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首页> 外文期刊>Journal of Biomolecular Structure and Dynamics >Protein flexibility and conformational states of Leishmania antigen eIF-4A: Identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling
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Protein flexibility and conformational states of Leishmania antigen eIF-4A: Identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling

机译：利什曼原虫抗原eIF-4A的蛋白质柔韧性和构象状态：使用比较基因组学和分子建模方法鉴定一种新的可能的蛋白质佐剂

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摘要

Recent homology modeling studies have identified specific residues (epitope) of the Leishmania RNA helicase protein (LmeIF) that stimulates production of IL-12 cytokine. However, question remains concerning how LmeIF's N-terminal moiety initiates adjuvant effects. Extensive molecular modeling combining the normal mode analysis (NMA) and molecular dynamics simulations, in the present study, has demonstrated that the LmeIF structure may exist in two different forms corresponding to the extended and collapsed (closed) states of the entire structure. The computational results showed that the two domains of the LmeIF structure tend to undergo large fluctuations in a concerted fashion and have strong effect on the solvent accessible surface of the epitope situated on the N-terminal structure. The conformational freedom of the C-terminal domains may explain why the entire LmeIF protein is not as active as the N-terminal moiety. Thereafter, a comparative genome analysis with subsequent homology modeling and molecular electrostatic potential (MEP) techniques allowed us to predict a novel and plausible RNA helicase (LI-helicase) from the Listeria source with adjuvant property as observed for the Leishmania eIF-4A protein. The structural folding and MEP maps revealed similar topologies of the epitope of both LmeIF and LI-helicase proteins and striking identity in the local disposition of the charged groups.
机译：最近的同源性建模研究已经确定了刺激IL-12细胞因子产生的利什曼原虫RNA解旋酶蛋白（LmeIF）的特定残基（表位）。然而，关于LmeIF的N末端部分如何引发佐剂作用仍存在疑问。在本研究中，结合正态分析（NMA）和分子动力学模拟的广泛分子建模表明，LmeIF结构可能以两种不同形式存在，分别对应于整个结构的扩展和折叠（闭合）状态。计算结果表明，LmeIF结构的两个结构域倾向于以一致的方式经历大的波动，并且对位于N端结构的表位的溶剂可及表面有很强的影响。 C末端结构域的构象自由可以解释为什么整个LmeIF蛋白不如N末端部分具有活性。此后，通过比较基因组分析以及随后的同源性建模和分子静电潜能（MEP）技术，我们可以从利斯特氏菌来源中预测出一种新颖且合理的RNA解旋酶（LI-解旋酶），并具有对利什曼原虫eIF-4A蛋白观察到的佐剂特性。结构折叠和MEP图显示了LmeIF和LI-解旋酶蛋白的表位的相似拓扑，并且在带电基团的局部位置具有惊人的同一性。

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