月別: 2023年6月

[Published online Journal of Computer Chemistry, Japan Vol.21, 134-136, by J-STAGE]
<Title:> シトクロムcの複合体形成過程の再現シミュレーション
<Author(s):> 下山　紘充, 重田　育照
<Abstract:> A 3-dimensional domain swapping (3D-DS) phenomenon is a promising way to make a stable multimer because interactions in the multimer is about the same as that of a monomer; it would be useful to artificially design a functional protein’s multimer. In this study, molecular dynamics (MD) simulation of cytochrome c(cyt c) that is known to form a 3D-DS dimer (PDB ID: 3NBS) was performed to study factors that enhance 3D-DS structure sampling. Our results show a difficulty of 3D-DS structure sampling and a necessity of a method such as the generalized ensemble method. The results also show the importance of a loop-flexibility to sample 3D-DS structure; when the bond and torsion angle potential coefficients are less than 10% of secondary structure, 3D-DS structures become easy to sample.
<Keywords:> Cytochrome c, 3D-DS dimer, MD Simulation, Generalized ensemble method, Go-like model
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 129-133, by J-STAGE]
<Title:> 汎用ニューラルネットワークポテンシャルを用いた 三元系ナノ合金のCO吸着特性の評価
<Author(s):> 綾子 田村, Gerardo VALADEZ HUERTA, 優輔 難波, 馨 久間, 通久 古山
<Corresponding author E-Mill:> ayako_tamura(at)shinshu-u.ac.jp
<Abstract:> Multi-element alloy nanoparticles have attracted attention for their potentially high catalytic properties. However, a high degree of freedom in configurations of metal atoms within nanoparticle increases the distinct adsorption sites, making it difficult to theoretically analyze its catalytic properties because the first-principles calculation requires a considerable computational cost. In this study, we develop a sequential scheme to calculate hundreds of adsorption sites by employing a pre-trained universal neural network potential named PFP. Our automated scheme is applied to CO single-molecule adsorption of CO onto PtRuIr ternary alloy nanoparticles. The calculation results are first compared with DFT results to confirm the accuracy. Adsorption energies in the alloy systems are widely distributed in comparison with those of the monometal counterparts, indicating that the alloy nanoparticle includes adsorption sites with various catalytic activities.
<Keywords:> Alloy nanoparticle, Universal neural network potential, CO adsorption
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0016/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 126-128, by J-STAGE]
<Title:> グラフニューラルネットワークによる有機遷移金属反応の学習
<Author(s):> 酒井　基至, 金重　光典, 安田　耕二
<Corresponding author E-Mill:> yasudak(at)imass.nagoya-u.ac.jp
<Abstract:> 深層学習による反応予測は，人が識別パターンを設計する必要がないため最近注目されている．しかし有機遷移金属反応は一見複雑で，深層学習の適応例は殆どなかった．我々は，論文や特許などから集めた数万件の実験反応を，素反応に分解したデータベースを構築し，グラフニューラルネットワークを用いて学習させた．最高で97.1%の精度で反応が予測できた．
<Keywords:> Graph neural network, Forward synthesis prediction, Organo transition metal reactions
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 118-122, by J-STAGE]
<Title:> 中分子の膜透過性に対する計算手法の検討
<Author(s):> 高橋　輝行, Hengphasatporn　Kowit, 原田　隆平, 重田　育照
<Abstract:> We used computational methods to predict the cell membrane permeability of a medium molecular drug, Bottromycin A2. We compared the three calculation methods, electronic structure calculation, molecular dynamics (MD) simulation, and empirical method, and examined which method was the best. As a result, we found that the first one is the best method among three methods treated, and that a prediction with high accuracy can be expected by increasing the number of experimental data.
<Keywords:> Membrane permeability, Medium Molecular Drug, Bottromycin A2, Cyclic Peptide, LogP
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0007/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 123-125, by J-STAGE]
<Title:> 抗体軽鎖四量体の立体構造の理論解析
<Author(s):> Lian　Duan, Hengphasatporn　Kowit, 重田　育照
<Abstract:> In this study, the trajectories of the four protomers corresponding to the light chain tetramers of human antibodies were obtained from MD simulations. The four protomers, which should be symmetrically constructed, were not completely symmetrical in the simulations. The DSSP analysis and 2D-RMSD analysis of the four protomers showed that although the secondary structure of the four protomers is approximately the same, the deconvolution of part of the α helix leads to the asymmetry of the overall structure in the simulation. Although the number of interactions within the protomers decreases, that between the protomers increases, making the overall energy more stable. We hypothesize that the deconvolution is caused by the formation of the α helix fragment in the tetramer, and the hydrogen bonding and van der Waals forces between the protomers lead to the breakage of the hydrogen bond within the protomers, further leading to the disappearance of the α helix.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0005/_article/-char/ja/