三种糖基化中间产物与小牛胸腺DNA相互作用的多光谱和分子动力学模拟  

Multispectral and molecular dynamics simulation studies of the interaction of three glycosylation intermediates with calf thymus DNA

作　　者：吴健妹 张国文[1] WU Jianmei;ZHANG Guowen(State Key Laboratory of Food Science and Technology,Nanchang University,Nanchang 330047,China)

机构地区：[1]南昌大学食品科学与技术国家重点实验室,江西南昌330047

出　　处：《南昌大学学报（理科版）》2023年第3期243-254,共12页Journal of Nanchang University(Natural Science)

基　　金：国家自然科学基金面上项目(22078143);江西省自然科学基金重点项目(20212ACB205010);食品科学与技术国家重点实验室项目(SKLF-ZZB-202136;SKLF-ZZA-201912)。

摘　　要：三种α-二羰基化合物:丙酮醛(MGO)、丁二酮(DA)和乙二醛(GO)作为常见的高反应活性的糖基化中间体,会对体内的生物大分子(如DNA)造成损伤。MGO、DA和GO与小牛胸腺DNA(ctDNA)的相互作用特性通过多光谱方法结合计算机模拟技术进行测定。紫外光谱分析表明,范德华力和氢键驱动MGO、DA和GO与ctDNA发生自发结合,分子动力学模拟中的各能量分布佐证了这一结论。在25℃下,MGO、DA和GO与ctDNA的结合常数接近经典的凹槽结合剂,其值分别为2.99×103、1.96×103和1.05×103L·mol-1。NaCl、单双链DNA、热变性、粘度和园二色谱实验证明了MGO、DA和GO与ctDNA均通过凹槽方式结合。分子对接直观显示了MGO、DA和GO是结合在DNA富含AT的小沟区,其中DT7和DA18是结合的活性位点。分子动力学模拟显示MGO-ctDNA复合物较游离ctDNA有更高的均方根偏差(RMSD)、回旋半径(Rg)和均方根波动(RMSF)值,说明MGO的结合使DNA结构部分松散,稳定性减弱。凝胶电泳实验表明,在赖氨酸和Cu2+存在下,MGO、DA和GO均能损伤质粒DNA,MGO和GO甚至会完全破坏DNA的超螺旋形态。Threeα-dicarbonyl compounds,methylglyoxal(MGO),diacetyl(DA)and glyoxal(GO)were common highly reactive glycosylation intermediates that can cause damage to biological macromolecules(e.g.DNA)in the body.The interaction properties of MGO,DA and GO with calf thymus DNA(ctDNA)were determined by multispectral methods combined with computer simulation techniques.Analysis of UV spectra indicated that MGO,DA and GO binding to ctDNA spontaneously were mainly driven by van der Waals forces and hydrogen bonding,and the energy distribution in molecular dynamics simulations supported this conclusion.The binding constants of MGO,DA and GO with ctDNA at 25℃were close to those of classical groove-binders,with corresponding values of 2.99×103,1.96×103 and 1.05×103 L·mol-1,respectively.NaCl,single and double-stranded DNA,thermal denaturation,viscosity and CD spectroscopy experiments demonstrated that MGO,DA and GO were all bound to ctDNA via groove binding.Molecular docking visualization showed that MGO,DA and GO were bound in the AT-rich minor groove region of DNA,with DT7 and DA18 being the active sites of binding.Molecular dynamics simulations of the MGO-ctDNA complex had higher root mean square deviation,radius of gyration,and root mean square fluctuation values than free DNA,indicating that the binding of MGO loosened and tended to destabilise parts of the DNA structure.Gel electrophoresis experiments showed that MGO,DA and GO could damage plasmid DNA in the presence of lysine and Cu 2+,and MGO and GO even completely disrupted the superhelical morphology of DNA.

关 键 词：糖基化中间产物 α-二羰基化合物 小牛胸腺DNA 相互作用 分子动力学模拟 

分 类 号：O657.3[理学—分析化学]