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Evolutionary Modes in Protein Observable Space: The Case of Thioredoxins

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Abstract

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.

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Acknowledgements

This work was partially funded by Sapienza, University of Rome (Progetto di Ateneo 2017). The authors gratefully acknowledge NVIDIA and CINECA for computational support.

Author information

Correspondence to Andrea Amadei or Marco D’Abramo.

Additional information

Handling Editor: Aaron Goldman.

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Del Galdo, S., Alba, J., Amadei, A. et al. Evolutionary Modes in Protein Observable Space: The Case of Thioredoxins. J Mol Evol 87, 175–183 (2019). https://doi.org/10.1007/s00239-019-09894-4

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Keywords

  • Protein evolution
  • Protein dynamics
  • Thioredoxin
  • Essential motions
  • Molecular dynamics