Two types of noncovalent bonding interactions are present in protein structures, specific and nonspecific. Nonspecific interactions are mostly hydrophobic and van der Waals. Specific interactions are largely electrostatic. While the hydrophobic effect is the major driving force in protein folding, electrostatic interactions are important in protein folding, stability, flexibility, and function. Here we review the role of close-range electrostatic interactions (salt bridges) and their networks in proteins. Salt bridges are formed by spatially proximal pairs of oppositely charged residues in native protein structures. Often salt-bridging residues are also close in the protein sequence and fall in the same secondary structural element, building block, autonomous folding unit, domain, or subunit, consistent with the hierarchical model for protein folding. Recent evidence also suggests that charged and polar residues in largely hydrophobic interfaces may act as hot spots for binding. Salt bridges are rarely found across protein parts which are joined by flexible hinges, a fact suggesting that salt bridges constrain flexibility and motion. While conventional chemical intuition expects that salt bridges contribute favorably to protein stability, recent computational and experimental evidence shows that salt bridges can be stabilizing or destabilizing. Due to systemic protein flexibility, reflected in small-scale side-chain and backbone atom motions, salt bridges and their stabilities fluctuate in proteins. At the same time, genome-wide, amino acid sequence composition, structural, and thermodynamic comparisons of thermophilic and mesophilic proteins indicate that specific interactions, such as salt bridges, may contribute significantly towards the thermophilic-mesophilic protein stability differential.
