Department of Chemical Science and Technology, University of Roma Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy.
Department of Chemistry, Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy.
J Mol Evol. 2019 Jul;87(4-6):175-183. doi: 10.1007/s00239-019-09894-4. Epub 2019 May 25.
In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from the crystallographic structures, we performed all-atom molecular dynamics simulations and compare the trajectories in terms of structural and dynamical properties. Interestingly, the structural properties related to the protein density (i.e. the number of residues divided by the excluded molecular volume) well describe the protein evolutionary behaviour. Our results also suggest that the changes in sequence as occurred during the evolution have affected the protein essential motions, allowing us to discriminate between ancient and extant proteins in terms of their dynamical behaviour. Such results are yet more evident when the bacterial, archaeal and eukaryotic thioredoxins are separately analysed.
在本文中，我们研究了一组由三种现存形式和七种实验室复活形式组成的十种硫氧还蛋白蛋白的结构和动力学演化行为。从晶体结构出发，我们进行了全原子分子动力学模拟，并根据结构和动力学特性对轨迹进行了比较。有趣的是，与蛋白质密度相关的结构特性（即残基数除以排除的分子体积）很好地描述了蛋白质的进化行为。我们的结果还表明，在进化过程中发生的序列变化影响了蛋白质的基本运动，使我们能够根据其动力学行为区分古老和现存的蛋白质。当分别分析细菌、古细菌和真核硫氧还蛋白时，这种结果更加明显。
