistical characterization of protein folding kinetics, and implemented it into an AFM-independent software module.<\/jats:p>\n               <jats:p>Availability: Software and documentation are available at http:\/\/code.google.com\/p\/refolding under Apache License 2.0.<\/jats:p>\n               <jats:p>Contact: \u00a0aioaneid@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq663","type":"journal-article","created":{"date-parts":[[2010,12,2]],"date-time":"2010-12-02T02:42:32Z","timestamp":1291257752000},"page":"423-425","source":"Crossref","is-referenced-by-count":6,"title":["Open source platform for the execution and analysis of mechanical refolding experiments"],"prefix":"10.1093","volume":"27","author":[{"given":"Daniel","family":"Aioanei","sequence":"first","affiliation":[{"name":"Department of Biochemistry \u2018G.Moruzzi\u2019, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Brucale","sequence":"additional","affiliation":[{"name":"Department of Biochemistry \u2018G.Moruzzi\u2019, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruno","family":"Samor\u00ed","sequence":"additional","affiliation":[{"name":"Department of Biochemistry \u2018G.Moruzzi\u2019, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,12,1]]},"reference":[{"key":"2023012511540650500_B1","doi-asserted-by":"crossref","first-page":"061916","DOI":"10.1103\/PhysRevE.80.061916","article-title":"Maximum likelihood estimation of protein kinetic parameters under weak assumptions from unfolding force spectroscopy experiments","volume":"80","author":"Aioanei","year":"2009","journal-title":"Phys. Rev. E"},{"key":"2023012511540650500_B2","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1126\/science.347575","article-title":"Models for the specific adhesion of cells to cells","volume":"200","author":"Bell","year":"1978","journal-title":"Science"},{"key":"2023012511540650500_B3","doi-asserted-by":"crossref","first-page":"4451","DOI":"10.1073\/pnas.0509016103","article-title":"The molecular elasticity of the insect flight muscle proteins projectin and kettin","volume":"103","author":"Bullard","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511540650500_B4","doi-asserted-by":"crossref","first-page":"1599","DOI":"10.1126\/science.8079175","article-title":"Entropic elasticity of lambda-phage DNA","volume":"265","author":"Bustamante","year":"1994","journal-title":"Science"},{"key":"2023012511540650500_B5","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1146\/annurev.biochem.72.121801.161542","article-title":"Mechanical processes in biochemistry","volume":"73","author":"Bustamante","year":"2004","journal-title":"Annu. Rev. Biochem."},{"key":"2023012511540650500_B6","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nmat1825","article-title":"Polyprotein of GB1 is an ideal artificial elastomeric protein","volume":"6","author":"Cao","year":"2007","journal-title":"Nat. Mater."},{"key":"2023012511540650500_B7","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1002\/anie.200502623","article-title":"Nonmechanical protein can have significant mechanical stability","volume":"45","author":"Cao","year":"2006","journal-title":"Angew. Chem."},{"key":"2023012511540650500_B8","doi-asserted-by":"crossref","first-page":"3694","DOI":"10.1073\/pnas.96.7.3694","article-title":"Mechanical and chemical unfolding of a single protein: a comparison","volume":"96","author":"Carrion-Vazquez","year":"1999","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511540650500_B9","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1126\/science.1092497","article-title":"Force-clamp spectroscopy monitors the folding trajectory of a single protein","volume":"303","author":"Fernandez","year":"2004","journal-title":"Science"},{"key":"2023012511540650500_B10","doi-asserted-by":"crossref","first-page":"2436","DOI":"10.1529\/biophysj.107.104422","article-title":"Force-clamp spectroscopy of single-protein monomers reveals the individual unfolding and folding pathways of I27 and ubiquitin","volume":"93","author":"Garcia-Manyes","year":"2007","journal-title":"Biophys. J."},{"key":"2023012511540650500_B11","doi-asserted-by":"crossref","first-page":"10534","DOI":"10.1073\/pnas.0901213106","article-title":"Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin","volume":"106","author":"Garcia-Manyes","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511540650500_B12","doi-asserted-by":"crossref","first-page":"10540","DOI":"10.1073\/pnas.0902090106","article-title":"Osmolyte-induced separation of the mechanical folding phases of ubiquitin","volume":"106","author":"Garcia-Manyes","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511540650500_B13","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1103\/RevModPhys.62.251","article-title":"Reaction-rate theory: fifty years after kramers","volume":"62","author":"H\u00e4nggi","year":"1990","journal-title":"Rev. Mod. Phys."},{"key":"2023012511540650500_B14","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/j.jmb.2010.07.059","article-title":"Measuring \u201cunmeasurable\u201d folding kinetics of proteins by single-molecule force spectroscopy","volume":"402","author":"Jollymore","year":"2010","journal-title":"J. Mol. Biol."},{"key":"2023012511540650500_B15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.physrep.2009.11.001","article-title":"Biomolecules under mechanical force","volume":"486","author":"Kumar","year":"2010","journal-title":"Phys. Rep."},{"key":"2023012511540650500_B16","volume-title":"Theory of Point Estimation","author":"Lehmann","year":"1998","edition":"2nd"},{"key":"2023012511540650500_B17","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1073\/pnas.98.2.468","article-title":"Stepwise unfolding of titin under force-clamp atomic force microscopy","volume":"98","author":"Oberhauser","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511540650500_B18","doi-asserted-by":"crossref","first-page":"215101","DOI":"10.1063\/1.2920475","article-title":"The load dependence of rate constants","volume":"128","author":"Walcott","year":"2008","journal-title":"J. Chem. Phys."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/423\/48863939\/bioinformatics_27_3_423.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/423\/48863939\/bioinformatics_27_3_423.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:02:54Z","timestamp":1674648174000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/3\/423\/320737"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,12,1]]},"references-count":18,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2011,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq663","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,2,1]]},"published":{"date-parts":[[2010,12,1]]}}}