Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase
| Autor: | Haifeng Jia, Yann R. Chemla, Sean P. Carney, Zaida Luthey-Schulten, Timothy M. Lohman, Wen Ma, Kevin D. Whitley |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Optical Tweezers
Base pair Science General Physics and Astronomy DNA Single-Stranded Sequence alignment Molecular Dynamics Simulation General Biochemistry Genetics and Molecular Biology Catalysis Article chemistry.chemical_compound Molecular dynamics Computational biophysics Single-molecule biophysics ATP hydrolysis DNA-binding proteins Escherichia coli A-DNA Multidisciplinary biology Chemistry Escherichia coli Proteins DNA Helicases Helicase General Chemistry Kinetics Optical tweezers biology.protein Biophysics Molecular modelling DNA |
| Zdroj: | Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021) Nature Communications |
| ISSN: | 2041-1723 |
| Popis: | 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. UvrD is a model helicase from the non-hexameric Superfamily 1. Here, the authors use optical tweezers to measure directly the stepwise translocation of UvrD along a DNA hairpin, and propose a mechanism in which UvrD moves one base pair at a time, but sequesters the nascent single strands, releasing them after a variable number of ATP hydrolysis cycles. |
| Databáze: | OpenAIRE |
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