1
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Goluguri RR, Ghosh C, Quintong J, Sadqi M, Muñoz V. How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors. Nucleic Acids Res 2024:gkae790. [PMID: 39287129 DOI: 10.1093/nar/gkae790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/22/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Most DNA scanning proteins uniquely recognize their cognate sequence motif and slide on DNA assisted by some sort of clamping interface. The pioneer transcription factors that control cell fate in eukaryotes must forgo both elements to gain access to DNA in naked and chromatin forms; thus, whether or how these factors scan naked DNA is unknown. Here, we use single-molecule techniques to investigate naked DNA scanning by the Engrailed homeodomain (enHD) as paradigm of highly promiscuous recognition and open DNA binding interface. We find that enHD scans naked DNA quite effectively, and about 200000-fold faster than expected for a continuous promiscuous slide. To do so, enHD scans about 675 bp of DNA in 100 ms and then redeploys stochastically to another location 530 bp afar in just 10 ms. During the scanning phase enHD alternates between slow- and medium-paced modes every 3 and 40 ms, respectively. We also find that enHD binds nucleosomes and does so with enhanced affinity relative to naked DNA. Our results demonstrate that pioneer-like transcription factors can in principle do both, target nucleosomes and scan active DNA efficiently. The hybrid scanning mechanism used by enHD appears particularly well suited for the highly complex genomic signals of eukaryotic cells.
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Affiliation(s)
- Rama Reddy Goluguri
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Catherine Ghosh
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Joshua Quintong
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Mourad Sadqi
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Victor Muñoz
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
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2
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Kamagata K, Itoh Y, Tan C, Mano E, Wu Y, Mandali S, Takada S, Johnson RC. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo. Nucleic Acids Res 2021; 49:8642-8664. [PMID: 34352099 PMCID: PMC8421229 DOI: 10.1093/nar/gkab658] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Miyazono KI, Wang D, Ito T, Tanokura M. Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI. Nucleic Acids Res 2020; 48:5106-5118. [PMID: 32232412 PMCID: PMC7229829 DOI: 10.1093/nar/gkaa184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023] Open
Abstract
R.PabI is a restriction DNA glycosylase that recognizes the sequence 5′-GTAC-3′ and hydrolyses the N-glycosidic bond of adenine in the recognition sequence. R.PabI drastically bends and unwinds the recognition sequence of double-stranded DNA (dsDNA) and flips the adenine and guanine bases in the recognition sequence into the catalytic and recognition sites on the protein surface. In this study, we determined the crystal structure of the R.PabI-dsDNA complex in which the dsDNA is drastically bent by the binding of R.PabI but the base pairs are not unwound. This structure is predicted to be important for the indirect readout of the recognition sequence by R.PabI. In the complex structure, wedge loops of the R.PabI dimer are inserted into the minor groove of dsDNA to stabilize the deformed dsDNA structure. A base stacking is distorted between the two wedge-inserted regions. R.PabI is predicted to utilize the distorted base stacking for the detection of the recognition sequence.
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Affiliation(s)
- Ken-Ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo 113-8657, Japan
| | - Delong Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomoko Ito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo 113-8657, Japan
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4
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Kamagata K, Mano E, Ouchi K, Kanbayashi S, Johnson RC. High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins. J Mol Biol 2018; 430:655-667. [PMID: 29307468 DOI: 10.1016/j.jmb.2018.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 01/02/2018] [Indexed: 01/25/2023]
Abstract
Architectural DNA-binding proteins function to regulate diverse DNA reactions and have the defining property of significantly changing DNA conformation. Although the 1D movement along DNA by other types of DNA-binding proteins has been visualized, the mobility of architectural DNA-binding proteins on DNA remains unknown. Here, we applied single-molecule fluorescence imaging on arrays of extended DNA molecules to probe the binding dynamics of three structurally distinct architectural DNA-binding proteins: Nhp6A, HU, and Fis. Each of these proteins was observed to move along DNA, and the salt concentration independence of the 1D diffusion implies sliding with continuous contact to DNA. Nhp6A and HU exhibit a single sliding mode, whereas Fis exhibits two sliding modes. Based on comparison of the diffusion coefficients and sizes of many DNA binding proteins, the architectural proteins are categorized into a new group distinguished by an unusually high free-energy barrier for 1D diffusion. The higher free-energy barrier for 1D diffusion by architectural proteins can be attributed to the large DNA conformational changes that accompany binding and impede rotation-coupled movement along the DNA grooves.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Aoba-ku, Sendai980-8577, Japan.
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Kana Ouchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Aoba-ku, Sendai980-8577, Japan
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA90095-1737, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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5
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Pan H, Bilinovich SM, Kaur P, Riehn R, Wang H, Williams DC. CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level. Nucleic Acids Res 2017. [PMID: 28637186 PMCID: PMC5587734 DOI: 10.1093/nar/gkx548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2. Single-molecule fluorescence tracking on DNA tightropes containing regions with CpG-rich and CpG-free regions reveals that MBD2 carries out unbiased 1D diffusion on CpG-rich DNA but subdiffusion on CpG-free DNA. In contrast, the protein stably and statically binds to methylated CpG (mCpG) regions. The intrinsically disordered region (IDR) on MBD2 both reduces exchange between mCpG sites along the DNA as well as the dissociation from DNA, acting like an anchor that restricts the dynamic mobility of the MBD domain. Unexpectedly, MBD2 binding to methylated CpGs induces DNA bending that is augmented by the IDR region of the protein. These results suggest that MBD2 targets NuRD to unmethylated or methylated CpG islands where its distinct dynamic binding modes help maintain open or closed chromatin, respectively.
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Affiliation(s)
- Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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6
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Kostiuk G, Dikic J, Schwarz FW, Sasnauskas G, Seidel R, Siksnys V. The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA. Nucleic Acids Res 2017; 45:5968-5979. [PMID: 28453854 PMCID: PMC5449598 DOI: 10.1093/nar/gkx294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
Endonucleases that generate DNA double strand breaks often employ two independent subunits such that the active site from each subunit cuts either DNA strand. Restriction enzyme BcnI is a remarkable exception. It binds to the 5΄-CC/SGG-3΄ (where S = C or G, ‘/’ designates the cleavage position) target as a monomer forming an asymmetric complex, where a single catalytic center approaches the scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements have previously shown that the same BcnI molecule cuts both DNA strands at the target site without dissociation from the DNA. Here, we analyse the BcnI DNA binding and target recognition steps at the single molecule level. We find, using FRET, that BcnI adopts either ‘open’ or ‘closed’ conformation in solution. Next, we directly demonstrate that BcnI slides over long distances on DNA using 1D diffusion and show that sliding is accompanied by occasional jumping events, where the enzyme leaves the DNA and rebinds immediately at a distant site. Furthermore, we quantify the dynamics of the BcnI interactions with cognate and non-cognate DNA, and determine the preferred binding orientation of BcnI to the target site. These results provide new insights into the intricate dynamics of BcnI–DNA interactions.
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Affiliation(s)
- Georgij Kostiuk
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Jasmina Dikic
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Friedrich W Schwarz
- BCUBE, Technische Universitaet Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Ralf Seidel
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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7
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Lee SH, Jin C, Cai E, Ge P, Ishitsuka Y, Teng KW, de Thomaz AA, Nall D, Baday M, Jeyifous O, Demonte D, Dundas CM, Park S, Delgado JY, Green WN, Selvin PR. Super-resolution imaging of synaptic and Extra-synaptic AMPA receptors with different-sized fluorescent probes. eLife 2017; 6:27744. [PMID: 28749340 PMCID: PMC5779237 DOI: 10.7554/elife.27744] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile extrasynaptic AMPAR pool. Using super-resolution microscopy, we examined how fluorophore size and photostability affected AMPAR trafficking outside of, and within, post-synaptic densities (PSDs) from rats. Organic fluorescent dyes (≈4 nm), quantum dots, either small (≈10 nm diameter; sQDs) or big (>20 nm; bQDs), were coupled to AMPARs via different-sized linkers. We find that >90% of AMPARs labeled with fluorescent dyes or sQDs were diffusing in confined nanodomains in PSDs, which were stable for 15 min or longer. Less than 10% of sQD-AMPARs were extrasynaptic and highly mobile. In contrast, 5-10% of bQD-AMPARs were in PSDs and 90-95% were extrasynaptic as previously observed. Contrary to the hypothesis that AMPAR entry is limited by the occupancy of open PSD 'slots', our findings suggest that AMPARs rapidly enter stable 'nanodomains' in PSDs with lifetime >15 min, and do not accumulate in extrasynaptic membranes.
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Affiliation(s)
- Sang Hak Lee
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Chaoyi Jin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - En Cai
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Pinghua Ge
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Yuji Ishitsuka
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Kai Wen Teng
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Andre A de Thomaz
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Duncan Nall
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Murat Baday
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Okunola Jeyifous
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Christopher M Dundas
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Sheldon Park
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Jary Y Delgado
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - William N Green
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Paul R Selvin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
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8
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Kamagata K, Murata A, Itoh Y, Takahashi S. Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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9
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Wang D, Miyazono KI, Tanokura M. Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA. Sci Rep 2016; 6:35197. [PMID: 27731370 PMCID: PMC5059719 DOI: 10.1038/srep35197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023] Open
Abstract
R.PabI is a type II restriction enzyme that recognizes the 5′-GTAC-3′ sequence and belongs to the HALFPIPE superfamily. Although most restriction enzymes cleave phosphodiester bonds at specific sites by hydrolysis, R.PabI flips the guanine and adenine bases of the recognition sequence out of the DNA helix and hydrolyzes the N-glycosidic bond of the flipped adenine in a similar manner to DNA glycosylases. In this study, we determined the structure of R.PabI in complex with double-stranded DNA without the R.PabI recognition sequence by X-ray crystallography. The 1.9 Å resolution structure of the complex showed that R.PabI forms a tetrameric structure to sandwich the double-stranded DNA and the tetrameric structure is stabilized by four salt bridges. DNA binding and DNA glycosylase assays of the R.PabI mutants showed that the residues that form the salt bridges (R70 and D71) are essential for R.PabI to find the recognition sequence from the sea of nonspecific sequences. R.PabI is predicted to utilize the tetrameric structure to bind nonspecific double-stranded DNA weakly and slide along it to find the recognition sequence.
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Affiliation(s)
- Delong Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken-Ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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10
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TALE proteins search DNA using a rotationally decoupled mechanism. Nat Chem Biol 2016; 12:831-7. [DOI: 10.1038/nchembio.2152] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/27/2016] [Indexed: 12/27/2022]
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11
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Xiong K, Blainey PC. Molecular sled sequences are common in mammalian proteins. Nucleic Acids Res 2016; 44:2266-73. [PMID: 26857546 PMCID: PMC4797294 DOI: 10.1093/nar/gkw035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/07/2016] [Indexed: 12/13/2022] Open
Abstract
Recent work revealed a new class of molecular machines called molecular sleds, which are small basic molecules that bind and slide along DNA with the ability to carry cargo along DNA. Here, we performed biochemical and single-molecule flow stretching assays to investigate the basis of sliding activity in molecular sleds. In particular, we identified the functional core of pVIc, the first molecular sled characterized; peptide functional groups that control sliding activity; and propose a model for the sliding activity of molecular sleds. We also observed widespread DNA binding and sliding activity among basic polypeptide sequences that implicate mammalian nuclear localization sequences and many cell penetrating peptides as molecular sleds. These basic protein motifs exhibit weak but physiologically relevant sequence-nonspecific DNA affinity. Our findings indicate that many mammalian proteins contain molecular sled sequences and suggest the possibility that substantial undiscovered sliding activity exists among nuclear mammalian proteins.
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Affiliation(s)
- Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
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12
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Brown MW, Kim Y, Williams GM, Huck JD, Surtees JA, Finkelstein IJ. Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions. Nat Commun 2016; 7:10607. [PMID: 26837705 PMCID: PMC4742970 DOI: 10.1038/ncomms10607] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/04/2016] [Indexed: 12/17/2022] Open
Abstract
DNA-binding proteins search for specific targets via facilitated diffusion along a crowded genome. However, little is known about how crowded DNA modulates facilitated diffusion and target recognition. Here we use DNA curtains and single-molecule fluorescence imaging to investigate how Msh2-Msh3, a eukaryotic mismatch repair complex, navigates on crowded DNA. Msh2-Msh3 hops over nucleosomes and other protein roadblocks, but maintains sufficient contact with DNA to recognize a single lesion. In contrast, Msh2-Msh6 slides without hopping and is largely blocked by protein roadblocks. Remarkably, the Msh3-specific mispair-binding domain (MBD) licences a chimeric Msh2-Msh6(3MBD) to bypass nucleosomes. Our studies contrast how Msh2-Msh3 and Msh2-Msh6 navigate on a crowded genome and suggest how Msh2-Msh3 locates DNA lesions outside of replication-coupled repair. These results also provide insights into how DNA repair factors search for DNA lesions in the context of chromatin.
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Affiliation(s)
- Maxwell W Brown
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Gregory M Williams
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - John D Huck
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - Jennifer A Surtees
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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13
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Tabaka M, Burdzy K, Hołyst R. Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: Application to in vivo data. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022721. [PMID: 26382446 DOI: 10.1103/physreve.92.022721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 06/05/2023]
Abstract
DNA-binding protein searches for its target, a specific site on DNA, by means of diffusion. The search process consists of many recurrent steps of one-dimensional diffusion (sliding) along the DNA chain and three-dimensional diffusion (hopping) after dissociation of a protein from the DNA chain. Here we propose a computational method that allows extracting the contribution of sliding and hopping to the search process in vivo from the measurements of the kinetics of the target search by the lac repressor in Escherichia coli [P. Hammar et al., Science 336, 1595 (2012)]. The method combines lattice Monte Carlo simulations with the Brownian excursion theory and includes explicitly steric constraints for hopping due to the helical structure of DNA. The simulation results including all experimental data reveal that the in vivo target search is dominated by sliding. The short-range hopping to the same base pair interrupts one-dimensional sliding while long-range hopping does not contribute significantly to the kinetics of the search of the target in vivo.
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Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Box 354350, Seattle, Washington 98195, USA
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Mechetin GV, Zharkov DO. Mechanisms of diffusional search for specific targets by DNA-dependent proteins. BIOCHEMISTRY (MOSCOW) 2015; 79:496-505. [PMID: 25100007 DOI: 10.1134/s0006297914060029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To perform their functions, many DNA-dependent proteins have to quickly locate specific targets against the vast excess of nonspecific DNA. Although this problem was first formulated over 40 years ago, the mechanism of such search remains one of the unsolved fundamental problems in the field of protein-DNA interactions. Several complementary mechanisms have been suggested: sliding, based on one-dimensional random diffusion along the DNA contour; hopping, in which the protein "jumps" between the closely located DNA fragments; macroscopic association-dissociation of the protein-DNA complex; and intersegmental transfer. This review covers the modern state of the problem of target DNA search, theoretical descriptions, and methods of research at the macroscopic (molecule ensembles) and microscopic (individual molecules) levels. Almost all studied DNA-dependent proteins search for specific targets by combined three-dimensional diffusion and one-dimensional diffusion along the DNA contour.
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Affiliation(s)
- G V Mechetin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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15
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Erie DA, Weninger KR. Single molecule studies of DNA mismatch repair. DNA Repair (Amst) 2014; 20:71-81. [PMID: 24746644 DOI: 10.1016/j.dnarep.2014.03.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/21/2014] [Accepted: 03/22/2014] [Indexed: 11/30/2022]
Abstract
DNA mismatch repair, which involves is a widely conserved set of proteins, is essential to limit genetic drift in all organisms. The same system of proteins plays key roles in many cancer related cellular transactions in humans. Although the basic process has been reconstituted in vitro using purified components, many fundamental aspects of DNA mismatch repair remain hidden due in part to the complexity and transient nature of the interactions between the mismatch repair proteins and DNA substrates. Single molecule methods offer the capability to uncover these transient but complex interactions and allow novel insights into mechanisms that underlie DNA mismatch repair. In this review, we discuss applications of single molecule methodology including electron microscopy, atomic force microscopy, particle tracking, FRET, and optical trapping to studies of DNA mismatch repair. These studies have led to formulation of mechanistic models of how proteins identify single base mismatches in the vast background of matched DNA and signal for their repair.
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Affiliation(s)
- Dorothy A Erie
- Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, United States
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16
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Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII. Protein Cell 2014; 5:357-68. [PMID: 24733184 PMCID: PMC3996161 DOI: 10.1007/s13238-014-0038-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 02/18/2014] [Indexed: 11/24/2022] Open
Abstract
DraIII is a type IIP restriction endonucleases (REases) that recognizes and creates a double strand break within the gapped palindromic sequence CAC↑NNN↓GTG of double-stranded DNA (↑ indicates nicking on the bottom strand; ↓ indicates nicking on the top strand). However, wild type DraIII shows significant star activity. In this study, it was found that the prominent star site is CAT↑GTT↓GTG, consisting of a star 5′ half (CAT) and a canonical 3′ half (GTG). DraIII nicks the 3′ canonical half site at a faster rate than the 5′ star half site, in contrast to the similar rate with the canonical full site. The crystal structure of the DraIII protein was solved. It indicated, as supported by mutagenesis, that DraIII possesses a ββα-metal HNH active site. The structure revealed extensive intra-molecular interactions between the N-terminal domain and the C-terminal domain containing the HNH active site. Disruptions of these interactions through site-directed mutagenesis drastically increased cleavage fidelity. The understanding of fidelity mechanisms will enable generation of high fidelity REases.
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17
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Khazanov N, Marcovitz A, Levy Y. Asymmetric DNA-search dynamics by symmetric dimeric proteins. Biochemistry 2013; 52:5335-44. [PMID: 23866074 DOI: 10.1021/bi400357m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We focus on dimeric DNA-binding proteins from two well-studied families: orthodox type II restriction endonucleases (REs) and transcription factors (TFs). Interactions of the protein's recognition sites with the DNA and, particularly, the contribution of each of the monomers to one-dimensional (1D) sliding along nonspecific DNA were studied using computational tools. Coarse-grained molecular dynamics simulations of DNA scanning by various TFs and REs provide insights into how the symmetry of a homodimer can be broken while they nonspecifically interact with DNA. The characteristics of protein sliding along DNA, such as the average sliding length, partitioning between 1D and 3D search, and the one-dimensional diffusion coefficient D1, strongly depend on the salt concentration, which in turn affects the probability of the two monomers adopting a cooperative symmetric sliding mechanism. Indeed, we demonstrate that maximal DNA search efficiency is achieved when the protein adopts an asymmetric search mode in which one monomer slides while its partner hops. We find that proteins classified as TFs have a higher affinity for the DNA, longer sliding lengths, and an increased probability of symmetric sliding in comparison with REs. Moreover, TFs can perform their biological function over a much wider range of salt concentrations than REs. Our results demonstrate that the different biological functions of DNA-binding proteins are related to the different nonspecific DNA search mechanisms they adopt.
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Affiliation(s)
- Netaly Khazanov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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18
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Arslan Z, Wurm R, Brener O, Ellinger P, Nagel-Steger L, Oesterhelt F, Schmitt L, Willbold D, Wagner R, Gohlke H, Smits SHJ, Pul U. Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucleic Acids Res 2013; 41:6347-59. [PMID: 23625968 PMCID: PMC3695520 DOI: 10.1093/nar/gkt315] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The adaptive immunity of bacteria against foreign nucleic acids, mediated by CRISPR (clustered regularly interspaced short palindromic repeats), relies on the specific incorporation of short pieces of the invading foreign DNA into a special genomic locus, termed CRISPR array. The stored sequences (spacers) are subsequently used in the form of small RNAs (crRNAs) to interfere with the target nucleic acid. We explored the DNA-binding mechanism of the immunization protein Csn2 from the human pathogen Streptococcus agalactiae using different biochemical techniques, atomic force microscopic imaging and molecular dynamics simulations. The results demonstrate that the ring-shaped Csn2 tetramer binds DNA ends through its central hole and slides inward, likely by a screw motion along the helical path of the enclosed DNA. The presented data indicate an accessory function of Csn2 during integration of exogenous DNA by end-joining.
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Affiliation(s)
- Zihni Arslan
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
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19
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Schwarz FW, Tóth J, van Aelst K, Cui G, Clausing S, Szczelkun MD, Seidel R. The helicase-like domains of type III restriction enzymes trigger long-range diffusion along DNA. Science 2013; 340:353-6. [PMID: 23599494 PMCID: PMC3646237 DOI: 10.1126/science.1231122] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Helicases are ubiquitous adenosine triphosphatases (ATPases) with widespread roles in genome metabolism. Here, we report a previously undescribed functionality for ATPases with helicase-like domains; namely, that ATP hydrolysis can trigger ATP-independent long-range protein diffusion on DNA in one dimension (1D). Specifically, using single-molecule fluorescence microscopy we show that the Type III restriction enzyme EcoP15I uses its ATPase to switch into a distinct structural state that diffuses on DNA over long distances and long times. The switching occurs only upon binding to the target site and requires hydrolysis of ~30 ATPs. We define the mechanism for these enzymes and show how ATPase activity is involved in DNA target site verification and 1D signaling, roles that are common in DNA metabolism: for example, in nucleotide excision and mismatch repair.
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Affiliation(s)
- Friedrich W. Schwarz
- DNA motors group, Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Júlia Tóth
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Kara van Aelst
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Guanshen Cui
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Sylvia Clausing
- DNA motors group, Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Mark D. Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Ralf Seidel
- DNA motors group, Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany
- Institute of Molecular Cell Biology, University of Münster, 48149 Münster, Germany
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Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level. Int J Mol Sci 2013; 14:3961-92. [PMID: 23429188 PMCID: PMC3588080 DOI: 10.3390/ijms14023961] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 01/13/2013] [Accepted: 02/04/2013] [Indexed: 12/13/2022] Open
Abstract
The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target DNA are the subject of intense investigations employing a variety of methods in biology. A large interest in these processes stems from the faster-than-diffusion association rates, explained in current models by a combination of 3D and 1D diffusion. Here, we present a review of the single-molecule approaches at the forefront of the study of protein-DNA interaction dynamics and target search in vitro and in vivo. Flow stretch, optical and magnetic manipulation, single fluorophore detection and localization as well as combinations of different methods are described and the results obtained with these techniques are discussed in the framework of the current facilitated diffusion model.
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Barbi M, Paillusson F. Protein–DNA Electrostatics. DYNAMICS OF PROTEINS AND NUCLEIC ACIDS 2013; 92:253-97. [DOI: 10.1016/b978-0-12-411636-8.00007-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Terakawa T, Kenzaki H, Takada S. p53 Searches on DNA by Rotation-Uncoupled Sliding at C-Terminal Tails and Restricted Hopping of Core Domains. J Am Chem Soc 2012; 134:14555-62. [DOI: 10.1021/ja305369u] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Tsuyoshi Terakawa
- Department of Biophysics
Graduate
School of Science, Kyoto University, Kyoto
606-8502 Japan
| | - Hiroo Kenzaki
- Department of Biophysics
Graduate
School of Science, Kyoto University, Kyoto
606-8502 Japan
| | - Shoji Takada
- Department of Biophysics
Graduate
School of Science, Kyoto University, Kyoto
606-8502 Japan
- CREST Japan Science and Technology Agency, Saitama 332-0012 Japan
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