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首页> 外文期刊>Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena >Molecular modeling, dynamics and docking studies of purine nucleoside phosphorylase from Streptococcus pyogenes.
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Molecular modeling, dynamics and docking studies of purine nucleoside phosphorylase from Streptococcus pyogenes.

机译：化脓性链球菌嘌呤核苷磷酸化酶的分子建模，动力学和对接研究。

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摘要

Purine Nucleoside Phosphorylase (PNP) catalyzes the reversible phosphorolysis of N-glycosidic bonds of purine nucleosides and deoxynucleosides, except for adenosine, to generate ribose 1-phosphate and the purine base. PNP has been submitted to intensive structural studies. This work describes for the first time a structural model of PNP from Streptococcus pyogenes (SpPNP). We modeled the complexes of SpPNP with six different ligands in order to determine the structural basis for specificity of these ligands against SpPNP. Molecular dynamics (MD) simulations were performed in order to evaluate the overall stability of SpPNP model. The analysis of the MD simulation was assessed mainly by principal component analysis (PCA) to explore the trimeric structure behavior. Structural comparison, between SpPNP and human PNP, was able to identify the main features responsible for differences in ligand-binding affinities, such as mutation in the purine-binding site and in the second phosphate-binding site. The PCA analysis suggests a different behavior for each subunit in the trimer structure.
机译：嘌呤核苷磷酸化酶（PNP）催化除腺苷外，嘌呤核苷和脱氧核苷的N-糖苷键可逆磷酸化，生成核糖1-磷酸和嘌呤碱基。 PNP已提交给深入的结构研究。这项工作首次描述了化脓性链球菌（SpPNP）的PNP结构模型。我们确定了具有六个不同配体的SpPNP的复合物，以确定这些配体对SpPNP的特异性的结构基础。为了评估SpPNP模型的整体稳定性，进行了分子动力学（MD）模拟。 MD模拟的分析主要通过主成分分析（PCA）进行评估，以探索三聚体的结构行为。 SpPNP和人PNP之间的结构比较能够确定导致配体结合亲和力差异的主要特征，例如嘌呤结合位点和第二个磷酸盐结合位点的突变。 PCA分析表明三聚体结构中每个亚基的行为不同。

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