scholarly journals DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Jing Wu ◽  
Alexandra de Paz ◽  
Bradley M. Zamft ◽  
Adam H. Marblestone ◽  
Edward S. Boyden ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Binding Strength ◽  
Y Family

Effects of electrostatic interactions on global folding and local conformational dynamics of a multidomain Y-family DNA polymerase

2021 ◽  
Author(s):  
Qing-Miao Nie ◽  
Li-Zhen Sun ◽  
Hai-Bin Li ◽  
Xiakun Chu ◽  
Jin Wang
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Electrostatic Interactions ◽  
Conformational Dynamics ◽  
Individual Domain ◽  
The Individual ◽  
Y Family

Electrostatic interactions can facilitate the folding of the multidomain DNA polymerase Dpo4 by refining the folding order of the individual domain and promote the functional conformational dynamics of Dpo4 during the DNA-binding recognition.

scholarly journals Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Xiakun Chu ◽  
Zucai Suo ◽  
Jin Wang
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Protein Interactions ◽  
Conformational Dynamics ◽  
Dna Lesions ◽  
Trade Off ◽  
Dna Polymerase Iv ◽  
Functional Dna ◽  
And Function ◽  
Y Family

The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to ‘U-shaped’ DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4–DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.

scholarly journals Single-stranded DNA-binding Protein Recruits DNA Polymerase V to Primer Termini on RecA-coated DNA

2008 ◽  
Vol 283 (13) ◽  
pp. 8274-8282 ◽  
Author(s):  
Gali Arad ◽  
Ayal Hendel ◽  
Claus Urbanke ◽  
Ute Curth ◽  
Zvi Livneh
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Single Stranded Dna ◽  
Dna Polymerase V

scholarly journals The Spacious Active Site of a Y-Family DNA Polymerase Facilitates Promiscuous Nucleotide Incorporation Opposite a Bulky Carcinogen-DNA Adduct

2004 ◽  
Vol 279 (35) ◽  
pp. 36951-36961 ◽  
Author(s):  
Rebecca A. Perlow-Poehnelt ◽  
Ilya Likhterov ◽  
David A. Scicchitano ◽  
Nicholas E. Geacintov ◽  
Suse Broyde
Keyword(s):  
Dna Polymerase ◽  
Active Site ◽  
Dna Adduct ◽  
Nucleotide Incorporation ◽  
Y Family

scholarly journals Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase

2008 ◽  
Vol 36 (12) ◽  
pp. 3867-3878 ◽  
Author(s):  
Jessica A. Brown ◽  
Sean A. Newmister ◽  
Kevin A. Fiala ◽  
Zucai Suo
Keyword(s):  
Dna Polymerase ◽  
Lesion Bypass ◽  
Double Base ◽  
Base Lesion ◽  
Y Family

scholarly journals Sloppy Bypass of an Abasic Lesion Catalyzed by a Y-family DNA Polymerase

2007 ◽  
Vol 282 (11) ◽  
pp. 8199-8206 ◽  
Author(s):  
Kevin A. Fiala ◽  
Zucai Suo
Keyword(s):  
Dna Polymerase ◽  
Y Family

scholarly journals The (I/Y)XGG Motif of Adenovirus DNA Polymerase Affects Template DNA Binding and the Transition from Initiation to Elongation

2001 ◽  
Vol 276 (32) ◽  
pp. 29846-29853 ◽  
Author(s):  
Arjan B. Brenkman ◽  
Marinus R. Heideman ◽  
Veronica Truniger ◽  
Margarita Salas ◽  
Peter C. van der Vliet
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Template Dna
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