Investigations on C-H• • •π interactions in RNA binding proteins

We have investigated the roles played by C-H center dot center dot center dot pi interactions in RNA binding proteins. There was an average of 55 C-H center dot center dot center dot pi interactions per protein and also there was an average of one significant C-H center dot center dot center dot pi interaction for every nine residues in the 59 RNA binding proteins studied. Main-chain to side-chain C-H center dot center dot center dot pi interactions is the predominant type of interactions in RNA binding proteins. The donor atom contribution to C-H center dot center dot center dot pi 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 center dot center dot center dot pi and side-chain to side-chain C-H center dot center dot center dot pi 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 center dot center dot center dot pi 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 center dot center dot center dot pi interactions. The secondary structure preference analysis of C-H center dot center dot center dot pi 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 center dot center dot center dot pi interactions are the predominant type of interactions in RNA binding proteins. More than 50% of C-H center dot center dot center dot pi interacting residues had a higher conservation score. Significant percentage of C-H center dot center dot center dot pi interacting residues had one or more stabilization centers. Seven percent of the theoretically predicted stabilizing residues were also involved in C-H center dot center dot center dot pi interactions and hence these residues may also contribute additional stability to RNA binding proteins. (c) 2007 Elsevier B.V. All rights reserved.