2′/3′‐O‐peptidyl Adenosine as a General Base Catalyst of its Own External Peptidyl Transfer: Implications for the Ribosome Catalytic Mechanism

Abstract

A physical organic study reveals general base catalysis by the 2′‐oxyanion of the peptidyl adenosine ethanolysis; this implies a proton‐shuttle role for the 2′‐OH of peptidyl tRNA A76 in the ribosome substrate‐assisted catalytic mechanism.

An Uncharged Amine in the Transition State of the Ribosomal Peptidyl Transfer Reaction

“…The third mechanism is a fully concerted reaction without intermediates and is a second variant of the "proton shuttle" proposal ( Figure 5). This mechanism requires that all bond formation, cleavage, and proton transfers occur simultaneously (Dorner, Polacek et al, 2002;Changalov, Ivanova et al, 2005). Each of these mechanisms can now be evaluated in light of the β nuc value determined for the ribosomal reaction.…”

“…The fully concerted "proton shuttle" mechanism with no intermediates ( Figure 5) (Dorner, Polacek et al, 2002;Changalov, Ivanova et al, 2005) requires that N-C bond formation, C-O bond cleavage, and proton-shuttling from the α-amine to the leaving group 3′-O all occur simultaneously. A near zero β nuc value is expected throughout the entire reaction coordinate as N-C bond formation occurs concurrently with α-amine proton abstraction.…”

Modulating the activity of the peptidyl transferase center of the ribosome

“…Hydrogen bonding between the 29-OH of A76 and the nucleophilic a-NH 2 group may help to position the nucleophile. Another attractive explanation for the importance of 29-OH of A76 of the P-site tRNA is its participation in a concerted proton shuttle that bridges the attacking a-NH 2 group and the leaving 39 oxygen of the P-site tRNA (Das et al 1999;Dorner et al 2002;Changalov et al 2005;Schmeing et al 2005a;Trobro and Å qvist 2005) The main role of ribosomal residues in the active site appears to provide a preorganized hydrogen-bond network that stabilizes the charged transition state (Schmeing et al 2005a;Trobro and Å qvist 2005). Additionally, they seem to protect pept-tRNA from premature hydrolysis by water when the A site is not filled by aa-tRNA ( Fig.…”

Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

“…The data included in the other three clusters differ more significantly from the experimental data. Cluster {2} consists mainly of methods which take into account the electron correlation, combined with basis sets without polarization functions or with basis sets including polarization functions but with a few primitives (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21). The other two clusters contain the HF method with or without polarization function in the basis sets (clusters {1} and {3}, respectively).…”

“…In addition, in Section 4.2 we report an approach to the automatic construction of the initial structures of transition states with desired atomic connectivity but unknown geometry using the same model reaction. We selected this reaction since it is a suitable model for elucidation of the mechanism of biosynthesis of peptide bonds in the ribosome, in connection with recent theoretical [13][14][15][16][17] and experimental [18][19][20] investigations.…”