Impact of Temperature on Structural Changes in nsp2 and nsp3 of CHIKV: Molecular Dynamics Simulations

Abstract

Authors have considered non-structural protease-2 (nsp2) and non-structural protease-3 (nsp3) of CHIKV for the investigation as they are involved in the replication of the virus and increases the infections in the human. CHIKV protease (nsp2), has a catalytic dyad (Cys1013/His1083) that processes viral polyproteins. Further, it has also been suggested that the catalytic dyad is interchangeable to a serine (proximal) and hence making called non-papain-like cysteine protease. Similarly, nsp3 plays important role during replication of CHIKV genome. In this work, we have investigated the effect of temperature on the structural stability of nsp2 and nsp3 of CHIKV. Although, we did not get any regular patter for change in the RMSD and RMSF for the nsp3 of CHIKV and observed that RMSD for nsp3 of CHIKV is acceptable at all the temperature (300, 325 and 350 K) but the minimum RMSD values are obtained at 325 K. Similarly, no regular pattern is observed for RMSF trajectories of nsp3 of CHIKV at different temperature and minimum fluctuations in the position of amino-acids at 325 K. Further, the RMSD and RMSF trajectories for nsp2 of CHIKV are investigated and observed a regular pattern in the RMSD and RMSF trajectories generated from MD simulations on increasing the temperature. In this, RMSD values are minimum at 300 K while the fluctuation in the position of amino-acids are maximum.