scholarly journals Architecture of Y-Family DNA Polymerases Relevant to Translesion DNA Synthesis as Revealed in Structural and Molecular Modeling Studies

2010 ◽  
Vol 2010 ◽  
pp. 1-20 ◽  
Author(s):  
Sushil Chandani ◽  
Christopher Jacobs ◽  
Edward L. Loechler
Keyword(s):  
Conformational Changes ◽  
Dna Polymerases ◽  
Class Versus ◽  
Lesion Bypass ◽  
Translesion Dna Synthesis ◽  
Protein Conformational Changes ◽  
Modeling Studies ◽  
Hydrophobic Amino Acids ◽  
Molecular Modeling Studies ◽  
Y Family

DNA adducts, which block replicative DNA polymerases (DNAPs), are often bypassed by lesion-bypass DNAPs, which are mostly in the Y-Family. Y-Family DNAPs can do non-mutagenic or mutagenic dNTP insertion, and understanding this difference is important, because mutations transform normal into tumorigenic cells. Y-Family DNAP architecture that dictates mechanism, as revealed in structural and modeling studies, is considered. Steps from adduct blockage of replicative DNAPs, to bypass by a lesion-bypass DNAP, to resumption of synthesis by a replicative DNAP are described. Catalytic steps and protein conformational changes are considered. One adduct is analyzed in greater detail: the major benzo[a]pyrene adduct , which is bypassed non-mutagenically (dCTP insertion) by Y-family DNAPs in the IV/-class and mutagenically (dATP insertion) by V/-class Y-Family DNAPs. Important architectural differences between IV/-class versus V/-class DNAPs are discussed, including insights gained by analyzing ~400 sequences each for bacterial DNAPs IV and V, along with sequences from eukaryotic DNAPs kappa, eta and iota. The little finger domains of Y-Family DNAPs do not show sequence conservation; however, their structures are remarkably similar due to the presence of a core of hydrophobic amino acids, whose exact identity is less important than the hydrophobic amino acid spacing.

scholarly journals Enzymatic Switching Between Archaeal DNA Polymerases Facilitates Abasic Site Bypass

2021 ◽  
Vol 12 ◽  
Author(s):  
Xu Feng ◽  
Baochang Zhang ◽  
Ruyi Xu ◽  
Zhe Gao ◽  
Xiaotong Liu ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Enzyme Kinetics ◽  
Dna Polymerases ◽  
Dna Lesions ◽  
Abasic Site ◽  
Lesion Bypass ◽  
Translesion Dna Synthesis ◽  
Kinetics Studies ◽  
Abasic Sites ◽  
Y Family

Abasic sites are among the most abundant DNA lesions encountered by cells. Their replication requires actions of specialized DNA polymerases. Herein, two archaeal specialized DNA polymerases were examined for their capability to perform translesion DNA synthesis (TLS) on the lesion, including Sulfolobuss islandicus Dpo2 of B-family, and Dpo4 of Y-family. We found neither Dpo2 nor Dpo4 is efficient to complete abasic sites bypass alone, but their sequential actions promote lesion bypass. Enzyme kinetics studies further revealed that the Dpo4’s activity is significantly inhibited at +1 to +3 site past the lesion, at which Dpo2 efficiently extends the primer termini. Furthermore, their activities are inhibited upon synthesis of 5–6 nt TLS patches. Once handed over to Dpo1, these substrates basically inactivate its exonuclease, enabling the transition from proofreading to polymerization of the replicase. Collectively, by functioning as an “extender” to catalyze further DNA synthesis past the lesion, Dpo2 bridges the activity gap between Dpo4 and Dpo1 in the archaeal TLS process, thus achieving more efficient lesion bypass.

scholarly journals Following DNA Chain Extension and Protein Conformational Changes in Crystals of a Y-Family DNA Polymerase via Raman Crystallography

Biochemistry ◽  
2013 ◽  
Vol 52 (29) ◽  
pp. 4881-4890 ◽  
Author(s):  
Shirly J. Espinoza-Herrera ◽  
Vineet Gaur ◽  
Zucai Suo ◽  
Paul R. Carey
Keyword(s):  
Dna Polymerase ◽  
Conformational Changes ◽  
Chain Extension ◽  
Protein Conformational Changes ◽  
Dna Chain ◽  
Y Family

scholarly journals Differential Roles for DNA Polymerases Eta, Zeta, and REV1 in Lesion Bypass of Intrastrand versus Interstrand DNA Cross-Links

2009 ◽  
Vol 30 (5) ◽  
pp. 1217-1230 ◽  
Author(s):  
J. Kevin Hicks ◽  
Colleen L. Chute ◽  
Michelle T. Paulsen ◽  
Ryan L. Ragland ◽  
Niall G. Howlett ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Dna Lesions ◽  
Dna Double Strand Breaks ◽  
Lesion Bypass ◽  
Translesion Dna Synthesis ◽  
Strand Breaks ◽  
Cycle Arrest ◽  
Interstrand Cross Links ◽  
Cross Links ◽  
Translesion Dna

ABSTRACT Translesion DNA synthesis (TLS) is a process whereby specialized DNA polymerases are recruited to bypass DNA lesions that would otherwise stall high-fidelity polymerases. We provide evidence that TLS across cisplatin intrastrand cross-links is performed by multiple translesion DNA polymerases. First, we determined that PCNA monoubiquitination by RAD18 is necessary for efficient bypass of cisplatin adducts by the TLS polymerases eta (Polη), REV1, and zeta (Polζ) based on the observations that depletion of these proteins individually leads to decreased cell survival, cell cycle arrest in S phase, and activation of the DNA damage response. Second, we showed that in addition to PCNA monoubiquitination by RAD18, the Fanconi anemia core complex is also important for recruitment of REV1 to stalled replication forks in cisplatin treated cells. Third, we present evidence that REV1 and Polζ are uniquely associated with protection against cisplatin and mitomycin C-induced chromosomal aberrations, and both are necessary for the timely resolution of DNA double-strand breaks associated with repair of DNA interstrand cross-links. Together, our findings indicate that REV1 and Polζ facilitate repair of interstrand cross-links independently of PCNA monoubiquitination and Polη, whereas RAD18 plus Polη, REV1, and Polζ are all necessary for replicative bypass of cisplatin intrastrand DNA cross-links.

scholarly journals Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases

2010 ◽  
Vol 39 (2) ◽  
pp. 609-622 ◽  
Author(s):  
Shanen M. Sherrer ◽  
Kevin A. Fiala ◽  
Jason D. Fowler ◽  
Sean A. Newmister ◽  
John M. Pryor ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Dna Polymerases ◽  
Lesion Bypass ◽  
Y Family

p-Trifluoroacetophenone Oxime Ester Derivatives: Synthesis, Antimicrobial and Cytotoxic Evaluation and Molecular Modeling Studies

2020 ◽  
Vol 17 (2) ◽  
pp. 169-183 ◽  
Author(s):  
İrem Bozbey ◽  
Suat Sari ◽  
Emine Şalva ◽  
Didem Kart ◽  
Arzu Karakurt
Keyword(s):  
Molecular Modeling ◽  
Neuroblastoma Cell ◽  
Neuroblastoma Cells ◽  
Cytotoxic Agents ◽  
Human Neuroblastoma Cell ◽  
Human Neuroblastoma ◽  
Modeling Studies ◽  
Broth Microdilution Method ◽  
Molecular Modeling Studies

Background: Azole antifungals are among the first-line drugs clinically used for the treatment of systemic candidiasis, a deadly type of fungal infection that threatens mostly immunecompromised and hospitalized patients. Some azole derivatives were also reported to have antiproliferative effects on cancer cells. Objective: In this study, 1-(4-trifluoromethylphenyl)-2-(1H-imidazol-1-yl)ethanone (3), its oxime (4), and a series of its novel oxime ester derivatives (5a-v) were synthesized and tested for their in vitro antimicrobial activities against certain ATCC standard strains of Candida sp. fungi and bacteria. The compounds were also tested for their cytotoxic effects against mouse fibroblast and human neuroblastoma cell lines. Molecular modeling studies were performed to provide insights into their possible mechanisms for antifungal and antibacterial actions. Methods: The compounds were synthesized by the reaction of various oximes with acyl chlorides. Antimicrobial activity of the compounds was determined according to the broth microdilution method. For the determination of cytotoxic effect, we used MTS assay. Molecular docking and QM/MM studies were performed to predict the binding mechanisms of the active compounds in the catalytic site of C. albicans CYP51 (CACYP51) and S. aureus flavohemoglobin (SAFH), the latter of which was created via homology modeling. Results: 5d, 5l, and 5t showed moderate antifungal activity against C. albicans, while 3, 5c, and 5r showed significant antibacterial activity against Staphylococcus aureus and Pseudomonas aeruginosa. Most of the compounds showed approximately 40-50% inhibition against the human neuroblastoma cells at 100 µM. In this line, 3 was the most potent with an IC50 value of 82.18 μM followed by 5a, 5o, and 5t. 3 and 5a were highly selective to the neuroblastoma cells. Molecular modelling results supported the hypothesis that our compounds were inhibitors of CAYP51 and SAFH. Conclusion: This study supports that oxime ester derivatives may be used for the development of new antimicrobial and cytotoxic agents.

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