Abstract
Type II DNA topoisomerases can catalyze the transport of one DNA segment through a transient break in another DNA segment by a complex mechanism of ATP hydrolysis. According to the hydrolysis process of two ATPs, a multi-state model is proposed to investigate the work cycle of DNA topoisomerase II. The rate of the opening and closing of the DNA topoisomerase gate is evaluated by determining the release rate of inorganic phosphates. The calculated results show that, under the condition of the high concentration of ATP, the work cycle of DNA topoisomerase II is about 0.84 s which is in agreement with the experimental data.
References
Baird CL, Harkins TT, Morris SK, Lindsley JE (1999) Topoisomerase II drives DNA transport by hydrolyzing one ATP. Proc Natl Acad Sci USA 96:13685–13690
Baird CL, Gordon MS, Andrenyak DM, Marecek JF, Lindsley JE (2001) The ATPase reaction cycle of yeast DNA topoisomerase II. Slow rates of ATP resynthesis and P(i) release. J Biol Chem 276:27893–27898
Bates AD, Maxwell A (2007) Energy coupling in type II topoisomerases: why do they hydrolyze ATP? Biochemistry 46:7929–7941
Collins TR, Hammes GG, Hsieh TS (2009) Analysis of the eukaryotic topoisomerase II DNA gate: a single-molecule FRET and structural perspective. Nucleic Acids Res 37:712–720
Ding H, Luo LF (2009) Kinetic model of the lysogeny/lysis switch of phage λ. Chin Phys Lett 26:098701
Guo WS, Luo LF, Li QZ (2002) A chemical kinetic theory on muscle contraction and spontaneous oscillation. Chem Phys Lett 363:471–478
Harkins TT, Lindsley JE (1998) Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 1. A DNA-dependent burst in ATP hydrolysis. Biochemistry 37:7292–7298
Harkins TT, Lewis TJ, Lindsley JE (1998) Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 2. Kinetic mechanism for the sequential hydrolysis of two ATP. Biochemistry 37:7299–7312
Holm C (1994) Coming undone: how to untangle a chromosome. Cell 77:955–957
Lindsley JE, Wang JC (1993) On the coupling between ATP usage and DNA transport by yeast DNA topoisomerase II. J Biol Chem 268:8096–8104
Maxwell A (1997) DNA gyrase as a drug target. Trends Microbiol 5:102–109
Miller KG, Liu LF, Englund PT (1981) A homogeneous type II DNA topoisomerase from HeLa cell nuclei. J Biol Chem 256: 9334–9339
Morris SK, Baird CL, Lindsley JE (2000) Steady-state and rapid kinetic analysis of topoisomerase II trapped as the closed-clamp intermediate by ICRF-193. J Biol Chem 275:2613–2618
Mueller-Planitz F, Herschlag D (2008) Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: a unifying kinetic and structural mechanism. J Biol Chem 283:17463–17476
Roca J (2009) Topoisomerase II: a fitted mechanism for the chromatin landscape. Nucleic Acids Res 37:721–730
Smiley RD, Collins TR, Hammes GG, Hsieh TS (2007) Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II. Proc Natl Acad Sci USA 104:4840–4845
Xie P (2010) Dynamics of strand passage catalyzed by topoisomerase II. Eur Biophys J 39:1251–1259
Acknowledgments
Supported by the National Natural Science Foundation of China (Grant No. 11047180 and 20973034), the Fundamental Research Funds for the Central Universities (ZYGX2009J081) and Scientific Research Startup Foundation of UESTC.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Ding, H., Lin, H. & Feng, J. The rate of opening and closing of the DNA gate for topoisomerase II. Theory Biosci. 132, 61–64 (2013). https://doi.org/10.1007/s12064-012-0163-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12064-012-0163-2