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