Cation-p interactions in structural biology (protein structureyelectrostatics)

Cation-p interactions in protein structures are identified and evaluated by using an energy-based criterion for selecting significant sidechain pairs. Cation-p interactions are found to be common among structures in the Protein Data Bank, and it is clearly demonstrated that, when a cationic sidechain (Lys or Arg) is near an aromatic sidechain (Phe, Tyr, or Trp), the geometry is biased toward one that would experience a favorable cation-p interaction. The sidechain of Arg is more likely than that of Lys to be in a cation-p interaction. Among the aromatics, a strong bias toward Trp is clear, such that over one-fourth of all tryptophans in the data bank experience an energetically significant cation-p interaction. The three-dimensional structure of a protein is determined by a delicate balance of weak interactions. Hydrogen bonds, salt bridges, and the hydrophobic effect all play roles in folding a protein and establishing its final structure. In addition, the cation-p interaction (1–3) is increasingly recognized as an important noncovalent binding interaction relevant to structural biology. Theoretical and experimental studies have shown that cation-p interactions can be quite strong, both in the gas phase and in aqueous media. A number of studies have established a role for cation-p interactions in biological recognition, especially in the binding of acetylcholine (4, 5). Here we present a detailed analysis of the extent and nature of cation-p interactions that are intrinsic to a protein’s structure and likely contribute to protein stability. We find that energetically significant cation-p interactions are common in proteins—a ‘‘typical’’ protein will contain several. We also have documented some significant preferences for certain amino acid pairs as partners in a cation-p interaction. Important early work indicated a role for cation-p interactions in protein structures. Following work by Levitt and Perutz (6–8) suggesting a hydrogen bond between aromatic and amino groups, Burley and Petsko identified the ‘‘amino aromatic’’ interaction (9), in which NH-containing groups tend to be positioned near aromatic rings within proteins. It is now appreciated that the interaction of a cationic group with an aromatic—a cation-p interaction—is much more favorable than an analogous interaction involving a neutral amine (10, 11). Important subsequent studies by Thornton (12–17) modified the Burley and Petsko analysis, especially with regard to the amino-aromatic ‘‘hydrogen bond.’’ In addition, explicit studies of Arg interacting with aromatic residues have been reported by Flocco and Mowbray (18) and by Thornton (14), and other efforts to search the Protein Data Bank (PDB) for cation-p interactions between ligands and proteins have been reported (19, 20). Previous protein database searches relied on geometric definitions of sidechain interactions, focusing on when a cationic sidechain displayed a certain distanceyangle relationship to an aromatic sidechain. The different geometries of Lys vs. Arg and Trp vs. PheyTyr can make such comparisons problematical. In addition, not all cation-aromatic contacts represent energetically favorable cation-p interactions. Unlike ion pairs, for which any close contact will be energetically favorable, a cation interaction with an aromatic can be attractive or repulsive. The electrostatic potential surfaces of the aromatics, which control such distinctions (1), can be complex, and it is difficult to clearly distinguish attractive from repulsive cation-aromatic contacts using geometric criteria alone. To circumvent this problem, and to put the diverse array of potential cation-p interactions on a more nearly equal footing, we have chosen to use energy-based, rather than geometrybased, criteria in this study. Our goals in this study are twofold. First, we wish to develop meaningful statistics for cation-p interactions for structures within the PDB (21). Second, we wish to develop a simple, unambiguous protocol for identifying cation-p interactions that can be easily applied by other workers. Within a protein, cation-p interactions can occur between the cationic sidechains of either lysine (Lys, K) or arginine (Arg, R) and the aromatic sidechains of phenylalanine (Phe, F), tyrosine (Tyr, Y) or tryptophan (Trp, W). Because histidine can participate in cation-p interactions as either a cation or as a p-system, depending on its protonation state, we do not consider histidine in this study. We assume Lys and Arg are always protonated.