Individual Domain Stability of Klenow-Like DNA Pol I ITB-1 Based on Molecular Dynamic Simulation

Hira Helwati^1,2, Santi Nurbaiti², Rukman Hertadi², Fida Madayanti Warganegara² and Akhmaloka²*

¹Department of Chemistry, University of Syahkuala, Banda Aceh Indonesia.

²Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institute, Teknologi Bandung, Jln Ganesha 10 Bandung - 40132 Indonesia.

Corresponding Author E-mail:loka@chem.itb.ac.id

ABSTRACT: The structural stability of individual domains in Klenow-like DNA polymerase I ITB-1 were carried out by molecular dynamics simulation. Based on Ca-root-mean square deviation (RMSD) at 300K, supported by root-mean-square fluctuation (RMSF), secondary structure and solvent accessible surface area (SASA) analysis suggested that the Klenow-like DNA Pol I ITB-1, 3'®5' exonuclease and 5’®3’ polymerase domains did not show significant change in the proteins structure during 10 ns MD simulation. These results suggested that both domains were stable and may have an independent folding at 300K. However, RMSD analysis at higher temperature (360 K) suggested that polymerase domain was the most unstable, indicated by increasing the RMSD value of the domain was faster than that the other two protein models. RMSD analysis at 360 K with extended times of simulation suggested that the structure of 3'®5' exonuclease domain required longer time to unfold than that polymerase domain. The MD simulation at 360 K suggested that interaction between 3’®5’ exonuclease and 5’®3’ polymerase domains have significant role in maintaining thermal stability of the whole structure of Klenow-like DNA Pol I ITB-1.

KEYWORDS: Klenow-like DNA Pol I ITB-1; protein stability; molecular dynamic simulation; imdividual domain

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