Lim Shion A, Hart Kathryn M, Harms Michael J, Marqusee Susan
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720.
Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):13045-13050. doi: 10.1073/pnas.1611781113. Epub 2016 Oct 31.
Proper folding of proteins is critical to producing the biological machinery essential for cellular function. The rates and energetics of a protein's folding process, which is described by its energy landscape, are encoded in the amino acid sequence. Over the course of evolution, this landscape must be maintained such that the protein folds and remains folded over a biologically relevant time scale. How exactly a protein's energy landscape is maintained or altered throughout evolution is unclear. To study how a protein's energy landscape changed over time, we characterized the folding trajectories of ancestral proteins of the ribonuclease H (RNase H) family using ancestral sequence reconstruction to access the evolutionary history between RNases H from mesophilic and thermophilic bacteria. We found that despite large sequence divergence, the overall folding pathway is conserved over billions of years of evolution. There are robust trends in the rates of protein folding and unfolding; both modern RNases H evolved to be more kinetically stable than their most recent common ancestor. Finally, our study demonstrates how a partially folded intermediate provides a readily adaptable folding landscape by allowing the independent tuning of kinetics and thermodynamics.
蛋白质的正确折叠对于产生细胞功能所必需的生物机制至关重要。蛋白质折叠过程的速率和能量学由其能量景观描述，这些信息编码在氨基酸序列中。在进化过程中，必须维持这种景观，以使蛋白质在生物学相关的时间尺度上折叠并保持折叠状态。目前尚不清楚蛋白质的能量景观在整个进化过程中究竟是如何维持或改变的。为了研究蛋白质的能量景观如何随时间变化，我们利用祖先序列重建来获取嗜温菌和嗜热菌核糖核酸酶H（RNase H）之间的进化历史，从而对RNase H家族祖先蛋白质的折叠轨迹进行了表征。我们发现，尽管序列差异很大，但在数十亿年的进化过程中，整体折叠途径是保守的。蛋白质折叠和展开的速率存在明显趋势；两种现代RNase H进化得比它们最近的共同祖先在动力学上更稳定。最后，我们的研究表明，部分折叠的中间体如何通过允许独立调节动力学和热力学来提供一个易于适应的折叠景观。
