scholarly journals Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase

2020 ◽  
Vol 477 (24) ◽  
pp. 4797-4810
Author(s):  
Hunmin Jung ◽  
Michael A. Hawkins ◽  
Seongmin Lee
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Dna Polymerase ◽  
Structural Basis ◽  
Base Pairing ◽  
Dna Damaging Agents ◽  
Guanine And Adenine ◽  
Induced Mutagenesis ◽  
Enol Tautomer ◽  
Structural Insights

The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively. The exocyclic amines of bases in DNA are hydrogen bond donors, while the carbonyl moiety generated by the base deamination acts as hydrogen bond acceptors, which can alter base pairing properties of the purines. Xanthine is known to base pair with both cytosine and thymine, while hypoxanthine predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA polymerase η (polη) catalyzing across xanthine and hypoxanthine. In the catalytic site of polη, the deaminated guanine (i.e. xanthine) forms three Watson–Crick-like hydrogen bonds with an incoming dCTP, indicating the O2-enol tautomer of xanthine involves in the base pairing. The formation of the enol tautomer appears to be promoted by the minor groove contact by Gln38 of polη. When hypoxanthine is at the templating position, the deaminated adenine uses its O6-keto tautomer to form two Watson–Crick hydrogen bonds with an incoming dCTP, providing the structural basis for the high promutagenicity of hypoxanthine.

scholarly journals Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion

2020 ◽  
Vol 477 (5) ◽  
pp. 937-951
Author(s):  
Hala Ouzon-Shubeita ◽  
Caroline K. Vilas ◽  
Seongmin Lee
Keyword(s):  
Dna Polymerase ◽  
Active Site ◽  
Cisplatin Resistance ◽  
Structural Basis ◽  
Abasic Site ◽  
Dna Polymerase Β ◽  
Dna Lesion ◽  
Human Dna ◽  
Optimal Conformation ◽  
Structural Insights

The cisplatin-1,2-d(GpG) (Pt-GG) intrastrand cross-link is the predominant DNA lesion generated by cisplatin. Cisplatin has been shown to predominantly induce G to T mutations and Pt-GG permits significant misincorporation of dATP by human DNA polymerase β (polβ). In agreement, polβ overexpression, which is frequently observed in cancer cells, is linked to cisplatin resistance and a mutator phenotype. However, the structural basis for the misincorporation of dATP opposite Pt-GG is unknown. Here, we report the first structures of a DNA polymerase inaccurately bypassing Pt-GG. We solved two structures of polβ misincorporating dATP opposite the 5′-dG of Pt-GG in the presence of Mg2+ or Mn2+. The Mg2+-bound structure exhibits a sub-optimal conformation for catalysis, while the Mn2+-bound structure is in a catalytically more favorable semi-closed conformation. In both structures, dATP does not form a coplanar base pairing with Pt-GG. In the polβ active site, the syn-dATP opposite Pt-GG appears to be stabilized by protein templating and pi stacking interactions, which resembles the polβ-mediated dATP incorporation opposite an abasic site. Overall, our results suggest that the templating Pt-GG in the polβ active site behaves like an abasic site, promoting the insertion of dATP in a non-instructional manner.

scholarly journals The structural basis of urea-induced protein unfolding in β-catenin

2014 ◽  
Vol 70 (11) ◽  
pp. 2840-2847 ◽  
Author(s):  
Chao Wang ◽  
Zhongzhou Chen ◽  
Xia Hong ◽  
Fangkun Ning ◽  
Haolin Liu ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Protein Unfolding ◽  
Protein Denaturation ◽  
Hydrophobic Interactions ◽  
Guanidine Hydrochloride ◽  
Structural Basis ◽  
General Mechanism ◽  
Nmr Analysis

Although urea and guanidine hydrochloride are commonly used to denature proteins, the molecular underpinnings of this process have remained unclear for a century. To address this question, crystal structures of β-catenin were determined at various urea concentrations. These structures contained at least 105 unique positions that were occupied by urea molecules, each of which interacted with the protein primarilyviahydrogen bonds. Hydrogen-bond competition experiments showed that the denaturing effects of urea were neutralized when polyethylene glycol was added to the solution. These data suggest that urea primarily causes proteins to unfold by competing and disrupting hydrogen bonds in proteins. Moreover, circular-dichroism spectra and nuclear magnetic resonance (NMR) analysis revealed that a similar mechanism caused protein denaturation in the absence of urea at pH levels greater than 12. Taken together, the results led to the conclusion that the disruption of hydrogen bonds is a general mechanism of unfolding induced by urea, high pH and potentially other denaturing agents such as guanidine hydrochloride. Traditionally, the disruption of hydrophobic interactions instead of hydrogen bonds has been thought to be the most important cause of protein denaturation.

scholarly journals Structural basis for the bypass of the major oxaliplatin–DNA adducts by human DNA polymerase η

2019 ◽  
Vol 476 (4) ◽  
pp. 747-758 ◽  
Author(s):  
Hala Ouzon-Shubeita ◽  
Meghan Baker ◽  
Myong-Chul Koag ◽  
Seongmin Lee
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Dna Polymerase ◽  
Dna Adducts ◽  
Structural Basis ◽  
Structural Studies ◽  
Translesion Dna Synthesis ◽  
Human Dna ◽  
Platinum Based Chemotherapy ◽  
Cross Links

Abstract Oxaliplatin, together with cisplatin, is among the most important drugs used in cancer chemotherapy. Oxaliplatin, which contains a bulky diaminocyclohexane (DACH) moiety, kills cancer cells mainly by producing (DACH)Pt–GpG intrastrand cross-links that impede transcription. The Pt–GpG tolerance by translesion DNA synthesis (TLS) polymerases contributes to the resistance of tumors to platinum-based chemotherapy. In particular, human DNA polymerase η (Polη) readily bypasses Pt–GpG adducts. While many structural studies have addressed how TLS polymerases interact with cisplatin–DNA adducts, a structure of DNA polymerase in complex with oxaliplatin–DNA adducts has not been reported, limiting our understanding of bypass of the bulky (DACH)Pt–GpG lesion by TLS polymerases. Herein, we report the first structure of DNA polymerase bound to oxaliplatinated DNA. We determined a crystal structure of Polη incorporating dCTP opposite the 3′G of the (DACH)Pt–GpG, which provides insights into accurate, efficient bypass of the oxaliplatin–GpG adducts by TLS polymerases. In the catalytic site of Polη, the 3′G of the (DACH)Pt–GpG formed three Watson–Crick hydrogen bonds with incoming dCTP and the primer terminus 3′-OH was optimally positioned for nucleotidyl transfer. To accommodate the bulky (DACH)Pt–GpG lesion, the Val59–Trp64 loop in the finger domain of Polη shifted from the positions observed in the corresponding Polη–cisplatin–GpG and undamaged structures, suggesting that the flexibility of the Val59–Trp64 loop allows the enzyme's bypass of the (DACH)Pt–GpG adducts. Overall, the Polη–oxaliplatin–GpG structure provides a structural basis for TLS-mediated bypass of the major oxaliplatin–DNA adducts and insights into resistance to platinum-based chemotherapy in humans.

scholarly journals Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Olga Rechkoblit ◽  
Robert E. Johnson ◽  
Angeliki Buku ◽  
Louise Prakash ◽  
Satya Prakash ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Active Site ◽  
Myeloid Leukemia ◽  
Local Perturbation ◽  
High Fidelity ◽  
Translesion Dna Synthesis ◽  
Induced Mutagenesis ◽  
Arac Treatment ◽  
Structural Insights ◽  
Acute Myeloid

Abstract Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.

Structural Basis for the Structure–Activity Behaviour of Oxaliplatin and its Enantiomeric Analogues: A Molecular Dynamics Study of Platinum-DNA Intrastrand Crosslink Adducts

2016 ◽  
Vol 69 (4) ◽  
pp. 379 ◽  
Author(s):  
Jing Yang ◽  
Jing Chen ◽  
Zibiao Li
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Conformational Dynamics ◽  
Structural Basis ◽  
Hydrogen Bond Formation ◽  
Damage Recognition ◽  
The Difference ◽  
Highly Correlated ◽  
Dynamics Simulations

The discrimination of Pt-GG adducts by mismatch repair proteins, DNA damage-recognition proteins, and translation DNA polymerases was thought to be vital in determining the toxicity, efficacy, and mutagenicity of platinum anti-tumour drugs. Studies on cis-diammine-Pt-GG (from cisplatin and carboplatin) and trans-R,R-diaminocyclohexane (DACH)-Pt-GG indicated that these proteins recognized the differences in conformation and conformational dynamics of Pt-DNA complexes. However, the structural basis of enantiomeric DACH-Pt-GG forms is unclear. Molecular dynamics simulations results presented here reveal that the conformational dynamics between trans-R,R-DACH-Pt-GG, trans-S,S-DACH-Pt-GG, cis-DACH-Pt-GG and undamaged DNA are distinct and depend on the chirality of DACH though their major conformations are similar. Trans-DACH-Pt was found to be energetically favoured over cis-DACH-Pt to form DNA adducts. Moreover, oxaliplatin and its cis-DACH analogues were found to preferentially form hydrogen bonds on the 3′ side of the Pt-GG adduct, whereas the S,S-DACH-Pt preferred the 5′ side. A three-centre hydrogen bond formed between cis1-DACH-Pt and DNA was observed, and the differences in hydrogen bond formation are highly correlated with differences in DNA conformational dynamics. Based on these results, it is suggested that the different bioactivities of oxaliplatin and its enantiomeric analogues were controlled by the difference in hydrogen bonds formation dynamics between DNA and the Pt moiety. Our molecular dynamics approach was demonstrated to be applicable to the study of stereoisomer conformations of platinum-DNA model, thereby suggesting its potential application as a tool for the study and design of new effective platinum-based drugs.

Hydrogen bonds in N-(3-chloro-2-benzo[b]thienocarbonyl)- and N-(2-benzo[b]thienocarbonyl)-N'-monosubstituted thioureas

1987 ◽  
Vol 52 (11) ◽  
pp. 2673-2679 ◽  
Author(s):  
Oľga Hritzová ◽  
Peter Kutschy ◽  
Ján Imrich ◽  
Thomas Schöffmann
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Strong Hydrogen Bond ◽  
Cyclic Form ◽  
Thiourea Derivatives

N-(3-Chloro-2-benzo[b]thienocarbonyl)-N'-monosubstituted thiourea derivatives undergo photocyclizations with lower yields than those obtained from analogous N',N'-disubstituted derivatives. This decreased reactivity is caused by the existence of a six-membered cyclic form with the very strong hydrogen bond NH···O=C. The possibility of formation of various conformers has been found with N-(2-benzo[b]thienocarbonyl)-N'-monosubstituted thiourea derivatives as a consequence of the rotation around the C(2)-C(O) connecting line.

Structural basis for recruitment of replicative DNA polymerase to PCNA

2008 ◽  
Vol 64 (a1) ◽  
pp. C308-C308
Author(s):  
H. Nishida ◽  
M. Tanabe ◽  
K. Mayanagi ◽  
S. Kiyonari ◽  
I. Yoshizumi ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Structural Basis
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