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Nakagawa H, Yonetani Y, Nakajima K, Ohira-Kawamura S, Kikuchi T, Inamura Y, Kataoka M, Kono H. Local dynamics coupled to hydration water determines DNA-sequence-dependent deformability. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022723. [PMID: 25215774 DOI: 10.1103/physreve.90.022723] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Indexed: 06/03/2023]
Abstract
Molecular dynamics (MD) simulations and quasielastic neutron scattering (QENS) experiments were conducted on two hydrated DNA dodecamers with distinct deformability: 5'CGCG[under AATT]̲CGCG3' and 5'CGCG[under TTAA]̲CGCG3'. The former is known to be rigid and the latter to be flexible. The mean-square displacements of DNA dodecamers exhibit so-called dynamical transition around 200-240 K for both sequences. To investigate the DNA-sequence-dependent dynamics, the dynamics of DNA and hydration water above the transition temperature were examined using both MD simulations and QENS experiments. The fluctuation amplitude of the AATT central tetramer is smaller, and its relaxation time is longer, than that observed in TTAA, suggesting that the AT step is kinetically more stable than TA. The sequence-dependent local base pair step dynamics correlates with the kinetics of breaking the hydrogen bond between DNA and hydration water. The sequence-dependent DNA base pair step fluctuations appear above the dynamical transition temperature. Together with these results, we conclude that DNA deformability is related to the local dynamics of the base pair steps, themselves coupled to hydration water in the minor groove.
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Affiliation(s)
- H Nakagawa
- Neutron Biophysics, Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Y Yonetani
- Molecular Modeling and Simulation, Quantum Beam Science Center, Japan Atomic Energy Agency, Kizugawa, Kyoto 619-0215, Japan
| | - K Nakajima
- J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - S Ohira-Kawamura
- J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - T Kikuchi
- J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Y Inamura
- J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - M Kataoka
- Neutron Biophysics, Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan and Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - H Kono
- Molecular Modeling and Simulation, Quantum Beam Science Center, Japan Atomic Energy Agency, Kizugawa, Kyoto 619-0215, Japan
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What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences. Biophys Chem 2012; 160:54-61. [DOI: 10.1016/j.bpc.2011.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 09/17/2011] [Accepted: 09/19/2011] [Indexed: 11/23/2022]
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Yonetani Y, Kono H. Sequence dependencies of DNA deformability and hydration in the minor groove. Biophys J 2009; 97:1138-47. [PMID: 19686662 PMCID: PMC2726331 DOI: 10.1016/j.bpj.2009.05.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 05/13/2009] [Accepted: 05/29/2009] [Indexed: 10/20/2022] Open
Abstract
DNA deformability and hydration are both sequence-dependent and are essential in specific DNA sequence recognition by proteins. However, the relationship between the two is not well understood. Here, systematic molecular dynamics simulations of 136 DNA sequences that differ from each other in their central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that this correlation can be illustrated by four typical cases. Most rigid basepair steps are highly likely to form an ordered hydration pattern composed of one water molecule forming a bridge between the bases of distinct strands, but a few exceptions favor another ordered hydration composed of two water molecules forming such a bridge. Steps with medium deformability can display both of these hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. A detailed picture of this correlation demonstrates that motions of hydration water molecules and DNA bases are tightly coupled with each other at the atomic level. These results contribute to our understanding of the entropic contribution from water molecules in protein or drug binding and could be applied for the purpose of predicting binding sites.
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Affiliation(s)
- Yoshiteru Yonetani
- Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto, Japan
| | - Hidetoshi Kono
- Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto, Japan
- Quantum Bioinformatics Team, Center for Computational Science and e-Systems, Japan Atomic Energy Agency, Kyoto, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
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Yonetani Y, Maruyama Y, Hirata F, Kono H. Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory. J Chem Phys 2008; 128:185102. [PMID: 18532849 DOI: 10.1063/1.2904865] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Because proteins and DNA interact with each other and with various small molecules in the presence of water molecules, we cannot ignore their hydration when discussing their structural and energetic properties. Although high-resolution crystal structure analyses have given us a view of tightly bound water molecules on their surface, the structural data are still insufficient to capture the detailed configurations of water molecules around the surface of these biomolecules. Thanks to the invention of various computational algorithms, computer simulations can now provide an atomic view of hydration. Here, we describe the apparent patterns of DNA hydration calculated by using two different computational methods: Molecular dynamics (MD) simulation and three-dimensional reference interaction site model (3D-RISM) theory. Both methods are promising for obtaining hydration properties, but until now there have been no thorough comparisons of the calculated three-dimensional distributions of hydrating water. This rigorous comparison showed that MD and 3D-RISM provide essentially similar hydration patterns when there is sufficient sampling time for MD and a sufficient number of conformations to describe molecular flexibility for 3D-RISM. This suggests that these two computational methods can be used to complement one another when evaluating the reliability of the calculated hydration patterns.
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Affiliation(s)
- Yoshiteru Yonetani
- Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto, Japan
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Auffinger P, Hashem Y. Nucleic acid solvation: from outside to insight. Curr Opin Struct Biol 2007; 17:325-33. [PMID: 17574833 DOI: 10.1016/j.sbi.2007.05.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 03/28/2007] [Accepted: 05/31/2007] [Indexed: 11/18/2022]
Abstract
Nucleic acids are polyanionic molecules that were historically considered to be solely surrounded by a shell of water molecules and a neutralizing cloud of monovalent and divalent cations. In this respect, recent experimental and theoretical reports demonstrate that water molecules within complex nucleic acid structures can display very long residency times, and assist drug binding and catalytic reactions. Finally, anions can also bind to these polyanionic systems. Many of these recent insights are provided by state-of-the-art molecular dynamics simulations of nucleic acid systems, which will be described together with relevant methodological issues.
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Affiliation(s)
- Pascal Auffinger
- Architecture et réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France.
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