Shigenori Tanaka

Kobe University, Kōbe, Hyōgo, Japan

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Publications (98)171.62 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: It is considered that Hoogsteen base pairs and DNA triplex structures play important roles in cellular processes even though these structures are less than duplexes of Watson-Crick base pairs. Molecular ions clearly affect the stability of DNA structures in vivo; however, the mechanisms are unknown. Here, we investigated the effects of sodium ions, choline ions, and tetramethylammonium ions on DNA triplexes using molecular dynamics simulations. We found that non-polar interactions, which are associated with van der Waals interactions, and solvent accessible surface area were more im-portant than polar or electrostatic interactions in determining the affinity of a molecular cation for the DNA groove areas. The free energy gain due to a cation that fit optimally within a DNA groove was larger than the free energy loss due to the effect of dehydration. Cations with shapes complementary to that of a particular DNA groove configuration stabilized triplex formation, but cations that disturbed hydrogen bonds between DNA bases were destabilizing. These stabilizing and destabi-lizing mechanisms of molecular cations were also applicable to a DNA duplex composed of Watson-Crick base pairs. The molecular-level view of cation interactions with DNA structures will guide de-sign of DNA devices, DNA-based drugs, and genetic therapies.
    The journal of physical chemistry. B. 07/2014;
  • Shigenori Tanaka, Miki Nakano
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    ABSTRACT: In this report the radial distribution functions (RDFs) of liquid water are calculated on the basis of the classical density functional theory combined with the reference interaction site model for molecular liquids. The bridge functions, which are neglected in the hypernetted-chain (HNC) approximation, are taken into account through the density expansion for the Helmholtz free energy functional up to the third order. A factorization approximation to the ternary direct correlation functions in terms of the site-site pair correlation functions is then employed in the expression of the bridge functions, thus leading to a closed set of integral equations for the determination of the RDFs. It is confirmed through numerical calculations that incorporation of the oxygen-oxygen bridge function substantially improves the poor descriptions by the HNC approximation at room temperature, e.g., for the second peak of the oxygen-oxygen RDF.
    Interdisciplinary sciences, computational life sciences. 05/2014;
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    ABSTRACT: Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
    Physical Chemistry Chemical Physics 04/2014; · 3.83 Impact Factor
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    ABSTRACT: The mechanism to fix helix 12 (H12) in the agonist/antagonist position, which is involved in controlling transcriptional activation, of the human estrogen receptor α ligand binding domain (hERαLBD) is studied by using fragment molecular orbital calculations at the Møller-Plesset second-order perturbation levels to analyze inter-fragment interaction energies (IFIEs), electrostatic potentials (ESPs) and atomic charges. The mutually attractive and complementary relationships between H12 and highly conserved Lys529/Lys362 are shown through the IFIEs and ESPs. The highly conserved Lys529 and Lys362 are found to have strong attractive interactions with the anionic residues of H12 in the agonist and antagonist positions, respectively, thus playing roles of charge clamps to fix H12. Additionally, intramolecular interactions between the neutral residues of H12 including LXXML motif and the other part of hERα are strengthened by the hydrogen bonds and polarization. It is noted that the highly conserved Asp351 forms a hydrogen bond with Leu540 of H12 in hERα-agonist complex, while it is also involved in stabilization of ligand binding in the hERα-antagonist complex. The charges of residues at the interface between H12 and the other part of hERα approach approximately neutral upon forming the agonist/antagonist binding conformation so as to relax the electrostatic repulsion caused by the negative charges of H12 and other part of hERα. Our observations would thus provide useful information to control the H12 position for regulation of transcription in hERα and other nuclear receptors.
    The Journal of Physical Chemistry B 04/2014; · 3.61 Impact Factor
  • Takeshi Matsuoka, Shigenori Tanaka, Kuniyoshi Ebina
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    ABSTRACT: We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achive a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics.
    Bio Systems 01/2014; · 1.27 Impact Factor
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    ABSTRACT: On the basis of available molecular structures registered in Protein Data Bank, we have theoretically carried out the interaction energy analysis for the complexes of influenza virus hemagglutinin (HA) proteins and sialosaccharide receptor analogs of host cells. Employing the fragment molecular orbital method for quantum-chemical calculations, the differences in magnitude and pattern of the interactions between the amino acid residues of avian-type (H7N3) or human-type (H7N9) HA and each saccharide part of avian or human receptor were studied in order to elucidate the molecular mechanism of avian-to-human infectious transmission of influenza virus. We have thus confirmed quantitatively that the mutations from the avian HA to the human HA significantly strengthened the binding affinity of human HA to human receptor, while retaining the affinity to avian receptor. In addition to direct effects regarding the changes of interactions between the altered residues and the receptors, we have also found the importance of indirect effects in which structural changes caused by the mutations play vital roles to modify the intermolecular interactions.
    Journal of Molecular Graphics and Modelling. 01/2014; 53:48–58.
  • Computational and Theoretical Chemistry. 01/2014;
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    ABSTRACT: Under physiological conditions, G-C base pairs are more stable than A-T base pairs. In a previous study, we showed that in the hydrated ionic liquid of choline dihydrogen phosphate, the stabilities of these base pairs are reversed. In the present study, we elucidated the unique binding interactions of choline ions with DNA atoms from a microscopic viewpoint using molecular dynamics simulations. Three times more choline ions bind to the DNA duplex than sodium ions. Sodium ions bind closely but not stably; in contrast, the choline ions bind through multiple hydrogen bonding networks with DNA atoms stably. The affinity of choline ion for the minor groove of A-T base pairs is more than two times that for other groove areas. In the narrow A-T minor groove, choline ion has high affinity for the ribose atoms of thymine. Choline ions also destabilize the formation of hydrogen bonds between G-C base pairs by binding to base atoms preferentially for both of duplex and single-strand DNA, which are associated with the bonds between G-C base pairs. Our new finding will not only lead to better control of DNA stability for use in DNA nanodevices, but also provide new insight into the stability of DNA duplexes under crowding conditions found in living cells.
    The Journal of Physical Chemistry B 10/2013; · 3.61 Impact Factor
  • Shigenori Tanaka, Miki Nakano
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    ABSTRACT: Density functional theory for molecular fluids developed by Donley et al. (J. Chem. Phys. 101 (1994) 3205) is extended to include the effects of orientation-dependent bridge functions associated with the inter-particle, triplet correlations. Resultant integral equations for the pair and direct correlation functions are solved for water, where the three-body direct correlation functions are approximated in terms of two-body functions. A test calculation employing a simple Gaussian form for the two-body function between the oxygen sites then provides a promising result to improve the description of the oxygen–oxygen correlations in liquid water at room temperature.
    Chemical Physics Letters 05/2013; 572:38–43. · 2.15 Impact Factor
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    ABSTRACT: We have applied the four-body corrected fragment molecular orbital (FMO4) method to the investigation of the interaction between an artificially designed peptide, with sequence of Arg1-Lys2-Leu3-Pro4-Asp5-Ala6 [Sano et al., Langmuir, 21 (2005) 3090], and the silica surface modeled by a large cluster model including 257 silicon atoms. The second-order Møller-Plesset perturbation calculation was accelerated by the Cholesky decomposition with adaptive metric technique (CDAM-MP2). Systematic analyses were made for inter-fragment interaction energies (IFIEs) with and without a statistical correction for screening. As the result, the importance of three charged residues (Arg1, Lys2 and Asp5) in the peptide-silica interaction was illuminated.
    Chemical Physics Letters 04/2013; 566:25–31. · 2.15 Impact Factor
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    ABSTRACT: We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design.
    Journal of molecular graphics & modelling 02/2013; 41C:31-42. · 2.17 Impact Factor
  • Miki Nakano, Kuniyoshi Ebina, Shigenori Tanaka
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    ABSTRACT: Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases.
    Journal of Molecular Modeling 01/2013; · 1.98 Impact Factor
  • Shigenori Tanaka, Miki Nakano
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    ABSTRACT: We have calculated the radial distribution functions (RDFs) of liquid water on the basis of the classical density functional theory combined with the reference interaction site model for molecular liquids. The density expansion for the Helmholtz free energy functional is retained up to the third order in order to take into account the effects of the bridge functions beyond the hypernetted-chain (HNC) approximation. The ternary direct correlation functions in the expression of the bridge functions are then given by a factorization approximation in terms of the site-site pair correlation functions, thus leading to a closed set of integral equations for the determination of the RDFs. We have obtained a numerical result in which a poor description by the HNC approximation for the second peak of the oxygen-oxygen RDF at room temperature has been improved to some extent by incorporating the oxygen-oxygen bridge function. Some directions toward more satisfactory agreement with computer simulation results are addressed as well.
    Chemical Physics. 01/2013;
  • Shigenori Tanaka, Chiduru Watanabe, Yoshio Okiyama
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    ABSTRACT: A theoretical scheme to evaluate effective, screened interactions between fragments is proposed within the framework of the fragment molecular orbital (FMO) method. In this theory, the presence of implicit, dielectric continuum solvent is not assumed, but only the information on bare, inter-fragment interaction energies obtained through the FMO calculation for explicit, molecular system is employed. The effective interactions with inclusion of entropic effect are then described and optimized as a consequence of inter-fragment correlations on the basis of classical-mechanical many-body theories. Test calculations for a simple model system and a realistic protein system are performed, and their implications are discussed.
    Chemical Physics Letters 01/2013; 556:272–277. · 2.15 Impact Factor
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    ABSTRACT: We have performed ab initio path integral Monte Carlo simulations for water trimer (H2O)3 system. The electron correlation effects have been taken into account up to the level of third-order Møller-Plesset (MP3) perturbation theory. Through comparisons of calculated geometrical properties of water trimer such as O–O distance, O–H–O angle, and torsional angle between O–H and O–O–O plane, the interplays among the nuclear quantum, thermal and electron correlation effects are analyzed quantitatively.
    Computational and Theoretical Chemistry 10/2012; 997:7-13. · 1.14 Impact Factor
  • Yosuke Suzuki, Shigenori Tanaka
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    ABSTRACT: We have developed a theoretical formulation for excitation energy transfer between structurally fluctuating dimer molecules in surrounding environments. On the basis of a generalized master equation in which a memory function plays a vital role, the temporal evolutions of the population densities of exciton at the donor and acceptor sites are described. By employing an ansatz form for the memory function, the competitive effects of dimeric coupling and bath modes are analyzed quantitatively, where the roles of oscillating electronic coupling are highlighted.
    Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 08/2012; 86(2).
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    ABSTRACT: We have performed ab initio path integral molecular dynamics and Monte Carlo simulations for water trimer and oligopeptide. In the first part, we illustrate the path integral molecular dynamics method based on fragment molecular orbital (FMO-PIMD) method. The FMO-PIMD method is applied to water trimer and glycine pentamer to investigate nuclear quantum effects on the structure and molecular interactions. In the second part, we employ the Møller-Plesset perturbation theory and discuss interplay of nuclear quantum effects and electron correlations.
    02/2012: pages 187-199; , ISBN: 9780841227507
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    ABSTRACT: The four-body corrected fragment molecular orbital (FMO4) method was implemented at the second-order Møller–Plesset perturbation (MP2) level. A series of accuracy tests relative to the previous two-body and three-body treatments were performed. As expected, FMO4 provided better accuracy in total energies in comparison with the reference values by regular MO calculations. A nonconventional fragmentation by separating main and side chains in amino acid residues was examined for Ala-pentamer and Chignolin, where the four-body corrections were shown to be substantial. A large complex of HIV-1 protease (total 198 residues) with lopinavir was calculated as well. Furthermore, this new FMO scheme was successfully applied to adamantane-shaped clusters with three-dimensional bonding framework.
    Chemical Physics Letters 01/2012; 523:128–133. · 2.15 Impact Factor
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    Shigenori Tanaka
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    ABSTRACT: Renormalization group method is applied to the study of vibrational energy transfer in protein molecule. An effective Lagrangian and associated equations of motion to describe the resonant energy transfer are analyzed in terms of the first-order perturbative renormalization group theory that has been developed as a unified tool for global asymptotic analysis. After the elimination of singular terms associated with the Fermi resonance, amplitude equations to describe the slow dynamics of vibrational energy transfer are derived, which recover the result obtained by a technique developed in nonlinear optics [S.J. Lade, Y.S. Kivshar, Phys. Lett. A 372 (2008) 1077].
    Journal of the Physical Society of Japan 08/2011; · 2.09 Impact Factor
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    ABSTRACT: Ab initio electronic-state calculations for influenza virus hemagglutinin (HA) trimer complexed with Fab antibody were performed on the basis of the fragment molecular orbital (FMO) method at the second and third-order Møller-Plesset (MP2 and MP3) perturbation levels. For the protein complex containing 2351 residues and 36,160 atoms, the inter-fragment interaction energies (IFIEs) were evaluated to illustrate the effective interactions between all the pairs of amino acid residues. By analyzing the calculated data on the IFIEs, we first discussed the interactions and their fluctuations between multiple domains contained in the trimer complex. Next, by combining the IFIE data between the Fab antibody and each residue in the HA antigen with experimental data on the hemadsorption activity of HA mutants, we proposed a protocol to predict probable mutations in HA. The proposed protocol based on the FMO-MP2.5 calculation can explain the historical facts concerning the actual mutations after the emergence of A/Hong Kong/1/68 influenza virus with subtype H3N2, and thus provides a useful methodology to enumerate those residue sites likely to mutate in the future.
    Journal of molecular graphics & modelling 07/2011; 30:110-9. · 2.17 Impact Factor

Publication Stats

406 Citations
171.62 Total Impact Points

Institutions

  • 2005–2014
    • Kobe University
      • • Department of Computational Science
      • • Graduate School of Human Development and Environment
      • • Graduate School of System Informatics
      • • Graduate School of Engineering
      Kōbe, Hyōgo, Japan
  • 2013
    • The University of Tokyo
      • Institute of Industrial Science
      Tokyo, Tokyo-to, Japan
  • 2006–2011
    • Mizuho Research Institute
      Edo, Tōkyō, Japan
    • National Institute of Health Sciences, Japan
      Edo, Tōkyō, Japan
  • 2009
    • Nagahama Institute of Bio-Science and Technology
      Нагахама, Shiga, Japan
    • Rikkyo University
      • Department of Chemistry
      Tokyo, Tokyo-to, Japan
  • 2005–2008
    • Brock University
      • Department of Chemistry
      St. Catharines, Ontario, Canada
  • 2007
    • Toyohashi University of Technology
      • Department of Knowledge-based Information Engineering
      Toyohasi, Aichi, Japan
  • 2003–2004
    • Toshiba Corporation
      Edo, Tōkyō, Japan