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Binding of the peptide deformylase on the ribosome surface modulates the structure and dynamics of the exit tunnel interior

Hugo McGrath, Michaela Černeková, View ORCID ProfileMichal H. Kolář
doi: https://doi.org/10.1101/2022.04.20.488877
Hugo McGrath
Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
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Michaela Černeková
Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
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Michal H. Kolář
Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
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  • ORCID record for Michal H. Kolář
  • For correspondence: michal@mhko.science
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Abstract

Proteosynthesis on ribosomes is regulated at many levels. Conformational changes of the ribosome, possibly induced by external factors, may transfer over large distances and contribute to the regulation. The molecular principles of this long-distance allostery within the ribosome remain poorly understood. Here, we use structural analysis and atomistic molecular dynamics simulations to investigate peptide deformylase (PDF), an enzyme that binds to the ribosome surface near the ribosomal protein uL22 during translation and chemically modifies the emerging nascent peptide. Our simulations of the entire ribosome–PDF complex reveal that the PDF undergoes a swaying motion on the ribosome surface at the sub-microsecond time scale. We show that the PDF affects the conformational dynamics of parts of the ribosome over distances of more than 5 nm. Using a supervised-learning algorithm we demonstrate that the exit tunnel is influenced by the presence or absence of PDF. Our findings suggest a possible effect of the PDF on the nascent peptide translocation through the ribosome exit tunnel.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Small main text corrections, Fig. 1 update, one extra Supplementary figure.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 26, 2022.
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Binding of the peptide deformylase on the ribosome surface modulates the structure and dynamics of the exit tunnel interior
Hugo McGrath, Michaela Černeková, Michal H. Kolář
bioRxiv 2022.04.20.488877; doi: https://doi.org/10.1101/2022.04.20.488877
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Binding of the peptide deformylase on the ribosome surface modulates the structure and dynamics of the exit tunnel interior
Hugo McGrath, Michaela Černeková, Michal H. Kolář
bioRxiv 2022.04.20.488877; doi: https://doi.org/10.1101/2022.04.20.488877

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