{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T10:43:38Z","timestamp":1783334618678,"version":"3.54.6"},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2013,12,12]],"date-time":"2013-12-12T00:00:00Z","timestamp":1386806400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003393","type":"journal-article","created":{"date-parts":[[2013,12,12]],"date-time":"2013-12-12T16:28:34Z","timestamp":1386865714000},"page":"e1003393","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":19,"title":["Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale"],"prefix":"10.1371","volume":"9","author":[{"given":"Michela","family":"Candotti","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"P\u00e9rez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carles","family":"Ferrer-Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Rueda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Meyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josep Llu\u00eds","family":"Gelp\u00ed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Modesto","family":"Orozco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2013,12,12]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0065-3233(08)60608-7","article-title":"Some factors in the interpretation of protein denaturation","volume":"14","author":"W Kauzmann","year":"1959","journal-title":"Adv Protein Chem"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1146\/annurev-physchem-032210-103531","article-title":"Role of solvation effects in protein denaturation: from thermodynamics to single molecules and back","volume":"62","author":"JL England","year":"2011","journal-title":"Annu Rev Phys Chem"},{"issue":"2\u20133","key":"ref3","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1016\/S0301-4622(03)00095-4","article-title":"Impact of urea on water structure: a clue to its properties as a denaturant?","volume":"105","author":"AK Soper","year":"2003","journal-title":"Biophys Chem"},{"issue":"24","key":"ref4","doi-asserted-by":"crossref","first-page":"7313","DOI":"10.1021\/bi970096i","article-title":"Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea","volume":"36","author":"J Tirado-Rives","year":"1997","journal-title":"Biochemistry"},{"issue":"9","key":"ref5","doi-asserted-by":"crossref","first-page":"5142","DOI":"10.1073\/pnas.0930122100","article-title":"The molecular basis for the chemical denaturation of proteins by urea","volume":"100","author":"BJ Bennion","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"39","key":"ref6","doi-asserted-by":"crossref","first-page":"15317","DOI":"10.1073\/pnas.0706251104","article-title":"Anatomy of energetic changes accompanying urea-induced protein denaturation","volume":"104","author":"M Auton","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"41","key":"ref7","doi-asserted-by":"crossref","first-page":"14760","DOI":"10.1073\/pnas.0404570101","article-title":"Aqueous urea solution destabilizes Abeta(16\u201322) oligomers","volume":"101","author":"DK Klimov","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"ref8","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1016\/j.bpj.2011.01.028","article-title":"Backbone and side-chain contributions in protein denaturation by urea","volume":"100","author":"DR Canchi","year":"2011","journal-title":"Biophys J"},{"issue":"23","key":"ref9","doi-asserted-by":"crossref","first-page":"7346","DOI":"10.1021\/ja069232+","article-title":"Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism","volume":"129","author":"EP O'Brien","year":"2007","journal-title":"J Am Chem Soc"},{"issue":"51","key":"ref10","doi-asserted-by":"crossref","first-page":"16126","DOI":"10.1021\/ja076216j","article-title":"Interaction of urea with amino acids: implications for urea-induced protein denaturation","volume":"129","author":"MC Stumpe","year":"2007","journal-title":"J Am Chem Soc"},{"issue":"11","key":"ref11","doi-asserted-by":"crossref","first-page":"e1000221","DOI":"10.1371\/journal.pcbi.1000221","article-title":"Polar or apolar\u2013the role of polarity for urea-induced protein denaturation","volume":"4","author":"MC Stumpe","year":"2008","journal-title":"PLoS Comput Biol"},{"issue":"9","key":"ref12","doi-asserted-by":"crossref","first-page":"3744","DOI":"10.1016\/j.bpj.2009.01.051","article-title":"Urea impedes the hydrophobic collapse of partially unfolded proteins","volume":"96","author":"MC Stumpe","year":"2009","journal-title":"Biophys J"},{"issue":"44","key":"ref13","doi-asserted-by":"crossref","first-page":"16928","DOI":"10.1073\/pnas.0808427105","article-title":"Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding","volume":"105","author":"L Hua","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"9358","DOI":"10.1039\/b925726h","article-title":"On the stability of chymotrypsin inhibitor 2 in a 10 M urea solution. The role of interaction energies for urea-induced protein denaturation","volume":"12","author":"M Lindgren","year":"2010","journal-title":"Phys Chem Chem Phys"},{"issue":"15","key":"ref15","doi-asserted-by":"crossref","first-page":"5933","DOI":"10.1073\/pnas.1216589110","article-title":"Towards an atomistic description of the urea-denatured state of proteins","volume":"2013 ; 110","author":"M Candotti","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"ref16","doi-asserted-by":"crossref","first-page":"2595","DOI":"10.1073\/pnas.0812588106","article-title":"Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group","volume":"106","author":"WK Lim","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"43","key":"ref17","doi-asserted-by":"crossref","first-page":"17200","DOI":"10.1021\/ja202849a","article-title":"Effect of urea on the -hairpin conformational ensemble and protein denaturation mechanism","volume":"133","author":"A Berteotti","year":"2011","journal-title":"J Am Chem Soc"},{"issue":"25","key":"ref18","doi-asserted-by":"crossref","first-page":"13518","DOI":"10.1073\/pnas.250473497","article-title":"Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation","volume":"97","author":"U Mayor","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures","volume":"247","author":"AG Murzin","year":"1995","journal-title":"J Mol Biol"},{"issue":"3","key":"ref20","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1073\/pnas.0605534104","article-title":"A consensus view of protein dynamics","volume":"104","author":"M Rueda","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1016\/j.str.2010.07.013","article-title":"MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories","volume":"18","author":"T Meyer","year":"2010","journal-title":"Structure"},{"issue":"6002","key":"ref22","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1126\/science.1187409","article-title":"Atomic-Level Characterization of the Structural Dynamics of Proteins","volume":"330","author":"DE Shaw","year":"2010","journal-title":"Science"},{"issue":"2","key":"ref23","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1006\/jmbi.1994.1017","article-title":"Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins","volume":"235","author":"VN Maiorov","year":"1994","journal-title":"J Mol Biol"},{"issue":"12","key":"ref24","doi-asserted-by":"crossref","first-page":"2485","DOI":"10.1110\/ps.ps.20801","article-title":"Thermodynamics of interactions of urea and guanidinium salts with protein surface: relationship between solute effects on protein processes and changes in water-accessible surface area","volume":"10","author":"ES Courtenay","year":"2001","journal-title":"Protein Sci"},{"issue":"22","key":"ref25","doi-asserted-by":"crossref","first-page":"6220","DOI":"10.1021\/jp066474n","article-title":"Aqueous Urea Solutions: Structure, Energetics, and Urea Aggregation","volume":"111","author":"MC Stumpe","year":"2007","journal-title":"J Phys Chem B"},{"issue":"1\u20132","key":"ref26","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.bpc.2010.05.004","article-title":"The affect of urea on the kinetics of local unfolding processes in chymotrypsin inhibitor 2","volume":"151","author":"M Lindgren","year":"2010","journal-title":"Biophys Chem"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2150","DOI":"10.1110\/ps.0306803","article-title":"A Consensus View of Fold Space: Combining SCOP, CATH, and the Dali Domain Dictionary","volume":"12","author":"R Day","year":"2003","journal-title":"Protein Sci"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0022-2836(77)80200-3","article-title":"The Protein Data Bank: A Computer-based Archival File For Macromolecular Structures","volume":"112","author":"FC Bernstein","year":"1977","journal-title":"J Mol Biol"},{"issue":"9","key":"ref29","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1093\/bioinformatics\/bts139","article-title":"MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations","volume":"28","author":"A Hospital","year":"2012","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1689","DOI":"10.1002\/jcc.20297","article-title":"Molecular modeling of organic and biomolecular systems using BOSS and MCPRO","volume":"26","author":"WL Jorgensen","year":"2005","journal-title":"J Comput Chem"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"WL Jorgensen","year":"1983","journal-title":"J Chem Phys"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/jp022049s","article-title":"Kirkwood-Buff derived force field for mixtures of urea and water","volume":"107","author":"S Weerasinghe","year":"2003","journal-title":"J Phys Chem B"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.theochem.2005.10.018","article-title":"Urea parametrization for molecular dynamics simulations","volume":"758","author":"A Caballero-Herrera","year":"2006","journal-title":"Journal of Molecular Structure: THEOCHEM"},{"issue":"6","key":"ref34","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1021\/ja00214a001","article-title":"The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin","volume":"110","author":"WL Jorgensen","year":"1988","journal-title":"J Am Chem Soc"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-atom empirical potential for molecular modeling and dynamics studies of proteins","volume":"102","author":"AD MacKerell","year":"1998","journal-title":"J Phys Chem B"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1002\/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F","article-title":"How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules","volume":"21","author":"J Wang","year":"2000","journal-title":"J Comp Chem"},{"issue":"9","key":"ref37","doi-asserted-by":"crossref","first-page":"L47","DOI":"10.1016\/j.bpj.2011.03.051","article-title":"How robust are protein folding simulations with respect to force field parameterization?","volume":"100","author":"S Piana","year":"2011","journal-title":"Biophys J"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A Smooth Particle Mesh Ewald Method,","volume":"103","author":"U Essmann","year":"1995","journal-title":"J Chem Phys"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","author":"J Phillips","year":"2005","journal-title":"J Comput Chem"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/0021-9991(83)90014-1","article-title":"RATTLE: A \u201cVelocity\u201d Version of the SHAKE Algorithm for Molecular Dynamics Calculations","volume":"52","author":"HC Andersen","year":"1983","journal-title":"Journal of Computational Physics"},{"issue":"2","key":"ref41","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"WL Jorgensen","year":"1983","journal-title":"J Chem Phys"},{"issue":"5","key":"ref42","doi-asserted-by":"crossref","first-page":"4177","DOI":"10.1063\/1.467468","article-title":"Constant pressure molecular dynamics algorithms","volume":"101","author":"GJ Martyna","year":"1994","journal-title":"J Chem Phys"},{"issue":"11","key":"ref43","doi-asserted-by":"crossref","first-page":"4613","DOI":"10.1063\/1.470648","article-title":"Constant pressure molecular dynamics simulation: The Langevin piston method","volume":"103","author":"SE Feller","year":"1995","journal-title":"J Chem Phys"},{"issue":"1","key":"ref44","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD - Visual Molecular Dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J Molec Graphics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003393","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,4]],"date-time":"2019-08-04T17:19:03Z","timestamp":1564939143000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003393"}},"subtitle":[],"editor":[{"given":"David","family":"van der Spoel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,12,12]]},"references-count":44,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2013,12,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003393","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12,12]]}}}