DnaB Helicase Activity Is Modulated by DNA Geometry and Force

• Published in: Biophysical journal Vol. 99; no. 7; pp. 2170 - 2179
• Main Authors: Ribeck, Noah, Kaplan, Daniel L., Bruck, Irina, Saleh, Omar A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 06-10-2010; Biophysical Society; The Biophysical Society
• Subjects: Base Pairing; Biological Assay; Biomechanical Phenomena - physiology; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - metabolism; DNA Replication; DnaB Helicases - chemistry; DnaB Helicases - metabolism; E coli; Enzyme kinetics; Escherichia coli; Escherichia coli - enzymology; Flexibility; Geometry; Kinetics; Models, Molecular; Nucleic Acid; Nucleic Acid Conformation; Proteins; Replication; Stimulation; Strands; Substrate Specificity; Winding
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2010.07.039

The replicative helicase for
Escherichia coli is DnaB, a hexameric, ring-shaped motor protein that encircles and translocates along ssDNA, unwinding dsDNA in advance of its motion. The microscopic mechanisms of DnaB are unknown; further, prior work has found that DnaB's activity is modified by other replication proteins, indicating some mechanistic flexibility. To investigate these issues, we quantified translocation and unwinding by single DnaB molecules in three tethered DNA geometries held under tension. Our data support the following conclusions: 1), Unwinding by DnaB is enhanced by force-induced destabilization of dsDNA. 2), The magnitude of this stimulation varies with the geometry of the tension applied to the DNA substrate, possibly due to interactions between the helicase and the occluded ssDNA strand. 3), DnaB unwinding and (to a lesser extent) translocation are interrupted by pauses, which are also dependent on force and DNA geometry. 4), DnaB moves slower when a large tension is applied to the helicase-bound strand, indicating that it must perform mechanical work to compact the strand against the applied force. Our results have implications for the molecular mechanisms of translocation and unwinding by DnaB and for the means of modulating DnaB activity.