Molecular dynamics simulations of the thermal stability of tteRBP and ecRBP
Xian-li Feng, Xi Zhao, Hui Yu, Tie-dong Sun, Xu-ri Huang [1]
Molecular Tour
The Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) and Escherichia coli ribose binding protein (ecRBP) are both members of the periplasmic binding protein (PBP) superfamily. PBP play many roles in prokaryotic ABC transport, chemotaxis and intercellular communication systems. The backbone structure of tteRBP (optimal activity temperature is 375 K, colored in yellow) and ecRBP (optimal activity temperature is 329 K, (colored in violet) [2] is very similar, but significantly different in thermal stability.
In order to investigate the thermal stability of tteRBP (crystal structure (2ioy) is in violet, tteRBP under the room temperature (300 K) is in magenta, tteRBP under the optimal activity temperature (375 K) is in darkmagenta) and ecRBP (crystal structure (2dri) is in yellow, ecRBP under the room temperature (300 K) is in orange, ecRBP under the optimal activity temperature (329 K) is in chocolate) molecular dynamics simulations were performed for investigating the dynamics changes of the two proteins. The results show that the overall structures of the ecRBP and tteRBP are well maintained at the two temperatures, respectively. The radius of gyration, solvent accessible surface area, salt bridges, side-chain interactions and hydrogen bonds of the two proteins are almost unchanged at the different temperatures, their conformations also have no obvious changes, moreover, the RMSIP reflect that the overall motion of tteRBP or ecRBP move along the same direction of the essential fluctuations at the different temperatures, respectively. The further analysis shows that the tteRBP and ecRBP both have strong side-chain interactions to maintain structural stability at the high temperatures, and they have different patterns of the intramolecular motion and flexibility at the two temperatures. At room temperature and the optimal activity temperature, the tteRBP has higher flexibility and more high flexible regions (tteRBP under the optimal activity temperature (375 K) is in darkmagenta with highly flexible regions colored in green and ecRBP under the optimal activity temperature (329 K) is in chocolate with highly flexible regions colored in lime) than the ecRBP. These are the most differences between tteRBP and ecRBP. So the higher flexibility of tteRBP 375 K has more advantageous to maintain overall structure stability and adapt to high temperature by the fine-tune structure with higher flexibility. According to article of Matthew et al., (2008)[2] we can conclude that the strong side-chain interactions and flexibility of backbone both are the key factors to maintain thermal stability of the two proteins.
