Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala 75124, Sweden.
Nucleic Acids Res. 2018 Feb 16;46(3):1362-1374. doi: 10.1093/nar/gkx1256.
We studied the effects of aminoglycosides and changing Mg2+ ion concentration on the accuracy of initial codon selection by aminoacyl-tRNA in ternary complex with elongation factor Tu and GTP (T3) on mRNA programmed ribosomes. Aminoglycosides decrease the accuracy by changing the equilibrium constants of 'monitoring bases' A1492, A1493 and G530 in 16S rRNA in favor of their 'activated' state by large, aminoglycoside-specific factors, which are the same for cognate and near-cognate codons. Increasing Mg2+ concentration decreases the accuracy by slowing dissociation of T3 from its initial codon- and aminoglycoside-independent binding state on the ribosome. The distinct accuracy-corrupting mechanisms for aminoglycosides and Mg2+ ions prompted us to re-interpret previous biochemical experiments and functional implications of existing high resolution ribosome structures. We estimate the upper thermodynamic limit to the accuracy, the 'intrinsic selectivity' of the ribosome. We conclude that aminoglycosides do not alter the intrinsic selectivity but reduce the fraction of it that is expressed as the accuracy of initial selection. We suggest that induced fit increases the accuracy and speed of codon reading at unaltered intrinsic selectivity of the ribosome.
我们研究了氨基糖苷类药物和改变 Mg2+ 离子浓度对氨酰-tRNA 在与延伸因子 Tu 和 GTP（T3）形成的三元复合物中与 mRNA 编程核糖体结合时初始密码子选择准确性的影响。氨基糖苷类药物通过改变 16S rRNA 中“监测碱基”A1492、A1493 和 G530 的平衡常数，有利于它们在大的、氨基糖苷类特异性因素的“激活”状态，对于同源和近同源密码子都是如此。增加 Mg2+ 浓度会降低准确性，因为 T3 从其在核糖体上的初始密码子和氨基糖苷类独立结合状态的解离速度减慢。氨基糖苷类药物和 Mg2+ 离子的不同准确性破坏机制促使我们重新解释以前的生化实验和现有高分辨率核糖体结构的功能意义。我们估计了准确性的热力学上限，即核糖体的“固有选择性”。我们得出结论，氨基糖苷类药物不会改变固有选择性，但会降低其作为初始选择准确性的表达比例。我们建议诱导契合增加了密码子阅读的准确性和速度，而核糖体的固有选择性不变。
