NH…π Interactions: Investigations on the Evidence and Consequences in RNA Binding Proteins

ABSTRACT

We have analyzed the role of N-H…π interactions in 59 RNA binding protein structures with relation to other factors like amino acid preference, secondary structural elements, solvent accessibility of a particular fold, conservation score, stabilization centers and stabilizing residues. There was an average of 12 N-H…π interactions per protein in the 59 proteins investigated and an average of one significant N-H…π interaction for every 37 amino acid residues in RNA binding proteins. 63% of the N-H…π interactions were computed to be inter-residue interactions, while the remaining 37% of the N-H…π interactions were found to be intra-residue interactions. The contribution of the main chain to side chain N-H…π mediated interactions was higher irrespective of the amino acids involved. Long-range N-H…π interactions appear to be the predominant type of interactions in RNA binding proteins. Arg, Asn, Asp, Gln, Glu, Ile, Leu, Lys and Ser preferred to be in helix. Ala, Cys, Phe, Thr, Trp, Tyr and Val were found to prefer strand conformation. Polar amino acid residues involved in N-H…π interactions were solvent exposed and most of the non polar residues involved in N-H…π interactions were excluded from the solvent. Most of the amino acid residues involved in N-H…π interactions might be conserved in RNA binding residues. The specificity is shown by residues not involved in N-H…π interactions as only a very small percentage of interacting residues are involved in RNA Binding. On the whole, the results of the present investigations on N-H…π interactions might be useful for intra protein-protein interactions and studies on inter-residue and intra-residue interactions.

Keywords: