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Alnajjar K, Wang K, Alvarado-Cruz I, Chavira C, Negahbani A, Nakhjiri M, Minard C, Garcia-Barboza B, Kashemirov BA, McKenna CE, Goodman MF, Sweasy JB. Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β. Biochemistry 2024; 63:1412-1422. [PMID: 38780930 PMCID: PMC11155676 DOI: 10.1021/acs.biochem.4c00065] [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: 02/03/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
The catalytic function of DNA polymerase β (pol β) fulfills the gap-filling requirement of the base excision DNA repair pathway by incorporating a single nucleotide into a gapped DNA substrate resulting from the removal of damaged DNA bases. Most importantly, pol β can select the correct nucleotide from a pool of similarly structured nucleotides to incorporate into DNA in order to prevent the accumulation of mutations in the genome. Pol β is likely to employ various mechanisms for substrate selection. Here, we use dCTP analogues that have been modified at the β,γ-bridging group of the triphosphate moiety to monitor the effect of leaving group basicity of the incoming nucleotide on precatalytic conformational changes, which are important for catalysis and selectivity. It has been previously shown that there is a linear free energy relationship between leaving group pKa and the chemical transition state. Our results indicate that there is a similar relationship with the rate of a precatalytic conformational change, specifically, the closing of the fingers subdomain of pol β. In addition, by utilizing analogue β,γ-CHX stereoisomers, we identified that the orientation of the β,γ-bridging group relative to R183 is important for the rate of fingers closing, which directly influences chemistry.
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Affiliation(s)
- Khadijeh
S. Alnajjar
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Katarina Wang
- Therapeutic
Radiology Department, Yale University, New Haven, Connecticut 06520, United States
| | - Isabel Alvarado-Cruz
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Cristian Chavira
- Fred
and Pamela Buffett Cancer Center and Eppley Institute for Cancer Research, Omaha, Nebraska 68198, United States
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Amirsoheil Negahbani
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Corinne Minard
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Beatriz Garcia-Barboza
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Myron F. Goodman
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department
of Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Joann B. Sweasy
- Fred
and Pamela Buffett Cancer Center and Eppley Institute for Cancer Research, Omaha, Nebraska 68198, United States
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Abstract
DNA polymerase beta (Pol β) is a 39 kD vertebrate polymerase that lacks proofreading ability, yet still maintains a moderate fidelity of DNA synthesis. Pol β is a key enzyme that functions in the base excision repair and non-homologous end joining pathways of DNA repair. Mechanisms of fidelity for Pol β are still being elucidated but are likely to involve dynamic conformational motions of the enzyme upon its binding to DNA and deoxynucleoside triphosphates. Recent studies have linked germline and somatic variants of Pol β with cancer and autoimmunity. These variants induce genomic instability by a number of mechanisms, including error-prone DNA synthesis and accumulation of single nucleotide gaps that lead to replication stress. Here, we review the structure and function of Pol β, and we provide insights into how structural changes in Pol β variants may contribute to genomic instability, mutagenesis, disease, cancer development, and impacts on treatment outcomes.
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Affiliation(s)
- Danielle L Sawyer
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ
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Purslow JA, Nguyen TT, Khatiwada B, Singh A, Venditti V. N 6-methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5. SCIENCE ADVANCES 2021; 7:7/34/eabi8215. [PMID: 34407931 PMCID: PMC8373141 DOI: 10.1126/sciadv.abi8215] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/29/2021] [Indexed: 05/13/2023]
Abstract
Alkbh5 catalyzes demethylation of the N 6-methyladenosine (m6A), an epigenetic mark that controls several physiological processes including carcinogenesis and stem cell differentiation. The activity of Alkbh5 comprises two coupled reactions. The first reaction involves decarboxylation of α-ketoglutarate (αKG) and formation of a Fe4+═O species. This oxyferryl intermediate oxidizes the m6A to reestablish the canonical base. Despite coupling between the two reactions being required for the correct Alkbh5 functioning, the mechanisms linking dioxygen activation to m6A binding are not fully understood. Here, we use solution NMR to investigate the structure and dynamics of apo and holo Alkbh5. We show that binding of m6A to Alkbh5 induces a metal-centered rearrangement of αKG that increases the exposed area of the metal, making it available for binding O2 Our study reveals the molecular mechanisms underlying activation of Alkbh5, therefore opening new perspectives for the design of novel strategies to control gene expression and cancer progression.
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Affiliation(s)
| | - Trang T Nguyen
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | - Aayushi Singh
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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Fijen C, Mahmoud MM, Kronenberg M, Kaup R, Fontana M, Towle-Weicksel JB, Sweasy JB, Hohlbein J. Using single-molecule FRET to probe the nucleotide-dependent conformational landscape of polymerase β-DNA complexes. J Biol Chem 2020; 295:9012-9020. [PMID: 32385112 PMCID: PMC7335799 DOI: 10.1074/jbc.ra120.013049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/07/2020] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic DNA polymerase β (Pol β) plays an important role in cellular DNA repair, as it fills short gaps in dsDNA that result from removal of damaged bases. Since defects in DNA repair may lead to cancer and genetic instabilities, Pol β has been extensively studied, especially its mechanisms for substrate binding and a fidelity-related conformational change referred to as "fingers closing." Here, we applied single-molecule FRET to measure distance changes associated with DNA binding and prechemistry fingers movement of human Pol β. First, using a doubly labeled DNA construct, we show that Pol β bends the gapped DNA substrate less than indicated by previously reported crystal structures. Second, using acceptor-labeled Pol β and donor-labeled DNA, we visualized dynamic fingers closing in single Pol β-DNA complexes upon addition of complementary nucleotides and derived rates of conformational changes. We further found that, while incorrect nucleotides are quickly rejected, they nonetheless stabilize the polymerase-DNA complex, suggesting that Pol β, when bound to a lesion, has a strong commitment to nucleotide incorporation and thus repair. In summary, the observation and quantification of fingers movement in human Pol β reported here provide new insights into the delicate mechanisms of prechemistry nucleotide selection.
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Affiliation(s)
- Carel Fijen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Mariam M Mahmoud
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Meike Kronenberg
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Rebecca Kaup
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mattia Fontana
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Jamie B Towle-Weicksel
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands; Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, The Netherlands.
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NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes. Biophys Rev 2019; 12:155-174. [PMID: 31838649 DOI: 10.1007/s12551-019-00609-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022] Open
Abstract
Allostery is a ubiquitous biological mechanism in which a distant binding site is coupled to and drastically alters the function of a catalytic site in a protein. Allostery provides a high level of spatial and temporal control of the integrity and activity of biomolecular assembles composed of proteins, nucleic acids, or small molecules. Understanding the physical forces that drive allosteric coupling is critical to harnessing this process for use in bioengineering, de novo protein design, and drug discovery. Current microscopic models of allostery highlight the importance of energetics, structural rearrangements, and conformational fluctuations, and in this review, we discuss the synergistic use of solution NMR spectroscopy and computational methods to probe these phenomena in allosteric systems, particularly protein-nucleic acid complexes. This combination of experimental and theoretical techniques facilitates an unparalleled detection of subtle changes to structural and dynamic equilibria in biomolecules with atomic resolution, and we provide a detailed discussion of specialized NMR experiments as well as the complementary methods that provide valuable insight into allosteric pathways in silico. Lastly, we highlight two case studies to demonstrate the adaptability of this approach to enzymes of varying size and mechanistic complexity.
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