Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations

Abstract

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.

Variations in the NSP4 gene of the type 2 porcine reproductive and respiratory syndrome virus isolated in China from 1996 to 2021

“…3CLSP plays an essential role in regulation of PRRSV replication, inhibition of the production of host IFN, and induction of host cell apoptosis. It has, therefore, emerged as an important target protein for further study of the pathogenesis of PRRSV [20][21][22]. NSP4 interacts with many types of host proteins, and it can cleave host proteins, which may be one of the main mechanisms by which PRRSV escapes detection by the host immune response.…”

Aspartic acid at residue 185 modulates the capacity of HP-PRRSV nsp4 to antagonize IFN-I expression

“…Like other RNA viruses in the order Nidovirales, such as EAV and severe acute respiratory syndrome coronavirus (SARS-CoV), PRRSVencoded proteases play a prominent role in virus replication. PRRSV nsp4 is responsible for most of the nonstructural protein processing to join into the virus replication (Aeksiri and Jantafong, 2017). PRRSV nsp4 has three domains, including two antiparallel β-barrels (called domain I and domain II, respectively) and an extra C-terminal α/β domain (domain III) (Tian et al, 2009).…”