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首页> 外文期刊>Drug Target Insights >In Silico Molecular Characterization of Cysteine Protease YopT from Yersinia pestis by Homology Modeling and Binding Site Identification
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In Silico Molecular Characterization of Cysteine Protease YopT from Yersinia pestis by Homology Modeling and Binding Site Identification

机译：同源性建模和结合位点鉴定的鼠疫耶尔森氏菌半胱氨酸蛋白酶YopT的计算机分子表征

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摘要

Plague is a major health concern and Yersinia pestis plays the central causal role in this disease. Yersinia pestis has developed resistance against the commonly available drugs. So, it is now a key concern to find a new drug target. Cysteine protease YopT enzyme is an important factor used by Yersinia pestis for pathogenesis in its host and it has the anti-phagocytic function of removal of C-termini lipid modification. The 3D structure of cysteine protease YopT of Yersinia pestis was determined by means of homology modeling through multiple alignments followed by intensive optimization and validation. The modeling was done by Phyre 2 and refined by ModRefiner. The obtained model was verified with structure validation programs such as PROCHECK, verify 3D and ERRAT for reliability. Interacting partners and active sites were also determined. PROCHECK analysis showed that 93% of the residues are in the most favored region, 5.9% are in the additional allowed region and 1.1% are in the generously allowed region of the Ramachandran plot. The verify 3D value of 0.78 indicates that the environmental profile of the model is good. SOPMA is employed for calculation of the secondary structural features of cysteine protease YopT. Active site determination through CASTp proposes that this protein can be utilized as a potential drug target. However, these findings should further be confirmed by wet lab studies for a targeted therapeutic agent design against Yersinia pestis.
机译：鼠疫是主要的健康问题，而鼠疫耶尔森菌在该疾病中起着重要的因果作用。鼠疫耶尔森氏菌对常用药物产生了抗药性。因此，现在是寻找新药目标的关键问题。半胱氨酸蛋白酶YopT酶是鼠疫耶尔森氏菌用于其宿主发病的重要因素，并且具有去除C-末端脂质修饰的抗吞噬功能。鼠疫耶尔森氏菌半胱氨酸蛋白酶YopT的3D结构是通过多重比对的同源性建模，然后进行深入的优化和验证来确定的。建模由Phyre 2完成，并由ModRefiner完善。通过结构验证程序（例如PROCHECK）验证了所获得的模型，验证了3D和ERRAT的可靠性。还确定了互动伙伴和活动站点。 PROCHECK分析表明，Ramachandran图中93％的残基位于最有利的区域，5.9％的残基位于允许的其他区域，而1.1％的残基位于慷慨的允许区域。验证的3D值为0.78表示模型的环境状况良好。 SOPMA用于计算半胱氨酸蛋白酶YopT的二级结构特征。通过CASTp进行的活性位点测定表明，该蛋白可用作潜在的药物靶标。但是，这些发现应通过湿实验室研究进一步证实，以针对鼠疫耶尔森氏菌进行靶向治疗。

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