Browse by author
Lookup NU author(s): Dr Kevin WhitleyORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
UvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. Previous estimates of its step size have been indirect, and a consensus on its stepping mechanism is lacking. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hexameric helicases.
Author(s): Carney SP, Ma W, Whitley KD, Jia H, Lohman TM, Luthey-Schulten Z, Chemla YR
Publication type: Article
Publication status: Published
Journal: Nature Communications
Year: 2021
Volume: 12
Online publication date: 01/12/2021
Acceptance date: 08/11/2021
Date deposited: 20/02/2025
ISSN (electronic): 2041-1723
Publisher: Springer Nature
URL: https://doi.org/10.1038/s41467-021-27304-6
DOI: 10.1038/s41467-021-27304-6
Data Access Statement: A reporting summary for this article is available as a Supplementary Information file. Source data are provided with this paper. The source data for Figs. 1–4 and Supplementary Figs. 1–10 are also available in the Illinois Data Bank repository at: https://doi.org/10.13012/B2IDB-5556865_V1. Intermediate structures from the simulations (Fig. 3b), as well as essential input and setup files needed to run the REST2 simulations in NAMD are provided in Supplementary Data 1. The structure deposited with PDB accession code 2IS2 was used to build the initial structure of the UvrD complex. The PDB accession codes for the other helicase structures aligned to that of UvrD are as follows: 1UAA (Rep), 3PJR (PcrA), 5LD2 (RecBCD), 1OYW (RecQ), 1A1V (NS3). Any other raw or processed data supporting the findings of this study are available from the corresponding author upon reasonable request. Source data are provided with this paper.
Altmetrics provided by Altmetric
