月別: 2021年10月

[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