Mosaic tile model for tRNA-enzyme recognition

• Published in: Nucleic acids research Vol. 21; no. 8; pp. 1941 - 1947
• Main Authors: Steinberg, S.V, Kisselev, L.L
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 25.04.1993
• Subjects: Algorithms; Amino Acids - metabolism; Amino Acyl-tRNA Synthetases - metabolism; aminoacyl-trna synthetase; binding sites; Escherichia coli; Escherichia coli - genetics; informational tiles; ligases; Models, Genetic; molecular conformation; nucleotide combinations; nucleotide sequences; Nucleotides - metabolism; RNA, Bacterial - metabolism; RNA, Transfer - metabolism; RNA, Transfer, Ala - metabolism; RNA, Transfer, Gln - metabolism; transfer RNA
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/21.8.1941

An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucleotide and its neighbours as they are defined by the tertiary structure of the molecule. Informational content of each tile is calculated as its probability to occur exclusively in a set of cognate tRNAs. Based on this algorithm the identity sites of E. coli tRNA(Ala) and tRNA(Gln) were determined. The results are in a good agreement with the biochemical data and provide new information about identity sites of these tRNAs.