The P-site A76 2′-OH acts as a peptidyl shuttle in a stepwise peptidyl transfer mechanism

Abstract

The P-site-A76-2′OH transfers the polypeptide chain to the A-site α-amine and A2451 facilitates this transfer by acting as proton shuttle.

Theoretical Study of the Mechanism of Ribosomal Peptide Bond Formation Using the ONIOM Method

“…Although the role of the 2′-OH group of A76 of peptidyl-tRNA is debatable, [33][34][35][36][37] we adopted a substrate-assisted catalysis model in which the 2′-OH group of A76 catalyzes peptide bond formation, 37) since this is consistent with experimental data and calculated models from previous mechanistic studies. 8,9,[12][13][14][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31]33,34) The optimized geometries of TS1 and TS2 are shown in Fig. 3.…”

“…Although this is inconsistent with the results of kinetic studies showing that the formation of the tetrahedral intermediate is rate-limiting, 8) a similar trend has been reported in theoretical calcula-tions of stepwise amide or peptide bond formation. [10][11][12][13][20][21][22][23][24][25][26][27][29][30][31] According to Rangelov et al, the height of the energy barrier of peptide bond formation is related to the angular deviation of the proton transfer route (O2′-H-O3′ or N-H-O2′) from linearity in the transition state. 12) Therefore, the larger angular deviation of Δθ O2′-H-O3′ = 47.5° at TS2 compared to that of Δθ N-H-O2′ = 20.3° at TS1 supports our conclusion that the ratelimiting step is TS2.…”

“…18) Quantum chemical calculations have been used to study both stepwise and concerted mechanisms. [20][21][22][23][24][25][26][27][28][29][30][31] In one study of systems containing 44-56 atoms of the PTC analyzed using the M06-2X/6-311 + G(d,p) level of theory, C-N bond formation and C-O bond cleavage were accompanied by proton transfer of the NH 2 group, 2′-OH group of A76, and water molecules in the transition states (proton-shuttle mechanism); these authors showed that a stepwise reaction was favored over a concerted one and that the 2′-OH group of rRNA A2451 in the active site of the ribosome stabilized the transition states through hydrogen bonding. 22) In a previous study, we demonstrated the stepwise mechanism of the peptidyl transfer reaction in a ribosome system consisting of 2354 atoms using the ONIOM method 23) (Fig.…”

Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids

“…Plausibly, this may actually reflect a somewhat more flexible structure, amenable to recognition of β-amino acids in addition to the canonical α-amino acids. Additionally, it should be noted that there are numerous reports suggesting that the ribose moiety of the 3′-terminal adenosine on aminoacyl-tRNA may also be an important factor in determining the facility of ribosomally mediated peptide bond formation. − Accordingly, the foregoing analysis, based only on ribosome structure, may not address all of the factors involved.…”

Quantum mechanics and molecular mechanics study of the reaction mechanism of quorum quenching enzyme: N-acyl homoserine lactonase with C6-HSL

“…This method has been successfully applied in exploring many enzymatic reactions. [21][22][23][24][25][39][40][41][42] To the best of our knowledge, this is the rst theoretical report regarding the catalytic reaction of AidH, which may provide important guides for the development of novel therapeutics against quorum sensing.…”