Molecular Dynamics Study On The Structure And Function Of Hyperthermophilic Protein Ssh10b

The hyperthermophilic proteins are found in archaea,which are considered as a class of highly conserved nucleic acid binding proteins,they play important roles in chromatin organization and gene regulation.The thermal stability of hyperthermophilic protein at high temperature and its structural properties have gained more attentions.The structural stability of hyperthermophilic protein Ssh10 b and the influence on conformation of RNA are studied by molecular dynamics simulations.The hyperthermophilic Ssh10 b from Sulfolobus shibatae is a member of the Sac10 b family,which binds RNA in vivo as a physiological substrate,and it has been postulated to play a key role in chromosomal organization in Archaea.Even though the crystal structure of Ssh10b-RNA was resolved successively by X-ray diffraction(PDB code: 3WBM),the detailed dynamic characteristics of Ssh10b-RNA are still unclear.In this study,molecular dynamics(MD)simulations at six temperatures(300 K,350 K,375 K,400 K,450 K and 500 K)were performed to investigate the mechanism of the structural stability of hyperthermophilic protein Ssh10 b and the influence on conformation of RNA.The simulation results indicate that RNA can be stabilized by Ssh10 b when the temperature rises up to 375 K.RNA is found to undergo conformational transition between A-RNA and A'-RNA when Ssh10 b binds to RNA at three different temperatures(300 K,350 K and 375 K).Salt bridges,hydrogen bonds and hydrophobic interactions are analyzed,and some residues have significant impact on the structural stability of the complex.This study will provide significant theoretical foundation for studying the structure and function of hyperthermophilic proteins and RNA.