NDLI: Mechanism of peptide bond synthesis on the ribosome

Content Provider	PubMed Central
Author	Stefan, Trobro Åqvist, Johan
Copyright Year	2005
Abstract	With the emergence of atomic-resolution crystal structures of bacterial ribosomal subunits, major advances in eliciting structure–function relationships of the translation process are underway. Nevertheless, the detailed mechanism of peptide bond synthesis that occurs on the large ribosomal subunit remains unknown. Separate x-ray structures of aminoacyl-tRNA and peptidyl-tRNA analogues bound to the ribosomal A- and P-sites, however, allow for structural modeling of the active complex in catalysis. Here, we combine available structural data to construct such a model of the peptidyl transfer reaction center with bound substrates. Molecular dynamics and free energy perturbation simulations then are used in combination with an empirical valence bond description of the reaction energy surface to examine possible catalytic mechanisms. Already, simulations of the reactant and tetrahedral intermediate states reveal a stable, preorganized H-bond network poised for catalysis. The most favorable mechanism is found not to involve any general acid–base catalysis by ribosomal groups but an intrareactant proton shuttling via the P-site adenine O2′ oxygen, which follows the attack of the A-site α-amino group on the P-site ester. The calculated rate enhancement for this mechanism is ≈105, and the catalytic effect is found to be entirely of entropic origin, in accordance with recent experimental data, and is associated with the reduction of solvent reorganization energy rather than with substrate alignment or proximity. This mechanism also explains the inability of 2′-deoxyadenine P-site substrates to promote peptidyl transfer. The observed H-bond network suggests an important structural role of several universally conserved rRNA residues.
Related Links	http://dx.doi.org/10.1073/pnas.0504043102
Ending Page	12400
Page Count	6
Starting Page	12395
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	35
Volume Number	102
Language	English
Publisher	National Academy of Sciences
Publisher Date	2005-08-30
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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