Study on the hydrolysis mechanism of phosphodiesterase 4 using molecular dynamics simulations

被引：9

作者：

Kang, N. S. ^{[1
]}

Chae, C. H. ^{[1
]}

Yoo, S. -E. ^{[1
]}

机构：

[1] Korea Res Inst Chem Technol, Taejon 305343, South Korea

来源：

MOLECULAR SIMULATION | 2006年 / 32卷 / 05期

关键词：

PDE4; cAMP; molecular dynamics simulation; hydrolysis mechanism; hydration pattern;

D O I：

10.1080/08927020600717111

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We carried out NPT molecular dynamics simulations in an explicit solvent to better understand the mechanism of cyclic adenosine monophosphates (cAMP) hydrolysis by phosphodiesterase 4 (PDE4) enzyme on atomic details and to obtain information on the dynamics characteristic of the catalytic domains of PDE4. In analyzing the water hydrogen-bond network around the active site, we also showed the importance of water in drug-protein interactions. In addition, we reported the characteristics of the hydration pattern and the dynamic distance distribution around the interesting residues. The results indicated that Asp318 plays the role of a general base that can activate water molecule for nucleophilic attack on cAMP. As expected, His160 plays the role of a proton donor for cAMP.

引用

页码：369 / 374

页数：6

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