Mechanistic alternatives for peptide bond formation on the ribosome.
Mechanistic alternatives for peptide bond formation on the ribosome.
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DOI：
10.1093/nar/gky367
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发表时间：
2018-06-20
影响因子：
14.9
通讯作者：
Åqvist J
中科院分区：
文献类型：
--
作者：
Kazemi M;Socan J;Himo F;Åqvist J
核糖体大亚基上的肽基转移反应依赖于胺亲核试剂的质子化状态，并表现出较大的动力学溶剂同位素效应（KSIE 108）。与此相反，相关的肽基-tRNA的水解反应参与终止显示KSIE为10.4和pH值-速率曲线指示碱催化。然而，目前还不清楚为什么这些反应应该进行不同的机制，实验数据表明。一种解释是两种竞争机制可能在肽基转移酶中心（PTC）中起作用。在此，我们通过重新研究先前提出的质子穿梭机制和测试一般碱催化也用于肽键形成的可行性来探索这种可能性。我们采用了活性中心的大簇模型，并通过密度泛函理论计算评估了不同的反应机理。在这些计算中，质子穿梭和一般的基础机制都产生的活化能与实验值。然而，只有质子穿梭机制被发现是与实验观察到的pH速率曲线和KSIE一致。这表明PTC促进了肽键形成的质子穿梭机制，同时禁止了一般碱催化，尽管排除一般碱催化的详细机制仍不清楚。
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.
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影响因子：
15
作者：
Åstrom, H;Limén, E;Strömberg, R
通讯作者：
Strömberg, R
影响因子：
16
作者：
Johansson, Magnus;Bouakaz, Elli;Ehrenberg, Mans
通讯作者：
Ehrenberg, Mans
影响因子：
--
作者：
Kingery, David A.;Pfund, Emmanuel;Strobel, Scott A.
通讯作者：
Strobel, Scott A.
DOI：
10.1073/pnas.171319598
发表时间：
2001-08-28
影响因子：
11.1
作者：
Bayfield, MA;Dahlberg, AE;Barta, A
通讯作者：
Barta, A
DOI：
10.1073/pnas.172404099
发表时间：
2002-09-03
影响因子：
11.1
作者：
Hansen, JL;Schmeing, TM;Steitz, TA
通讯作者：
Steitz, TA