1
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Figueroa Blanco DR, Vidossich P, De Vivo M. Correct Nucleotide Selection Is Confined at the Binding Site of Polymerase Enzymes. J Chem Inf Model 2024; 64:5285-5294. [PMID: 38901009 DOI: 10.1021/acs.jcim.4c00696] [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: 06/22/2024]
Abstract
DNA polymerases (Pols) add incoming nucleotides (deoxyribonucleoside triphosphate (dNTPs)) to growing DNA strands, a crucial step for DNA synthesis. The insertion of correct (vs incorrect) nucleotides relates to Pols' fidelity, which defines Pols' ability to faithfully replicate DNA strands in a template-dependent manner. We and others have demonstrated that reactant alignment and correct base pairing at the Pols catalytic site are crucial structural features to fidelity. Here, we first used equilibrium molecular simulations to demonstrate that the local dynamics at the protein-DNA interface in the proximity of the catalytic site is different when correct vs incorrect dNTPs are bound to polymerase β (Pol β). Formation and dynamic stability of specific interatomic interactions around the incoming nucleotide influence the overall binding site architecture. This explains why certain Pols' mutants can affect the local catalytic environment and influence the selection of correct vs incorrect nucleotides. In particular, this is here demonstrated by analyzing the interaction network formed by the residue R283, whose mutant R283A has an experimentally measured lower capacity of differentiating correct (G:dCTP) vs incorrect (G:dATP) base pairing in Pol β. We also used alchemical free-energy calculations to quantify the G:dCTP →G:dATP transformation in Pol β wild-type and mutant R283A. These results correlate well with the experimental trend, thus corroborating our mechanistic insights. Sequence and structural comparisons with other Pols from the same family suggest that these findings may also be valid in similar enzymes.
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Affiliation(s)
- David Ricardo Figueroa Blanco
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
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2
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Dong Y, Wang J, Chen L, Chen H, Dang S, Li F. Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics. Chem Soc Rev 2024; 53:6830-6859. [PMID: 38829187 DOI: 10.1039/d3cs00774j] [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: 06/05/2024]
Abstract
Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.
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Affiliation(s)
- Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Jingping Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Ling Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Haonan Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Shuangbo Dang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
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3
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Salehi H, Cheheregani Rad A, Raza A, Djalovic I, Prasad PVV. The comparative effects of manganese nanoparticles and their counterparts (bulk and ionic) in Artemisia annua plants via seed priming and foliar application. FRONTIERS IN PLANT SCIENCE 2023; 13:1098772. [PMID: 36743542 PMCID: PMC9893273 DOI: 10.3389/fpls.2022.1098772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
The world has experienced an unprecedented boom in nanotechnology. Nanoparticles (NPs) are likely to act as biostimulants in various plants due to having high surface/volume value. However, understanding the actual effect of NPs is essential to discriminate them from other counterparts in terms of being applicable, safe and cost-effective. This study aimed to assay the impact of manganese(III) oxide (Mn2O3)-NPs via seed-priming (SP) and a combination of SP and foliar application (SP+F) on Artemisia. annua performance at several times intervals and comparison with other available manganese (Mn) forms. Our findings indicate that SP with MnSO4 and Mn2O3-NPs stimulates the processes that occur prior to germination and thus reduces the time for radicle emergence. In both applications (i.e., SP and +F), none of the Mn treatments did show adverse phytotoxic on A. annua growth at morpho-physio and biochemical levels except for Mn2O3, which delayed germination and further plant growth, subsequently. Besides, from physio-biochemical data, it can be inferred that the general mechanism mode of action of Mn is mainly attributed to induce the photosynthetic processes, stimulate the superoxide dismutase (SOD) activity, and up-regulation of proline and phenolic compounds. Therefore, our results showed that both enzymatic and non-enzymatic antioxidants could be influenced by the application of Mn treatments in a type-dependent manner. In general, this study revealed that Mn2O3-NPs at the tested condition could be used as biostimulants to improve germination, seedling development and further plant growth. However, they are not as effective as MnSO4 treatments. Nonetheless, these findings can be used to consider and develop Mn2O3-NPs priming in future studies to improve seed germination and seedling quality in plants.
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Affiliation(s)
- Hajar Salehi
- Laboratory of Plant Cell Biology, Department of Biology, Bu-Ali Sina University, Hamedan, Iran
| | | | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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4
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Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Int J Mol Sci 2022; 23:ijms23126373. [PMID: 35742812 PMCID: PMC9224347 DOI: 10.3390/ijms23126373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.
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5
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Visualizing Rev1 catalyze protein-template DNA synthesis. Proc Natl Acad Sci U S A 2020; 117:25494-25504. [PMID: 32999062 DOI: 10.1073/pnas.2010484117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During DNA replication, replicative DNA polymerases may encounter DNA lesions, which can stall replication forks. One way to prevent replication fork stalling is through the recruitment of specialized translesion synthesis (TLS) polymerases that have evolved to incorporate nucleotides opposite DNA lesions. Rev1 is a specialized TLS polymerase that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts. Lesion bypass is accomplished using a unique protein-template mechanism in which the templating base is evicted from the DNA helix and the incoming dCTP hydrogen bonds with an arginine side chain of Rev1. To understand the protein-template mechanism at an atomic level, we employed a combination of time-lapse X-ray crystallography, molecular dynamics simulations, and DNA enzymology on the Saccharomyces cerevisiae Rev1 protein. We find that Rev1 evicts the templating base from the DNA helix prior to binding the incoming nucleotide. Binding the incoming nucleotide changes the conformation of the DNA substrate to orient it for nucleotidyl transfer, although this is not coupled to large structural changes in Rev1 like those observed with other DNA polymerases. Moreover, we found that following nucleotide incorporation, Rev1 converts the pyrophosphate product to two monophosphates, which drives the reaction in the forward direction and prevents pyrophosphorolysis. Following nucleotide incorporation, the hydrogen bonds between the incorporated nucleotide and the arginine side chain are broken, but the templating base remains extrahelical. These postcatalytic changes prevent potentially mutagenic processive synthesis by Rev1 and facilitate dissociation of the DNA product from the enzyme.
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6
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Lv J, Dong Y, Gu Z, Yang D. Programmable DNA Nanoflowers for Biosensing, Bioimaging, and Therapeutics. Chemistry 2020; 26:14512-14524. [DOI: 10.1002/chem.202002242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/02/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Jigang Lv
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Yuhang Dong
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Zi Gu
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Dayong Yang
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
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7
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Howard MJ, Horton JK, Zhao ML, Wilson SH. Lysines in the lyase active site of DNA polymerase β destabilize nonspecific DNA binding, facilitating searching and DNA gap recognition. J Biol Chem 2020; 295:12181-12187. [PMID: 32647014 PMCID: PMC7443498 DOI: 10.1074/jbc.ra120.013547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/07/2020] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase (pol) β catalyzes two reactions at DNA gaps generated during base excision repair, gap-filling DNA synthesis and lyase-dependent 5´-end deoxyribose phosphate removal. The lyase domain of pol β has been proposed to function in DNA gap recognition and to facilitate DNA scanning during substrate search. However, the mechanisms and molecular interactions used by pol β for substrate search and recognition are not clear. To provide insight into this process, a comparison was made of the DNA binding affinities of WT pol β, pol λ, and pol μ, and several variants of pol β, for 1-nt-gap-containing and undamaged DNA. Surprisingly, this analysis revealed that mutation of three lysine residues in the lyase active site of pol β, 35, 68, and 72, to alanine (pol β KΔ3A) increased the binding affinity for nonspecific DNA ∼11-fold compared with that of the WT. WT pol μ, lacking homologous lysines, displayed nonspecific DNA binding behavior similar to that of pol β KΔ3A, in line with previous data demonstrating both enzymes were deficient in processive searching. In fluorescent microscopy experiments using mouse fibroblasts deficient in PARP-1, the ability of pol β KΔ3A to localize to sites of laser-induced DNA damage was strongly decreased compared with that of WT pol β. These data suggest that the three lysines in the lyase active site destabilize pol β when bound to DNA nonspecifically, promoting DNA scanning and providing binding specificity for gapped DNA.
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Affiliation(s)
- Michael J Howard
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA.
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8
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Howard MJ, Cavanaugh NA, Batra VK, Shock DD, Beard WA, Wilson SH. DNA polymerase β nucleotide-stabilized template misalignment fidelity depends on local sequence context. J Biol Chem 2020; 295:529-538. [PMID: 31801827 PMCID: PMC6956524 DOI: 10.1074/jbc.ra119.010594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/03/2019] [Indexed: 01/07/2023] Open
Abstract
DNA polymerase β has two DNA-binding domains that interact with the opposite sides of short DNA gaps. These domains contribute two activities that modify the 5' and 3' margins of gapped DNA during base excision repair. DNA gaps greater than 1 nucleotide (nt) pose an architectural and logistical problem for the two domains to interact with their respective DNA termini. Here, crystallographic and kinetic analyses of 2-nt gap-filling DNA synthesis revealed that the fidelity of DNA synthesis depends on local sequence context. This was due to template dynamics that altered which of the two template nucleotides in the gap served as the coding nucleotide. We observed that, when a purine nucleotide was in the first coding position, DNA synthesis fidelity was similar to that observed with a 1-nt gap. However, when the initial templating nucleotide was a pyrimidine, fidelity was decreased. If the first templating nucleotide was a cytidine, there was a significantly higher probability that the downstream template nucleotide coded for the incoming nucleotide. This dNTP-stabilized misalignment reduced base substitution and frameshift deletion fidelities. A crystal structure of a binary DNA product complex revealed that the cytidine in the first templating site was in an extrahelical position, permitting the downstream template nucleotide to occupy the coding position. These results indicate that DNA polymerase β can induce a strain in the DNA that modulates the position of the coding nucleotide and thereby impacts the identity of the incoming nucleotide. Our findings demonstrate that "correct" DNA synthesis can result in errors when template dynamics induce coding ambiguity.
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Affiliation(s)
- Michael J. Howard
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Nisha A. Cavanaugh
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Vinod K. Batra
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - David D. Shock
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - William A. Beard
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, To whom correspondence should be addressed:
Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T. W. Alexander Dr., P. O. Box 12233, MD F1–12, Research Triangle Park, NC 27709-2233. Tel.:
984-287-3451; E-mail:
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9
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DeRose EF, Kirby TW, Mueller GA, Beard WA, Wilson SH, London RE. Transitions in DNA polymerase β μs-ms dynamics related to substrate binding and catalysis. Nucleic Acids Res 2019; 46:7309-7322. [PMID: 29917149 PMCID: PMC6101544 DOI: 10.1093/nar/gky503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/24/2018] [Indexed: 11/12/2022] Open
Abstract
DNA polymerase β (pol β) plays a central role in the DNA base excision repair pathway and also serves as an important model polymerase. Dynamic characterization of pol β from methyl-TROSY 13C-1H multiple quantum CPMG relaxation dispersion experiments of Ile and Met sidechains and previous backbone relaxation dispersion measurements, reveals transitions in μs-ms dynamics in response to highly variable substrates. Recognition of a 1-nt-gapped DNA substrate is accompanied by significant backbone and sidechain motion in the lyase domain and the DNA binding subdomain of the polymerase domain, that may help to facilitate binding of the apoenzyme to the segments of the DNA upstream and downstream from the gap. Backbone μs-ms motion largely disappears after formation of the pol β-DNA complex, giving rise to an increase in uncoupled μs-ms sidechain motion throughout the enzyme. Formation of an abortive ternary complex using a non-hydrolyzable dNTP results in sidechain motions that fit to a single exchange process localized to the catalytic subdomain, suggesting that this motion may play a role in catalysis.
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Affiliation(s)
- Eugene F DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas W Kirby
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Geoffrey A Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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10
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Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublié S, Loria J, Sweasy JB. I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity. Nucleic Acids Res 2019; 46:10740-10756. [PMID: 30239932 PMCID: PMC6237750 DOI: 10.1093/nar/gky825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/05/2018] [Indexed: 11/14/2022] Open
Abstract
DNA polymerase β (pol β) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol β must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol β‘s ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol β to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol β.
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Affiliation(s)
- Cary Liptak
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mariam M Mahmoud
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Marcus V Moreno
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Kyle East
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Khadijeh S Alnajjar
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ji Huang
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jamie B Towle-Weicksel
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - J Patrick Loria
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- To whom correspondence should be addressed. Tel: +203 436 2518; Fax: +203 436 6144; . Correspondence may also be addressed to Joann B. Sweasy. Tel: +203 737 2626; Fax: +203 785 6309;
| | - Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- To whom correspondence should be addressed. Tel: +203 436 2518; Fax: +203 436 6144; . Correspondence may also be addressed to Joann B. Sweasy. Tel: +203 737 2626; Fax: +203 785 6309;
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11
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Beard WA, Wilson SH. DNA polymerase beta and other gap-filling enzymes in mammalian base excision repair. Enzymes 2019; 45:1-26. [PMID: 31627875 DOI: 10.1016/bs.enz.2019.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA polymerase β plays a central role in the base excision DNA repair pathway that cleanses the genome of apurinic/apyrimidinic (AP) sites. AP sites arise in DNA from spontaneous base loss and DNA damage-specific glycosylases that hydrolyze the N-glycosidic bond between the deoxyribose and damaged base. AP sites are deleterious lesions because they can be mutagenic and/or cytotoxic. DNA polymerase β contributes two enzymatic activities, DNA synthesis and lyase, during the repair of AP sites; these activities reside on carboxyl- and amino-terminal domains, respectively. Accordingly, its cellular, structural, and kinetic attributes have been extensively characterized and it serves as model enzyme for the nucleotidyl transferase reaction utilized by other replicative, repair, and trans-lesion DNA polymerases.
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Affiliation(s)
- William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Durham, NC, United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Durham, NC, United States.
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12
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
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13
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Chen K, Lv J, Wang G, Yu X, Xu X, Zhu G, Shao Z, Wang D, Tang C, Cai S. Changes of serum trace elements in early stage trauma and its correlation with injury severity score. Medicine (Baltimore) 2018; 97:e10077. [PMID: 29879011 PMCID: PMC5999505 DOI: 10.1097/md.0000000000010077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Severe trauma can cause secondary multiple organ dysfunction syndrome and death. The absolute and relative concentrations of trace elements in both critical care and conventional treatment, which can lead to acute trace element deficiency, constitute an important mechanism of multiple organ dysfunction syndrome (MODS)/multiple organ failure (MOF). METHODS We investigated the changes in serum Cu, Zn, and Fe in early stage trauma of patients with the high injury severity score (ISS) and correlated the change in trace elements with ISS. Blood samples were collected within an hour of admittance and the patients were scored according to ISS. We collected clinical data records and ISS score values, and determined serum Fe, Zn, and Cu by inductively coupled plasma mass spectrometry. RESULTS Compared with the control group, the serum Zn and Fe values of trauma patients were decreased. There was no significant difference in serum Cu between the patients and the control group. In the trauma group, the serum Zn and Fe were lower than that of the minor injury group, and the difference of Cu concentration was not statistically significant. CONCLUSIONS Serum Zn and Fe levels in patients with multiple trauma fractures were significantly different than those in the normal group, suggesting that Zn and Fe need to be monitored in the early stage of trauma.
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Affiliation(s)
- Kaihong Chen
- The Second Affiliated Hospital of Shantou University Medical College
| | - Junyao Lv
- Department of Forensic Medicine, Shantou University Medical College, Shantou, Guangdong Province, People's Republic of China
| | - Guanghuan Wang
- The Second Affiliated Hospital of Shantou University Medical College
| | - Xiaojun Yu
- Department of Forensic Medicine, Shantou University Medical College, Shantou, Guangdong Province, People's Republic of China
| | - Xiaohu Xu
- Department of Forensic Medicine, Shantou University Medical College, Shantou, Guangdong Province, People's Republic of China
| | - Guanghui Zhu
- Department of Forensic Medicine, Shantou University Medical College, Shantou, Guangdong Province, People's Republic of China
| | - Zhuying Shao
- The Second Affiliated Hospital of Shantou University Medical College
| | - Dian Wang
- Department of Forensic Medicine, Shantou University Medical College, Shantou, Guangdong Province, People's Republic of China
| | - Chang Tang
- Department of Forensic Medicine, Shantou University Medical College, Shantou, Guangdong Province, People's Republic of China
| | - Shanqing Cai
- Department of Forensic Medicine, Shantou University Medical College, Shantou, Guangdong Province, People's Republic of China
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14
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Shock DD, Freudenthal BD, Beard WA, Wilson SH. Modulating the DNA polymerase β reaction equilibrium to dissect the reverse reaction. Nat Chem Biol 2017; 13:1074-1080. [PMID: 28759020 PMCID: PMC5605435 DOI: 10.1038/nchembio.2450] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 06/28/2017] [Indexed: 12/20/2022]
Abstract
DNA polymerases catalyze efficient and high fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, removing the DNA primer terminus and generating deoxynucleoside triphosphates. Since pyrophosphorolysis can influence polymerase fidelity and sensitivity to chain-terminating nucleosides, we analyzed pyrophosphorolysis with human DNA polymerase β and found the reaction to be inefficient. The lack of a thio-elemental effect indicated that it was limited by a non-chemical step. Utilizing a pyrophosphate analog, where the bridging oxygen is replaced with an imido-group (PNP), increased the rate of the reverse reaction and displayed a large thio-elemental effect indicating that chemistry was now rate determining. Time-lapse crystallography with PNP captured structures consistent with a chemical equilibrium that favored the reverse reaction. These results highlight the importance of the bridging atom between the β- and γ-phosphates of the incoming nucleotide in reaction chemistry, enzyme conformational changes, and overall reaction equilibrium.
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Affiliation(s)
- David D Shock
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Bret D Freudenthal
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
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15
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Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure 2016; 24:1863-1875. [PMID: 27642161 DOI: 10.1016/j.str.2016.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 11/24/2022]
Abstract
High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis.
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16
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Zhang Y, Baranovskiy AG, Tahirov ET, Tahirov TH, Pavlov YI. Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction. DNA Repair (Amst) 2016; 43:24-33. [PMID: 27235627 DOI: 10.1016/j.dnarep.2016.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/09/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022]
Abstract
DNA polymerases (pols) are sophisticated protein machines operating in the replication, repair and recombination of genetic material in the complex environment of the cell. DNA pol reactions require at least two divalent metal ions for the phosphodiester bond formation. We explore two understudied roles of metals in pol transactions with emphasis on polα, a crucial enzyme in the initiation of DNA synthesis. We present evidence that the combination of many factors, including the structure of the template/primer, the identity of the metal, the metal turnover in the pol active site, and the influence of the concentration of nucleoside triphosphates, affect DNA pol synthesis. On the poly-dT70 template, the increase of Mg(2+) concentration within the range typically used for pol reactions led to the severe loss of the ability of pol to extend DNA primers and led to a decline in DNA product sizes when extending RNA primers, simulating the effect of "counting" of the number of nucleotides in nascent primers by polα. We suggest that a high Mg(2+) concentration promotes the dynamic formation of unconventional DNA structure(s), thus limiting the apparent processivity of the enzyme. Next, we found that Zn(2+) supported robust polα reactions when the concentration of nucleotides was above the concentration of ions; however, there was only one nucleotide incorporation by the Klenow fragment of DNA pol I. Zn(2+) drastically inhibited polα, but had no effect on Klenow, when Mg(2+) was also present. It is possible that Zn(2+) perturbs metal-mediated transactions in pol active site, for example affecting the step of pyrophosphate removal at the end of each pol cycle necessary for continuation of polymerization.
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Affiliation(s)
- Yinbo Zhang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States
| | - Emin T Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.
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17
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Kim T, Freudenthal BD, Beard WA, Wilson SH, Schlick T. Insertion of oxidized nucleotide triggers rapid DNA polymerase opening. Nucleic Acids Res 2016; 44:4409-24. [PMID: 27034465 PMCID: PMC4872097 DOI: 10.1093/nar/gkw174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/04/2016] [Indexed: 11/21/2022] Open
Abstract
A novel mechanism is unveiled to explain why a pro-mutagenic nucleotide lesion (oxidized guanine, 8-oxoG) causes the mammalian DNA repair polymerase-β (pol-β) to rapidly transition to an inactive open conformation. The mechanism involves unexpected features revealed recently in time-lapse crystallography. Specifically, a delicate water network associated with a lesion-stabilizing auxilliary product ion Mg(p) triggers a cascade of events that leads to poor active site geometry and the rupture of crucial molecular interactions between key residues in both the anti(8-oxoG:C) and syn(8-oxoG:A) systems. Once the base pairs in these lesioned systems are broken, dislocation of both Asp192 (a metal coordinating ligand) and the oxoG phosphate group (PO4) interfere with the hydrogen bonding between Asp192 and Arg258, whose rotation toward Asp192 is crucial to the closed-to-open enzyme transition. Energetically, the lesioned open states are similar in energy to those of the corresponding closed complexes after chemistry, in marked contrast to the unlesioned pol-β anti(G:C) system, whose open state is energetically higher than the closed state. The delicate surveillance system offers a fundamental protective mechanism in the cell that triggers DNA repair events which help deter insertion of oxidized lesions.
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Affiliation(s)
- Taejin Kim
- Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY 10003, USA
| | - Bret D Freudenthal
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY 10003, USA Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
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18
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Dahl JM, Lieberman KR, Wang H. Modulation of DNA Polymerase Noncovalent Kinetic Transitions by Divalent Cations. J Biol Chem 2016; 291:6456-70. [PMID: 26797125 PMCID: PMC4813572 DOI: 10.1074/jbc.m115.701797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/02/2016] [Indexed: 11/06/2022] Open
Abstract
Replicative DNA polymerases (DNAPs) require divalent metal cations for phosphodiester bond formation in the polymerase site and for hydrolytic editing in the exonuclease site. Me(2+) ions are intimate architectural components of each active site, where they are coordinated by a conserved set of amino acids and functional groups of the reaction substrates. Therefore Me(2+) ions can influence the noncovalent transitions that occur during each nucleotide addition cycle. Using a nanopore, transitions in individual Φ29 DNAP complexes are resolved with single-nucleotide spatial precision and sub-millisecond temporal resolution. We studied Mg(2+) and Mn(2+), which support catalysis, and Ca(2+), which supports deoxynucleoside triphosphate (dNTP) binding but not catalysis. We examined their effects on translocation, dNTP binding, and primer strand transfer between the polymerase and exonuclease sites. All three metals cause a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Me(2+) also promotes an increase in the backward translocation rate that is dependent upon the primer terminal 3'-OH group. Me(2+) modulates the translocation rates but not their response to force, suggesting that Me(2+) does not affect the distance to the transition state of translocation. Absent Me(2+), the primer strand transfer pathway between the polymerase and exonuclease sites displays additional kinetic states not observed at >1 mm Me(2+). Complementary dNTP binding is affected by Me(2+) identity, with Ca(2+) affording the highest affinity, followed by Mn(2+), and then Mg(2+). Both Ca(2+) and Mn(2+) substantially decrease the dNTP dissociation rate relative to Mg(2+), while Ca(2+) also increases the dNTP association rate.
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Affiliation(s)
- Joseph M Dahl
- From the Departments of Biomolecular Engineering and
| | | | - Hongyun Wang
- Applied Mathematics and Statistics, University of California, Santa Cruz, California 95064
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19
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Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH. Substrate-induced DNA polymerase β activation. J Biol Chem 2014; 289:31411-22. [PMID: 25261471 DOI: 10.1074/jbc.m114.607432] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerases and substrates undergo conformational changes upon forming protein-ligand complexes. These conformational adjustments can hasten or deter DNA synthesis and influence substrate discrimination. From structural comparison of binary DNA and ternary DNA-dNTP complexes of DNA polymerase β, several side chains have been implicated in facilitating formation of an active ternary complex poised for chemistry. Site-directed mutagenesis of these highly conserved residues (Asp-192, Arg-258, Phe-272, Glu-295, and Tyr-296) and kinetic characterization provides insight into the role these residues play during correct and incorrect insertion as well as their role in conformational activation. The catalytic efficiencies for correct nucleotide insertion for alanine mutants were wild type ∼ R258A > F272A ∼ Y296A > E295A > D192A. Because the efficiencies for incorrect insertion were affected to about the same extent for each mutant, the effects on fidelity were modest (<5-fold). The R258A mutant exhibited an increase in the single-turnover rate of correct nucleotide insertion. This suggests that the wild-type Arg-258 side chain generates a population of non-productive ternary complexes. Structures of binary and ternary substrate complexes of the R258A mutant and a mutant associated with gastric carcinomas, E295K, provide molecular insight into intermediate structural conformations not appreciated previously. Although the R258A mutant crystal structures were similar to wild-type enzyme, the open ternary complex structure of E295K indicates that Arg-258 stabilizes a non-productive conformation of the primer terminus that would decrease catalysis. Significantly, the open E295K ternary complex binds two metal ions indicating that metal binding cannot overcome the modified interactions that have interrupted the closure of the N-subdomain.
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Affiliation(s)
- William A Beard
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - David D Shock
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Vinod K Batra
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Rajendra Prasad
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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20
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Abstract
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DNA
polymerase (pol) β is a small eukaryotic DNA polymerase
composed of two domains. Each domain contributes an enzymatic activity
(DNA synthesis and deoxyribose phosphate lyase) during the repair
of simple base lesions. These domains are termed the polymerase and
lyase domains, respectively. Pol β has been an excellent model
enzyme for studying the nucleotidyl transferase reaction and substrate
discrimination at a molecular level. In this review, recent crystallographic
studies of pol β in various liganded and conformational states
during the insertion of right and wrong nucleotides as well as during
the bypass of damaged DNA (apurinic sites and 8-oxoguanine) are described.
Structures of these catalytic intermediates provide unexpected insights
into mechanisms by which DNA polymerases enhance genome stability.
These structures also provide an improved framework that permits computational
studies to facilitate the interpretation of detailed kinetic analyses
of this model enzyme.
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Affiliation(s)
- William A Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive, P.O. Box 12233, MD F3-01, Research Triangle Park, North Carolina 27709, United States
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21
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Koag MC, Lee S. Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase β. J Am Chem Soc 2014; 136:5709-21. [PMID: 24694247 PMCID: PMC4004240 DOI: 10.1021/ja500172d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Human
DNA polymerase β (polβ) inserts, albeit slowly,
T opposite the carcinogenic lesion O6-methylguanine (O6MeG) ∼30-fold
more frequently than C. To gain insight into this promutagenic process,
we solved four ternary structures of polβ with an incoming dCTP
or dTTP analogue base-paired with O6MeG in the presence of active-site
Mg2+ or Mn2+. The Mg2+-bound structures
show that both the O6MeG·dCTP/dTTP–Mg2+ complexes
adopt an open protein conformation, staggered base pair, and one active-site
metal ion. The Mn2+-bound structures reveal that, whereas
the O6Me·dCTP–Mn2+ complex assumes the similar
altered conformation, the O6MeG·dTTP–Mn2+ complex
adopts a catalytically competent state with a closed protein conformation
and pseudo-Watson–Crick base pair. On the basis of these observations,
we conclude that polβ slows nucleotide incorporation opposite
O6MeG by inducing an altered conformation suboptimal for catalysis
and promotes mutagenic replication by allowing Watson–Crick-mode
for O6MeG·T but not for O6MeG·C in the enzyme active site.
The O6MeG·dTTP–Mn2+ ternary structure, which
represents the first structure of mismatched polβ ternary complex
with a closed protein conformation and coplanar base pair, the first
structure of pseudo-Watson–Crick O6MeG·T formed in the
active site of a DNA polymerase, and a rare, if not the first, example
of metal-dependent conformational activation of a DNA polymerase,
indicate that catalytic metal-ion coordination is utilized as a kinetic
checkpoint by polβ and is crucial for the conformational activation
of polβ. Overall, our structural studies not only explain the
promutagenic polβ catalysis across O6MeG but also provide new
insights into the replication fidelity of polβ.
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Affiliation(s)
- Myong-Chul Koag
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
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22
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Kirby TW, Derose EF, Beard WA, Shock DD, Wilson SH, London RE. Substrate rescue of DNA polymerase β containing a catastrophic L22P mutation. Biochemistry 2014; 53:2413-22. [PMID: 24655288 PMCID: PMC4004254 DOI: 10.1021/bi5001855] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
DNA polymerase (pol)
β is a multidomain enzyme with two enzymatic
activities that plays a central role in the overlapping base excision
repair and single-strand break repair pathways. The high frequency
of pol β variants identified in tumor-derived tissues suggests
a possible role in the progression of cancer, making the determination
of the functional consequences of these variants of interest. Pol
β containing a proline substitution for leucine 22 in the lyase
domain (LD), identified in gastric tumors, has been reported to exhibit
severe impairment of both lyase and polymerase activities. Nuclear
magnetic resonance (NMR) spectroscopic evaluations of both pol β
and the isolated LD containing the L22P mutation demonstrate destabilization
sufficient to result in LD-selective unfolding with minimal structural
perturbations to the polymerase domain. Unexpectedly, addition of
single-stranded or hairpin DNA resulted in partial refolding of the
mutated lyase domain, both in isolation and for the full-length enzyme.
Further, formation of an abortive ternary complex using Ca2+ and a complementary dNTP indicates that the fraction of pol β(L22P)
containing the folded LD undergoes conformational activation similar
to that of the wild-type enzyme. Kinetic characterization of the polymerase
activity of L22P pol β indicates that the L22P mutation compromises
DNA binding, but nearly wild-type catalytic rates can be observed
at elevated substrate concentrations. The organic osmolyte trimethylamine N-oxide (TMAO) is similarly able to induce folding and kinetic
activation of both polymerase and lyase activities of the mutant.
Kinetic data indicate synergy between the TMAO cosolvent and substrate
binding. NMR data indicate that the effect of the DNA results primarily
from interaction with the folded LD(L22P), while the effect of the
TMAO results primarily from destabilization of the unfolded LD(L22P).
These studies illustrate that substrate-induced catalytic activation
of pol β provides an optimal enzyme conformation even in the
presence of a strongly destabilizing point mutation. Accordingly,
it remains to be determined whether this mutation alters the threshold
of cellular repair activity needed for routine genome maintenance
or whether the “inactive” variant interferes with DNA
repair.
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Affiliation(s)
- Thomas W Kirby
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences , Research Triangle Park, North Carolina 27709, United States
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23
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Li Y, Freudenthal BD, Beard WA, Wilson SH, Schlick T. Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways. J Am Chem Soc 2014; 136:3630-9. [PMID: 24511902 PMCID: PMC7032070 DOI: 10.1021/ja412701f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To interpret recent structures of the R283K mutant of human DNA repair enzyme DNA polymerase β (pol β) differing in the number of Mg(2+) ions, we apply transition path sampling (TPS) to assess the effect of differing ion placement on the transition from the open one-metal to the closed two-metal state. We find that the closing pathway depends on the initial ion position, both in terms of the individual transition states and associated energies. The energy barrier of the conformational pathway varies from 25 to 58 kJ/mol, compared to the conformational energy barrier of 42 kJ/mol for the wild-type pol β reported previously. Moreover, we find a preferred ion route located in the center of the enzyme, parallel to the DNA. Within this route, the conformational pathway is similar to that of the overall open to closed transition of pol β, but outside it, especially when the ion starts near active site residues Arg258 and Asp190, the conformational pathway diverges significantly. Our findings should apply generally to pol β, since R283K is relatively far from the active site; further experimental and computational work are required to confirm this. Our studies also underscore the common feature that less active mutants have less stable closed states than their open states, in marked contrast to the wild-type enzyme, where the closed state is significantly more stable than the open form.
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Affiliation(s)
- Yunlang Li
- Department of Chemistry and Courant Institute of
Mathematical Sciences, New York University, 251 Mercer Street, New York, NY
10012
| | - Bret D. Freudenthal
- Laboratory of Structural Biology, National
Institute of Environmental Health Sciences, National Institutes of Health, Bethesda,
Research Triangle Park, NC 27709
| | - William A. Beard
- Laboratory of Structural Biology, National
Institute of Environmental Health Sciences, National Institutes of Health, Bethesda,
Research Triangle Park, NC 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National
Institute of Environmental Health Sciences, National Institutes of Health, Bethesda,
Research Triangle Park, NC 27709
| | - Tamar Schlick
- Department of Chemistry and Courant Institute of
Mathematical Sciences, New York University, 251 Mercer Street, New York, NY
10012
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24
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Koag MC, Min K, Lee S. Structural basis for promutagenicity of 8-halogenated guanine. J Biol Chem 2014; 289:6289-98. [PMID: 24425881 DOI: 10.1074/jbc.m113.537803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
8-Halogenated guanine (haloG), a major DNA adduct formed by reactive halogen species during inflammation, is a promutagenic lesion that promotes misincorporation of G opposite the lesion by various DNA polymerases. Currently, the structural basis for such misincorporation is unknown. To gain insights into the mechanism of misincorporation across haloG by polymerase, we determined seven x-ray structures of human DNA polymerase β (polβ) bound to DNA bearing 8-bromoguanine (BrG). We determined two pre-catalytic ternary complex structures of polβ with an incoming nonhydrolyzable dGTP or dCTP analog paired with templating BrG. We also determined five binary complex structures of polβ in complex with DNA containing BrG·C/T at post-insertion and post-extension sites. In the BrG·dGTP ternary structure, BrG adopts syn conformation and forms Hoogsteen base pairing with the incoming dGTP analog. In the BrG·dCTP ternary structure, BrG adopts anti conformation and forms Watson-Crick base pairing with the incoming dCTP analog. In addition, our polβ binary post-extension structures show Hoogsteen BrG·G base pair and Watson-Crick BrG·C base pair. Taken together, the first structures of haloG-containing DNA bound to a protein indicate that both BrG·G and BrG·C base pairs are accommodated in the active site of polβ. Our structures suggest that Hoogsteen-type base pairing between G and C8-modified G could be accommodated in the active site of a DNA polymerase, promoting G to C mutation.
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Affiliation(s)
- Myong-Chul Koag
- From the Division of Medicinal Chemistry, College of Pharmacy, the University of Texas, Austin, Texas 78712
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25
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Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublié S. The E295K cancer variant of human polymerase β favors the mismatch conformational pathway during nucleotide selection. J Biol Chem 2013; 288:34850-60. [PMID: 24133209 DOI: 10.1074/jbc.m113.510891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
DNA polymerase β (pol β) is responsible for gap filling synthesis during repair of damaged DNA as part of the base excision repair pathway. Human pol β mutations were recently identified in a high percentage (∼30%) of tumors. Characterization of specific cancer variants is particularly useful to further the understanding of the general mechanism of pol β while providing context to disease contribution. We showed that expression of the carcinoma variant E295K induces cellular transformation. The poor polymerase activity exhibited by the variant was hypothesized to be caused by the destabilization of proper active site assembly by the glutamate to lysine mutation. Here, we show that this variant exhibits an unusual preference for binding dCTP opposite a templating adenine over the cognate dTTP. Biochemical studies indicate that the noncognate competes with the cognate nucleotide for binding to the polymerase active site with the noncognate incorporation a function of higher affinity and not increased activity. In the crystal structure of the variant bound to dA:dCTP, the fingers domain closes around the mismatched base pair. Nucleotide incorporation is hindered because key residues in the polymerase active site are not properly positioned for nucleotidyl transfer. In contrast to the noncognate dCTP, neither the cognate dTTP nor its nonhydrolyzable analog induced fingers closure, as isomorphous difference Fourier maps show that the cognate nucleotides are bound to the open state of the polymerase. Comparison with published structures provides insight into the structural rearrangements within pol β that occur during the process of nucleotide discrimination.
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Affiliation(s)
- Brian E Eckenroth
- From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405 and
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26
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Gouge J, Rosario S, Romain F, Beguin P, Delarue M. Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism. J Mol Biol 2013; 425:4334-52. [PMID: 23856622 DOI: 10.1016/j.jmb.2013.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 11/19/2022]
Abstract
Terminal deoxynucleotidyltransferase (Tdt) is a non-templated eukaryotic DNA polymerase of the polX family that is responsible for the random addition of nucleotides at the V(D)J junctions of immunoglobulins and T-cell receptors. Here we describe a series of high-resolution X-ray structures that mimic the pre-catalytic state, the post-catalytic state and a competent state that can be transformed into the two other ones in crystallo via the addition of dAMPcPP and Zn(2+), respectively. We examined the effect of Mn(2+), Co(2+) and Zn(2+) because they all have a marked influence on the kinetics of the reaction. We demonstrate a dynamic role of divalent transition metal ions bound to site A: (i) Zn(2+) (or Co(2+)) in Metal A site changes coordination from octahedral to tetrahedral after the chemical step, which explains the known higher affinity of Tdt for the primer strand when these ions are present, and (ii) metal A has to leave to allow the translocation of the primer strand and to clear the active site, a typical feature for a ratchet-like mechanism. Except for Zn(2+), the sugar puckering of the primer strand 3' terminus changes from C2'-endo to C3'-endo during catalysis. In addition, our data are compatible with a scheme where metal A is the last component that binds to the active site to complete its productive assembly, as already inferred in human pol beta. The new structures have potential implications for modeling pol mu, a closely related polX implicated in the repair of DNA double-strand breaks, in a complex with a DNA synapsis.
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Affiliation(s)
- Jérôme Gouge
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 rue du Dr Roux, 75015 Paris, France
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27
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Freudenthal BD, Beard WA, Wilson SH. DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Nucleic Acids Res 2012; 41:1848-58. [PMID: 23267011 PMCID: PMC3561998 DOI: 10.1093/nar/gks1276] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A major base lesion resulting from oxidative stress is 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxoG) that has ambiguous coding potential. Error-free DNA synthesis involves 8-oxoG adopting an anti-conformation to base pair with cytosine whereas mutagenic bypass involves 8-oxoG adopting a syn-conformation to base pair with adenine. Left unrepaired the syn-8-oxoG/dAMP base pair results in a G–C to T–A transversion. During base excision repair of this mispair, DNA polymerase (pol) β is confronted with gap filling opposite 8-oxoG. To determine how pol β discriminates between anti- and syn-8-oxoG, we introduced a point mutation (R283K) to alter insertion specificity. Kinetic studies demonstrate that this substitution results in an increased fidelity opposite 8-oxoG. Structural studies with R283K pol β show that the binary DNA complex has 8-oxoG in equilibrium between anti- and syn-forms. Ternary complexes with incoming dCTP resemble the wild-type enzyme, with templating anti-8-oxoG base pairing with incoming cytosine. In contrast to wild-type pol β, the ternary complex of the R283K mutant with an incoming dATP-analogue and templating 8-oxoG resembles a G–A mismatched structure with 8-oxoG adopting an anti-conformation. These results demonstrate that the incoming nucleotide is unable to induce a syn-8-oxoG conformation without minor groove DNA polymerase interactions that influence templating (anti-/syn-equilibrium) of 8-oxoG while modulating fidelity.
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Affiliation(s)
- Bret D Freudenthal
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, PO Box 12233, Research Triangle Park, NC 27709-2233, USA
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Schlick T, Arora K, Beard WA, Wilson SH. Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms. Theor Chem Acc 2012; 131:1287. [PMID: 23459563 DOI: 10.1007/s00214-012-1287-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In recent papers, there has been a lively exchange concerning theories for enzyme catalysis, especially the role of protein dynamics/pre-chemistry conformational changes in the catalytic cycle of enzymes. Of particular interest is the notion that substrate-induced conformational changes that assemble the polymerase active site prior to chemistry are required for DNA synthesis and impact fidelity (i.e., substrate specificity). High-resolution crystal structures of DNA polymerase β representing intermediates of substrate complexes prior to the chemical step are available. These structures indicate that conformational adjustments in both the protein and substrates must occur to achieve the requisite geometry of the reactive participants for catalysis. We discuss computational and kinetic methods to examine possible conformational change pathways that lead from the observed crystal structure intermediates to the final structures poised for chemistry. The results, as well as kinetic data from site-directed mutagenesis studies, are consistent with models requiring pre-chemistry conformational adjustments in order to achieve high fidelity DNA synthesis. Thus, substrate-induced conformational changes that assemble the polymerase active site prior to chemistry contribute to DNA synthesis even when they do not represent actual rate-determining steps for chemistry.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA. Courant Institute of Mathematical Sciences, New York, University, 251 Mercer Street, New York, NY 10012, USA
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29
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Freudenthal BD, Beard WA, Wilson SH. Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure 2012; 20:1829-37. [PMID: 22959623 PMCID: PMC3496073 DOI: 10.1016/j.str.2012.08.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 11/23/2022]
Abstract
DNA polymerase and substrate conformational changes are essential for high-fidelity DNA synthesis. Structures of DNA polymerase (pol) β in complex with DNA show the enzyme in an "open" conformation. Subsequent to binding the nucleotide, the polymerase "closes" around the nascent base pair with two metals positioned for chemistry. However, structures of substrate/active site intermediates prior to closure are lacking. By destabilizing the closed complex, we determined unique ternary complex structures of pol β with correct and incorrect incoming nucleotides bound to the open conformation. These structures reveal that Watson-Crick hydrogen bonding is assessed upon initial complex formation. Importantly, nucleotide-bound states representing intermediate metal coordination states occur with active site assembly. The correct, but not incorrect, nucleotide maintains Watson-Crick hydrogen bonds during interconversion of these states. These structures indicate that the triphosphate of the incoming nucleotide undergoes rearrangement prior to closure, providing an opportunity to deter misinsertion and increase fidelity.
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Affiliation(s)
- Bret D. Freudenthal
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
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30
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Li Y, Gridley CL, Jaeger J, Sweasy JB, Schlick T. Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. J Am Chem Soc 2012; 134:9999-10010. [PMID: 22651551 PMCID: PMC3383778 DOI: 10.1021/ja300361r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mutations in DNA polymerase β (pol β) have been associated with approximately 30% of human tumors. The E295K mutation of pol β has been linked to gastric carcinoma via interference with base excision repair. To interpret the different behavior of E295K as compared to wild-type pol β in atomic and energetic detail, we resolve a binary crystal complex of E295K at 2.5 Å and apply transition path sampling (TPS) to delineate the closing pathway of the E295K pol β mutant. Conformational changes are important components in the enzymatic pathway that lead to and ready the enzyme for the chemical reaction. Our analyses show that the closing pathway of E295K mutant differs from the wild-type pol β in terms of the individual transition states along the pathway, associated energies, and the active site conformation in the final closed form of the mutant. In particular, the closed state of E295K has a more distorted active site than the active site in the wild-type pol β. In addition, the total energy barrier in the conformational closing pathway is 65 ± 11 kJ/mol, much higher than that estimated for both correct (e.g., G:C) and incorrect (e.g., G:A) wild-type pol β systems (42 ± 8 and 45 ± 7 kJ/mol, respectively). In particular, the rotation of Arg258 is the rate-limiting step in the conformational pathway of E295K due to unfavorable electrostatic and steric interactions. The distorted active site in the closed relative to open state and the high energy barrier in the conformational pathway may explain in part why the E295K mutant is observed to be inactive. Interestingly, however, following the closing of the thumb but prior to the rotation of Arg258, the E295K mutant complex has a similar energy level as compared to the wild-type pol β. This suggests that the E295K mutant may associate with DNA with similar affinity, but it may be hampered in continuing the process of chemistry. Supporting experimental data come from the observation that the catalytic activity of wild-type pol β is hampered when E295K is present: this may arise from the competition between E295K and wild-type enzyme for the DNA. These combined results suggest that the low insertion efficiency of E295K mutant as compared to wild-type pol β may be related to a closed form distorted by unfavorable electrostatic and steric interactions between Arg258 and other key residues. The active site is thus less competent for proceeding to the chemical reaction, which may also involve a higher reaction barrier than the wild-type or may not be possible in this mutant. Our analysis also suggests further experiments for other mutants to test the above hypothesis and dissect the roles of steric and electrostatic factors on enzyme behavior.
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Affiliation(s)
- Yunlang Li
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012
| | - Chelsea L. Gridley
- Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Joachim Jaeger
- Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
- Division of Genetics, Wadsworth Center NYS-DOH, New Scotland Avenue, Albany, NY 12208, USA
| | - Joann B. Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208040, New Haven, CT 06520, USA
| | - Tamar Schlick
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012
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31
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Nemec AA, Donigan KA, Murphy DL, Jaeger J, Sweasy JB. Colon cancer-associated DNA polymerase β variant induces genomic instability and cellular transformation. J Biol Chem 2012; 287:23840-9. [PMID: 22573322 DOI: 10.1074/jbc.m112.362111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rapidly advancing technology has resulted in the generation of the genomic sequences of several human tumors. We have identified several mutations of the DNA polymerase β (pol β) gene in human colorectal cancer. We have demonstrated that the expression of the pol β G231D variant increased chromosomal aberrations and induced cellular transformation. The transformed phenotype persisted in the cells even once the expression of G231D was extinguished, suggesting that it resulted as a consequence of genomic instability. Biochemical analysis revealed that its catalytic rate was 140-fold slower than WT pol β, and this was a result of the decreased binding affinity of nucleotides by G231D. Residue 231 of pol β lies in close proximity to the template strand of the DNA. Molecular modeling demonstrated that the change from a small and nonpolar glycine to a negatively charged aspartate resulted in a repulsion between the template and residue 231 leading to the distortion of the dNTP binding pocket. In addition, expression of G231D was insufficient to rescue pol β-deficient cells treated with chemotherapeutic agents suggesting that these agents may be effectively used to treat tumors harboring this mutation. More importantly, this suggests that the G231D variant has impaired base excision repair. Together, these data indicate that the G231D variant plays a role in driving cancer.
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Affiliation(s)
- Antonia A Nemec
- Department of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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32
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Berlow RB, Swain M, Dalal S, Sweasy JB, Loria JP. Substrate-dependent millisecond domain motions in DNA polymerase β. J Mol Biol 2012; 419:171-82. [PMID: 22446382 DOI: 10.1016/j.jmb.2012.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 02/02/2023]
Abstract
DNA polymerase β (Pol β) is a 39-kDa enzyme that performs the vital cellular function of repairing damaged DNA. Mutations in Pol β have been linked to various cancers, and these mutations are further correlated with altered Pol β enzymatic activity. The fidelity of correct nucleotide incorporation into damaged DNA is essential for Pol β repair function, and several studies have implicated conformational changes in Pol β as a determinant of this repair fidelity. In this work, the rate constants for domain motions in Pol β have been determined by solution NMR relaxation dispersion for the apo and substrate-bound, binary forms of Pol β. In apo Pol β, molecular motions, primarily isolated to the DNA lyase domain, are observed to occur at 1400 s(-1). Additional analysis suggests that these motions allow apo Pol β to sample a conformation similar to the gapped DNA-substrate-bound form. Upon binding DNA, these lyase domain motions are significantly quenched, whereas evidence for conformational motions in the polymerase domain becomes apparent. These NMR studies suggest an alteration in the dynamic landscape of Pol β due to substrate binding. Moreover, a number of the flexible residues identified in this work are also the location of residues, which upon mutation lead to cancer phenotypes in vivo, which may be due to the intimate role of protein motions in Pol β fidelity.
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Affiliation(s)
- Rebecca B Berlow
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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