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Protein-RNA interactions: a structural analysis

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journal contribution
posted on 2023-06-08, 10:09 authored by Susan Jones, David T A Daley, Nicholas M Luscombe, Helen M Berman, Janet M Thornton
A detailed computational analysis of 32 protein¿RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein¿double-stranded DNA and protein¿single-stranded DNA complexes. The interface properties of the protein¿RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein¿RNA and protein¿DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein¿RNA complexes, backbone contacts were more dominant in the protein¿DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.

History

Publication status

  • Published

File Version

  • Published version

Journal

Nucleic Acids Research

ISSN

0305-1048

Issue

4

Volume

29

Page range

943-954

Pages

12.0

Department affiliated with

  • Biochemistry Publications

Notes

SJ wrote the algorithms, conducted the analysis and was the corresponding author

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2012-02-06

First Open Access (FOA) Date

2016-03-22

First Compliant Deposit (FCD) Date

2017-03-06

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