Aeksiri Niran, Jantafong Tippawan
Center for Agriculture Biotechnology, Faculty of Agriculture, Natural Resources, and Environment, Naresuan University, Phitsanulok 65000, Thailand; Department of Agricultural Sciences, Faculty of Agriculture, Natural Resources, and Environment, Naresuan University, Phitsanulok 65000, Thailand.
Department of Virology and Immunology, Faculty of Veterinary Medicine, Mahanakorn University of Technology, Thailand.
J Mol Graph Model. 2017 Jun;74:125-134. doi: 10.1016/j.jmgm.2017.03.015. Epub 2017 Mar 24.
Porcine reproductive and respiratory virus (PRRSV) causes major economic concerns for the swine industry worldwide. We have performed molecular dynamics simulations (MD) and principle component analysis (PCA) to investigate the role of the catalytic triad and conformational dynamics of type I and type II of nsp4 PRRSV. The results showed that the RMSF of residues 136-142 near the active site of all models was highly flexible. Moreover, we identified the effect of single structural mutations of the catalytic triad. The percentage of residue with a 0.1nm RMSF value and PCA results revealed that the mutations affected domain I and II suggesting the wild types were more stable than the mutants. At the catalytic triad, the distances between H39 and S118 were very flexible while the distances between H39 and D64 were very stable. H39, D64 and S118 showed high occupancy percentage of the hydrogen bond interaction with many residues that are conserved in PRRSVAS, PRRSVES, LDVC, LDVP and EAV. Moreover, S118 of wild-type protein formed H-bonds with T134 and G135 but these interactions were lost in PRRSVAV (S118A) and PRRSVES (S117A) indicating that the substitution of important H-bond interaction in PRRSVAS (S118A) and PRRSVES (S117A) affected the flexibility around the catalytic triad, conformation and proteolytic activity. Overall, our study may provide the structural basic of the catalytic triad and be useful for testing the protein activity in future experiments.
猪繁殖与呼吸综合征病毒（PRRSV）给全球养猪业带来了重大经济问题。我们进行了分子动力学模拟（MD）和主成分分析（PCA），以研究PRRSV非结构蛋白4（nsp4）I型和II型催化三联体的作用及其构象动力学。结果表明，所有模型活性位点附近136 - 142位残基的均方根波动（RMSF）具有高度灵活性。此外，我们确定了催化三联体单个结构突变的影响。具有0.1nm RMSF值的残基百分比和PCA结果表明，这些突变影响了结构域I和II，这表明野生型比突变体更稳定。在催化三联体处，组氨酸39（H39）与丝氨酸118（S118）之间的距离非常灵活，而H39与天冬氨酸64（D64）之间的距离非常稳定。H39、D64和S118与PRRSVAS、PRRSVES、LDVC、LDVP和EAV中许多保守残基形成氢键相互作用的占有率很高。此外，野生型蛋白的S118与苏氨酸134（T134）和甘氨酸135（G135）形成氢键，但在PRRSVAV（S118A）和PRRSVES（S117A）中这些相互作用消失，这表明PRRSVAS（S118A）和PRRSVES（S117A）中重要氢键相互作用的取代影响了催化三联体周围的灵活性、构象和蛋白水解活性。总体而言，我们的研究可能为催化三联体提供结构基础，并有助于在未来实验中测试蛋白活性。
