Quantum chemical study of ester aminolysis catalyzed by a single adenine: a reference reaction for the ribosomal peptide synthesis.
Herein we report the results of a HF/6-31+G** and B3LYP/6-31+G** computational investigation of the title reaction for the peptide bond synthesis catalyzed by a single adenine. This system constitutes a reference reaction to study the basic chemical events that have been proposed to occur at the peptidyl transferase active site of ribosomes on the basis of structural determinations (Science 2000, 239, 920--931). Thus, the analysis of the geometry, charge distribution, and energetics of the critical structures involved in this title reaction yields insight into the catalytic mode of action of RNA molecules. Our computational results give further support to the hypotheses that the activated nucleotide A2451 in the ribosome acts as a base catalyst and that this role is similar to that of the His residue in the catalytic triad of serine proteases.
Suárez
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Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, Oviedo 33006, Spain.
Merz
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D000085:Acetates / Q000737:chemistry; D000225:Adenine / Q000737:chemistry*; D001665:Binding Sites; D002384:Catalysis; D008744:Methylamines / Q000737:chemistry; D008956:Models, Chemical; D010455:Peptides / Q000138:chemical synthesis; D011789:Quantum Theory; D012269:Ribosomal Proteins / Q000138:chemical synthesis*; D012270:Ribosomes / Q000737:chemistry
D000085:Acetates; D008744:Methylamines; D010455:Peptides; D012269:Ribosomal Proteins; C027451:methylamine; D000225:Adenine; C046923:methyl acetate