{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T11:38:04Z","timestamp":1767181084223,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006295","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,8,14]],"date-time":"2018-08-14T00:00:00Z","timestamp":1534204800000}}],"reference-count":49,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2018,8,2]],"date-time":"2018-08-02T00:00:00Z","timestamp":1533168000000},"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.1006295","type":"journal-article","created":{"date-parts":[[2018,8,2]],"date-time":"2018-08-02T13:27:37Z","timestamp":1533216457000},"page":"e1006295","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["The permeation mechanism of organic cations through a CNG mimic channel"],"prefix":"10.1371","volume":"14","author":[{"given":"Luisa M. R.","family":"Napolitano","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arin","family":"Marchesi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Rodriguez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matteo","family":"De March","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0612-7948","authenticated-orcid":true,"given":"Silvia","family":"Onesti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9164-7907","authenticated-orcid":true,"given":"Alessandro","family":"Laio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Torre","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,8,2]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1152\/physrev.00008.2002","article-title":"Cyclic nucleotide-gated ion channels","volume":"82","author":"UB Kaupp","year":"2002","journal-title":"Physiol Rev"},{"key":"ref2","article-title":"Handbook of Ion Channels","author":"J Zheng","year":"2015","journal-title":"Journal of Chemical Information and Modeling"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1113\/jphysiol.1993.sp019497","article-title":"The Permeability of the Cgmp-Activated Channel to Organic Cations in Retinal Rods of the Tiger Salamander","volume":"460","author":"C Picco","year":"1993","journal-title":"J Physiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/phy2.148","article-title":"Multiple mechanisms underlying rectification in retinal cyclic nucleotide-gated (CNGA1) channels","volume":"1","author":"M Arcangeletti","year":"2013","journal-title":"Physiol Rep"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"E3619","DOI":"10.1073\/pnas.1503334112","article-title":"A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels","volume":"112","author":"LMR Napolitano","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1085\/jgp.72.4.409","article-title":"Potassium channels as multi-ion single-file pores","volume":"72","author":"B Hille","year":"1978","journal-title":"J Gen Physiol"},{"key":"ref7","article-title":"Ion Channels of Excitable Membranes","author":"B Hille","year":"2001"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/S0006-3495(99)77184-5","article-title":"Physical origin of selectivity in ionic channels of biological membranes","volume":"76","author":"A Laio","year":"1999","journal-title":"Biophys J"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/35009114","article-title":"Ion permeation mechanism of the potassium channel","volume":"404","author":"J \u00c5qvist","year":"2000","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/35102067","article-title":"Energetics of ion conduction through the K+ channel","volume":"414","author":"S Bern\u00e8che","year":"2001","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1038\/nature02943","article-title":"Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands","volume":"431","author":"SY Noskov","year":"2004","journal-title":"Nature"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"16074","DOI":"10.1073\/pnas.0903226106","article-title":"Atypical mechanism of conduction in potassium channels","volume":"106","author":"S Furini","year":"2009","journal-title":"Proc Natl Acad Sci"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1085\/jgp.60.5.588","article-title":"Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons","volume":"60","author":"F Bezanilla","year":"1972","journal-title":"J Gen Physiol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.280.5360.69","article-title":"The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity","volume":"280","author":"DA Doyle","year":"1998","journal-title":"Science"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1085\/jgp.200609633","article-title":"Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels","volume":"129","author":"SY Noskov","year":"2007","journal-title":"J Gen Physiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1113\/jphysiol.1984.sp015352","article-title":"Non-Selective Conductance in Calcium Channels of Frog Muscle: Calcium Selectivity in a Single-File Pore","volume":"353","author":"W Almers","year":"1984","journal-title":"J Physiol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/309453a0","article-title":"Mechanism of ion permeation through calcium channels","volume":"309","author":"P Hess","year":"1984","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1126\/science.7618108","article-title":"Permeation selectivity by competition in a delayed rectifier potassium channel","volume":"269","author":"SJ Korn","year":"1995","journal-title":"Science"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1113\/jphysiol.1955.sp005291","article-title":"The potassium permeability of a giant nerve fibre","volume":"128","author":"AL Hodgkin","year":"1955","journal-title":"J Physiol"},{"key":"ref20","first-page":"1","article-title":"Protein interactions central to stabilizing the K","author":"DB Sauer","year":"2011","journal-title":"PNAS"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1016\/j.bbamem.2016.02.019","article-title":"Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel","volume":"1858","author":"D Medovoy","year":"2016","journal-title":"Biochim Biophys Acta\u2014Biomembr"},{"key":"ref22","article-title":"Equilibrium selectivity alone does not create K + -selective ion conduction in K + channels","volume":"4","author":"S Liu","year":"2013","journal-title":"Nat Commun"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1085\/jgp.201511371","article-title":"Determinants of cation transport selectivity: Equilibrium binding and transport kinetics","volume":"146","author":"SW Lockless","year":"2015","journal-title":"J Gen Physiol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1073\/pnas.1013636108","article-title":"Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites","volume":"108","author":"MG Derebe","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1073\/pnas.1013643108","article-title":"Structural studies of ion permeation and Ca2+ blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore","volume":"108","author":"MG Derebe","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/35102009","article-title":"Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 \u00c5 resolution","volume":"414","author":"Y Zhou","year":"2001","journal-title":"Nature"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"4553","DOI":"10.1021\/jp067873l","article-title":"A Bias-Exchange Approach to Protein Folding","volume":"111","author":"S Piana","year":"2007","journal-title":"J Phys Chem B"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"5075","DOI":"10.1113\/jphysiol.2012.238352","article-title":"A ring of threonines in the inner vestibule of the pore of CNGA1 channels constitutes a binding site for permeating ions","volume":"590","author":"A Marchesi","year":"2012","journal-title":"J Physiol"},{"key":"ref29","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000452","article-title":"A kinetic model of Trp-cage folding from multiple biased molecular dynamics simulations","volume":"5","author":"F Marinelli","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"3002","DOI":"10.1073\/pnas.1319054111","article-title":"A repulsion mechanism explains magnesium permeation and selectivity in CorA","volume":"111","author":"O Dalmas","year":"2014","journal-title":"Proc Natl Acad Sci"},{"key":"ref31","article-title":"Evolving Methods for Macromolecular Crystallography","author":"AGW Leslie","year":"2007","journal-title":"Evolving Methods for Macromolecular Crystallography"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1107\/S0907444909047337","article-title":"XDS","volume":"66","author":"W Kabsch","year":"2010","journal-title":"Acta Crystallogr Sect D Biol Crystallogr"},{"key":"ref33","first-page":"1","article-title":"XDS","author":"W Kabsch","year":"2010","journal-title":"Acta Cryst (2010) D66, 125\u2013132 [101107\/S0907444909047337]"},{"key":"ref34","first-page":"760","article-title":"Collaborative Computational Project, Number 4 (1994). The CCP4 Suite: programs for protein crystallography","volume":"D50","year":"1994","journal-title":"Acta Crystallogr"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.sbi.2015.07.003","article-title":"Assessing and maximizing data quality in macromolecular crystallography","author":"PA Karplus","year":"2015","journal-title":"Current Opinion in Structural Biology"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/S0076-6879(97)76068-3","article-title":"Detecting and overcoming crystal twinning","author":"TO Yeates","year":"1997","journal-title":"Methods in Enzymology"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1107\/S0907444911001314","article-title":"REFMAC5 for the refinement of macromolecular crystal structures","volume":"67","author":"GN Murshudov","year":"2011","journal-title":"Acta Crystallogr Sect D Biol Crystallogr"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1107\/S0907444904019158","article-title":"Coot: Model-building tools for molecular graphics","volume":"60","author":"P Emsley","year":"2004","journal-title":"Acta Crystallogr Sect D Biol Crystallogr"},{"key":"ref39","article-title":"PyMOL User\u2019s Guide","author":"WL Delano","year":"2004","journal-title":"DeLano Scientific LLC"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2051","DOI":"10.1002\/jcc.20748","article-title":"Performance of the general amber force field in modeling aqueous POPC membrane bilayers","volume":"28","author":"B J\u00f3j\u00e1rt","year":"2007","journal-title":"J Comput Chem"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.cpc.2013.09.018","article-title":"PLUMED 2: New feathers for an old bird","volume":"185","author":"GA Tribello","year":"2014","journal-title":"Comput Phys Commun"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/S0010-4655(00)00215-0","article-title":"Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations","volume":"135","author":"M Souaille","year":"2001","journal-title":"Comput Phys Commun"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.cpc.2017.04.009","article-title":"METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations","volume":"217","author":"T Giorgino","year":"2017","journal-title":"Comput Phys Commun"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1085\/jgp.114.3.377","article-title":"Cyclic nucleotide-gated channels. Pore topology studied through the accessibility of reporter cysteines","volume":"114","author":"a Becchetti","year":"1999","journal-title":"J Gen Physiol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"3283","DOI":"10.1016\/S0006-3495(02)75329-0","article-title":"Movement of the C-helix during the gating of cyclic nucleotide-gated channels","volume":"83","author":"M Mazzolini","year":"2002","journal-title":"Biophys J"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1021\/ja01288a032","article-title":"Individual Activity Coefficients of Ions in Aqueous Solutions","volume":"59","author":"J Kielland","year":"1937","journal-title":"J Am Chem Soc"},{"key":"ref47","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms1972","article-title":"Gating of cyclic nucleotide-gated channels is voltage dependent","volume":"3","author":"A Marchesi","year":"2012","journal-title":"Nat Commun"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1113\/jphysiol.1990.sp018061","article-title":"Currents carried by monovalent cations through cyclic GMP-activated channels in excised patches from salamander rods","volume":"424","author":"A Menini","year":"1990","journal-title":"J Physiol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1113\/jphysiol.1995.sp020858","article-title":"The multi-ion nature of the cGMP-gated channel from vertebrate rods","volume":"487","author":"F Sesti","year":"1995","journal-title":"J Physiol"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006295","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,8,14]],"date-time":"2018-08-14T00:00:00Z","timestamp":1534204800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006295","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T23:18:50Z","timestamp":1540250330000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006295"}},"subtitle":[],"editor":[{"given":"Avner","family":"Schlessinger","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,2]]},"references-count":49,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2018,8,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006295","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,8,2]]}}}