000130728 001__ 130728
000130728 005__ 20240131210810.0
000130728 0247_ $$2doi$$a10.1039/c5cp04504e
000130728 0248_ $$2sideral$$a92784
000130728 037__ $$aART-2015-92784
000130728 041__ $$aeng
000130728 100__ $$0(orcid)0000-0002-1896-7805$$aGalano-Frutos, J.$$uUniversidad de Zaragoza
000130728 245__ $$aThe mechanism of water/ion exchange at a protein surface: A weakly bound chloride in Helicobacter pylori apoflavodoxin
000130728 260__ $$c2015
000130728 5060_ $$aAccess copy available to the general public$$fUnrestricted
000130728 5203_ $$aBinding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes such as protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism of chloride/water exchange at a protein surface (that of the apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal a variety of chloride exit routes and residence times; the latter is related to specific coordination modes of the anion. The role of solvent molecules in the mechanism of chloride unbinding has been studied in detail. We see no temporary increase in chloride coordination along the release process. Instead, the coordination of new water molecules takes place in most cases after the chloride/protein atom release event has begun. Moreover, the distribution function of water entrance events into the first chloride solvation shell peaks after chloride protein atom dissociation events. All these observations together seem to indicate that water molecules simply fill the vacancies left by the previously coordinating protein residues. We thus propose a step-by-step dissociation pathway in which protein/chloride interactions gradually break down before new water molecules progressively fill the vacant positions left by protein atoms. As observed for other systems, water molecules associated with bound chloride or with protein atoms have longer residence times than those bound to the free anion. The implications of the exchange mechanism proposed for the binding of the FMN (Flavin Mononucleotide) protein cofactor are discussed.
000130728 536__ $$9info:eu-repo/grantAgreement/ES/MINECO/BFU2013-47064-P$$9info:eu-repo/grantAgreement/ES/MINECO/BIO2014-57314-REDT
000130728 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
000130728 590__ $$a4.449$$b2015
000130728 591__ $$aPHYSICS, ATOMIC, MOLECULAR & CHEMICAL$$b6 / 35 = 0.171$$c2015$$dQ1$$eT1
000130728 591__ $$aCHEMISTRY, PHYSICAL$$b32 / 144 = 0.222$$c2015$$dQ1$$eT1
000130728 592__ $$a1.725$$b2015
000130728 593__ $$aPhysics and Astronomy (miscellaneous)$$c2015$$dQ1
000130728 593__ $$aPhysical and Theoretical Chemistry$$c2015$$dQ1
000130728 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/acceptedVersion
000130728 700__ $$0(orcid)0000-0001-5775-483X$$aMorón, M.C.$$uUniversidad de Zaragoza
000130728 700__ $$0(orcid)0000-0002-2879-9200$$aSancho, J.$$uUniversidad de Zaragoza
000130728 7102_ $$11002$$2060$$aUniversidad de Zaragoza$$bDpto. Bioq.Biolog.Mol. Celular$$cÁrea Bioquímica y Biolog.Mole.
000130728 7102_ $$12003$$2395$$aUniversidad de Zaragoza$$bDpto. Física Materia Condensa.$$cÁrea Física Materia Condensada
000130728 773__ $$g17, 43 (2015), 28635-28646$$pPhys. chem. chem. phys.$$tPhysical chemistry chemical physics$$x1463-9076
000130728 8564_ $$s2268591$$uhttps://zaguan.unizar.es/record/130728/files/texto_completo.pdf$$yPostprint
000130728 8564_ $$s1555273$$uhttps://zaguan.unizar.es/record/130728/files/texto_completo.jpg?subformat=icon$$xicon$$yPostprint
000130728 909CO $$ooai:zaguan.unizar.es:130728$$particulos$$pdriver
000130728 951__ $$a2024-01-31-19:16:23
000130728 980__ $$aARTICLE