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Alonso-Sarduy L, De Los Rios P, Benedetti F, Vobornik D, Dietler G, Kasas S, Longo G. Real-time monitoring of protein conformational changes using a nano-mechanical sensor. PLoS One 2014; 9:e103674. [PMID: 25077809 PMCID: PMC4117498 DOI: 10.1371/journal.pone.0103674] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/01/2014] [Indexed: 11/24/2022] Open
Abstract
Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center stage in protein research. As an example, Topoisomerases are particularly interesting enzymes capable of managing tangled and supercoiled double-stranded DNA, thus facilitating many physiological processes. In this work, we describe the use of a cantilever-based nanomotion sensor to characterize the dynamics of human topoisomerase II (Topo II) enzymes and their response to different kinds of ligands, such as ATP, which enhance the conformational dynamics. The sensitivity and time resolution of this sensor allow determining quantitatively the correlation between the ATP concentration and the rate of Topo II conformational changes. Furthermore, we show how to rationalize the experimental results in a comprehensive model that takes into account both the physics of the cantilever and the dynamics of the ATPase cycle of the enzyme, shedding light on the kinetics of the process. Finally, we study the effect of aclarubicin, an anticancer drug, demonstrating that it affects directly the Topo II molecule inhibiting its conformational changes. These results pave the way to a new way of studying the intrinsic dynamics of proteins and of protein complexes allowing new applications ranging from fundamental proteomics to drug discovery and development and possibly to clinical practice.
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Affiliation(s)
- Livan Alonso-Sarduy
- Laboratory of Physics of Living Matter, Institute of Physics of Biological Systems, School of Basic Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Paolo De Los Rios
- Laboratory of Statistical Biophysics, Institute of Theoretical Physics, School of Basic Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Laboratory of Physics of Living Matter, Institute of Physics of Biological Systems, School of Basic Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Dusan Vobornik
- Laboratory of Physics of Living Matter, Institute of Physics of Biological Systems, School of Basic Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, Institute of Physics of Biological Systems, School of Basic Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Sandor Kasas
- Laboratory of Physics of Living Matter, Institute of Physics of Biological Systems, School of Basic Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
- Faculty of Biology and Medicine, Department of Fundamental Neurosciences, Lausanne University, Lausanne, Switzerland
| | - Giovanni Longo
- Laboratory of Physics of Living Matter, Institute of Physics of Biological Systems, School of Basic Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
- Istituto Superiore di Sanità, Rome, Italy
- * E-mail:
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Zhang Z, Liu Y, Xie P, Li W, Dou S, Wang P. Studying the interaction between gyrase and DNA using magnetic tweezers. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ding H, Lin H, Feng J. The rate of opening and closing of the DNA gate for topoisomerase II. Theory Biosci 2012; 132:61-4. [PMID: 22890500 DOI: 10.1007/s12064-012-0163-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 07/25/2012] [Indexed: 11/30/2022]
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.
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Affiliation(s)
- Hui Ding
- Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
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Bailly C. Contemporary challenges in the design of topoisomerase II inhibitors for cancer chemotherapy. Chem Rev 2012; 112:3611-40. [PMID: 22397403 DOI: 10.1021/cr200325f] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Christian Bailly
- Centre de Recherche et Développement, Institut de Recherche Pierre Fabre, Toulouse, France.
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