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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
Base pairing plays a pivotal role in DNA functions and replication fidelity. But while the complementarity between Watson-Crick matched bases is generally believed to arise from the different number of hydrogen bonds in G|C pairs versus A|T, the energetics of these interactions are heavily renormalized by the aqueous solvent. Employing large-scale Monte Carlo simulations, we have extracted the solvent contribution to the free energy for canonical and some noncanonical and stacked base pairs. For all of them, the solvent's contribution to the base pairing free energy is exclusively destabilizing. While the direct hydrogen bonding interactions in the G|C pair is much stronger than A|T, the thermodynamic resistance produced by the solvent also pushes back much stronger against G|C compared to A|T, generating an only ∼1 kcal/mol free energy difference between them. We have profiled the density of water molecules in the solvent adjacent to the bases and observed a "freezing" behavior where waters are recruited into the gap between the bases to compensate for the unsatisfied hydrogen bonds between them. A very small number of water molecules that are associated with the Watson-Crick donor/acceptor atoms turn out to be responsible for the majority of the solvent's thermodynamic resistance to base pairing. The absence or presence of these near-field waters can be used to enhance fidelity during DNA replication.
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Nikoomanzar A, Vallejo D, Chaput JC. Elucidating the Determinants of Polymerase Specificity by Microfluidic-Based Deep Mutational Scanning. ACS Synth Biol 2019; 8:1421-1429. [PMID: 31081325 DOI: 10.1021/acssynbio.9b00104] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Engineering polymerases to synthesize artificial genetic polymers with unique backbone structures is limited by a general lack of understanding about the structural determinants that govern substrate specificity. Here, we report a high-throughput microfluidic-based approach for mapping sequence-function relationships that combines droplet-based optical polymerase sorting with deep mutational scanning. We applied this strategy to map the finger subdomain of a replicative DNA polymerase isolated from Thermococcus kodakarensis (Kod). The enrichment profile provides an unbiased view of the ability of each mutant to synthesize threose nucleic acid, which was used as a model non-natural genetic polymer. From a single round of sorting, we discovered two cases of positive epistasis and demonstrate the near inversion of substrate specificity from a double mutant variant. This effort indicates that polymerase specificity may be governed by a small number of highly specific residues that can be elucidated by deep mutational scanning without the need for iterative rounds of directed evolution.
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Affiliation(s)
- Ali Nikoomanzar
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - Derek Vallejo
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - John C Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
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Oertell K, Florián J, Haratipour P, Crans DC, Kashemirov BA, Wilson SH, McKenna CE, Goodman MF. A Transition-State Perspective on Y-Family DNA Polymerase η Fidelity in Comparison with X-Family DNA Polymerases λ and β. Biochemistry 2019; 58:1764-1773. [PMID: 30839203 DOI: 10.1021/acs.biochem.9b00087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deoxynucleotide misincorporation efficiencies can span a wide 104-fold range, from ∼10-2 to ∼10-6, depending principally on polymerase (pol) identity and DNA sequence context. We have addressed DNA pol fidelity mechanisms from a transition-state (TS) perspective using our "tool-kit" of dATP- and dGTP-β,γ substrate analogues in which the pyrophosphate leaving group (p Ka4 = 8.9) has been replaced by a series of bisphosphonates covering a broad acidity range spanning p Ka4 values from 7.8 (CF2) to 12.3 [C(CH3)2]. Here, we have used a linear free energy relationship (LFER) analysis, in the form of a Brønsted plot of log( kpol) versus p Ka4, for Y-family error-prone pol η and X-family pols λ and β to determine the extent to which different electrostatic active site environments alter kpol values. The apparent chemical rate constant ( kpol) is the rate-determining step for the three pols. The pols each exhibit a distinct catalytic signature that differs for formation of right (A·T) and wrong (G·T) incorporations observed as changes in slopes and displacements of the Brønsted lines, in relation to a reference LFER. Common to this signature among all three pols is a split linear pattern in which the analogues containing two halogens show kpol values that are systematically lower than would be predicted from their p Ka4 values measured in aqueous solution. We discuss how metal ions and active site amino acids are responsible for causing "effective" p Ka4 values that differ for dihalo and non-dihalo substrates as well as for individual R and S stereoisomers for CHF and CHCl.
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Affiliation(s)
- Keriann Oertell
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts, and Sciences , University of Southern California , University Park Campus , Los Angeles , California 90089 , United States
| | - Jan Florián
- Department of Chemistry and Biochemistry , Loyola University Chicago , 1032 West Sheridan Road , Chicago , Illinois 60660 , United States
| | - Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences , University of Southern California , University Park Campus , Los Angeles , California 90089 , United States
| | - Debbie C Crans
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences , University of Southern California , University Park Campus , Los Angeles , California 90089 , United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina 27709 , United States
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences , University of Southern California , University Park Campus , Los Angeles , California 90089 , United States
| | - Myron F Goodman
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts, and Sciences , University of Southern California , University Park Campus , Los Angeles , California 90089 , United States.,Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences , University of Southern California , University Park Campus , Los Angeles , California 90089 , United States
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