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Liu B, Qi Y, Wang X, Gao X, Yao Y, Zhang L. Investigation of the Flipping Dynamics of 1, N6-Ethenoadenine in Alkyladenine DNA Glycosylase. J Phys Chem B 2024; 128:1606-1617. [PMID: 38331753 DOI: 10.1021/acs.jpcb.3c06853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Alkyladenine DNA glycosylase (AAG) is an essential enzyme responsible for maintaining genome integrity by repairing several DNA lesions damaged by alkylation or deamination. Understanding how it can recognize and excise the lesions thus lays the foundation for therapeutic treatment against lesion-associated diseases or cancers. However, the molecular details of how the lesion can be distinguished from the matched base by AAG and how it enters the cleavage site, ready for excision, are not fully elucidated. In this study, we have revealed the molecular details of the flipping dynamics of 1, N6-ethenoadenine (εA) not only in the form of free double-stranded DNA (dsDNA) but also in the form of the AAG-dsDNA complex. Our MD simulations and PMF calculations have shown that the flipping of εA and dA is thermodynamically disfavored in the free dsDNA, even though εA has a lower flipping energy barrier than dA. By sharp contrast, the flipping of εA is thermodynamically favored in AAG with an obvious free energy drop, while dA is equally stabilized before and after the flipping. Moreover, a comparison of the PMFs in the forms of free dsDNA and the AAG-dsDNA complex has pinpointed the role of AAG in discriminating εA against dA and facilitating the flipping of εA. Besides, the flipping process is simulated along the major and minor grooves, and our results have additionally demonstrated that the flipping is not directional in the free dsDNA while flipping along the major groove is kinetically more favorable than the minor groove in the AAG-dsDNA complex. Overall, our study has offered molecular insights into the flipping dynamics of εA and revealed its discrimination mechanism by AAG, which is expected to guide further enzyme engineering for therapeutic applications.
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Affiliation(s)
- Bin Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Qi
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaowei Wang
- Department of Chemical and Biological Engineering and Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Yuan Yao
- Department of Chemical and Biological Engineering and Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fuzhou, Fujian 361005, China
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Diatlova EA, Mechetin GV, Zharkov DO. Distinct Mechanisms of Target Search by Endonuclease VIII-like DNA Glycosylases. Cells 2022; 11:cells11203192. [PMID: 36291061 PMCID: PMC9600533 DOI: 10.3390/cells11203192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 12/02/2022] Open
Abstract
Proteins that recognize specific DNA sequences or structural elements often find their cognate DNA lesions in a processive mode, in which an enzyme binds DNA non-specifically and then slides along the DNA contour by one-dimensional diffusion. Opposite to the processive mechanism is distributive search, when an enzyme binds, samples and releases DNA without significant lateral movement. Many DNA glycosylases, the repair enzymes that excise damaged bases from DNA, use processive search to find their cognate lesions. Here, using a method based on correlated cleavage of multiply damaged oligonucleotide substrates we investigate the mechanism of lesion search by three structurally related DNA glycosylases—bacterial endonuclease VIII (Nei) and its mammalian homologs NEIL1 and NEIL2. Similarly to another homologous enzyme, bacterial formamidopyrimidine–DNA glycosylase, NEIL1 seems to use a processive mode to locate its targets. However, the processivity of Nei was notably lower, and NEIL2 exhibited almost fully distributive action on all types of substrates. Although one-dimensional diffusion is often regarded as a universal search mechanism, our results indicate that even proteins sharing a common fold may be quite different in the ways they locate their targets in DNA.
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Affiliation(s)
- Evgeniia A. Diatlova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Grigory V. Mechetin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence:
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Huang R, Zhou PK. DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther 2021; 6:254. [PMID: 34238917 PMCID: PMC8266832 DOI: 10.1038/s41392-021-00648-7] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China.
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Da LT, Yu J. Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process. Nucleic Acids Res 2019; 46:5410-5425. [PMID: 29762710 PMCID: PMC6009601 DOI: 10.1093/nar/gky386] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive. Here, we employ the Markov State Model (MSM) constructed from extensive all-atom molecular dynamics (MD) simulations to reveal the complete base-flipping process for a G.T mispair at a tens of microsecond timescale. Our studies identify critical intermediates of the mispaired dT during its extrusion process and reveal the key TDG residues involved in the inter-state transitions. Notably, we find an active role of TDG in promoting the intrahelical nt eversion, sculpturing the DNA backbone, and penetrating into the DNA minor groove. Three additional TDG substrates, namely dU, 5fC, and 5caC, are further tested to evaluate the substituent effects of various chemical modifications of the pyrimidine ring on base-flipping dynamics.
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Affiliation(s)
- Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100193, China
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Taylor EL, Kesavan PM, Wolfe AE, O'Brien PJ. Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase. Biochemistry 2018; 57:4440-4454. [PMID: 29940097 DOI: 10.1021/acs.biochem.8b00531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) recognizes many alkylated and deaminated purine lesions and excises them to initiate the base excision DNA repair pathway. AAG employs facilitated diffusion to rapidly scan nonspecific sites and locate rare sites of damage. Nonspecific DNA binding interactions are critical to the efficiency of this search for damage, but little is known about the binding footprint or the affinity of AAG for nonspecific sites. We used biochemical and biophysical approaches to characterize the binding of AAG to both undamaged and damaged DNA. Although fluorescence anisotropy is routinely used to study DNA binding, we found unexpected complexities in the data for binding of AAG to DNA. Systematic comparison of different fluorescent labels and different lengths of DNA allowed binding models to be distinguished and demonstrated that AAG can bind with high affinity and high density to nonspecific DNA. Fluorescein-labeled DNA gave the most complex behavior but also showed the greatest potential to distinguish specific and nonspecific binding modes. We suggest a unified model that is expected to apply to many DNA binding proteins that exhibit affinity for nonspecific DNA. Although AAG strongly prefers to excise lesions from duplex DNA, nonspecific binding is comparable for single- and double-stranded nonspecific sites. The electrostatically driven binding of AAG to small DNA sites (∼5 nucleotides of single-stranded and ∼6 base pairs of duplex) facilitates the search for DNA damage in chromosomal DNA, which is bound by nucleosomes and other proteins.
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Affiliation(s)
- Erin L Taylor
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Preethi M Kesavan
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Abigail E Wolfe
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Patrick J O'Brien
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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Howard MJ, Wilson SH. Processive searching ability varies among members of the gap-filling DNA polymerase X family. J Biol Chem 2017; 292:17473-17481. [PMID: 28893909 DOI: 10.1074/jbc.m117.801860] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/29/2017] [Indexed: 11/06/2022] Open
Abstract
DNA repair proteins must locate rare damaged sites within the genome. DNA polymerase β (Pol β), a member of the DNA polymerase X family that is involved in base excision repair, uses a processive hopping search mechanism to locate substrates. This effectively enhances its search footprint on DNA, increasing the probability of locating damaged sites. Processive searching has been reported or proposed for many DNA-binding proteins, raising the question of how widespread or specific to certain enzymes the ability to perform this function is. To provide insight into this question, we compared the ability of three homologous DNA Pol X family members to perform a processive search for 1-nucleotide gaps in DNA using a previously developed biochemical assay. We found that at near-predicted physiological ionic strengths, the intramolecular searching ability of Pol β is at least 4-fold higher than that of Pol μ and ∼2-fold higher than that of Pol λ. Pol β also was able to perform intersegmental transfer with the intersegmental searching ability of Pol β being at least 6- and ∼2-fold higher than that of Pols μ and λ, respectively. Mutational analysis suggested that differences in the N-terminal domains of these polymerases are responsible for the varying degrees of searching competence. Of note, the differences in processive searching ability observed among the DNA Pol X family members correlated with their proposed biological functions in base excision repair and nonhomologous end joining.
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Affiliation(s)
- Michael J Howard
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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