Investigations on unconventional hydrogen bonds in RNA binding proteins: The role of CH⋯O [dbnd]C interactions

Abstract

We have investigated the roles played by C H⋯O C interactions in RNA binding proteins. There was an average of 78 C H⋯O C interactions per protein and also there was an average of one significant C H⋯O C interaction for every 6 residues in the 59 RNA binding proteins studied. Main chain–Main chain (MM) C H⋯O C interactions are the predominant type of interactions in RNA binding proteins. The donor atom contribution to C H⋯O C interactions was mainly from aliphatic residues. The acceptor atom contribution for MM C H⋯O C interactions was mainly from Val, Phe, Leu, Ile, Arg and Ala. The secondary structure preference analysis of C H⋯O C interacting residues showed that, Arg, Gln, Glu and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Ile, Leu, Lys, Met, Phe, Trp and Val preferred to be in strand conformation. Most of the C H⋯O C interacting polar amino acid residues were solvent exposed while, majority of the C H⋯O C interacting non polar residues were excluded from the solvent. Long and medium-range C H⋯O C interactions are the predominant type of interactions in RNA binding proteins. More than 50% of C H⋯O C interacting residues had a higher conservation score. Significant percentage of C H⋯O C interacting residues had one or more stabilization centers. Sixty-six percent of the theoretically predicted stabilizing residues were also involved in C H⋯O C interactions and hence these residues may also contribute additional stability to RNA binding proteins.