title: Active and passive mechanisms of helicases.
abstract: In this work, we discuss the active or passive character of helicases. In the past years, several studies have used the theoretical framework proposed by Betterton and Julicher [Betterton, M.D. and Julicher, F. (2005) Opening of nucleic-acid double strands by helicases: active versus passive opening. Phys. Rev. E, 71, 11904-11911.] to analyse the unwinding data and assess the mechanism of the helicase under study (active versus passive). However, this procedure has given rise to apparently contradictory interpretations: helicases exhibiting similar behaviour have been classified as both active and passive enzymes [Johnson, D.S., Bai, L. Smith, B.Y., Patel, S.S. and Wang, M.D. (2007) Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell, 129, 1299-1309; Lionnet, T., Spiering, M.M., Benkovic, S.J., Bensimon, D. and Croquette, V. (2007) Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism Proc. Natl Acid. Sci., 104, 19790-19795]. In this work, we show that when the helicase under study has not been previously well characterized (namely, if its step size and rate of slippage are unknown) a multi-parameter fit to the afore-mentioned model can indeed lead to contradictory interpretations. We thus propose to differentiate between active and passive helicases on the basis of the comparison between their observed translocation velocity on single-stranded nucleic acid and their unwinding rate of double-stranded nucleic acid (with various GC content and under different tensions). A threshold separating active from passive behaviour is proposed following an analysis of the reported activities of different helicases. We study and contrast the mechanism of two helicases that exemplify these two behaviours: active for the RecQ helicase and passive for the gp41 helicase.
authors.affiliation: Laboratoire de Physique Statistique, Ecole Normale Superieure, UPMC Univ Paris 06, Universit Paris Diderot, CNRS, 24 rue Lhomond, 75005 Paris, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Manosas
authors.forename: Xu Guang
authors.initials: XG
authors.lastname: Xi
authors.forename: David
authors.initials: D
authors.lastname: Bensimon
authors.forename: Vincent
authors.initials: V
authors.lastname: Croquette
mesh_terms: D055162:Biocatalysis; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004265:DNA Helicases / Q000378:metabolism*; D008954:Models, Biological; D053484:RecQ Helicases / Q000378:metabolism*; D014764:Viral Proteins / Q000378:metabolism*
chemical_list: D014764:Viral Proteins; C063983:gene 41 protein, Enterobacteria phage T4; D004247:DNA; C506724:RecQ protein, E coli; D004265:DNA Helicases; D053484:RecQ Helicases