Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase

  1. Xiakun Chu
  2. Zucai Suo
  3. Jin Wang  Is a corresponding author
  1. Stony Brook University, United States
  2. Florida State University, United States

Abstract

The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to "U-shaped' folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4-DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.

Data availability

The necessary files for setting up Gromacs (version 4.5.7 with PLUMED version 2.5.0) simulations and analysis programs/scripts are publicly available at https://osf.io/qu5ve/.

The following data sets were generated

Article and author information

Author details

  1. Xiakun Chu

    Chemistry, Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3166-7070
  2. Zucai Suo

    Department of Biomedical Sciences, Florida State University, Tallahassee, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3871-3420
  3. Jin Wang

    Chemistry, Stony Brook University, Stony Brook, United States
    For correspondence
    jin.wang.1@stonybrook.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2841-4913

Funding

National Institute of General Medical Sciences (R01GM124177)

  • Zucai Suo
  • Jin Wang

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Yibing Shan, DE Shaw Research, United States

Publication history

  1. Received: June 26, 2020
  2. Accepted: October 16, 2020
  3. Accepted Manuscript published: October 20, 2020 (version 1)
  4. Version of Record published: November 4, 2020 (version 2)

Copyright

© 2020, Chu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Xiakun Chu
  2. Zucai Suo
  3. Jin Wang
(2020)
Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase
eLife 9:e60434.
https://doi.org/10.7554/eLife.60434

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