カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.20, 116-118, by J-STAGE]
<Title:> デジタルアニーラ前処理空間探索と拡張アンサンブル法による環状ペプチド分子の高速安定構造探索
<Author(s):> 谷田　義明, 佐藤　博之, 眞鍋　敏夫, 島　千絵子
<Corresponding author E-Mill:> tanida.yoshiaki(at)fujitsu.com
<Abstract:> Cyclization generally stabilizes the bioactive conformation of the peptide and increases its affinity for the target. However, since cyclic peptides frequently adopt multiple conformations in solution, the structural information is not fully understood in experiments, and the relationship between structure and function is not well understood. We demonstrate the practical possibilities of using a combination of a special purpose computing engine (Digital Annealer) and REST2 (replica exchange with solute tempering) simulation in “ab initio” structure prediction of macrocyclic peptides.
<Keywords:> Macrocyclic peptide, Digital Annealer, Lattice protein model, REST2, Structure prediction, Cluster analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0036/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 119-122, by J-STAGE]
<Title:> DSSC用のトリフェニルアミンドナーベース有機色素におけるベンゾチアジアゾールを補助置換基とした時の効果の解析
<Author(s):> 山崎　直人, 野村　泰志, 森川　大
<Corresponding author E-Mill:> nomuray(at)shinshu-u.ac.jp
<Abstract:> It has been reported that the introduction of a 2, 1, 3-benzothiadiazole (BTD) into an organic dye used in dye sensitized solar cells (DSSC) makes its conversion efficiency improve. In this study, we examine the effects of BTD’s from viewpoints of its number and position, for DSSC with triphenylamine (TPA) as a donor moiety and cyanoacrylic acid (CA) as an acceptor one. And it is found that the best optical response was obtained when only one BTD was introduced on the side of the acceptor moiety.
<Keywords:> Organic dyes, Dye sensitized solar cells, Conjugation order, Optoelectronic properties, Benzothiadiazole
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 94-96, by J-STAGE]
<Title:> HSP90とコシャペロンp23複合体の安定性に関するシミュレーション研究
<Author(s):> 松倉　里紗, 宮下　尚之
<Corresponding author E-Mill:> miya(at)waka.kindai.ac.jp
<Abstract:> Heat Shock Protein 90 (HSP90) has been known as one of the molecular chaperone proteins, and it supports the correct folding of client proteins. It has been getting attention as the target protein for an anti-cancer drug because the client proteins sometimes include the critical proteins of progressing cancer. In the HSP90 chaperon cycle, several co-chaperones and substrates interact with HSP90 in turn. In this study, we focused on the interaction between HSP90 and p23, which is one of the co-chaperones. After the HSP90 dimer forms the closed conformation, the p23 and ATP bind to the HSP90. However, the detailed interaction among them has not been clear yet. To clear the mechanism of the interaction among HSP90, ATP, and p23, we performed the all-atom molecular dynamics simulations of ATP bound/unbound HSP90 with/without p23. We found that the domain swapping in HSP90 closed conformation is essential for the stable binding between HSP90 and p23, and the ATP binding supports the stability of the HSP90 and p23 complex.
<Keywords:> Molecular Dynamics Simulation, Co-chaperone, Heat Shock Protein 90, Chaperone cycle, Computational Biophysics
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0044/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 100-102, by J-STAGE]
<Title:> 3次元畳み込みニューラルネットワークの転移学習を用いたブロック共重合体の応力ひずみ曲線予測
<Author(s):> 川口　裕靖, 伊藤　真利子, 青柳　岳司, 大西　立顕
<Corresponding author E-Mill:> hironobukawaguchi(at)rikkyo.ac.jp
<Abstract:> The simulation to obtain stress-strain curves of block copolymers requires large computational resources. As an alternative to simulation, a method for high-throughput prediction of stress-strain curves using a three-dimensional convolutional neural network has been reported. In this study, we incorporated shortcut coupling into the neural network and performed pre-training and transfer learning in a step-by-step manner to successfully predict the stress-strain curve with high accuracy while reducing the training cost.
<Keywords:> Block copolymers, Microphase separation, Stress-strain curve, Deep learning, 3D convolutional neural network
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 89-91, by J-STAGE]
<Title:> エラストマーの一軸伸長における重み付きネットワーク構造の変化
<Author(s):> 伊藤　真利子, 天本　義史, 大西　立顕
<Corresponding author E-Mill:> marikoito.rnu1(at)gmail.com
<Abstract:> Previous studies on elastomers have revealed that the physical property of elastomers can be affected by the topological feature of their network structure. In the paper, for the simulation data of construction and elongation of elastomers, we analyzed the weighted network structure of each elastomer, where each node is a crosslinking point and the distance between crosslinking points is incorporated into the weight of a link. We derived centrality of each link based on the idea of closeness centrality in complex networks. We found that how the centrality of each node changes during elongation was significantly affected by the concentration under which crosslinking reaction was carried out, implicating that the weighted network structure of elastomer changed differently according to the reaction concentration.
<Keywords:> Elastomers, Network polymer, Complex networks, Weighted network, Closeness centrality
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 103-105, by J-STAGE]
<Title:> ランダムフォレストを用いた結晶性高分子のX線散乱回折データの解析
<Author(s):> 髙橋　数冴, 天本　義史, 菊武　裕晃, 伊藤　真利子, 高原　淳, 大西　立顕
<Corresponding author E-Mill:> takaha5.26(at)gmail.com
<Abstract:> Crystalline polymers have a hierarchical structure in which polymer chains are folded. Although each hierarchical structure strongly affects the physical properties of crystalline polymers, it is hard to describe the relationship between the formation conditions, crystal structure and physical properties. We used Random Forest regression to comprehensively investigate the relationship between these features of polylactic acid (PLA), a biodegradable crystalline polymer. It was suggested that important features for mechanical property and biodegradability, where the trade-off relationship between them is a significant issue of PLA, are related to the different level crystal structures. This shows that it is possible to use Random Forest for complex prediction of crystalline polymer properties to search for important forming conditions and crystal structures.
<Keywords:> Random Forest, Importance, Crystalline polymers, Polylactic acid, X-ray diffraction and scattering
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0042/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 97-99, by J-STAGE]
<Title:> ヘモグロビンのアロステリック制御に関するデータ科学的研究
<Author(s):> 田中　美帆, 高橋　由芽, 高見　慧, 北村　勇吉, 長岡　正隆
<Corresponding author E-Mill:> kitamura.yuhkichi(at)shizuoka.ac.jp
<Abstract:> In this letter, we investigated the contribution of bridging hydrogen bonds (BHB) via Cl^– on the T-R transition of human adult hemoglobin (HbA). We applied the time-series clustering method to time-series data of the αβ dimer rotation angle φ and the total number of the BHBs. Compared with the above two results, we have concluded that Cl^–-BHBs do not significantly contribute to the structural regulation of HbA.
<Keywords:> Keyword Hemoglobin, Allostery regulation, Chloride ion, Bridging hydrogen bond, Time-series clustering method
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0045/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 92-93, by J-STAGE]
<Title:> FMO結晶エネルギーを用いた結晶構造予測の高精度化
<Author(s):> 内海　洋平, 梅田　大貴, 奥脇　弘次, 小畑　繁昭, 中山　尚史, 後藤　仁志, 古石　誉之, 福澤　薫, 米持　悦生
<Corresponding author E-Mill:> k-fukuzawa(at)hoshi.ac.jp
<Abstract:> The aim of this study is to improve the accuracy of crystal structure prediction for Target XXIII, which was the target of the 6th Crystal Structure Prediction Blind Test (CSP6), by using the fragment molecular orbital (FMO) method. The intermolecular interaction analysis revealed that the dispersion interaction is stronger than the electrostatic interaction in all crystal polymorphs. In our method, the three correct structures included in the predicted structures were located within the top five. Furthermore, it was possible to evaluate the stability of polymorphs by the difference of intramolecular hydrogen bonds.
<Keywords:> Polymorphism, Crystal structure prediction, CONFLEX, Fragment molecular orbital method, ABINI-MP
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0041/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.7, -, by J-STAGE]
<Title:> Development of a Protein-Gene Motif Dictionary System for One-Stop Motif Analysis
<Author(s):> Masahiro OHTOMO, Hiroaki KATO
<Corresponding author E-Mill:> ohtomo(at)kuicr.kyoto-u.ac.jp
<Abstract:> The amino acid sequence of a protein is closely related to its structure and function. This is especially true for particular structural features called motifs, which are well-reserved sites in genome sequences. Biological data, such as the data for biopolymers, are rapidly increasing. Constructing a database for efficient analysis is important for identifying the structure and function of unknown biological data. Here, we constructed a protein-gene motif dictionary system for several model species using NoSQL, a database management system. This dictionary stored protein sequence motifs based on PROSITE, along with their corresponding mRNA sequences. Additionally, the database stored 3D structural information of the corresponding protein sequence motifs. The protein-gene dictionary has 49,265 registered entries, 120,047 sequence motifs, and 57,452 3D structural motifs from 7 model species. Software tools with graphical user interface were also developed to assist with intuitive search and analysis using the system. As a result, we discovered that zinc protease motif had co-occurrence with the cysteine switch motif. It was followed by the cysteine switch motif with a gap of 117 to 293 amino acids, however, its 3D Euclidean distance was preserved at around 12 .
<Keywords:> Protein motif, Nucleotide motif, Protein-gene motif dictionary, 3D structural motif, PROSITE, Co-occurrence motif analysis
<URL:> https://www.jstage.jst.go.jp/article/jccjie/7/0/7_2020-0008/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.7, -, by J-STAGE]
<Title:> Effect of meso-Substitution on the Selectivity of the Propene Reaction by Fe(IV)OCl Porphyrin: a Density Functional Theory Mechanistic Study
<Author(s):> Zhifeng MA, Masahiko HADA
<Corresponding author E-Mill:> hada(at)tmu.ac.jp
<Abstract:> We have performed density functional theory (DFT) calculations of C=C epoxidation and C-H hydroxylation of propene using a model of Fe(IV)OCl porphyrin cation radical complexes with fluorine and methyl groups as meso-substituents of the porphyrin ring. By gas-phase DFT calculations, it is found that fluorine substitution enhances the reactivity. According to detailed electronic feature analysis of the reactant complexes and transition states, electron-withdrawing groups at the meso-position stabilize the electron acceptor orbital of the complex more than the electron donation orbital of the substrate, leading to a decrease in the energy gap between these orbitals, and a lower energy barrier. More importantly, fluorine substitution for the pull effect makes hydroxylation favorable, whereas methyl substitution makes epoxidation preferable. The selective oxidation reactivity of Fe(IV)OCl porphyrin is largely ascribed to the effect of meso-substitution on the amount of electron transfer from propene to Fe(IV)OCl porphyrin. Additionally, we analyzed intersystem crossing between the quartet and sextet spin states using the potential energy surfaces (PESs), and the crossing seam between the quartet and sextet PESs occurs at around transition state TS1.
<Keywords:> Density functional theory, meso-substitution effect, Oxoiron(IV) porphyrin, Electronic structure, Molecular orbital
<URL:> https://www.jstage.jst.go.jp/article/jccjie/7/0/7_2020-0011/_html