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Biochemistry (Moscow)

, Volume 79, Issue 7, pp 643–652 | Cite as

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

  • Honggucun Zhang
  • Chunhua Li
  • Feng Yang
  • Jiguo Su
  • Jianjun Tan
  • Xiaoyi Zhang
  • Cunxin Wang
Article

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.

Key words

cation-pi interactions protein-RNA interfaces sequence and structural specificities electrostatic energy ab initio 

Abbreviations

Ade

adenine

Benz

benzene

Cyt

cytidine

Gua

guanosine

Ura

uridine

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Copyright information

© Pleiades Publishing, Ltd. 2014

Authors and Affiliations

  1. 1.College of Life Science and BioengineeringBeijing University of TechnologyBeijingChina
  2. 2.College of ScienceYanshan UniversityQinhuangdaoChina

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