The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin

摘要: Binding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism chloride/water exchange at a surface (that apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal variety chloride exit routes and residence times; latter is related to specific coordination modes anion. The role solvent molecules in unbinding has been studied detail. see no temporary increase along release process. Instead, new water takes place most cases after chloride/protein atom event begun. Moreover, distribution function entrance events into first solvation shell peaks dissociation events. All these observations together seem indicate that simply fill vacancies left by previously coordinating residues. thus propose step-by-step pathway which protein/chloride interactions gradually break down before progressively vacant positions atoms. As observed for other systems, associated with bound atoms longer times than those free implications proposed binding FMN (Flavin Mononucleotide) cofactor are discussed.