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Domain motions of Klenow-like DNA polymerase I ITB-1 in the absence of substrate
Nurbaiti S.a, Nagao H.b, Saito H.b, Hertadi R.a, Martoprawiro M.A.a, Akhmalokaa
a Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Indonesia
b Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Japan
[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]Domain motions in proteins have long been recognized to have critical function in binding and recognition of ligands, enzymatic activities, and regulations. The motion of Klenow-like DNA Polymerase I ITB-1 domain in the absence of substrate has been analyzed by molecular dynamics (MD) simulation for a period of 8.5 ns. The root-mean-square fluctuation’s and snapshot analysis showed that the fingers and thumb subdomains are the most flexible regions. Further analysis based on principal component and cross-correlation to the MD trajectory showed that 3’→;5′ exonuclease and 5’→6;3′ polymerase domains exhibited anticorrelated motion. Furthermore, the communication between residues belonged to the 3’→5′ exonuclease domain appeared as correlated motion, in contrast to the residues inside 5’→3′ polymerase domain represented by thumb and fingers subdomains showed anticorrelated motion. In addition, the surface electrostatic potential analysis showed that the interface between thumb and fingers subdomains has positive charges, this might due to caused repulsion of the subdomains resulting periodical motion even without substrates. © IJIB.[/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]Cross-correlation map,Domain motion,Electrostatic potential,Molecular dynamic,Principal component analysis[/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]