嘧啶核苷磷酸化酶的α和α/β结构域刚性移动的动力学模拟  

Dynamics Simulation of Rigid Body Movement of the α and α/β Domains of Pyrimidine Nucleoside Phosphorylase

作　　者：高雪峰[1] 黄旭日[1] 孙延波[1] 

机构地区：[1]吉林大学理论化学研究所,理论化学计算国家重点实验室,长春130023

出　　处：《高等学校化学学报》2003年第10期1885-1886,共2页Chemical Journal of Chinese Universities

基　　金：教育部骨干教师基金;吉林省杰出青年基金资助

摘　　要：Pyrimidine nucleoside phosphorylase(PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. The enzyme has two structure states: non-active opened structure and active closed structure. During change from non-active opened structure to active closed structure, the protein loop connecting domain α to domain α/β becomes bent remarkablely, which results in two domains closed up, and binding pocket reduce obviously. Setting about from the inactive-open X-ray structure, applying the method of molecular dynamic simulation, putting the ligand in the active-pocket, we carry out a dynamic simulation in the CVFF force-field for the entire system. The structures obstained are more approximately to the active-close X-ray structures, it proves that the rigid movement of the domains is arouse by the inducing effect of the ligand molecules.Pyrimidine nucleoside phosphorylase(PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. The enzyme has two structure states: non-active opened structure and active closed structure. During change from non-active opened structure to active closed structure, the protein loop connecting domain α to domain α/β becomes bent remarkablely, which results in two domains closed up, and binding pocket reduce obviously. Setting about from the inactive-open X-ray structure, applying the method of molecular dynamic simulation, putting the ligand in the active-pocket, we carry out a dynamic simulation in the CVFF force-field for the entire system. The structures obstained are more approximately to the active-close X-ray structures, it proves that the rigid movement of the domains is arouse by the inducing effect of the ligand molecules.

关 键 词：嘧啶核苷磷酸化酶 α结构 α/β结构域 刚性移动 动力学模拟 诱导作用 

分 类 号：Q555.4[生物学—生物化学] Q503