title: Ions and the protein surface revisited: extensive molecular dynamics simulations and analysis of protein structures in alkali-chloride solutions.
abstract: Proteins interact with ions in various ways. The surface of proteins has an innate capability to bind ions, and it is also influenced by the screening of the electrostatic potential owing to the presence of salts in the bulk solution. Alkali metal ions and chlorides interact with the protein surface, but such interactions are relatively weak and often transient. In this paper, computer simulations and analysis of protein structures are used to characterize the interactions between ions and the protein surface. The results show that the ion-binding properties of protein residues are highly variable. For example, alkali metal ions are more often associated with aspartate residues than with glutamates, whereas chlorides are most likely to be located near arginines. When comparing NaCl and KCl solutions, it was found that certain surface residues attract the anion more strongly in NaCl. This study demonstrates that protein-salt interactions should be accounted for in the planning and execution of experiments and simulations involving proteins, particularly if subtle structural details are sought after.
authors.affiliation: School of Natural Sciences, Linnæus University, 391 82 Kalmar, Sweden. ran.friedman@lnu.se
authors.forename: Ran
authors.initials: R
authors.lastname: Friedman
mesh_terms: D000468:Alkalies / Q000737:chemistry*; D000682:Amyloid / Q000737:chemistry / Q000378:metabolism; D002712:Chlorides / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D016333:HIV Protease / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D056004:Molecular Dynamics Simulation; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D038601:Ribosomal Protein S6 / Q000737:chemistry / Q000378:metabolism; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties
chemical_list: D000468:Alkalies; D000682:Amyloid; D002712:Chlorides; D005656:Fungal Proteins; D011506:Proteins; D038601:Ribosomal Protein S6; D012996:Solutions; D012997:Solvents; D016333:HIV Protease