Cation-pi interactions at non-redundant protein--RNA interfaces

Biochemistry (Mosc). 2014 Jul;79(7):643-52. doi: 10.1134/S0006297914070062.

Abstract

Cation-pi interactions have proved to be important in proteins and protein-ligand complexes. Here, cation-pi interactions are analyzed for 282 non-redundant protein-RNA interfaces. The statistical results show that this kind of interactions exists in 65% of the interfaces. The four RNA bases are ranked as Gua>Ade>Ura>Cyt according to their propensity to participate in cation-pi interactions. The corresponding ranking for the involved amino acid residues is: Arg>Lys>Asn>Gln. The same trends are obtained based on the empirical energy calculation. The Arg-Gua pairs have the greatest stability and are also most frequently observed. The number of cation-pi pairs involving unpaired bases is 2.5 times as many as those involving paired bases. Hence, cation-pi interactions show sequence and structural specificities. For the bicyclic bases, Gua and Ade, their 5-atom rings participate in cation-pi interactions somewhat more than the 6-atom rings, with percentages of 54 and 46%, respectively, which is due to the higher cation-pi participation proportion (63%) of 5-atom rings in the paired bases. These results give a general view of cation-pi interactions at protein-RNA interfaces and are helpful in understanding the specific recognition between protein and RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Cations / chemistry
  • Computer Simulation
  • Models, Molecular
  • Protein Binding
  • Quantum Theory
  • RNA-Binding Proteins / chemistry*
  • Sodium / chemistry*
  • Thermodynamics

Substances

  • Amino Acids
  • Cations
  • RNA-Binding Proteins
  • Sodium