title: Cation-pi interactions at non-redundant protein--RNA interfaces.
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.
authors.affiliation: College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China. zhgc1988@gmail.com.
authors.forename: Honggucun
authors.initials: H
authors.lastname: Zhang
authors.forename: Chunhua
authors.initials: C
authors.lastname: Li
authors.forename: Feng
authors.initials: F
authors.lastname: Yang
authors.forename: Jiguo
authors.initials: J
authors.lastname: Su
authors.forename: Jianjun
authors.initials: J
authors.lastname: Tan
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Zhang
authors.forename: Cunxin
authors.initials: C
authors.lastname: Wang
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D002412:Cations / Q000737:chemistry; D003198:Computer Simulation; D008958:Models, Molecular; D011485:Protein Binding; D011789:Quantum Theory; D016601:RNA-Binding Proteins / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D002412:Cations; D016601:RNA-Binding Proteins; D012964:Sodium