Investigations on C–H⋯π interactions in RNA binding proteins

Abstract

We have investigated the roles played by C–H⋯π interactions in RNA binding proteins. There was an average of 55 C–H⋯π interactions per protein and also there was an average of one significant C–H⋯π interaction for every nine residues in the 59 RNA binding proteins studied. Main-chain to side-chain C–H⋯π interactions is the predominant type of interactions in RNA binding proteins. The donor atom contribution to C–H⋯π interactions was mainly from Phe, Tyr, Trp, Pro, Gly, Lys, His and Ala residues. The acceptor atom contribution to main-chain to side-chain C–H⋯π and side-chain to side-chain C–H⋯π interactions was mainly from Phe and Tyr residues. On the contrary, the acceptor atoms of Trp residues contributed to all the four types of C–H⋯π interactions. Also, Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain five-member aromatic ring and side-chain to side-chain C–H⋯π interactions. The secondary structure preference analysis of C–H⋯π interacting residues showed that, Arg, Gln, Glu, His, Ile, Leu, Lys, Met, Phe and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Trp and Val preferred to be in strand conformation. Long-range C–H⋯π interactions are the predominant type of interactions in RNA binding proteins. More than 50% of C–H⋯π interacting residues had a higher conservation score. Significant percentage of C–H⋯π interacting residues had one or more stabilization centers. Seven percent of the theoretically predicted stabilizing residues were also involved in C–H⋯π interactions and hence these residues may also contribute additional stability to RNA binding proteins.