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首页> 外文期刊>Journal of Molecular Modeling >Molecular modeling and dynamics studies of purine nucleoside phosphorylase from Bacteroides fragilis
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Molecular modeling and dynamics studies of purine nucleoside phosphorylase from Bacteroides fragilis

机译：脆弱拟杆菌的嘌呤核苷磷酸化酶的分子建模和动力学研究

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摘要

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of N-ribosidic bonds of purine nucleosides and deoxynucleosides, except adenosine, to generate ribose 1-phosphate and the purine base. This work describes for the first time a structural model of PNP from Bacteroides fragilis (Bf). We modeled the complexes of BfPNP with six different ligands in order to determine the structural basis for specificity of these ligands against BfPNP. Comparative analysis of the model of BfPNP and the structure of HsPNP allowed identification of structural features responsible for differences in the computationally determined ligand affinities. The molecular dynamics (MD) simulation was assessed to evaluate the overall stability of the BfPNP model. The superposition of the final onto the initial minimized structure shows that there are no major conformational changes from the initial model, which is consistent with the relatively low root mean square deviation (RMSD). The results indicate that the structure of the model was stable during MD, and does not exhibit loosely structured loop regions or domain terminals.
机译：嘌呤核苷磷酸化酶（PNP）催化除腺苷以外的嘌呤核苷和脱氧核苷的N-核糖键的可逆磷酸化反应，生成核糖1-磷酸和嘌呤碱基。这项工作首次描述了脆弱拟杆菌（Bf）的PNP结构模型。为了确定这些配体对BfPNP的特异性的结构基础，我们对BfPNP与六个不同配体的复合物进行了建模。通过对BfPNP模型和HsPNP结构的比较分析，可以鉴定造成计算确定的配体亲和力差异的结构特征。评估分子动力学（MD）模拟以评估BfPNP模型的整体稳定性。最终物到初始最小化结构上的叠加表明，与初始模型相比，没有重大构象变化，这与相对较低的均方根偏差（RMSD）相一致。结果表明，该模型的结构在MD期间是稳定的，并且没有表现出松散的环状区域或域末端。

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  • 来源
    《Journal of Molecular Modeling》 |2009年第8期|913-922|共10页
  • 作者

    Ivani Pauli; Luis Fernando Saraiva Macedo Timmers; Rafael Andrade Caceres; Luiz Augusto Basso; Diógenes Santiago Santos; Walter Filgueira de Azevedo Jr.;

  • 作者单位

    Laboratório de Bioquímica Estrutural Faculdade de Biociências Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre RS Brazil;

    Laboratório de Bioquímica Estrutural Faculdade de Biociências Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre RS Brazil;

    Laboratório de Bioquímica Estrutural Faculdade de Biociências Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre RS Brazil;

    Programa de Pós-Graduação em Medicina e Ciências da Saúde Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre RS Brazil;

    Programa de Pós-Graduação em Medicina e Ciências da Saúde Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre RS Brazil;

    Laboratório de Bioquímica Estrutural Faculdade de Biociências Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre RS Brazil;

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  • 原文格式 PDF
  • 正文语种 eng
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  • 关键词

    Bacteroides fragilis; Bioinformatics; Drug-design; Molecular dynamics; Molecular modeling;

    机译：脆弱拟杆菌;生物信息学;药物设计;分子动力学;分子建模;

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