1
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Tian J, Dong X, Wu T, Wen P, Liu X, Zhang M, An X, Shi D. Revealing the conformational dynamics of UDP-GlcNAc recognition by O-GlcNAc transferase via Markov state model. Int J Biol Macromol 2024; 256:128405. [PMID: 38016609 DOI: 10.1016/j.ijbiomac.2023.128405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
The O-linked N-acetylglucosamine (O-GlcNAc) glycosylation is a critical post-translational modification and closely linked to various physiological and pathological conditions. The O-GlcNAc transferase (OGT) functions as the only glycosyltransferase of O-GlcNAc glycosylation by transferring GlcNAc from UDP-GlcNAc to serine or threonine residues on protein substrates. The interaction mode of UDP-GlcNAc against OGT has been preliminarily revealed by the crystal structures, yet an atomic-level comprehension for the conformational dynamics of the recognition process remains elusive. Here, we construct the Markov state model based on extensive all-atom molecular dynamics (MD) simulations with an aggregated simulation time of ∼9 μs, and reveal that the UDP-GlcNAc recognition process by OGT encompasses four key metastable states, occurring within an estimated timescale of ∼10 μs. During UDP-GlcNAc recognition process, we find the pyrophosphate moiety (P2O52-) initially anchors to the active pocket via salt bridge and hydrogen bonds, facilitating subsequent binding of the uridine and GlcNAc moieties. Furthermore, the functional roles of K842 involved in the salt bridge with P2O52- were evaluated through extra mutant MD simulations. Overall, our study provides valuable insights into the UDP-GlcNAc recognition mechanism by OGT, which could further aid in mechanistic studies of O-GlcNAc glycosylation and drug development targeting on OGT.
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Affiliation(s)
- Jiaqi Tian
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xin Dong
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Tianshuo Wu
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Pengbo Wen
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xin Liu
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Mengying Zhang
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xiaoli An
- School of Chemical Engineering, Institute of Pharmaceutical Engineering Technology and Application, Sichuan University of Science & Engineering, Xueyuan Street 180, Huixing Road, Zigong 643000, Sichuan, China.
| | - Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China.
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2
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Chang Y, Zeng X, Peng S, Lai R, Yang M, Wang D, Zhou X, Shao Y. All-or-None Selectivity in Probing Polarity-Determined Trinucleotide Repeat Foldings with a Parity Resolution by a Beyond-Size-Matching Ligand. Anal Chem 2023; 95:3746-3753. [PMID: 36745842 DOI: 10.1021/acs.analchem.2c04810] [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: 02/08/2023]
Abstract
Abnormal amplification of trinucleotide repeats (TNRs) is associated with neurodegenerative diseases by forming a particular hairpin bulge. It is well known that the polarity and parity of TNRs can regulate the formed hairpin structures. Therefore, there is a great challenge to efficiently discriminate the hairpin structures of TNRs with substantial selectivity. Herein, we developed a fluorescent ligand of pseudohypericin (Pse) with a beyond-size-matching (BSM) geometry to selectively sense hairpin structures of GTC and CTG TNRs. The GTC hairpin structures can bind with Pse dominantly at extreme T-T mismatches by the virtue of their most extrahelical conformations, while there is no binding event to occur with the polarity-inverted counterpart CTG hairpin structures because of the limited space provided by their intrahelical T-T mismatches. In addition, this all-or-none response with the polarity-dependent folding (PoDF) is independent of the length of these TNRs. Interestingly, the parity-dependent folding (PaDF) of GTC hairpin structures can also be resolved. Besides pure TNRs, the competency of this BSM ligand to sense the PoDF and PaDF effects was also generalized to DNAs with TNRs occurring at loop and stem end regions. To our knowledge, this is the first experimental observation with the state-of-the-art performance over the fluorescence measurement of PoDF and PaDF in TNRs. Our work provides an expedient way to elucidate the TNR folding by designing ligands having BSM features.
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Affiliation(s)
- Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Mujing Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
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3
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Hong X, Song K, Rahman MU, Wei T, Zhang Y, Da LT, Chen HF. Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. J Chem Inf Model 2023; 63:605-618. [PMID: 36607244 DOI: 10.1021/acs.jcim.2c01177] [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: 01/07/2023]
Abstract
Leukocyte adhesion deficiency-1 (LAD-1) disorder is a severe immunodeficiency syndrome caused by deficiency or mutation of β2 integrin. The phosphorylation on threonine 758 of β2 integrin acts as a molecular switch inhibiting the binding of filamin. However, the switch mechanism of site-specific phosphorylation at the atom level is still poorly understood. To resolve the regulation mechanism, all-atom molecular dynamics simulation and Markov state model were used to study the dynamic regulation pathway of phosphorylation. Wild type system possessed lower binding free energy and fewer number of states than the phosphorylated system. Both systems underwent local disorder-to-order conformation conversion when achieving steady states. To reach steady states, wild type adopted less number of transition paths/shortest path according to the transition path theory than the phosphorylated system. The underlying phosphorylated regulation pathway was from P1 to P0 and then P4 state, and the main driving force should be hydrogen bond and hydrophobic interaction disturbing the secondary structure of phosphorylated states. These studies will shed light on the pathogenesis of LAD-1 disease and lay a foundation for drug development.
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Affiliation(s)
- Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Kaiyuan Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Ting Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yan Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Lin-Tai Da
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai200240, China
- Shanghai Center for Bioinformation Technology, Shanghai200240, China
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4
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Xi K, Zhu L. Automated Path Searching Reveals the Mechanism of Hydrolysis Enhancement by T4 Lysozyme Mutants. Int J Mol Sci 2022; 23:ijms232314628. [PMID: 36498954 PMCID: PMC9736071 DOI: 10.3390/ijms232314628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteriophage T4 lysozyme (T4L) is a glycosidase that is widely applied as a natural antimicrobial agent in the food industry. Due to its wide applications and small size, T4L has been regarded as a model system for understanding protein dynamics and for large-scale protein engineering. Through structural insights from the single conformation of T4L, a series of mutations (L99A,G113A,R119P) have been introduced, which have successfully raised the fractional population of its only hydrolysis-competent excited state to 96%. However, the actual impact of these substitutions on its dynamics remains unclear, largely due to the lack of highly efficient sampling algorithms. Here, using our recently developed travelling-salesman-based automated path searching (TAPS), we located the minimum-free-energy path (MFEP) for the transition of three T4L mutants from their ground states to their excited states. All three mutants share a three-step transition: the flipping of F114, the rearrangement of α0/α1 helices, and final refinement. Remarkably, the MFEP revealed that the effects of the mutations are drastically beyond the expectations of their original design: (a) the G113A substitution not only enhances helicity but also fills the hydrophobic Cavity I and reduces the free energy barrier for flipping F114; (b) R119P barely changes the stability of the ground state but stabilizes the excited state through rarely reported polar contacts S117OG:N132ND2, E11OE1:R145NH1, and E11OE2:Q105NE2; (c) the residue W138 flips into Cavity I and further stabilizes the excited state for the triple mutant L99A,G113A,R119P. These novel insights that were unexpected in the original mutant design indicated the necessity of incorporating path searching into the workflow of rational protein engineering.
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5
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Wang SD, Zhang RB, Eriksson LA. Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base. Nucleic Acids Res 2022; 50:9072-9082. [PMID: 35979954 PMCID: PMC9458442 DOI: 10.1093/nar/gkac691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
The static and dynamic structures of DNA duplexes affected by 5S-Tg (Tg, Thymine glycol) epimers were studied using MD simulations and Markov State Models (MSMs) analysis. The results show that the 5S,6S-Tg base caused little perturbation to the helix, and the base-flipping barrier was determined to be 4.4 kcal mol-1 through the use of enhanced sampling meta-eABF calculations, comparable to 5.4 kcal mol-1 of the corresponding thymine flipping. Two conformations with the different hydrogen bond structures between 5S,6R-Tg and A19 were identified in several independent MD trajectories. The 5S,6R-Tg:O6HO6•••N1:A19 hydrogen bond is present in the high-energy conformation displaying a clear helical distortion, and near barrier-free Tg base flipping. The low-energy conformation always maintains Watson-Crick base pairing between 5S,6R-Tg and A19, and 5S-Tg base flipping is accompanied by a small barrier of ca. 2.0 KBT (T = 298 K). The same conformations are observed in the MSMs analysis. Moreover, the transition path and metastable structures of the damaged base flipping are for the first time verified through MSMs analysis. The data clearly show that the epimers have completely different influence on the stability of the DNA duplex, thus implying different enzymatic mechanisms for DNA repair.
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Affiliation(s)
- Shu-dong Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street No. 5, Zhongguancun, Haidan District, 100081 Beijing, China
| | - Ru-bo Zhang
- Correspondence may also be addressed to Ru-bo Zhang.
| | - Leif A Eriksson
- To whom correspondence should be addressed. Tel: +46 31 786 9117;
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6
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Wang L, Xi K, Zhu L, Da LT. DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base Flipping. J Chem Inf Model 2022; 62:3213-3226. [PMID: 35708296 DOI: 10.1021/acs.jcim.2c00091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human alkyladenine DNA glycosylase (AAG) is a key enzyme that corrects a broad range of alkylated and deaminated nucleobases to maintain genomic integrity. When encountering the lesions, AAG adopts a base-flipping strategy to extrude the target base from the DNA duplex to its active site, thereby cleaving the glycosidic bond. Despite its functional importance, the detailed mechanism of such base extrusion and how AAG distinguishes the lesions from an excess of normal bases both remain elusive. Here, through the Markov state model constructed on extensive all-atom molecular dynamics simulations, we find that the alkylated nucleobase (N3-methyladenine, 3MeA) everts through the DNA major groove. Two key AAG motifs, the intercalation and E131-N146 motifs, play active roles in bending/pressing the DNA backbone and widening the DNA minor groove during 3MeA eversion. In particular, the intercalated residue Y162 is involved in buckling the target site at the early stage of 3MeA eversion. Our traveling-salesman based automated path searching algorithm further revealed that a non-target normal adenine tends to be trapped in an exo site near the active site, which however barely exists for a target base 3MeA. Collectively, these results suggest that the Markov state model combined with traveling-salesman based automated path searching acts as a promising approach for studying complex conformational changes of biomolecules and dissecting the elaborate mechanism of target recognition by this unique enzyme.
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Affiliation(s)
- Lingyan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kun Xi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, P. R. China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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7
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Wang L, Song K, Yu J, Da LT. Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process. Acta Biochim Biophys Sin (Shanghai) 2022; 54:796-806. [PMID: 35593467 PMCID: PMC9828053 DOI: 10.3724/abbs.2022050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA glycosylase, as one member of DNA repair machineries, plays an essential role in correcting mismatched/damaged DNA nucleotides by cleaving the N-glycosidic bond between the sugar and target nucleobase through the base excision repair (BER) pathways. Efficient corrections of these DNA lesions are critical for maintaining genome integrity and preventing premature aging and cancers. The target-site searching/recognition mechanisms and the subsequent conformational dynamics of DNA glycosylase, however, remain challenging to be characterized using experimental techniques. In this review, we summarize our recent studies of sequential structural changes of thymine DNA glycosylase (TDG) during the DNA repair process, achieved mostly by molecular dynamics (MD) simulations. Computational simulations allow us to reveal atomic-level structural dynamics of TDG as it approaches the target-site, and pinpoint the key structural elements responsible for regulating the translocation of TDG along DNA. Subsequently, upon locating the lesions, TDG adopts a base-flipping mechanism to extrude the mispaired nucleobase into the enzyme active-site. The constructed kinetic network model elucidates six metastable states during the base-extrusion process and suggests an active role of TDG in flipping the intrahelical nucleobase. Finally, the molecular mechanism of product release dynamics after catalysis is also summarized. Taken together, we highlight to what extent the computational simulations advance our knowledge and understanding of the molecular mechanism underlying the conformational dynamics of TDG, as well as the limitations of current theoretical work.
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Affiliation(s)
- Lingyan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Kaiyuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jin Yu
- Department of Physics and AstronomyDepartment of ChemistryNSF-Simons Center for Multiscale Cell Fate ResearchUniversity of CaliforniaIrvineCA92697USA
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China,Correspondence address. Tel: +86-21-34207348; E-mail:
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8
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Tarantino ME, Delaney S. Kinetic Analysis of the Effect of N-Terminal Acetylation on Thymine DNA Glycosylase. Biochemistry 2022; 61:895-908. [PMID: 35436101 PMCID: PMC9117521 DOI: 10.1021/acs.biochem.1c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thymine DNA glycosylase (TDG) is tasked with initiating DNA base excision repair by recognizing and removing T, U, the chemotherapeutic 5-fluorouracil (5-FU), and many other oxidized and halogenated pyrimidine bases. TDG contains a long, unstructured N-terminus that contains four known sites of acetylation: lysine (K) residues 59, 83, 84, and 87. Here, K to glutamine (Q) mutants are used as acetyl-lysine (AcK) analogues to probe the effect of N-terminal acetylation on the kinetics of TDG. We find that mimicking acetylation affects neither the maximal single-turnover rate kmax nor the turnover rate kTO, indicating that the steps after initial binding, through chemistry and product release, are not affected. Under subsaturating conditions, however, acetylation changes the processing of U substrates. Subtle differences among AcK analogues are revealed with 5-FU in single-stranded DNA. We propose that the subtleties observed among the AcK analogues may be amplified on the genomic scale, leading to regulation of TDG activity. N-terminal acetylation, though, may also play a structural, rather than kinetic role in vivo.
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Affiliation(s)
- Mary E. Tarantino
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, United States
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9
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Westwood MN, Johnson CC, Oyler NA, Meints GA. Kinetics and thermodynamics of BI-BII interconversion altered by T:G mismatches in DNA. Biophys J 2022; 121:1691-1703. [PMID: 35367235 PMCID: PMC9117933 DOI: 10.1016/j.bpj.2022.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/26/2021] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
T:G mismatches in DNA result in humans primarily from deamination of methylated CpG sites. They are repaired by redundant systems, such as thymine DNA glycosylase (TDG) and methyl-binding domain enzyme (MBD4), and maintenance of these sites has been implicated in epigenetic processes. The process by which these enzymes identify a canonical DNA base in the incorrect basepairing context remains a mystery. However, the conserved contacts of the repair enzymes with the DNA backbone suggests a role for protein-phosphate interaction in the recognition and repair processes. We have used 31P NMR to investigate the energetics of DNA backbone BI-BII interconversion, and for this work have focused on alterations to the activation barriers to interconversion and the effect of a mismatch compared with canonical DNA. We have found that alterations to the ΔG of interconversion for T:G basepairs are remarkably similar to U:G basepairs in the form of stepwise differences in ΔG of 1-2 kcal/mol greater than equivalent steps in unmodified DNA, suggesting a universality of this result for TDG substrates. Likewise, we see perturbations to the free energy (∼1 kcal/mol) and enthalpy (2-5 kcal/mol) of activation for the BI-BII interconversion localized to the phosphates flanking the mismatch. Overall our results strongly suggest that the perturbed backbone energetics in T:G basepairs play a significant role in the recognition process of DNA repair enzymes.
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Affiliation(s)
- M N Westwood
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri
| | - C C Johnson
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri
| | - Nathan A Oyler
- Department of Chemistry, University of Missouri-Kansas City, Kansas City, Missouri
| | - Gary A Meints
- Department of Chemistry and Biochemistry, Missouri State University, Springfield, Missouri.
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10
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Huskova A, Landova B, Boura E, Silhan J. The rate of formation and stability of abasic site interstrand crosslinks in the DNA duplex. DNA Repair (Amst) 2022; 113:103300. [PMID: 35255312 DOI: 10.1016/j.dnarep.2022.103300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/03/2022]
Abstract
DNA interstrand crosslinks (ICLs) strands pose an impenetrable barrier for DNA replication. Different ICLs are known to recruit distinct DNA repair pathways. NEIL3 glycosylase has been known to remove an abasic (Ap) site derived DNA crosslink (Ap-ICL). An Ap-ICL forms spontaneously from the Ap site with an adjacent adenine in the opposite strand. Lack of genetic models and a poor understanding of the fate of these lesions leads to many questions about the occurrence and the toxicity of Ap-ICL in cells. Here, we investigate the circumstances of Ap-ICL formation. With an array of different oligos, we have investigated the rates of formation, the yields, and the stability of Ap-ICL. Our findings point out how different bases in the vicinity of the Ap site change crosslink formation in vitro. We reveal that AT-rich rather than GC-rich regions in the surrounding Ap site lead to higher rates of Ap-ICL formation. Overall, our data reveal that Ap-ICL can be formed in virtually any DNA sequence context surrounding a hot spot of a 5'-Ap-dT pair, albeit with significantly different rates and yields. Based on Ap-ICL formation in vitro, we attempt to predict the number of Ap-ICLs in the cell.
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Affiliation(s)
- Andrea Huskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Barbora Landova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic.
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11
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Beierlein F, Volkenandt S, Imhof P. Oxidation Enhances Binding of Extrahelical 5-Methyl-Cytosines by Thymine DNA Glycosylase. J Phys Chem B 2022; 126:1188-1201. [PMID: 35109648 DOI: 10.1021/acs.jpcb.1c09896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA repair protein thymine DNA glycosylase (TDG) removes mispaired or damaged bases, such as oxidized methyl-cytosine, from DNA by cleavage of the glycosidic bond between the sugar and the target base flipped into the enzyme's active site. The enzyme is active against formyl-cytosine and carboxyl-cytosine, whereas the lower oxidized hydroxymethyl-cytosine and methyl-cytosine itself are not processed by the enzyme. Molecular dynamics simulations with thermodynamic integration of TDG complexed to DNA carrying one of four different (oxidized) methyl-cytosine bases in extrahelcial conformation, methyl-cytosine (mC), hydroxymethyl-cytosine (hmC), formyl-cytosine (fC), or carboxyl-cytosine (caC), show a more favorable binding affinity of the higher oxidized forms, fC and caC, than the nonsubstrate bases hmC and mC. Despite rather comparable, reaction-competent conformations of the flipped bases in the active site of the enzyme, more and stronger interactions with active site residues account for the preferred binding of the higher oxidized bases. Binding of the negatively charged caC and the neutral fC are strengthened by interactions with positively charged His151. Our calculated proton affinities find this protonation state of His151 the preferred one in the presence of caC and conceivable in the presence of fC as well as increasing the binding affinity toward the two bases. Discrimination of the substrate bases is further achieved by the backbone of Tyr152 that forms a strong hydrogen bond to the carboxyl and formyl oxygen atoms of caC and fC, respectively, a contact that is completely lacking in mC and much weaker in hmC. Overall, our computational results indicate that the enzyme discriminates the different oxidation forms of methyl-cytosine already at the formation of the extrahelical complexes.
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Affiliation(s)
- Frank Beierlein
- Department for Chemistry and Pharmacy Computer Chemistry Centre, Friedrich-Alexander University (FAU) Erlangen Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander University (FAU) Erlangen Nürnberg, Martensstraße 1, 91058 Erlangen, Germany
| | - Senta Volkenandt
- Department for Chemistry and Pharmacy Computer Chemistry Centre, Friedrich-Alexander University (FAU) Erlangen Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany.,Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Petra Imhof
- Department for Chemistry and Pharmacy Computer Chemistry Centre, Friedrich-Alexander University (FAU) Erlangen Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany.,Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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12
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Wang SD, Eriksson LA, Zhang RB. Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond. J Chem Inf Model 2022; 62:386-398. [PMID: 34994562 PMCID: PMC8790752 DOI: 10.1021/acs.jcim.1c01169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Damaged or mismatched
DNA bases are normally thought to be able
to flip out of the helical stack, providing enzymes with access to
the faulty genetic information otherwise hidden inside the helix.
Thymine glycol (Tg) is one of the most common products of nucleic
acid damage. However, the static and dynamic structures of DNA duplexes
affected by 5R-Tg epimers are still not clearly understood, including
the ability of these to undergo spontaneous base flipping. Structural
effects of the 5R-Tg epimers on the duplex DNA are herein studied
using molecular dynamics together with reliable DFT based calculations.
In comparison with the corresponding intact DNA, the cis-5R,6S-Tg epimer base causes little perturbation to the duplex DNA,
and a barrier of 4.9 kcal mol–1 is obtained by meta-eABF
for cis-5R,6S-Tg base flipping out of the duplex
DNA, comparable to the 5.4 kcal mol–1 obtained for
the corresponding thymine flipping in intact DNA. For the trans-5R,6R-Tg epimer, three stable local structures were
identified, of which the most stable disrupts the Watson–Crick
hydrogen-bonded G5/C20 base pair, leading to conformational distortion
of the duplex. Interestingly, the relative barrier height of the 5R-Tg
flipping is only 1.0 kcal mol–1 for one of these trans-5R,6R-Tg epimers. Water bridge interactions were identified
to be essential for 5R-Tg flipping. The study clearly demonstrates
the occurrence of partial trans-5R,6R-Tg epimer flipping
in solution.
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Affiliation(s)
- Shu Dong Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street no 5, Zhongguancun, Haidian District, 100081 Beijing, China
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9c, 405 30 Göteborg, Sweden
| | - Ru Bo Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street no 5, Zhongguancun, Haidian District, 100081 Beijing, China
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13
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Konovalov K, Unarta IC, Cao S, Goonetilleke EC, Huang X. Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning. JACS AU 2021; 1:1330-1341. [PMID: 34604842 PMCID: PMC8479766 DOI: 10.1021/jacsau.1c00254] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 05/19/2023]
Abstract
Markov state models (MSMs) based on molecular dynamics (MD) simulations are routinely employed to study protein folding, however, their application to functional conformational changes of biomolecules is still limited. In the past few years, the field of computational chemistry has experienced a surge of advancements stemming from machine learning algorithms, and MSMs have not been left out. Unlike global processes, such as protein folding, the application of MSMs to functional conformational changes is challenging because they mostly consist of localized structural transitions. Therefore, it is critical to properly select a subset of structural features that can describe the slowest dynamics of these functional conformational changes. To address this challenge, we recommend several automatic feature selection methods such as Spectral-OASIS. To identify states in MSMs, the chosen features can be subject to dimensionality reduction methods such as TICA or deep learning based VAMPNets to project MD conformations onto a few collective variables for subsequent clustering. Another challenge for the application of MSMs to the study of functional conformational changes is the ability to comprehend their biophysical mechanisms, as MSMs built for these processes often require a large number of states. We recommend the recently developed quasi-MSMs (qMSMs) to address this issue. Compared to MSMs, qMSMs encode the non-Markovian dynamics via the generalized master equation and can significantly reduce the number of states. As a result, qMSMs can be built with a handful of states to facilitate the interpretation of functional conformational changes. In the wake of machine learning, we believe that the rapid advancement in the MSM methodology will lead to their wider application in studying functional conformational changes of biomolecules.
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Affiliation(s)
- Kirill
A. Konovalov
- Department
of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Hong
Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
| | - Ilona Christy Unarta
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Hong
Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
| | - Siqin Cao
- Department
of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Hong
Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
| | - Eshani C. Goonetilleke
- Department
of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Hong
Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
| | - Xuhui Huang
- Department
of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Hong
Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
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14
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Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms. Molecules 2021; 26:molecules26195728. [PMID: 34641273 PMCID: PMC8510025 DOI: 10.3390/molecules26195728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Thymine DNA Glycosylase (TDG) is an enzyme of the base excision repair mechanism and removes damaged or mispaired bases from DNA via hydrolysis of the glycosidic bond. Specificity is of high importance for such a glycosylase, so as to avoid the damage of intact DNA. Among the substrates reported for TDG are mispaired uracil and thymine but also formyl-cytosine and carboxyl-cytosine. Methyl-cytosine and hydroxylmethyl-cytosine are, in contrast, not processed by the TDG enzyme. We have in this work employed molecular dynamics simulations to explore the conformational dynamics of DNA carrying a formyl-cytosine or carboxyl-cytosine and compared those to DNA with the non-cognate bases methyl-cytosine and hydroxylmethyl-cytosine, as amino and imino tautomers. Whereas for the mispairs a wobble conformation is likely decisive for recognition, all amino tautomers of formyl-cytosine and carboxyl-cytosine exhibit the same Watson–Crick conformation, but all imino tautomers indeed form wobble pairs. The conformational dynamics of the amino tautomers in free DNA do not exhibit differences that could be exploited for recognition, and also complexation to the TDG enzyme does not induce any alteration that would indicate preferable binding to one or the other oxidised methyl-cytosine. The imino tautomers, in contrast, undergo a shift in the equilibrium between a closed and a more open, partially flipped state, towards the more open form upon complexation to the TDG enzyme. This stabilisation of the more open conformation is most pronounced for the non-cognate bases methyl-cytosine and hydroxyl-cytosine and is thus not a likely mode for recognition. Moreover, calculated binding affinities for the different forms indicate the imino forms to be less likely in the complexed DNA. These findings, together with the low probability of imino tautomers in free DNA and the indifference of the complexed amino tautomers, suggest that discrimination of the oxidised methyl-cytosines does not take place in the initial complex formation.
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15
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Zhu Y, Li Z, Wang P, Qiu QM, Ma H, Li H. The Research of G-Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes. Front Chem 2021; 9:709777. [PMID: 34277575 PMCID: PMC8278404 DOI: 10.3389/fchem.2021.709777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
A detailed understanding of the mismatched base-pairing interactions in DNA will help reveal genetic diseases and provide a theoretical basis for the development of targeted drugs. Here, we utilized mononucleotide fragment to simulate mismatch DNA interactions in a local hydrophobic microenvironment. The bipyridyl-type bridging ligands were employed as a mild stabilizer to stabilize the GG mismatch containing complexes, allowing mismatch to be visualized based on X-ray crystallography. Five single crystals of 2′-deoxyguanosine–5′–monophosphate (dGMP) metal complexes were designed and obtained via the process of self-assembly. Crystallographic studies clearly reveal the details of the supramolecular interaction between mononucleotides and guest intercalators. A novel guanine–guanine base mismatch pattern with unusual (high anti)–(high anti) type of arrangement around the glycosidic angle conformations was successfully constructed. The solution state 1H–NMR, ESI–MS spectrum studies, and UV titration experiments emphasize the robustness of this g–motif in solution. Additionally, we combined the methods of single-crystal and solution-, solid-state CD spectrum together to discuss the chirality of the complexes. The complexes containing the g–motif structure, which reduces the energy of the system, following the solid-state CD signals, generally move in the long-wave direction. These results provided a new mismatched base pairing, that is g–motif. The interaction mode and full characterizations of g–motif will contribute to the study of the mismatched DNA interaction.
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Affiliation(s)
- Yanhong Zhu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Zhongkui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Pengfei Wang
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Qi-Ming Qiu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Hongwei Ma
- Analytical and Testing Centre, Beijing Institute of Technology, Beijing, China
| | - Hui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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16
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Nehzati S, Summers AO, Dolgova NV, Zhu J, Sokaras D, Kroll T, Pickering IJ, George GN. Hg(II) Binding to Thymine Bases in DNA. Inorg Chem 2021; 60:7442-7452. [PMID: 33938732 DOI: 10.1021/acs.inorgchem.1c00735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The compounds of mercury can be highly toxic and can interfere with a range of biological processes, although many aspects of the mechanism of toxicity are still obscure or unknown. One especially intriguing property of Hg(II) is its ability to bind DNA directly, making interstrand cross-links between thymine nucleobases in AT-rich sequences. We have used a combination of small molecule X-ray diffraction, X-ray spectroscopies, and computational chemistry to study the interactions of Hg(II) with thymine. We find that the energetically preferred mode of thymine binding in DNA is to the N3 and predict only minor distortions of the DNA structure on binding one Hg(II) to two cross-adjacent thymine nucleotides. The preferred geometry is predicted to be twisted away from coplanar through a torsion angle of between 32 and 43°. Using 1-methylthymine as a model, the bis-thymine coordination of Hg(II) is found to give a highly characteristic X-ray spectroscopic signature that is quite distinct from other previously described biological modes of binding of Hg(II). This work enlarges and deepens our view of significant biological targets of Hg(II) and demonstrates tools that can provide a characteristic signature for the binding of Hg(II) to DNA in more complex matrices including intact cells and tissues, laying the foundation for future studies of mechanisms of mercury toxicity.
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Affiliation(s)
- Susan Nehzati
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Anne O Summers
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Natalia V Dolgova
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Jianfeng Zhu
- Saskatchewan Structural Sciences Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Ingrid J Pickering
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Graham N George
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
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17
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Gillet N, Bartocci A, Dumont E. Assessing the sequence dependence of pyrimidine-pyrimidone (6-4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation. J Chem Phys 2021; 154:135103. [PMID: 33832258 DOI: 10.1063/5.0041332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Sequence dependence of the (6-4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities. Moreover, REST2 simulations allow us to probe structures possibly important for damaged DNA recognition.
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Affiliation(s)
- Natacha Gillet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Alessio Bartocci
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Elise Dumont
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
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18
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Tian J, Wang L, Da LT. Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition. Nucleic Acids Res 2021; 49:1278-1293. [PMID: 33469643 PMCID: PMC7897493 DOI: 10.1093/nar/gkaa1252] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Thymine DNA glycosylase (TDG), as a repair enzyme, plays essential roles in maintaining the genome integrity by correcting several mismatched/damaged nucleobases. TDG acquires an efficient strategy to search for the lesions among a vast number of cognate base pairs. Currently, atomic-level details of how TDG translocates along DNA as it approaches the lesion site and the molecular mechanisms of the interplay between TDG and DNA are still elusive. Here, by constructing the Markov state model based on hundreds of molecular dynamics simulations with an integrated simulation time of ∼25 μs, we reveal the rotation-coupled sliding dynamics of TDG along a 9 bp DNA segment containing one G·T mispair. We find that TDG translocates along DNA at a relatively faster rate when distant from the lesion site, but slows down as it approaches the target, accompanied by deeply penetrating into the minor-groove, opening up the mismatched base pair and significantly sculpturing the DNA shape. Moreover, the electrostatic interactions between TDG and DNA are found to be critical for mediating the TDG translocation. Notably, several uncharacterized TDG residues are identified to take part in regulating the conformational switches of TDG occurred in the site-transfer process, which warrants further experimental validations.
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Affiliation(s)
- Jiaqi Tian
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lingyan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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19
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Levintov L, Paul S, Vashisth H. Reaction Coordinate and Thermodynamics of Base Flipping in RNA. J Chem Theory Comput 2021; 17:1914-1921. [PMID: 33594886 DOI: 10.1021/acs.jctc.0c01199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack of atomistic details on complex rearrangements in neighboring bases. In this work, we applied transition path sampling (TPS) methods to study base flipping in a double-stranded RNA (dsRNA) molecule that is known to interact with RNA-editing enzymes through this mechanism. We obtained an ensemble of 1000 transition trajectories to describe the base-flipping process. We used the likelihood maximization method to determine the refined reaction coordinate (RC) consisting of two collective variables (CVs), a distance and a dihedral angle between nucleotides that form stacking interactions with the flipping base. The free energy profile projected along the refined RC revealed three minima, two corresponding to the initial and final states and one for a metastable state. We suggest that the metastable state likely represents a wobbled conformation of nucleobases observed in NMR studies that is often characterized as the flipped state. The analyses of reactive trajectories further revealed that the base flipping is coupled to a global conformational change in a stem-loop of dsRNA.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Sanjib Paul
- Department of Chemistry, New York University, New York 10003, New York, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
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20
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Vatta M, Lyons B, Heney KA, Lidster T, Merrill AR. Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies. Toxins (Basel) 2021; 13:toxins13010055. [PMID: 33450958 PMCID: PMC7828395 DOI: 10.3390/toxins13010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 11/16/2022] Open
Abstract
Scabin is a mono-ADP-ribosyltransferase toxin/enzyme and possible virulence factor produced by the agriculture pathogen, Streptomyces scabies. Recently, molecular dynamic approaches and MD simulations revealed its interaction with both NAD+ and DNA substrates. An Essential Dynamics Analysis identified a crab-claw-like mechanism, including coupled changes in the exposed motifs, and the Rβ1-RLa-NLc-STTβ2-WPN-WARTT-(QxE)ARTT sequence motif was proposed as a catalytic signature of the Pierisin family of DNA-acting toxins. A new fluorescence assay was devised to measure the kinetics for both RNA and DNA substrates. Several protein variants were prepared to probe the Scabin-NAD-DNA molecular model and to reveal the reaction mechanism for the transfer of ADP-ribose to the guanine base in the DNA substrate. The results revealed that there are several lysine and arginine residues in Scabin that are important for binding the DNA substrate; also, key residues such as Asn110 in the mechanism of ADP-ribose transfer to the guanine base were identified. The DNA-binding residues are shared with ScARP from Streptomyces coelicolor but are not conserved with Pierisin-1, suggesting that the modification of guanine bases by ADP-ribosyltransferases is divergent even in the Pierisin family.
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Affiliation(s)
- Maritza Vatta
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Bronwyn Lyons
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada;
| | - Kayla A. Heney
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada;
| | - Taylor Lidster
- Department of Biological Sciences, Brock University, St. Catherines, ON L2S 3A1, Canada;
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: ; Fax: +1-519-837-1802
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21
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Wang X, Unarta IC, Cheung PPH, Huang X. Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models. Curr Opin Struct Biol 2020; 67:69-77. [PMID: 33126140 DOI: 10.1016/j.sbi.2020.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/28/2020] [Accepted: 10/07/2020] [Indexed: 01/01/2023]
Abstract
Functional conformational changes of proteins can facilitate numerous biological events in cells. The Markov state model (MSM) built from molecular dynamics simulations provide a powerful approach to study them. We here introduce a protocol that is tailor-made for constructing MSMs to study the functional conformational changes of proteins. In this protocol, one of the important steps is to select proper molecular features that can collectively describe the slowest timescales of conformational changes of interest. We recommend spectral oASIS, the modified version of oASIS, as a promising approach for automatic feature selection. Recently developed deep learning methods could also serve efficient approaches for selecting features and finding collective variables. Using DNA repair enzymes and RNA polymerases as examples, we review recent applications of MSMs to elucidate molecular mechanisms of functional conformational changes. Finally, we discuss remaining challenges and future perspectives for constructing MSMs to study functional conformational changes of proteins.
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Affiliation(s)
- Xiaowei Wang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Ilona Christy Unarta
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Kowloon, 4Hong Kong Center for Neurodegenerative Diseases, Hong Kong
| | - Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Kowloon, 4Hong Kong Center for Neurodegenerative Diseases, Hong Kong.
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22
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Li S, Da LT. Key structural motifs in Thymine DNA glycosylase responsible for recognizing certain DNA bent conformation revealed by atomic simulations. Biochem Biophys Res Commun 2020; 526:953-959. [PMID: 32291075 DOI: 10.1016/j.bbrc.2020.03.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 10/24/2022]
Abstract
Knowledge of how DNA bending facilitates the target-base searching by Thymine DNA glycosylase (TDG) is of major importance for unraveling the recognition mechanism between DNA and TDG in DNA repair process. An atomic-level understanding of the initial encounter between TDG and DNA before base-flipping, however, is still elusive. Here, we employ all-atom molecular dynamics (MD) simulations with an integrated simulation time of ∼3 μs to investigate how TDG responses to different DNA bending conformations. By constructing several TDG-DNA complexes with varied DNA bend angles (ranging from ∼0° to 60°), we pinpoint the key TDG motifs responsible for recognizing certain DNA bending conformations. Particularly, several positively charged residues, i.e., Lys232, Lys240, and Lys246, are critical for the tight binding with DNA backbones. Importantly, the roll-angle patterns, rather than the tilt and twist angles, are found to be strongly correlated with the extent of DNA bending, which in turn, governs the TDG recognition. Further comparisons between the naked and TDG-bound DNA conformations reveal that the TDG binding can impose a substantial DNA deformation, resulting in profound roll-angle alterations. Our studies warrant further experimental validations and provide deep structural insights into the recognition mechanism between TDG and DNA during their initial encounter.
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Affiliation(s)
- Shuang Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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23
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Kaur R, Nikkel DJ, Wetmore SD. Computational studies of DNA repair: Insights into the function of monofunctional DNA glycosylases in the base excision repair pathway. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge Alberta Canada
| | - Dylan J. Nikkel
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge Alberta Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge Alberta Canada
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24
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Da LT, Lin M. Opening dynamics of HIV-1 gp120 upon receptor binding is dictated by a key hydrophobic core. Phys Chem Chem Phys 2019; 21:26003-26016. [PMID: 31764922 DOI: 10.1039/c9cp04613e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
HIV-1 entry is mediated firstly by the molecular recognition between the viral glycoprotein gp120 and its receptor CD4 on host T-cells. As a key antigen that can be targeted by neutralizing antibodies, gp120 has been a focus for extensive studies with efforts to understand its structural properties and conformational dynamics upon receptor binding. An atomistic-level revelation of gp120 opening dynamics activated by CD4, however, is still unknown. Here, by constructing a Markov State Model (MSM) based on hundreds of Molecular Dynamics (MD) simulations with an aggregated simulation time of ∼20 microseconds (μs), we identify the key metastable states of gp120 during its opening dynamics upon CD4 binding. The MSM provides a clear dynamic model whereby the identified metastable states coexist and can reach an equilibrium. More importantly, a hydrophobic core flanked by variable loops (V1V2 and V3) and the β20/21 region plays an essential role in triggering the gp120 opening. Any destabilizing effects introduced into the hydrophobic core, therefore, can be expected to promote transition of gp120 to an open state. Moreover, the variable loops demonstrate high flexibilities in fully open gp120. In particular, the V3 region is capable of exploring both closed and open conformations, even with the V1/V2 loops largely adopting an open form. In addition, the bridging sheet formation in gp120 is likely induced by the incoming co-receptor/antibody recognitions, since the V1/V2 structure is highly heterogeneous so that the bridging-sheet formed conformation is not the most populated state. Our studies provide deep insights into the dynamic features of gp120 and its molecular recognitions to the broadly neutralizing antibodies, which guides future attempts to design more effective gp120 immunogens.
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Affiliation(s)
- Lin-Tai Da
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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25
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Satange R, Chuang CY, Neidle S, Hou MH. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Res 2019; 47:8899-8912. [PMID: 31361900 PMCID: PMC6895262 DOI: 10.1093/nar/gkz653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chien-Ying Chuang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
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Tian J, Liu F, Xu Z, Shi J, Liang T, Zhang Y, Da LT. Regulatory Role of One Critical Catalytic Loop of Polypeptide N-Acetyl-Galactosaminyltransferase-2 in Substrate Binding and Catalysis during Mucin-Type O-Glycosylation. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jiaqi Tian
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Feng Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhijue Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jingjing Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tao Liang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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27
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Maffeo C, Chou HY, Aksimentiev A. Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations. ADVANCED THEORY AND SIMULATIONS 2019; 2:1800191. [PMID: 31728433 PMCID: PMC6855400 DOI: 10.1002/adts.201800191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Han-Yi Chou
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
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28
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Almutairi M, Mohammad Alhadeq A, Almeer R, Almutairi M, Alzahrani M, Semlali A. Effect of the thymine-DNA glycosylase rs4135050 variant on Saudi smoker population. Mol Genet Genomic Med 2019; 7:e00590. [PMID: 30779328 PMCID: PMC6465727 DOI: 10.1002/mgg3.590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/13/2018] [Accepted: 01/02/2019] [Indexed: 12/22/2022] Open
Abstract
Background Thymine‐DNA glycosylase (TDG) is an essential DNA‐repair enzyme which works in both epigenetic regulation and genome maintenance. It is also responsible for efficient correction of multiple endogenous DNA lesions which occur commonly in mammalian genomes. Research of genetic variants such as SNPs, resulting in disease, is predicted to yield clinical advancements through the identification of sensitive genetic markers and the development of disease prevention and therapy. To that end, the main objective of the present study is to identify the possible interactions between cigarette smoking and the rs4135050 variant of the TDG gene, situated in the intron position, among Saudi individuals. Methods TDG rs4135050 (A/T) was investigated by genotyping 239, and 235 blood specimens were obtained from nonsmokers and smokers of cigarette respectively. Results T allele frequency was found which showed a significant protective effect on Saudi male smokers (OR = 0.64, p = 0.0187) compared to nonsmoking subjects, but not in female smokers. Furthermore, smokers aged less than 29 years, the AT and AT+TT genotypes decreased more than four times the risk of initiation of smoking related‐diseases compare to the ancestral AA homozygous genotype. Paradoxically, the AT (OR = 3.88, p = 0.0169) and AT+TT (OR = 2.86, p = 0.0420) genotypes were present at a higher frequency in smoking patients aged more than 29 years as compared to nonsmokers at the same ages. Conclusion Depending on the gender and age of patients, TDG rs4135050 may provide a novel biomarker for the early diagnosis and prevention of several diseases caused by cigarette smoking.
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Affiliation(s)
- Mikhlid Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | | | - Rafa Almeer
- Zoology Department, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Alzahrani
- Biology Department, College of Science, Al Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Abdelhabib Semlali
- Groupe de Recherche en Écologie Buccale, Université Laval, Québec, Québec, Canada.,Department of Biochemistry, College of Science, King Saud University, Kingdom of Saudi Arabia, Riyadh
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Kanaan N, Imhof P. Interactions of the DNA Repair Enzyme Human Thymine DNA Glycosylase with Cognate and Noncognate DNA. Biochemistry 2018; 57:5654-5665. [PMID: 30067350 DOI: 10.1021/acs.biochem.8b00409] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycosylases specifically recognize and flip their target base out of the DNA helix into the enzyme's active site. Our simulations show that a partially flipped state, already present in free DNA carrying a T:G mispair, becomes the more probable state compared to the closed state after binding of thymine DNA glycosylase (TDG). Paired thymine (T:A) or methyl-cytosine (mC:G) does not exhibit a partially flipped state in free or complexed DNA. Important enzyme-DNA interactions exhibit significant strength in the intrahelical and extrahelical TDG-DNA complexes. The computed binding free energy differences suggest these interactions account for the stabilization of the partially flipped state, thereby driving the T:G mispair toward base flip. In the fully flipped state, the cognate base thymine is significantly better accommodated in the enzyme's active site than noncognate bases are, suggesting the hydrolysis step as the last of several stages at which base recognition can be achieved.
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Affiliation(s)
- Natalia Kanaan
- Institute of Theoretical Physics , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
| | - Petra Imhof
- Institute of Theoretical Physics , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
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30
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Tarantino ME, Dow BJ, Drohat AC, Delaney S. Nucleosomes and the three glycosylases: High, medium, and low levels of excision by the uracil DNA glycosylase superfamily. DNA Repair (Amst) 2018; 72:56-63. [PMID: 30268365 DOI: 10.1016/j.dnarep.2018.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 01/19/2023]
Abstract
Human cells express the UDG superfamily of glycosylases, which excise uracil (U) from the genome. The three members of this structural superfamily are uracil DNA glycosylase (UNG/UDG), single-strand selective monofunctional uracil DNA glycosylase (SMUG1), and thymine DNA glycosylase (TDG). We previously reported that UDG is efficient at removing U from DNA packaged into nucleosome core particles (NCP) and is minimally affected by the histone proteins when acting on an outward-facing U in the dyad region. In an effort to determine whether this high activity is a general property of the UDG superfamily of glycosylases, we compare the activity of UDG, SMUG1, and TDG on a U:G wobble base pair using NCP assembled from Xenopus laevis histones and the Widom 601 positioning sequence. We found that while UDG is highly active, SMUG1 is severely inhibited on NCP and this inhibition is independent of sequence context. Here we also provide the first report of TDG activity on an NCP, and found that TDG has an intermediate level of activity in excision of U and is severely inhibited in its excision of T. These results are discussed in the context of cellular roles for each of these enzymes.
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Affiliation(s)
- Mary E Tarantino
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, United States
| | - Blaine J Dow
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, United States
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, United States; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD, 21201, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, 02912, United States.
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