The Role of Interface Domain Interactions on Thermal Stability of DNA polymerase I ITB-1

ABSTRACT

Temperature-induced unfolding of Klenow-like DNA Pol I ITB-1 was investigated by molecular dynamic simulation, focusing on the key factors that stabilizing the protein. The result showed that the protein unfolded initially by disruptions of the interface between of 5’→3’polymerase and 3’→5’ exonuclease domains. Several amino acid residues, Lys374-Glu489 and Lys381-Glu487, form salt bridges at the interface domain and played an important role in the contact between the two domains. These interactions were examined through in silico mutation by comparing the free-energy solvation changes between the wild type and the mutants. The disruption of salt bridges by replacing Glu to Gln at position 487 and 489 caused positive value of ΔΔ_Gsolv, suggesting that the proteins were more unstable. While the substitution of Glu to Asp at position 487 and 489 preserved the electrostatic interaction. The last two mutants showed negative value of ΔΔ_Gsolv, suggesting that the proteins were more stable. All the data suggested that the salt bridges between Lys374-Glu489 and Lys381-Glu487 have an essential role in maintaining the stability of the interface domain of DNA Pol I ITB-1, and thus, the whole structure of the protein.

Keywords:

crystallization, DNA polymerase I ITB-1, molecular dynamic simulation, salt bridges, free-energy calculation.