Protein-RNA interactions: Structural analysis and functional classes

Ellis, Jonathan J., Broom, Mark and Jones, Susan (2007) Protein-RNA interactions: Structural analysis and functional classes. Proteins, 66 4: 903-911. doi:10.1002/prot.21211

Author Ellis, Jonathan J.
Broom, Mark
Jones, Susan
Title Protein-RNA interactions: Structural analysis and functional classes
Journal name Proteins   Check publisher's open access policy
ISSN 0887-3585
Publication date 2007-03
Sub-type Article (original research)
DOI 10.1002/prot.21211
Volume 66
Issue 4
Start page 903
End page 911
Total pages 9
Place of publication John Wiley and Sons
Publisher Hoboken, NJ, United States
Language eng
Formatted abstract
A data set of 89 protein-RNA complexes has been extracted from the Protein Data Bank, and the nucleic acid recognition sites characterized through direct contacts, accessible surface area, and secondary structure motifs. The differences between RNA recognition sites that bind to RNAs in functional classes has also been analyzed. Analysis of the complete data set revealed that van der Waals interactions are more numerous than hydrogen bonds and the contacts made to the nucleic acid backbone occur more frequently than specific contacts to nucleotide bases. Of the base-specific contacts that were observed, contacts to guanine and adenine occurred most frequently. The most favored amino acid-nucleotide pairings observed were lysine-phosphate, tyrosine-uracil, arginine-phosphate, phenylalanine-adenine and tryptophan-guanine. The amino acid propensities showed that positively charged and polar residues were favored as expected, but also so were tryptophan and glycine. The propensities calculated for the functional classes showed trends similar to those observed for the complete data set. However, the analysis of hydrogen bond and van der Waal contacts showed that in general proteins complexed with messenger RNA, transfer RNA and viral RNA have more base specific contacts and less backbone contacts than expected, while proteins complexed with ribosomal RNA have less base-specific contacts than the expected. Hence, whilst the types of amino acids involved in the interfaces are similar, the distribution of specific contacts is dependent upon the functional class of the RNA bound.
Keyword Protein-RNA interactions
RNA binding proteins
Structural analysis
Interaction propensity
Nucleic Acid Recognition
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collections: ERA 2012 Admin Only
School of Chemistry and Molecular Biosciences
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