Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
Nat Chem. 2023 Mar;15(3):308-318. doi: 10.1038/s41557-022-01091-z. Epub 2022 Dec 5.
The specific activity of enzymes can be altered over long timescales in cells by synonymous mutations that alter a messenger RNA molecule's sequence but not the encoded protein's primary structure. How this happens at the molecular level is unknown. Here, we use multiscale modelling of three Escherichia coli enzymes (type III chloramphenicol acetyltransferase, D-alanine-D-alanine ligase B and dihydrofolate reductase) to understand experimentally measured changes in specific activity due to synonymous mutations. The modelling involves coarse-grained simulations of protein synthesis and post-translational behaviour, all-atom simulations to test robustness and quantum mechanics/molecular mechanics calculations to characterize enzymatic function. We show that changes in codon translation rates induced by synonymous mutations cause shifts in co-translational and post-translational folding pathways that kinetically partition molecules into subpopulations that very slowly interconvert to the native, functional state. Structurally, these states resemble the native state, with localized misfolding near the active sites of the enzymes. These long-lived states exhibit reduced catalytic activity, as shown by their increased activation energies for the reactions they catalyse.
在细胞中，通过同义突变可以在很长的时间尺度上改变酶的特定活性，而同义突变会改变信使 RNA 分子的序列，但不会改变编码蛋白质的一级结构。这种情况在分子水平上是如何发生的尚不清楚。在这里，我们使用三种大肠杆菌酶（III 型氯霉素乙酰转移酶、D-丙氨酸-D-丙氨酸连接酶 B 和二氢叶酸还原酶）的多尺度建模来理解由于同义突变导致的特定活性的实验测量变化。该建模涉及蛋白质合成和翻译后行为的粗粒模拟、全原子模拟以测试稳健性以及量子力学/分子力学计算以表征酶功能。我们表明，同义突变引起的密码子翻译速率的变化导致共翻译和翻译后折叠途径发生变化，从而在动力学上将分子分成亚群，这些亚群非常缓慢地相互转化为天然的、功能性状态。从结构上看，这些状态类似于天然状态，酶的活性部位附近存在局部错误折叠。这些长寿命状态表现出降低的催化活性，正如它们催化的反应的增加的活化能所表明的那样。
