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Protein-protein docking with large-scale backbone flexibility

View ORCID ProfileMateusz Kurcinski, View ORCID ProfileSebastian Kmiecik, View ORCID ProfileMateusz Zalewski, View ORCID ProfileAndrzej Kolinski
doi: https://doi.org/10.1101/2021.02.22.432196
Mateusz Kurcinski
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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Sebastian Kmiecik
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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  • For correspondence: sebastian.kmiecik@gmail.com
Mateusz Zalewski
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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Andrzej Kolinski
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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Abstract

Structure prediction of protein-protein complexes is one of the most critical challenges in computational structural biology. It is often difficult to predict the complex structure, even for relatively rigid proteins. Modeling significant structural flexibility in protein docking remains an unsolved problem. This work demonstrates a protein-protein docking protocol with enhanced sampling that accounts for large-scale backbone flexibility. The docking protocol starts from unbound x-ray structures and is not using any binding site information. In docking, one protein partner undergoes multiple fold rearrangements, rotations, and translations during docking simulations, while the other protein exhibits small backbone fluctuations. Including significant backbone flexibility during the search for the binding site has been made possible using the CABS coarse-grained protein model and Replica Exchange Monte Carlo dynamics. In our simulations, we obtained acceptable quality models for the set of 12 protein-protein complexes, while for selected cases, models were close to high accuracy.

Competing Interest Statement

The authors have declared no competing interest.

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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-ND 4.0 International license.
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Posted February 23, 2021.
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Protein-protein docking with large-scale backbone flexibility
Mateusz Kurcinski, Sebastian Kmiecik, Mateusz Zalewski, Andrzej Kolinski
bioRxiv 2021.02.22.432196; doi: https://doi.org/10.1101/2021.02.22.432196
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Protein-protein docking with large-scale backbone flexibility
Mateusz Kurcinski, Sebastian Kmiecik, Mateusz Zalewski, Andrzej Kolinski
bioRxiv 2021.02.22.432196; doi: https://doi.org/10.1101/2021.02.22.432196

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