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Journal of Computer-Aided Molecular Design

, Volume 31, Issue 12, pp 1063–1072 | Cite as

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

  • Josephine Alba
  • Maria Jose Marcaida
  • Jesus Prieto
  • Guillermo Montoya
  • Rafael MolinaEmail author
  • Marco D’AbramoEmail author
Article

Abstract

I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.

Keywords

Endonuclease I-DmoI X-ray Molecular dynamics Protein dynamics and activity Electric field 

Notes

Acknowledgements

This work was supported by Ministero dell’Istruzione, Università e Ricerca (R. Levi-Montalcini fellow to M.D.) and by Sapienza, University of Rome (Grant “Ateneo 2015”). We acknowledge CINECA Supercomputing Center, NVIDIA Academic Program, the Dept. of Chemistry for computational resources and the staffs at ALBA and SLS synchrotrons for helping in data collection.

Author contributions

JA performed the Molecular Dynamics simulations; MJM performed the crystallization assays and X-ray data collection; MJM and RM carried out the crystal data processing, model building and refinement; RM, MJM, JP and GM were involved in the crystallographic analysis; J.A. and R.M. prepared the figures; JA and MD analysed the trajectories; RM and MD discussed the data and wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no competing financial interests.

Supplementary material

10822_2017_87_MOESM1_ESM.docx (460 kb)
Supplementary material 1 (DOCX 459 KB)

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Department of ChemistrySapienza University of RomeRomeItaly
  2. 2.Institute of Bioengineering, School of Life SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
  3. 3.Spanish National Cancer CenterMadridSpain
  4. 4.Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
  5. 5.Deparment of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano”CSICMadridSpain

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