A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

Wang, Qiang; Gao, Jun; Zhang, Dongju

doi:10.1016/j.chemphys.2015.01.011

Cited by 7 publications

(6 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, what is clear is that all published computational investigations of reaction paths do predict a late TS on the ribosome, dominated by C−O bond breaking ( 7–9 , 12 , 20 , 25–31 ). There is, however, some confusion here due to the fact that some works ( 20 , 27 , 28 ) equate the rate-limiting TS with the elementary chemical step that has the highest energy barrier, and not with the TS that has the highest energy relative to the reactant complex, which is the correct kinetic definition. Besides the stepwise type of mechanism involving a transient tetrahedral intermediate, a fully concerted mechanism has also been proposed in several studies ( 26 , 29–31 ).…”

Section: Introductionmentioning

confidence: 99%

Mechanistic alternatives for peptide bond formation on the ribosome

Kazemi

Sočan

Himo

et al. 2018

Nucleic Acids Research

View full text Add to dashboard Cite

The peptidyl transfer reaction on the large ribosomal subunit depends on the protonation state of the amine nucleophile and exhibits a large kinetic solvent isotope effect (KSIE ∼8). In contrast, the related peptidyl-tRNA hydrolysis reaction involved in termination shows a KSIE of ∼4 and a pH-rate profile indicative of base catalysis. It is, however, unclear why these reactions should proceed with different mechanisms, as the experimental data suggests. One explanation is that two competing mechanisms may be operational in the peptidyl transferase center (PTC). Herein, we explored this possibility by re-examining the previously proposed proton shuttle mechanism and testing the feasibility of general base catalysis also for peptide bond formation. We employed a large cluster model of the active site and different reaction mechanisms were evaluated by density functional theory calculations. In these calculations, the proton shuttle and general base mechanisms both yield activation energies comparable to the experimental values. However, only the proton shuttle mechanism is found to be consistent with the experimentally observed pH-rate profile and the KSIE. This suggests that the PTC promotes the proton shuttle mechanism for peptide bond formation, while prohibiting general base catalysis, although the detailed mechanism by which general base catalysis is excluded remains unclear.

show abstract

Section: Introductionmentioning

confidence: 99%

Mechanistic alternatives for peptide bond formation on the ribosome

Kazemi

Sočan

Himo

et al. 2018

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Without the presence of any intermediate species, C-N bond formation is completed simultaneously with the C-O bond cleavage and proton transfer. Alternatively, several theoretical investigations have also examined stepwise mechanisms of peptide formation, in which C-N bond forms asynchronously with the C-O bond cleavage through a neutral intermediate where the proton from α-amino group is transferred to the carbonyl oxygen atom [ 11 , 21 , 22 , 23 ]. There are experimental evidences that the peptide formation reaction proceeds in a stepwise way.…”

Section: Resultsmentioning

confidence: 99%

“…Replacement of its 2′-OH with -F or -OCH 3 drastically decreases the ribosome’s activity [ 16 ]. Though previous mechanism studies confirmed that A2451 can either activate the proton donor function of the 2′-OH of A76 or stabilize the transition state via hydrogen bonding with A76, it is thought to play only a single role as a hydrogen bond donor in the reaction [ 11 , 21 , 22 , 23 ]. However, our results show that the 2′-OH of A2451 indeed serves as both the proton donor and acceptor to shuttle the proton between 2′-OH of A76 and W1.…”

Section: Resultsmentioning

confidence: 99%

“…In addition to W3 located between 2′ and 3′ hydroxyls of A76, a second water molecule (W2) is seen between N of A2602 and 2′ hydroxyl of U2584 in the structure of the Haloarcula marismortui (Hma) 50S complexed with substrate analogs [ 2 , 10 ]. Computational mechanism study identified that W2 stabilizes the oxyanion in the transition state via extensive hydrogen bond network centered around this water molecule [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…Previous studies of the ribosome have emphasized the importance of water, which mediates in proton transfer in peptide formation reaction [ 11 , 13 , 14 ]. QM/MM (Quantum Mechanics/Molecular Mechanics) simulation performed by Świderek et al confirmed that a W3-mediated eight-membered ring transition state experiences an energy barrier of 27.60 kcal·mol −1 , significantly lower than 33.90 kcal·mol −1 of the six-membered ring proton shuttle mechanism, in which no water is involved [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study

et al. 2017

View full text Add to dashboard Cite

In this work, we have investigated a novel distal proton shuttle mechanism of ribosome catalyzed peptide bond formation reaction. The reaction was found to follow a two-step mechanism. A distal water molecule located about 6.1 Å away from the attacking amine plays as a proton acceptor and results in a charge-separated intermediate that is stabilized by the N terminus of L27 and the A-site A76 5′-phosphate. The ribose A2451 bridges the proton shuttle pathway, thus plays critical role in the reaction. The calculated 27.64 kcal·mol−1 free energy barrier of the distal proton shuttle mechanism is lower than that of eight-membered ring transition state. The distal proton shuttle mechanism studied in this work can provide new insights into the important biological peptide synthesis process.

show abstract