Torres R A, Bruice T C
Department of Chemistry, University of California, Santa Barbara, CA 93106, USA.
Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11077-82. doi: 10.1073/pnas.95.19.11077.
We have performed molecular dynamics (MD) calculations by using one of the recently solved crystal structures of a hammerhead ribozyme. By rotating the alpha, beta, gamma, delta, epsilon, and zeta torsion angles of the phosphate linkage of residue 17, the nucleobase at the cleavage site was slightly rotated out of the active site toward the solution. Unconstrained MD simulations exceeding 1 ns were performed on this starting structure solvated in water with explicit counter ions and two Mg2+ ions at the active site. Our results reveal that near attack conformations consistently were formed in the simulation. These near attack conformations are characterized by assumption of the 2'-hydroxyl to a near in-line position for attack on the -O-(PO2-)-O- phosphorous. Also during the time course of the MD study, one Mg2+ moved immediately to associate with a pro-R phosphate oxygen in the conserved core region, and the second Mg2+ remained associated with the pro-R oxygen on the phosphate linkage undergoing hydrolysis. These results are in accord with a one-metal ion mechanism of catalysis and give insight into the possible roles of many of the conserved residues in the ribozyme.
我们利用最近解析出的一种锤头状核酶晶体结构进行了分子动力学（MD）计算。通过旋转17号残基磷酸键的α、β、γ、δ、ε和ζ扭转角，切割位点处的核碱基稍微从活性位点转出，朝向溶液。对该起始结构在水中进行了超过1纳秒的无约束MD模拟，其中含有明确的抗衡离子，且活性位点处有两个Mg2+离子。我们的结果表明，在模拟中始终会形成接近攻击的构象。这些接近攻击的构象的特征是2'-羟基处于接近直线的位置，以便对-O-(PO2-)-O-磷进行攻击。同样在MD研究的时间进程中，一个Mg2+立即移动并与保守核心区域中的前-R磷酸氧结合，第二个Mg2+则仍与正在水解的磷酸键上的前-R氧结合。这些结果与单金属离子催化机制相符，并深入了解了核酶中许多保守残基可能发挥的作用。
