[vc_empty_space][vc_empty_space]
Individual domain stability of Klenow-like DNA Pol I ITB-1 based on molecular dynamic simulation
Helwati H.a,b, Nurbaiti S.b, Hertadi R.b, Warganegara F.M.b, Akhmalokab
a Department of Chemistry, University of Syahkuala, Indonesia
b Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institute, Teknologi Bandung, Indonesia
[vc_row][vc_column][vc_row_inner][vc_column_inner][vc_separator css=”.vc_custom_1624529070653{padding-top: 30px !important;padding-bottom: 30px !important;}”][/vc_column_inner][/vc_row_inner][vc_row_inner layout=”boxed”][vc_column_inner width=”3/4″ css=”.vc_custom_1624695412187{border-right-width: 1px !important;border-right-color: #dddddd !important;border-right-style: solid !important;border-radius: 1px !important;}”][vc_empty_space][megatron_heading title=”Abstract” size=”size-sm” text_align=”text-left”][vc_column_text]The structural stability of individual domains in Klenow-like DNA polymerase IITB-1 were earned 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 IITB-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.[/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Author keywords” size=”size-sm” text_align=”text-left”][vc_column_text][/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Indexed keywords” size=”size-sm” text_align=”text-left”][vc_column_text]Domain interaction,Imdividual domain,Klenow-like DNA Pol I ITB-1,Molecular dynamic simulation,Protein stability[/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Funding details” size=”size-sm” text_align=”text-left”][vc_column_text][/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”DOI” size=”size-sm” text_align=”text-left”][vc_column_text][/vc_column_text][/vc_column_inner][vc_column_inner width=”1/4″][vc_column_text]Widget Plumx[/vc_column_text][/vc_column_inner][/vc_row_inner][/vc_column][/vc_row][vc_row][vc_column][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][/vc_column][/vc_row]