化学位移是核磁共振波谱(nuclear magnetic resonance spectrum,NMR)的一项重要参数,由于其对原子周围化学环境十分敏感,因此化学位移的理论计算在生物大分子的结构预测中扮演着重要的角色[1-2]。目前预测生物大分子NMR化学位移的理论...化学位移是核磁共振波谱(nuclear magnetic resonance spectrum,NMR)的一项重要参数,由于其对原子周围化学环境十分敏感,因此化学位移的理论计算在生物大分子的结构预测中扮演着重要的角色[1-2]。目前预测生物大分子NMR化学位移的理论方法主要分为两类:一类是从实验数据拟合得到的经验或者半经验方法[3-4];另一类是基于量子力学理论的从头计算方法[5-7]。与前者相比,量子力学方法不依赖数据集,针对不同体系具有很好的移植性。由于量子力学方法需要的计算时间随计算体系的大小呈多项式增长,因此人们基于“化学局域性”原理发展了分块量子化学方法来提高计算效率。本课题组长期致力于分块量子化学方法的发展,针对生物大分子的NMR化学位移精确预测发展了自动分块的大分子NMR化学位移计算方法(automated fragmentation,AF-NMR)。本文简要介绍本课题组在这方面的研究进展。展开更多
As the major and abundant type of glucosinolates(GL)in plants,sinigrin has potential functions in promoting health and insect defense.The final step in the biosynthesis of sinigrin core structure is highly representat...As the major and abundant type of glucosinolates(GL)in plants,sinigrin has potential functions in promoting health and insect defense.The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds,which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase(SOT).However,due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL,little is known about this sulfonation process.Fortunately,the crystal structure of SOT 18 from Arabidopsis thaliana(At SOT18)containing the substance(sinigrin)similar to 3-methylthiopropyl GL has been determined.To understand the enzymatic mechanism,we employed molecular dynamics(MD)simulation and quantum mechanics combined with molecular mechanics(QM/MM)methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18.The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism.Moreover,Lys93,Thr96,Thr97,Tyr130,His155,and two enzyme peptide chains(Pro92-Lys93 and Gln95-Thr96-Thr97)play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry.Particularly,His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process.The presently proposed concerted dissociative mechanism explains the role of At SOT18 in sinigrin biosynthesis,and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.展开更多
文摘化学位移是核磁共振波谱(nuclear magnetic resonance spectrum,NMR)的一项重要参数,由于其对原子周围化学环境十分敏感,因此化学位移的理论计算在生物大分子的结构预测中扮演着重要的角色[1-2]。目前预测生物大分子NMR化学位移的理论方法主要分为两类:一类是从实验数据拟合得到的经验或者半经验方法[3-4];另一类是基于量子力学理论的从头计算方法[5-7]。与前者相比,量子力学方法不依赖数据集,针对不同体系具有很好的移植性。由于量子力学方法需要的计算时间随计算体系的大小呈多项式增长,因此人们基于“化学局域性”原理发展了分块量子化学方法来提高计算效率。本课题组长期致力于分块量子化学方法的发展,针对生物大分子的NMR化学位移精确预测发展了自动分块的大分子NMR化学位移计算方法(automated fragmentation,AF-NMR)。本文简要介绍本课题组在这方面的研究进展。
基金supported by the National Natural Science Foundation of China(No.21973005)。
文摘As the major and abundant type of glucosinolates(GL)in plants,sinigrin has potential functions in promoting health and insect defense.The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds,which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase(SOT).However,due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL,little is known about this sulfonation process.Fortunately,the crystal structure of SOT 18 from Arabidopsis thaliana(At SOT18)containing the substance(sinigrin)similar to 3-methylthiopropyl GL has been determined.To understand the enzymatic mechanism,we employed molecular dynamics(MD)simulation and quantum mechanics combined with molecular mechanics(QM/MM)methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18.The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism.Moreover,Lys93,Thr96,Thr97,Tyr130,His155,and two enzyme peptide chains(Pro92-Lys93 and Gln95-Thr96-Thr97)play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry.Particularly,His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process.The presently proposed concerted dissociative mechanism explains the role of At SOT18 in sinigrin biosynthesis,and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.
