Abstract.
Three recently observed facts of the translocation of actual hexameric and nonstructural (NS) helicases are related to the various physical quantities and are in accordance with the recently proposed mechanical mechanism: a) the translocation of hexameric helicases might be led by either the N-terminal domain (NTD) or C-terminal domain (CTD) depending on which domain has a smaller central pore, b) the translocation speed (vt) of the ring-shaped helicases and NS helicases decreased with decreasing applied tension, and c) a large difference in the vt of the NS helicase was observed for the helicase translocating on DNA and RNA. These findings are the effects of the physical quantities of the helicase/nuclei acid strands on the translocation of helicases and are difficult to explain with biochemical models. We predict that a similar behavior as described in b) and c) is also shown by hexameric helicases. The validity of the mechanical mechanism is demonstrated in simulation experiments.
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M.R. Singleton, M.S. Dillingham, D.B. Wigley, Annu. Rev. Biochem. 76, 23 (2007)
J.L. Kim, K.A. Morgenstern, J.P. Griffith, M.D. Dwyer, J.A. Thomson, M.A. Murcko, C. Lin, P.R. Caron, Structure 6, 89 (1998)
H.S. Subramanya, L.E. Bird, J.A. Brannigan, D.B. Wigley, Nature 384, 379 (1996)
N. Yao, T. Hesson, M. Cable, Z. Hong, A.D. Kwong, H.V. Le, P.C. Weber, Nat. Struct. Biol. 4, 463 (1997)
M.K. Levin, M. Gurjar, S.S. Patel, Nat. Struct. Mol. Biol. 12, 429 (2005)
S. Korolev, J. Hseih, G.H. Gauss, T.M. Lohman, G. Waksman, Cell 90, 636 (1997)
A. Chakraborty, D. Wang, Y.W. Ebright, Y. Korlann, E. Kortkhonjia, T. Kim, S. Chowdhury, S. Wigneshweraraj, H. Irschik, R. Jansen, B.T. Nixon, J. Knight, S. Weiss, R. Ebright, Science 337, 591 (2012)
M.E. O’Donnell, H. Li, Nat. Struct. Mol. Biol. 25, 122 (2018)
C.-T. Lin, F. Tritschler, K.S. Lee, M. Gu, C.M. Rice, T. Ha, Protein Sci. 26, 1391 (2017)
E.J. Enemark, L. Joshua-Tor, Nature 442, 270 (2006)
P. Guo, Z. Zhao, J. Haak, S. Wang, D. Wu, B. Meng, T. Weitao, Biotechn. Adv. 32, 853 (2014)
M.E. Douglas, F.A. Ali, A. Costa, J.F.X. Diffley, Nature 555, 265 (2018)
N.D. Thomsen, J.M. Berger, Cell 139, 523 (2009)
D.S. Johnson, L. Bai, B.Y. Smith, S.S. Patel, M.D. Wang, Cell 129, 1299 (2007)
A. Wolfe, K. Phipps, T. Weitao, Cell Biosci. 4, 31 (2014)
Y.C. Chou, J. Phys. D 51, 135401 (2018)
R. Georgescu, Z. Yuan, L. Bai, R. de Luna Almeida Santos, J. Sun, D. Zhang, O. Yurieva, H. Li, M.E. O’Donnell, Proc. Natl. Acad. Sci. U.S.A. 114, E697 (2017)
O. Itsathitphaisarn, R.A. Wing, W.K. Eliason, J. Wang, T.A. Steitz, Cell 151, 267 (2012)
E.A. Toth, Y. Li, M.R. Sawaya, Y. Cheng, T. Ellenberger, Cell 12, 1113 (2003)
P.M. Matias, S. Gorynia, P. Donner, M.A. Carrondo, J. Biol. Chem. 281, 38918 (2006)
T.H. Massey, C.P. Mercogliano, J. Yates, D.J. Sherratt, J. Lowe, Mol. Cell 23, 457 (2006)
M. Manosas, X.G. Xi, D. Bensimon, V. Crowuette, Nucl. Acids Res. 38, 5518 (2010)
P. Xie, Biophys. Chem. 211, 49 (2016)
S.S. Patel, I. Donmez, J. Biol. Chem. 281, 18265 (2006)
A.Y. Grosberg, A.R. Khokhlov, Statistical Physics of Macromolecules (American Institute of Physics, 1994)
H. Chen, S.P. Meisburger, S.A. Pabit, J.L. Sutton, W.W. Webb, L. Pollack, Proc. Natl. Acad. Sci. U.S.A. 109, 799 (2012)
L.A. Amos, D. Schliper, Advances in Protein Chemistry, Vol. 71 (Elsevier Academic Press, 2005) p. 257
T. Fujii, A.H. Iwane, T. Yanahida, K. Namba, Nature 467, 724 (2010)
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Chou, Y.C. Mechanical mechanism for the translocation of hexameric and nonstructural helicases: Dependence on physical parameters. Eur. Phys. J. E 43, 21 (2020). https://doi.org/10.1140/epje/i2020-11944-1
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DOI: https://doi.org/10.1140/epje/i2020-11944-1