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Protein-RNA interactions: a structural analysis

Jones, S; Daley, DT; Luscombe, NM; Berman, HM; Thornton, JM; (2001) Protein-RNA interactions: a structural analysis. Nucleic Acids Research , 29 (4) 943 - 954. 10.1093/nar/29.4.943. Green open access

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Abstract

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.

Type: Article
Title: Protein-RNA interactions: a structural analysis
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/nar/29.4.943
Publisher version: http://dx.doi.org/10.1093/nar/29.4.943
Language: English
Additional information: PMCID: PMC29619 Originally published in the Oxford University Press journal Nucleic Acids Research.
Keywords: Base Pairing, Binding Sites, Computational Biology, DNA, Databases as Topic, Guanine, Hydrogen Bonding, Internet, Models, Molecular, Protein Binding, Protein Structure, Secondary, RNA, RNA-Binding Proteins, Uracil
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/22315
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