scholarly journals Global Conformational Dynamics of a Y-Family DNA Polymerase during Catalysis

PLoS Biology ◽  
2009 ◽  
Vol 7 (10) ◽  
pp. e1000225 ◽  
Author(s):  
Cuiling Xu ◽  
Brian A. Maxwell ◽  
Jessica A. Brown ◽  
Likui Zhang ◽  
Zucai Suo
Keyword(s):  
Dna Polymerase ◽  
Conformational Dynamics ◽  
Y Family

scholarly journals Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment

2013 ◽  
Vol 42 (4) ◽  
pp. 2555-2563 ◽  
Author(s):  
Alfonso Brenlla ◽  
Radoslaw P. Markiewicz ◽  
David Rueda ◽  
Louis J. Romano
Keyword(s):  
Dna Polymerase ◽  
Single Molecule ◽  
Base Pair ◽  
Conformational Dynamics ◽  
Binary Complex ◽  
Translesion Dna Synthesis ◽  
Dna Polymerase Iv ◽  
Y Family ◽  
Dntp Binding ◽  
Base Pair Insertion

Abstract Y-family DNA polymerases play a crucial role in translesion DNA synthesis. Here, we have characterized the binding kinetics and conformational dynamics of the Y-family polymerase Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) using single-molecule fluorescence. We find that in the absence of dNTPs, the binary complex shuttles between two different conformations within ∼1 s. These data are consistent with prior crystal structures in which the nucleotide binding site is either occupied by the terminal base pair (preinsertion conformation) or empty following Dpo4 translocation by 1 base pair (insertion conformation). Most interestingly, on dNTP binding, only the insertion conformation is observed and the correct dNTP stabilizes this complex compared with the binary complex, whereas incorrect dNTPs destabilize it. However, if the n+1 template base is complementary to the incoming dNTP, a structure consistent with a misaligned template conformation is observed, in which the template base at the n position loops out. This structure provides evidence for a Dpo4 mutagenesis pathway involving a transient misalignment mechanism.

scholarly journals DNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis

2012 ◽  
Vol 287 (16) ◽  
pp. 13040-13047 ◽  
Author(s):  
Brian A. Maxwell ◽  
Cuiling Xu ◽  
Zucai Suo
Keyword(s):  
Dna Polymerase ◽  
Conformational Dynamics ◽  
Dna Lesion ◽  
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 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 Using Exciton-Coupled Probe Spectroscopy to Investigate the Roles of Local DNA Conformational Dynamics in Processive DNA Polymerase Holoenzyme Formation

2021 ◽  
Vol 120 (3) ◽  
pp. 32a
Author(s):  
Patrick J. Herbert ◽  
Dylan Heussman ◽  
Jack Maurer ◽  
Steven E. Weitzel ◽  
Peter H. von Hippel ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Conformational Dynamics ◽  
Probe Spectroscopy
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