title: The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations.
abstract: Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short (+)N-H⋯O(-) bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm(-1). It is caused by the asymmetric stretching vibrations of the (+)N-H⋯O(-) fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.
authors.affiliation: Mendeleev University of Chemical Technology, Moscow, Russia.
authors.forename: M V
authors.initials: MV
authors.lastname: Vener
authors.affiliation: Photochemistry Center of the Russian Academy of Sciences, Moscow, Russia.
authors.forename: A V
authors.initials: AV
authors.lastname: Odinokov
authors.affiliation: Free University, Berlin, Germany.
authors.forename: C
authors.initials: C
authors.lastname: Wehmeyer
authors.affiliation: Martin-Luther-Universität Halle-Wittenberg, Halle, Germany.
authors.forename: D
authors.initials: D
authors.lastname: Sebastiani
mesh_terms: D001120:Arginine / Q000737:chemistry / Q000528:radiation effects*; D018698:Glutamic Acid / Q000737:chemistry / Q000528:radiation effects*; D007259:Infrared Rays; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry* / Q000528:radiation effects*; D012492:Salts / Q000737:chemistry / Q000528:radiation effects*; D013055:Spectrophotometry, Infrared; D014732:Vibration
chemical_list: D010455:Peptides; D012492:Salts; D018698:Glutamic Acid; D001120:Arginine