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Volume 67, Issue 3
Displaying 1-10 of 10 articles from this issue
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Comprehensive Papers
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Chie MOTONO, M. Michael GROMIHA2010 Volume 67 Issue 3 Pages 151-163
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSThe cold shock protein (CSP) from hyperthermophile Thermotoga maritima (TmCSP) is only marginally stable at 353 K, the optimum environmental temperature Topt for T. maritima. In comparison, homologous CSPs from mesophilic E. coli and B. subtilis are at least 5 times more stable at 310 K, the Topt for the mesophiles. Yet at room temperature, TmCSP is more stable than its homologues. This unique observation suggests that kinetic, rather than thermodynamic, barriers towards unfolding might help TmCSP native structure at high temperatures. High temperature (600 K) complete unfolding MD simulations of TmCSP support our hypothesis and reveal an unfolding scheme unique to TmCSP. For all the studied homologues of TmCSP, the unfolding process first starts at the C-terminal region and the N-terminal region unfolds last. But for TmCSP, unfolding starts at both terminals simultaneously. In TmCSP, the C-terminal region is better fortified and has better interactions with the N-terminal region due to the charged residues, R2, E47, E49, H61, K63 and E66, being in spatial vicinity. The electrostatic interactions among these residues are unique to TmCSP. Consistently, the room temperature MD simulations show that TmCSP is more rigid at its N- and C- termini as compared to its homologues from E. coli, B. subtilis and B. caldolyticus.
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Shi-aki HYODO, Masao DOI2010 Volume 67 Issue 3 Pages 164-178
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSIn order to confirm the fundamental issues of the multi-scale modeling and the procedure of coarse-graining in polymer simulations, the differences and similarities of several kinds of mesoscopic simulation methods, especially the coarse-graining particle dynamics and the dynamical density functional methods, were critically compared and analyzed based on our recent published works. We mainly discuss the fundamental differences of the description of coarse-graining procedure between the macroscopic and microscopic points of view. We conclude that though there still exists a wide gap between the methods, a critical comparison between the two will bring us a step towards quantitative multi-scale modeling.
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Takahisa YAMATO2010 Volume 67 Issue 3 Pages 179-186
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSMolecular functions of folded proteins are investigated in the light of biophysical computations. In particular, we have focused on the molecular mechanism of photoreceptor proteins. Using theoretical/computational techniques, I study what happens in these photoreceptor proteins after light illumination and how these proteins convert light energy into conformational changes. Vibrational relaxations and molecular dynamics play crucial roles in heat, energy and signal transfer processes. I introduced a new concept of site-site energy conductivity and successfully characterized the intramolecular communication chart of the photoactive yellow protein. Analysis of the electron-tunneling pathways of the DNA photolyase derived from Anacystis nidulans revealed the active role of the protein environment in the electron transfer. I observed busy trafficking of electron-tunneling currents at the methionine residue, Met-353. Interestingly, the amino acid conservation pattern of Met-353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyase.
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Original Papers
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Tomoyuki KINJO, Yuko MURAYAMA, Kenji IMAI, Toshihisa MUNEKATA, Shi-aki ...2010 Volume 67 Issue 3 Pages 187-191
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSProton conductivity of polymer electrolyte membrane is one of the important properties for application in high performance fuel cell vehicles. In general, increase of acid density enhances proton conductivity, however, it also leads to swelling and weakening of the membrane by water absorption. In this paper, we report a coarse-grained simulation of polymer electrolyte membrane to seek a desirable molecular geometry for the compatibility of high proton conductivity and water resistance. Molecular geometries, which have hydrophilic blocks encompassed with hydrophobic blocks, show relatively good compatibility within our present study.
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Miho YUKAWA, Hanae MORIWAKI, Taichi MURAKAMI, Hirohito IKEDA, Yukiko I ...2010 Volume 67 Issue 3 Pages 192-197
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSThe inclusion complexes of two β-lactam antibiotics, ampicillin (ABPC) and amoxicillin (AMPC), with β-cyclodextrin in aqueous solution has been studied by semi-empirical molecular orbital method. In a strongly acid solution, two different types of complexes with a 1 : 1 stoichiometry were formed. Complex_Ph, in which the phenyl ring of β-lactam antibiotics was oriented towards the cavity of CD, and Complex_Pe, in which the penam ring was oriented towards the cavity. In neutral or basic solution, only Complex_Ph was formed. These results match the results of microcalorimetry and 1H NMR spectroscopy.
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Masaki MINE, Naohito URAKAMI, Koji NOZAKI, Takashi YAMAMOTO2010 Volume 67 Issue 3 Pages 198-202
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSOrganic thin-films are recently used in various functional devices. In this short report, molecular dynamics simulations are performed to study crystallization and thin-film formation in n-alkane C19H40 on solid substrates of various types. Irrespective of detailed geometrical structures of the substrate, the chains generally tend to lie parallel to the substrate if the substrate is highly attractive, while they align perpendicular to the substrate of weak attraction. If the substrate has a medium level of attraction, detailed atomic-level structure of the substrate is found to play important roles in determining chain orientations within the thin films.
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Mitsuhiro FUKUDA, Yoshinori TAMAI, Nozomu SUZUKI, Hiroaki KIKUCHI2010 Volume 67 Issue 3 Pages 203-208
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSFree-energy related properties for small molecules in poly(dimethylsiloxane) (PDMS) have been evaluated using a test-particle-insertion method with the excluded volume map sampling (EVMS). The excess chemical potential (solubility) and solvation energy in PDMS at 298 K were calculated for five noble gases (He, Ne, Ar, Kr, Xe) and for five hydrocarbon gases (CH4, C2H6, C3H8, C2H4, C3H6). The bulk configurations of PDMS composed of 8 chains of CH3-(Si(CH3)2-O-)301-Si(CH3)3 were obtained by the molecular dynamics simulation with NPT ensemble. The solubility coefficients obtained by the EVMS method showed a good agreement with the experimental values. The solvation entropy for the respective gas molecule was also evaluated from the solubility enthalpy and the excess chemical potential both of which were calculated during the test-particle-insertion method. The relations of these free-energy related properties with the molecular size based on the Lenard-Jones size parameter or Lenard-Jones force constants are discussed.
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Susumu KAWAUCHI, Masayuki KANEKO, Tatsuya IMASE, Yoshiaki TAGUCHI, Chu ...2010 Volume 67 Issue 3 Pages 209-213
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSThe dependence of the degree of polymerization (n) for poly(p-hydroxybenzoic acid) on its dipole moment (μ) and hyperpolarizability (β) shows a high linearity for B3LYP and MP2 calculations. Both μ and β indicate that B3LYP/6-31G(d) gives higher values than those of MP2/6-31G(d). In addition, for all the basis sets considered here, μ and β show a high linearity with n. For both B3LYP and MP2, μ and β calculated with 6-31G(d) and 6-311G(d) give similar values, while those calculated with 6-31+G(d) and 6-311+G(d) give similar values, also. Furthermore, it was found that the addition of a diffuse function improves μ and β values.
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Yoshihito INAI, Haruki OGAWA2010 Volume 67 Issue 3 Pages 214-223
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSWe have investigated theoretical conformational feature of an isolated poly(lactic acid) (PLA) chain involving a racemic unit at the central position. Two polymers were employed, one with the sequence of 25 units of L-lactic acid (1) and one in which the 13th position is substituted by the D-isomer (1-D). In both PLAs, several initial conformers were geometry-optimized with the semi-empirical molecular orbital method. The energy value of each converged structure was re-evaluated with DFT single-point computation. In the optimization of 1 from eight periodic conformers, a “g-t”-helical conformer was found to be the most stable. In the case of 1-D, most of the corresponding eight structures were energetically destabilized or deformed at around the central position. The D-isomer incorporated into the most stable “g-t”-helical conformer of 1 led the whole chain to a triangle-like shape that reduced the edge-to-edge distance by ca. 25%. The present simulation reveals that the introduction of a single heterochiral unit into a long homochiral PLA chain generates large conformational flexibility to vary its physicochemical properties.
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Notes
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Shin-ichi SAWADA, Tetsuya YAMAKI, Taku OZAWA, Akihiro SUZUKI, Takayuki ...2010 Volume 67 Issue 3 Pages 224-227
Published: 2010
Released on J-STAGE: March 25, 2010
JOURNAL FREE ACCESSWe investigated for the first time the mesoscopic structure of crosslinked-polytetrafluoroethylene (cPTFE) based radiation-grafted polymer electrolyte membranes (PEMs) by using dissipative particle dynamics (DPD) simulation. Based on the molecular structures, the fully-hydrated PEM systems were constructed with coarse-grained particles representing several atom groups. In the equilibrium state, water appeared to percolate into poly(styrene sulfonic acid) (PSSA) graft chains to give a mixed phase, separated from the hydrophobic PTFE chains. This phase-separation picture is quite different from that of Nafion, in which only water particles were gathered excluding any polymer parts (formation of a so-called water cluster). In order to obtain a deep insight into the phase-separation structure, the radial distribution function between water particles was calculated. As a result, there were found to be small water clusters with a diameter of only 1.8 nm in the water/grafts mixture regions.
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