Homology modeling and molecular dynamics study on N-acetylneuraminate lyase
Homology modeling and molecular dynamics study on N-acetylneuraminate lyase
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DOI：
10.1007/s00894-008-0398-5
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发表时间：
2009-03-01
影响因子：
2.2
通讯作者：
Zhang, Hong-Xing
中科院分区：
文献类型：
--
作者：
Chu, Hui-Ying;Zheng, Qing-Chuan;Zhang, Hong-Xing
采用同源建模技术、分子力学和分子动力学方法，建立并完善了人n -乙酰神经胺酸裂解酶（hNAL, EC 4.1.3.3）的三维结构模型。通过Profile-3D和PROCHECK对该模型进行了进一步评估，证实了改进后的模型是可靠的。此外，底物（唾液酸和KDO）与hNAL活性位点的对接结果表明，hNAL可以裂解唾液酸和KDO。Thr51和Tyr143可能是关键的氨基酸残基，因为它们与底物有很强的氢键相互作用，这与Izard等人的实验结果很好地吻合（Structure 2: 361-369）。doi: 10.1016 / s0969 - 2126(00) 00038 - 1(1994))。通过对接研究，我们还发现Asp176和Ser218仅与唾液酸形成氢键，因此，它们可能有助于唾液酸与hNAL稳定相互作用。
With homology modeling techniques, molecular mechanics and molecular dynamics methods, a 3D structure model of N-acetylneuraminate lyase from human ( hNAL, EC 4.1.3.3) was created and refined. This model was further assessed by Profile-3D and PROCHECK, which confirms that the refined model is reliable. Furthermore, the docking results of the substrates ( sialic acid and KDO) into the active site of hNAL indicate that hNAL can cleave the sialic acid and KDO. Thr51 and Tyr143 may be the key amino acids residues as they have strong hydrogen bonding interactions with the substrates, which is in good agreement with the experimental results by Izard et al. ( Structure 2: 361-369. doi:10.1016/S0969-2126(00)00038-1 (1994)). From the docking studies, we also suggest that Asp176 and Ser218 only form hydrogen bonds with sialic acid, therefore, they may help sialic acid interact with hNAL steadly.