Cation–pi Interactions at Non-redundant Protein–RNA Interfaces

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Honggucun Zhang¹, Chunhua Li^1*, Feng Yang¹, Jiguo Su², Jianjun Tan¹, Xiaoyi Zhang¹, and Cunxin Wang^1*

¹College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; fax: 86-10-67392837; E-mail: zhgc1988@gmail.com; chunhuali@bjut.edu.cn; fyang@bjut.edu.cn; xiaoyizhang@bjut.edu.cn; cxwang@bjut.edu.cn

²College of Science, Yanshan University, Qinhuangdao 066004, China; E-mail: jiguosu@bjut.edu.cn

^* To whom correspondence should be addressed.

Received December 23, 2013; Revision received March 31, 2014

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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.

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KEY WORDS: cation–pi interactions, protein–RNA interfaces, sequence and structural specificities, electrostatic energy, ab initio

DOI: 10.1134/S0006297914070062

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