Dynamics of strand passage catalyzed by topoisomerase II.

European Biophysics Journal : EBJ
Ping Xie

Abstract

DNA topoisomerase II is a homodimeric molecular machine that uses ATP hydrolysis to untangle DNA by passing one double-stranded DNA duplex (T-segment) through another double-stranded duplex (G-segment). However, despite extensive studies, the dynamics of ATP-dependent T-transport is still not very clear. Here, based on the proposal that transport of the T-segment through the transiently cleaved G-segment and the opened C-gate of the enzyme is via a free diffusion mechanism, the dynamics of T-transport are studied theoretically. Our results show that, to complete passage of the strand with nearly 100% efficiency, the C-gate is required to open by a width that is only slightly larger than the width of DNA duplex and for a time shorter than 100 micros in the presence of several k (B) T binding affinities of the T-segment for the B' domains. The results are implied by our understanding of the opening and closing dynamics of the C-gate. Moreover, the dependence of chemomechanical coupling efficiency on degrees of DNA supercoiling by gyrases can also be explained by using our results. On the basis of these theoretical results and previous experimental data, a modified two-gate model for chemomechanical coupling of the topoisomerase I...Continue Reading

References

Jan 18, 1996·Nature·J M BergerJ C Wang
Apr 30, 1996·Proceedings of the National Academy of Sciences of the United States of America·J RocaJ C Wang
Feb 1, 1996·Current Opinion in Structural Biology·J M Berger, J C Wang
Jan 1, 1996·Annual Review of Biochemistry·J C Wang
Aug 28, 1997·Nature·J H Morais CabralR C Liddington
Apr 9, 1998·Biophysical Journal·C H WigginsR E Goldstein
Sep 28, 1998·Biochimica Et Biophysica Acta·D A Burden, N Osheroff
Jul 27, 1999·The Journal of Biological Chemistry·S Olland, J C Wang
Nov 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·C L BairdJ E Lindsley
Jun 8, 2001·Annual Review of Biochemistry·J J Champoux
Feb 19, 2002·The Journal of Biological Chemistry·Valérie LamourDino Moras
Dec 14, 2002·The Journal of Biological Chemistry·Camilla SkouboeAnni H Andersen
Sep 10, 2003·Proceedings of the National Academy of Sciences of the United States of America·Scott ClassenJames M Berger
May 14, 2004·Annual Review of Biophysics and Biomolecular Structure·Kevin D Corbett, James M Berger
Jan 14, 2005·The Journal of Biological Chemistry·Jerrylaine VaughnJohn L Nitiss
Aug 16, 2005·The Journal of Biological Chemistry·Hua WeiGregory L Verdine
Oct 26, 2005·Biochemical Society Transactions·A J Schoeffler, J M Berger
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·R Derike SmileyTao-Shih Hsieh
Jun 22, 2007·Biochemistry·Andrew D Bates, Anthony Maxwell
Nov 3, 2007·Biochimica Et Biophysica Acta·Ping XiePeng-Ye Wang
Apr 12, 2008·The Journal of Biological Chemistry·Felix Mueller-Planitz, Daniel Herschlag
May 27, 2008·Biochimica Et Biophysica Acta·Ping Xie
Dec 9, 2008·Nucleic Acids Research·Joaquim Roca

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Citations

Aug 15, 2012·Theory in Biosciences = Theorie in Den Biowissenschaften·Hui DingJuan Feng

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