Radhakrishnan Ravi
Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Biophys J. 2007 Oct 1;93(7):2391-9. doi: 10.1529/biophysj.107.104661. Epub 2007 Jun 1.
By employing classical molecular dynamics, correlation analysis of coupling between slow and fast dynamical modes, and free energy (umbrella) sampling using classical as well as mixed quantum mechanics molecular mechanics force fields, we uncover a possible pathway for phosphoryl transfer in the self-cleaving reaction of the minimal hammerhead ribozyme. The significance of this pathway is that it initiates from the minimal hammerhead crystal structure and describes the reaction landscape as a conformational rearrangement followed by a covalent transformation. The delineated mechanism is catalyzed by two metal (Mg(2+)) ions, proceeds via an in-line-attack by CYT 17 O2' on the scissile phosphorous (ADE 1.1 P), and is therefore consistent with the experimentally observed inversion configuration. According to the delineated mechanism, the coupling between slow modes involving the hammerhead backbone with fast modes in the cleavage site appears to be crucial for setting up the in-line nucleophilic attack.
通过运用经典分子动力学、慢动力学模式与快动力学模式之间耦合的相关分析以及使用经典和混合量子力学分子力学力场的自由能（伞形）采样，我们揭示了最小锤头状核酶自切割反应中磷酰基转移的一条可能途径。该途径的重要意义在于它起始于最小锤头状晶体结构，并将反应图景描述为构象重排后伴随共价转化。所描绘的机制由两个金属（Mg(2+)）离子催化，通过CYT 17 O2'对可切割磷（ADE 1.1 P）的内攻击进行，因此与实验观察到的构型翻转一致。根据所描绘的机制，涉及锤头状主链的慢模式与切割位点的快模式之间的耦合对于建立内亲核攻击似乎至关重要。
