1
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Gao Y, Wei C, Luo L, Tang Y, Yu Y, Li Y, Xing J, Pan X. Membrane-assisted tariquidar access and binding mechanisms of human ATP-binding cassette transporter P-glycoprotein. Front Mol Biosci 2024; 11:1364494. [PMID: 38560519 PMCID: PMC10979361 DOI: 10.3389/fmolb.2024.1364494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
The human multidrug transporter P-glycoprotein (P-gp) is physiologically essential and of key relevance to biomedicine. Recent structural studies have shed light on the mode of inhibition of the third-generation inhibitors for human P-gp, but the molecular mechanism by which these inhibitors enter the transmembrane sites remains poorly understood. In this study, we utilized all-atom molecular dynamics (MD) simulations to characterize human P-gp dynamics under a potent inhibitor, tariquidar, bound condition, as well as the atomic-level binding pathways in an explicit membrane/water environment. Extensive unbiased simulations show that human P-gp remains relatively stable in tariquidar-free and bound states, while exhibiting a high dynamic binding mode at either the drug-binding pocket or the regulatory site. Free energy estimations by partial nudged elastic band (PNEB) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method identify two energetically favorable binding pathways originating from the cytoplasmic gate with an extended tariquidar conformation. Interestingly, free tariquidar in the lipid membrane predominantly adopts extended conformations similar to those observed at the regulatory site. These results suggest that membrane lipids may preconfigure tariquidar into an active ligand conformation for efficient binding to the regulatory site. However, due to its conformational plasticity, tariquidar ultimately moves toward the drug-binding pocket in both pathways, explaining how it acts as a substrate at low concentrations. Our molecular findings propose a membrane-assisted mechanism for the access and binding of the third-generation inhibitors to the binding sites of human P-gp, and offer deeper insights into the molecule design of more potent inhibitors against P-gp-mediated drug resistance.
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Affiliation(s)
- Yingjie Gao
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Caiyan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Lanxin Luo
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Yang Tang
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yongzhen Yu
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yaling Li
- Department of Pharmacy, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Juan Xing
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Xianchao Pan
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
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2
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Duan L, Zhao Y, Zhang X, Cui X, Meng Q, Zhang C. Fluorescent adenine analogues with ESPT characteristic utilized for real-time detecting DNA adduct. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 282:121675. [PMID: 35914355 DOI: 10.1016/j.saa.2022.121675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
The 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG) is the representative damaged nucleoside that may increase the risk of developing diseases. Accordingly, the selective detection of 8-oxoG in DNA with minimal disturbance to the native structure is important to have an in-depth understanding of the formation mechanism and becomes an attractive tool for genomic research. To identify the DNA adduct in real-time efficiently, a series of quasi-intrinsic optical probes are performed based on the natural adenine, which has preference to form a stable base pair with 8-oxoG in the syn conformation. The calculations revealed that the A-analogues in solution could bring red-shifted absorption spectra and bright photoluminescence arisen from the additional π-conjugation by means of fluorophore modification and the ring expansion. Especially, A1 possesses large Stokes shifts and the highest fluorescence intensity in emission, which is proposed as the biosensor to monitor the optical changes in the presence and absence of the considered 8-oxoG. It is found that the fluorescence is insensitive to base pairing with thymine, while the excited state intermolecular proton transfer (ESPT) induced efficient fluorescence quenching is observed upon pairing with the 8-oxoG. To evaluate the direct usefulness of the bright adenine analogues in biological environment, we further examined the influences of linking deoxyribose on the absorption and emission, which are consistent with the experimental data.
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Affiliation(s)
- Lingjie Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Yu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Xiao Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Xixi Cui
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
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3
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Fallon L, Belfon KA, Raguette L, Wang Y, Stepanenko D, Cuomo A, Guerra J, Budhan S, Varghese S, Corbo CP, Rizzo RC, Simmerling C. Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket. J Am Chem Soc 2021; 143:11349-11360. [PMID: 34270232 PMCID: PMC8315243 DOI: 10.1021/jacs.1c00556] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Indexed: 02/08/2023]
Abstract
The SARS-CoV-2 coronavirus is an enveloped, positive-sense single-stranded RNA virus that is responsible for the COVID-19 pandemic. The spike is a class I viral fusion glycoprotein that extends from the viral surface and is responsible for viral entry into the host cell and is the primary target of neutralizing antibodies. The receptor binding domain (RBD) of the spike samples multiple conformations in a compromise between evading immune recognition and searching for the host-cell surface receptor. Using atomistic simulations of the glycosylated wild-type spike in the closed and 1-up RBD conformations, we map the free energy landscape for RBD opening and identify interactions in an allosteric pocket that influence RBD dynamics. The results provide an explanation for experimental observation of increased antibody binding for a clinical variant with a substitution in this pocket. Our results also suggest the possibility of allosteric targeting of the RBD equilibrium to favor open states via binding of small molecules to the hinge pocket. In addition to potential value as experimental probes to quantify RBD conformational heterogeneity, small molecules that modulate the RBD equilibrium could help explore the relationship between RBD opening and S1 shedding.
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Affiliation(s)
- Lucy Fallon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Kellon A.A. Belfon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Lauren Raguette
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Yuzhang Wang
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Darya Stepanenko
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Abbigayle Cuomo
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jose Guerra
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Stephanie Budhan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Sarah Varghese
- Undergraduate Program in Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher P. Corbo
- Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Robert C. Rizzo
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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4
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Fallon L, Belfon KAA, Raguette L, Wang Y, Stepanenko D, Cuomo A, Guerra J, Budhan S, Varghese S, Corbo CP, Rizzo RC, Simmerling C. Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket. J Am Chem Soc 2021. [PMID: 34270232 DOI: 10.26434/chemrxiv.13502646.v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The SARS-CoV-2 coronavirus is an enveloped, positive-sense single-stranded RNA virus that is responsible for the COVID-19 pandemic. The spike is a class I viral fusion glycoprotein that extends from the viral surface and is responsible for viral entry into the host cell and is the primary target of neutralizing antibodies. The receptor binding domain (RBD) of the spike samples multiple conformations in a compromise between evading immune recognition and searching for the host-cell surface receptor. Using atomistic simulations of the glycosylated wild-type spike in the closed and 1-up RBD conformations, we map the free energy landscape for RBD opening and identify interactions in an allosteric pocket that influence RBD dynamics. The results provide an explanation for experimental observation of increased antibody binding for a clinical variant with a substitution in this pocket. Our results also suggest the possibility of allosteric targeting of the RBD equilibrium to favor open states via binding of small molecules to the hinge pocket. In addition to potential value as experimental probes to quantify RBD conformational heterogeneity, small molecules that modulate the RBD equilibrium could help explore the relationship between RBD opening and S1 shedding.
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Affiliation(s)
- Lucy Fallon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Kellon A A Belfon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Lauren Raguette
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Yuzhang Wang
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Darya Stepanenko
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Abbigayle Cuomo
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jose Guerra
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Stephanie Budhan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Sarah Varghese
- Undergraduate Program in Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher P Corbo
- Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Robert C Rizzo
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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5
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Gillet N, Bartocci A, Dumont E. Assessing the sequence dependence of pyrimidine-pyrimidone (6-4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation. J Chem Phys 2021; 154:135103. [PMID: 33832258 DOI: 10.1063/5.0041332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Sequence dependence of the (6-4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities. Moreover, REST2 simulations allow us to probe structures possibly important for damaged DNA recognition.
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Affiliation(s)
- Natacha Gillet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Alessio Bartocci
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Elise Dumont
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
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6
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Ghoreishi D, Cerutti DS, Fallon Z, Simmerling C, Roitberg AE. Fast Implementation of the Nudged Elastic Band Method in AMBER. J Chem Theory Comput 2019; 15:4699-4707. [PMID: 31314523 PMCID: PMC7291791 DOI: 10.1021/acs.jctc.9b00329] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We present a fast implementation of the nudged elastic band (NEB) method into the particle mesh Ewald molecular dynamics module of the Amber software package for both central processing units (CPU) and graphics processing units (GPU). The accuracy of the new implementation has been validated for three cases: a conformational change of alanine dipeptide, the α-helix to β-sheet transition in polyalanine, and a large conformational transition in the human 8-oxoguanine-DNA glycosylase with DNA complex (OGG1-DNA). Timing benchmark tests were performed on the explicitly solvated OGG1-DNA system containing ∼50 000 atoms. The GPU-optimized implementation of NEB achieves a more than two orders of magnitude speedup compared with the previous CPU implementation performed with a two-core CPU processor. The speed and scalable features of this implementation will enable NEB applications on larger and more complex systems.
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Affiliation(s)
- Delaram Ghoreishi
- Department of Physics, University of Florida, Gainesville, Florida 32611, United States
| | - David S. Cerutti
- Laboratory for Biomolecular Simulation Research, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Zachary Fallon
- Department of Chemistry, and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, 11794, United States
| | - Carlos Simmerling
- Department of Chemistry, and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, 11794, United States
| | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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7
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Da LT, Yu J. Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process. Nucleic Acids Res 2019; 46:5410-5425. [PMID: 29762710 PMCID: PMC6009601 DOI: 10.1093/nar/gky386] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive. Here, we employ the Markov State Model (MSM) constructed from extensive all-atom molecular dynamics (MD) simulations to reveal the complete base-flipping process for a G.T mispair at a tens of microsecond timescale. Our studies identify critical intermediates of the mispaired dT during its extrusion process and reveal the key TDG residues involved in the inter-state transitions. Notably, we find an active role of TDG in promoting the intrahelical nt eversion, sculpturing the DNA backbone, and penetrating into the DNA minor groove. Three additional TDG substrates, namely dU, 5fC, and 5caC, are further tested to evaluate the substituent effects of various chemical modifications of the pyrimidine ring on base-flipping dynamics.
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Affiliation(s)
- Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100193, China
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8
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Endutkin AV, Zharkov DO. Critical Sites of DNA Backbone Integrity for Damaged Base Removal by Formamidopyrimidine-DNA Glycosylase. Biochemistry 2019; 58:2740-2749. [PMID: 31120733 DOI: 10.1021/acs.biochem.9b00134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA glycosylases, the enzymes that initiate base excision DNA repair, recognize damaged bases through a series of precisely orchestrated movements. Most glycosylases sharply kink the DNA axis at the lesion site and extrude the target base from the DNA double helix into the enzyme's active site. Little attention has been paid so far to the role of the physical continuity of the DNA backbone in allowing the required conformational distortion. Here, we analyze base excision by formamidopyrimidine-DNA glycosylase (Fpg) from substrates keeping all phosphates but containing a nick within three nucleotides of the lesion in either DNA strand. Four phosphoester linkages at the damaged nucleotide and two nucleotides 3' to it were essential for Fpg activity, while the breakage of the others, even at the same critical phosphates, had no effect or even stimulated the reaction. Reduction of the likelihood of hydrogen bonding at the nicks by using dideoxynucleotides as their 3'-terminal groups was more detrimental for the activity. All phosphoester bonds in the complementary strand were dispensable for base excision, but nicks close to the orphaned nucleotide caused early termination of damaged strand cleavage. Elastic network analysis of Fpg-DNA structures showed that the vibrational motions of the critical phosphates are strongly correlated, in part due to the presence of the protein. Overall, our results suggest that mechanical forces propagating along the DNA backbone play a critical role in the correct conformational distortion of DNA by Fpg and possibly by other target base-everting DNA glycosylases.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
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9
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Abstract
7,8-Dihydro-8-oxoguanine (oxoG) is the most abundant oxidative DNA lesion with dual coding properties. It forms both Watson–Crick (anti)oxoG:(anti)C and Hoogsteen (syn)oxoG:(anti)A base pairs without a significant distortion of a B-DNA helix. DNA polymerases bypass oxoG but the accuracy of nucleotide incorporation opposite the lesion varies depending on the polymerase-specific interactions with the templating oxoG and incoming nucleotides. High-fidelity replicative DNA polymerases read oxoG as a cognate base for A while treating oxoG:C as a mismatch. The mutagenic effects of oxoG in the cell are alleviated by specific systems for DNA repair and nucleotide pool sanitization, preventing mutagenesis from both direct DNA oxidation and oxodGMP incorporation. DNA translesion synthesis could provide an additional protective mechanism against oxoG mutagenesis in cells. Several human DNA polymerases of the X- and Y-families efficiently and accurately incorporate nucleotides opposite oxoG. In this review, we address the mutagenic potential of oxoG in cells and discuss the structural basis for oxoG bypass by different DNA polymerases and the mechanisms of the recognition of oxoG by DNA glycosylases and dNTP hydrolases.
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10
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Kladova OA, Grin IR, Fedorova OS, Kuznetsov NA, Zharkov DO. Conformational Dynamics of Damage Processing by Human DNA Glycosylase NEIL1. J Mol Biol 2019; 431:1098-1112. [DOI: 10.1016/j.jmb.2019.01.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
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11
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Votaw KA, McCullagh M. Characterization of the Search Complex and Recognition Mechanism of the AlkD-DNA Glycosylase. J Phys Chem B 2018; 123:95-105. [PMID: 30525620 DOI: 10.1021/acs.jpcb.8b09555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA damage is a routine problem for cells, and pathways such as base excision repair have evolved to protect the genome by using DNA glycosylases to first recognize and excise lesions. The search mechanism of these enzymes is of particular interest due to the seemingly intractable problem of probing the billions of base pairs in the genome for potential damage. It has been hypothesized that glycosylases form multiple protein-DNA conformational states to efficiently search and recognize DNA lesions, ultimately only flipping out the damaged substrate into the active site. A unique DNA glycosylase, the Bacillus cereus AlkD enzyme, has been shown to excise damaged DNA without flipping the nucleobase into a protein binding pocket following lesion recognition. Here, we use microsecond-scale all-atom molecular dynamics simulations to characterize the AlkD recognition mechanism, putting it in perspective with other DNA glycosylases. We first identify and describe two distinct enzyme-DNA conformations of AlkD: the search complex (SC) and excision complex (EC). The SC is distinguished by the linearity of DNA, changes in four helical parameters in the vicinity of the lesion, and changes in distance between active site residues and the DNA. Free DNA simulations are used to demonstrate that the DNA structural deviations and increased active site interactions present in the EC are initiated by the recognition of a methylation-induced signal in the rises both 5' to the methylation and opposing this base. Our results support the hypothesis that subtle geometric distortions in DNA are recognized by AlkD and are consequently probed to initiate concerted protein and DNA conformational changes which prime excise without additional intermediate states. This mechanism is shown to be consistent among the three methylated DNA sequences that have been crystallized bound to AlkD.
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Affiliation(s)
- Kevin A Votaw
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523, United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523, United States
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12
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Endutkin AV, Koptelov SS, Popov AV, Torgasheva NA, Lomzov AA, Tsygankova AR, Skiba TV, Afonnikov DA, Zharkov DO. Residue coevolution reveals functionally important intramolecular interactions in formamidopyrimidine-DNA glycosylase. DNA Repair (Amst) 2018; 69:24-33. [DOI: 10.1016/j.dnarep.2018.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]
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13
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Li H, Endutkin AV, Bergonzo C, Fu L, Grollman A, Zharkov DO, Simmerling C. DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase. J Am Chem Soc 2017; 139:2682-2692. [PMID: 28098999 DOI: 10.1021/jacs.6b11433] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8 and H7). Human 8-oxoguanine glycosylase 1 (OGG1) can locate and remove 8-oxoG through extrusion and excision. To date, it remains unclear how OGG1 efficiently distinguishes 8-oxoG from a large excess of undamaged DNA bases. We recently showed that formamidopyrimidine-DNA glycosylase (Fpg), a bacterial functional analog of OGG1, can selectively facilitate eversion of oxoG by stabilizing several intermediate states, and it is intriguing whether OGG1 also employs a similar mechanism in lesion recognition. Here, we use molecular dynamics simulations to explore the mechanism by which OGG1 discriminates between 8-oxoG and guanine along the base-eversion pathway. The MD results suggest an important role for kinking of the DNA by the glycosylase, which positions DNA phosphates in a way that assists lesion recognition during base eversion. The computational predictions were validated through experimental enzyme assays on phosphorothioate substrate analogs. Our simulations suggest that OGG1 distinguishes between 8-oxoG and G using their chemical dissimilarities not only at the active site but also at earlier stages during base eversion, and this mechanism is at least partially conserved in Fpg despite a lack of structural homology. The similarity also suggests that lesion recognition through multiple gating steps may be a common theme in DNA repair. Our results provide new insight into how enzymes can exploit kinetics and DNA conformational changes to probe the chemical modifications present in DNA lesions.
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Affiliation(s)
| | - Anton V Endutkin
- Novosibirsk State University , 2 Pirogova Street, Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue, Novosibirsk 630090, Russia
| | | | - Lin Fu
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | | | - Dmitry O Zharkov
- Novosibirsk State University , 2 Pirogova Street, Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue, Novosibirsk 630090, Russia
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14
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Knips A, Zacharias M. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage. Sci Rep 2017; 7:41324. [PMID: 28128222 PMCID: PMC5269681 DOI: 10.1038/srep41324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/16/2016] [Indexed: 01/31/2023] Open
Abstract
The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.
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Affiliation(s)
- Alexander Knips
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany
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15
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Tomsett M, Maffucci I, Le Bailly BAF, Byrne L, Bijvoets SM, Lizio MG, Raftery J, Butts CP, Webb SJ, Contini A, Clayden J. A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal. Chem Sci 2017; 8:3007-3018. [PMID: 28451368 PMCID: PMC5380885 DOI: 10.1039/c6sc05474a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/24/2017] [Indexed: 11/21/2022] Open
Abstract
Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.
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Affiliation(s)
- Michael Tomsett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Bryden A F Le Bailly
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Liam Byrne
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Stefan M Bijvoets
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - M Giovanna Lizio
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - James Raftery
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Craig P Butts
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Simon J Webb
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Jonathan Clayden
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
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16
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La Rosa G, Zacharias M. Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA. Nucleic Acids Res 2016; 44:9591-9599. [PMID: 27651459 PMCID: PMC5175360 DOI: 10.1093/nar/gkw827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/04/2016] [Accepted: 09/08/2016] [Indexed: 01/20/2023] Open
Abstract
Oxidation of guanine (Gua) to form 7,8-dihydro-8-oxoguanine (8oxoG) is a frequent mutagenic DNA lesion. DNA repair glycosylases such as the bacterial MutM can effciently recognize and eliminate the 8oxoG damage by base excision. The base excision requires a 8oxoG looping out (flipping) from an intrahelical base paired to an extrahelical state where the damaged base is in the enzyme active site. It is still unclear how the damage is identified and flipped from an energetically stable stacked and paired state without any external energy source. Free energy simulations have been employed to study the flipping process for globally deformed DNA conformational states. DNA deformations were generated by systematically untwisting the DNA to mimic its conformation in repair enzyme encounter complex. The simulations indicate that global DNA untwisting deformation toward the enzyme bound form alone (without protein) significantly reduces the penalty for damage flipping to about half of the penalty observed in regular DNA. The finding offers a mechanistic explanation how binding free energy that is transformed to binding induced DNA deformation facilitates flipping and helps to rapidly detect a damaged base. It is likely of general relevance since repair enzyme binding frequently results in significant deformation of the target DNA.
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Affiliation(s)
- Giuseppe La Rosa
- Physik-Department T38, Technische Universität München, James-Franck-Straße 1, D-85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, James-Franck-Straße 1, D-85748 Garching, Germany
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17
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Li H, Endutkin AV, Bergonzo C, Campbell AJ, de los Santos C, Grollman A, Zharkov DO, Simmerling C. A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine-DNA glycosylase. Nucleic Acids Res 2015; 44:683-94. [PMID: 26553802 PMCID: PMC4737139 DOI: 10.1093/nar/gkv1092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/08/2015] [Indexed: 01/29/2023] Open
Abstract
In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre to achieve their exquisite specificity. It is widely believed that substrate recognition by such enzymes involves a series of conformational changes in the enzyme-DNA complex with sequential gates favoring cognate DNA and rejecting nonsubstrates. However, direct evidence for such mechanism is limited to a few systems. We report that discrimination between the oxidative DNA lesion, 8-oxoguanine (oxoG) and its normal counterpart, guanine, by the repair enzyme, formamidopyrimidine-DNA glycosylase (Fpg), likely involves multiple gates. Fpg uses an aromatic wedge to open the Watson-Crick base pair and everts the lesion into its active site. We used molecular dynamics simulations to explore the eversion free energy landscapes of oxoG and G by Fpg, focusing on structural and energetic details of oxoG recognition. The resulting energy profiles, supported by biochemical analysis of site-directed mutants disturbing the interactions along the proposed path, show that Fpg selectively facilitates eversion of oxoG by stabilizing several intermediate states, helping the rapidly sliding enzyme avoid full extrusion of every encountered base for interrogation. Lesion recognition through multiple gating intermediates may be a common theme in DNA repair enzymes.
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Affiliation(s)
- Haoquan Li
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Christina Bergonzo
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Arthur J Campbell
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Carlos de los Santos
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Arthur Grollman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
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18
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Kuznetsov NA, Bergonzo C, Campbell AJ, Li H, Mechetin GV, de los Santos C, Grollman AP, Fedorova OS, Zharkov DO, Simmerling C. Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition. Nucleic Acids Res 2014; 43:272-81. [PMID: 25520195 PMCID: PMC4288190 DOI: 10.1093/nar/gku1300] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Formamidopyrimidine-DNA glycosylase (Fpg) excises 8-oxoguanine (oxoG) from DNA but ignores normal guanine. We combined molecular dynamics simulation and stopped-flow kinetics with fluorescence detection to track the events in the recognition of oxoG by Fpg and its mutants with a key phenylalanine residue, which intercalates next to the damaged base, changed to either alanine (F110A) or fluorescent reporter tryptophan (F110W). Guanine was sampled by Fpg, as evident from the F110W stopped-flow traces, but less extensively than oxoG. The wedgeless F110A enzyme could bend DNA but failed to proceed further in oxoG recognition. Modeling of the base eversion with energy decomposition suggested that the wedge destabilizes the intrahelical base primarily through buckling both surrounding base pairs. Replacement of oxoG with abasic (AP) site rescued the activity, and calculations suggested that wedge insertion is not required for AP site destabilization and eversion. Our results suggest that Fpg, and possibly other DNA glycosylases, convert part of the binding energy into active destabilization of their substrates, using the energy differences between normal and damaged bases for fast substrate discrimination.
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Affiliation(s)
- Nikita A Kuznetsov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Christina Bergonzo
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Arthur J Campbell
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Haoquan Li
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Grigory V Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Carlos de los Santos
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Arthur P Grollman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Olga S Fedorova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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19
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Di Russo NV, Martí MA, Roitberg AE. Underlying thermodynamics of pH-dependent allostery. J Phys Chem B 2014; 118:12818-26. [PMID: 25318010 DOI: 10.1021/jp507971v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the effects of coupling protein protonation and conformational states is critical to the development of drugs targeting pH sensors and to the rational engineering of pH switches. In this work, we address this issue by performing a comprehensive study of the pH-regulated switch from the closed to the open conformation in nitrophorin 4 (NP4) that determines its pH-dependent activity. Our calculations show that D30 is the only amino acid that has two significantly different pKas in the open and closed conformations, confirming its critical role in regulating pH-dependent behavior. In addition, we describe the free-energy landscape of the conformational change as a function of pH, obtaining accurate estimations of free-energy barriers and equilibrium constants using different methods. The underlying thermodynamic model of the switch workings suggests the possibility of tuning the observed pKa only through the conformational equilibria, keeping the same conformation-specific pKas, as evidenced by the proposed K125L mutant. Moreover, coupling between the protonation and conformational equilibria results in efficient regulation and pH-sensing around physiological pH values only for some combinations of protonation and conformational equilibrium constants, placing constraints on their possible values and leaving a narrow space for protein molecular evolution. The calculations and analysis presented here are of general applicability and provide a guide as to how more complex systems can be studied, offering insight into how pH-regulated allostery works of great value for designing drugs that target pH sensors and for rational engineering of pH switches beyond the common histidine trigger.
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Affiliation(s)
- Natali V Di Russo
- Quantum Theory Project and Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
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20
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Alkylpurine glycosylase D employs DNA sculpting as a strategy to extrude and excise damaged bases. PLoS Comput Biol 2014; 10:e1003704. [PMID: 24992034 PMCID: PMC4081403 DOI: 10.1371/journal.pcbi.1003704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/19/2014] [Indexed: 01/05/2023] Open
Abstract
Alkylpurine glycosylase D (AlkD) exhibits a unique base excision strategy. Instead of interacting directly with the lesion, the enzyme engages the non-lesion DNA strand. AlkD induces flipping of the alkylated and opposing base accompanied by DNA stack compression. Since this strategy leaves the alkylated base solvent exposed, the means to achieve enzymatic cleavage had remained unclear. We determined a minimum energy path for flipping out a 3-methyl adenine by AlkD and computed a potential of mean force along this path to delineate the energetics of base extrusion. We show that AlkD acts as a scaffold to stabilize three distinct DNA conformations, including the final extruded state. These states are almost equivalent in free energy and separated by low barriers. Thus, AlkD acts by sculpting the global DNA conformation to achieve lesion expulsion from DNA. N-glycosidic bond scission is then facilitated by a backbone phosphate group proximal to the alkylated base. DNA repair efficiency is critically dependent on the function of DNA glycosylases. These versatile enzymes perform a remarkably discriminating search for DNA lesions, followed by damage-specific base extrusion into to the enzyme's active site and removal of the damaged bases. Our work elucidates the mechanism of Bacillus cereus AlkD, representative of a superfamily of alkylpurine glycosylase enzymes that function differently from all other known glycosylases. AlkD does not employ any direct contacts to the alkylated lesion. Instead, it relies on DNA backbone contacts to extrude the lesion's base-pairing partner. The alkylated base is flipped into solvent allowing N-glycosidic bond hydrolysis to occur with no apparent assistance from any protein side chains. Our work contributes to understanding of this unique base extrusion and excision strategy. We determined a minimum energy path for flipping out a 3-methyl adenine base by AlkD and computed an effective free energy profile for this transition. We show that lesion extrusion relies on DNA sculpting to break up the process into two steps characterized by low free energy barriers and a stable intermediate. AlkD provides a rigid scaffold to accommodate the three distinct DNA conformations and positions a phosphate group to facilitate scission of the alkylated base.
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21
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Cannan WJ, Tsang BP, Wallace SS, Pederson DS. Nucleosomes suppress the formation of double-strand DNA breaks during attempted base excision repair of clustered oxidative damages. J Biol Chem 2014; 289:19881-93. [PMID: 24891506 DOI: 10.1074/jbc.m114.571588] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Exposure to ionizing radiation can produce multiple, clustered oxidative lesions in DNA. The near simultaneous excision of nearby lesions in opposing DNA strands by the base excision repair (BER) enzymes can produce double-strand DNA breaks (DSBs). This attempted BER accounts for many of the potentially lethal or mutagenic DSBs that occur in vivo. To assess the impact of nucleosomes on the frequency and pattern of BER-dependent DSB formation, we incubated nucleosomes containing oxidative damages in opposing DNA strands with selected DNA glycosylases and human apurinic/apyrimidinic endonuclease 1. Overall, nucleosomes substantially suppressed DSB formation. However, the degree of suppression varied as a function of (i) the lesion type and DNA glycosylase tested, (ii) local sequence context and the stagger between opposing strand lesions, (iii) the helical orientation of oxidative lesions relative to the underlying histone octamer, and (iv) the distance between the lesion cluster and the nucleosome edge. In some instances the binding of a BER factor to one nucleosomal lesion appeared to facilitate binding to the opposing strand lesion. DSB formation did not invariably lead to nucleosome dissolution, and in some cases, free DNA ends resulting from DSB formation remained associated with the histone octamer. These observations explain how specific structural and dynamic properties of nucleosomes contribute to the suppression of BER-generated DSBs. These studies also suggest that most BER-generated DSBs will occur in linker DNA and in genomic regions associated with elevated rates of nucleosome turnover or remodeling.
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Affiliation(s)
- Wendy J Cannan
- From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405
| | - Betty P Tsang
- From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405
| | - Susan S Wallace
- From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405
| | - David S Pederson
- From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405
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22
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Temelso B, Alser KA, Gauthier A, Palmer AK, Shields GC. Structural Analysis of α-Fetoprotein (AFP)-like Peptides with Anti-Breast-Cancer Properties. J Phys Chem B 2014; 118:4514-26. [DOI: 10.1021/jp500017b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Berhane Temelso
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Katherine A. Alser
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Arianne Gauthier
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Amber Kay Palmer
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - George C. Shields
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
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23
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Li HJ, Lai CT, Pan P, Yu W, Liu N, Bommineni GR, Garcia-Diaz M, Simmerling C, Tonge PJ. A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA. ACS Chem Biol 2014; 9:986-93. [PMID: 24527857 PMCID: PMC4004265 DOI: 10.1021/cb400896g] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/14/2014] [Indexed: 01/01/2023]
Abstract
Slow-onset enzyme inhibitors are of great interest for drug discovery programs since the slow dissociation of the inhibitor from the drug-target complex results in sustained target occupancy leading to improved pharmacodynamics. However, the structural basis for slow-onset inhibition is often not fully understood, hindering the development of structure-kinetic relationships and the rational optimization of drug-target residence time. Previously we demonstrated that slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA correlated with motions of a substrate-binding loop (SBL) near the active site. In the present work, X-ray crystallography and molecular dynamics simulations have been used to map the structural and energetic changes of the SBL that occur upon enzyme inhibition. Helix-6 within the SBL adopts an open conformation when the inhibitor structure or binding kinetics is substrate-like. In contrast, slow-onset inhibition results in large-scale local refolding in which helix-6 adopts a closed conformation not normally populated during substrate turnover. The open and closed conformations of helix-6 are hypothesized to represent the EI and EI* states on the two-step induced-fit reaction coordinate for enzyme inhibition. These two states were used as the end points for nudged elastic band molecular dynamics simulations resulting in two-dimensional potential energy profiles that reveal the barrier between EI and EI*, thus rationalizing the binding kinetics observed with different inhibitors. Our findings indicate that the structural basis for slow-onset kinetics can be understood once the structures of both EI and EI* have been identified, thus providing a starting point for the rational control of enzyme-inhibitor binding kinetics.
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Affiliation(s)
- Huei-Jiun Li
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Cheng-Tsung Lai
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Pan Pan
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Weixuan Yu
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Nina Liu
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Gopal R. Bommineni
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Miguel Garcia-Diaz
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Carlos Simmerling
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Peter J. Tonge
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
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24
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Galindo‐Murillo R, Bergonzo C, Cheatham TE. Molecular Modeling of Nucleic Acid Structure: Setup and Analysis. ACTA ACUST UNITED AC 2014; 56:7.10.1-21. [DOI: 10.1002/0471142700.nc0710s56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | - Christina Bergonzo
- Department of Medicinal Chemistry, University of Utah Salt Lake City Utah
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, University of Utah Salt Lake City Utah
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25
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Dršata T, Kara M, Zacharias M, Lankaš F. Effect of 8-oxoguanine on DNA structure and deformability. J Phys Chem B 2013; 117:11617-22. [PMID: 24028561 DOI: 10.1021/jp407562t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
8-Oxoguanine (oxoG) is an abundant product of oxidative DNA damage. It is removed by repair glycosylases, but exactly how the enzymes recognize oxoG in the large surplus of undamaged bases is not fully understood. The lesion may induce changes in the properties of naked DNA that facilitate the recognition. In this work, we assess the effect of oxoG on DNA structure and mechanical deformability. We performed extensive unrestrained, atomic resolution molecular dynamics simulations to parametrize a nonlocal, rigid base mechanical model of DNA. Our data indicate that oxoG induces unwinding of the base pair step at the 5'-side of the lesion. This brings the damaged DNA closer to its conformation in the initial complex with bacterial glycosylase MutM. The untwisting is partially caused by different BII substate populations and is further enhanced by the base-sugar repulsion within oxoG. On the other hand, our analysis shows that damaged and undamaged DNA have very similar harmonic stiffness. These results suggest an indirect readout component of the MutM-DNA initial complex formation. They also help one to understand the effect of oxoG on the formation of nucleosomes and looped gene regulatory complexes.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstı́ 2, 166 10, Praha 6, Czech Republic
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26
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Cao L, Lv C, Yang W. Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium Simulation Study. J Chem Theory Comput 2013; 9:10.1021/ct400198q. [PMID: 24250279 PMCID: PMC3829643 DOI: 10.1021/ct400198q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA base extrusion is a crucial component of many biomolecular processes. Elucidating how bases are selectively extruded from the interiors of double-strand DNAs is pivotal to accurately understanding and efficiently sampling this general type of conformational transitions. In this work, the on-the-path random walk (OTPRW) method, which is the first generalized ensemble sampling scheme designed for finite-temperature-string path optimizations, was improved and applied to obtain the minimum free energy path (MFEP) and the free energy profile of a classical B-DNA major-groove base extrusion pathway. Along the MFEP, an intermediate state and the corresponding transition state were located and characterized. The MFEP result suggests that a base-plane-elongation event rather than the commonly focused base-flipping event is dominant in the transition state formation portion of the pathway; and the energetic penalty at the transition state is mainly introduced by the stretching of the Watson-Crick base pair. Moreover to facilitate the essential base-plane-elongation dynamics, the surrounding environment of the flipped base needs to be intimately involved. Further taking the advantage of the extended-dynamics nature of the OTPRW Hamiltonian, an equilibrium generalized ensemble simulation was performed along the optimized path; and based on the collected samples, several base-flipping (opening) angle collective variables were evaluated. In consistence with the MFEP result, the collective variable analysis result reveals that none of these commonly employed flipping (opening) angles alone can adequately represent the base extrusion pathway, especially in the pre-transition-state portion. As further revealed by the collective variable analysis, the base-pairing partner of the extrusion target undergoes a series of in-plane rotations to facilitate the base-plane-elongation dynamics. A base-plane rotation angle is identified to be a possible reaction coordinate to represent these in-plane rotations. Notably, these in-plane rotation motions may play a pivotal role in determining the base extrusion selectivity.
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Affiliation(s)
- Liaoran Cao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
| | - Chao Lv
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
| | - Wei Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306
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Cai Y, Zheng H, Ding S, Kropachev K, Schwaid AG, Tang Y, Mu H, Wang S, Geacintov NE, Zhang Y, Broyde S. Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility. Chem Res Toxicol 2013; 26:1115-25. [PMID: 23758590 DOI: 10.1021/tx400156a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The crystal structure of Rad4/Rad23, the yeast homolog of the human nucleotide excision repair (NER) lesion recognition factor XPC-RAD23B ( Min , J. H. and Pavletich , N. P. ( 2007 ) Nature 449 , 570 - 575 ) reveals that the lesion-partner base is flipped out of the helix and binds to amino acids of the protein. This suggests the hypothesis that the flipping of this partner base must overcome a free energy barrier, which constitutes one element contributing to changes in the thermodynamic properties induced by the DNA damage and sensed by the recognition protein. We explored this hypothesis by computing complete flipping free energy profiles for two lesions derived from the procarcinogenic polycyclic aromatic hydrocarbons (PAHs), dibenzo[a,l]pyrene (DB[a,l]P) and benzo[a]pyrene (B[a]P), R-trans-anti-DB[a,l]P-N(6)-dA (R-DB[a,l]P-dA) and R-trans-anti-B[a]P-N(6)-dA (R-B[a]P-dA), and the corresponding unmodified duplex. The DB[a,l]P and B[a]P adducts differ in number and organization of their aromatic rings. We integrate these results with prior profiles for the R-trans-anti-DB[a,l]P-dG adduct ( Zheng , H. et al. ( 2010 ) Chem. Res. Toxicol. 23 , 1868 - 1870 ). All adopt conformational themes involving intercalation of the PAH aromatic ring system into the DNA duplex; however, R-DB[a,l]P-dA and R-B[a]P-dA intercalate from the major groove, while R-DB[a,l]P-dG intercalates from the minor groove. These structural differences produce different computed van der Waals stacking interaction energies between the flipping partner base with the lesion aromatic ring system and adjacent bases; we find that the better the stacking, the higher the relative flipping free energy barrier and hence lower flipping probability. The better relative NER susceptibilities correlate with greater ease of flipping in these three differently intercalated lesions. In addition to partner base flipping, the Rad4/Rad23 crystal structure shows that a protein-β-hairpin, BHD3, intrudes from the major groove side between the DNA strands at the lesion site. We present a molecular modeling study for the R-DB[a,l]P-dG lesion in Rad4/Rad23 showing BHD3 β-hairpin intrusion with lesion eviction, and we hypothesize that lesion steric effects play a role in the recognition of intercalated adducts.
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Affiliation(s)
- Yuqin Cai
- Department of Biology, New York University , New York, New York 10003, United States
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Franco D, Sgrignani J, Bussi G, Magistrato A. Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations. J Chem Inf Model 2013; 53:1371-87. [DOI: 10.1021/ci4001647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Duvan Franco
- International School for Advances Studies (SISSA/ISAS), via Bonomea 265,
Trieste, Italy
| | - Jacopo Sgrignani
- CNR-IOM-DEMOCRITOS National Simulation Center C/o SISSA, via Bonomea 265,
Trieste, Italy
| | - Giovanni Bussi
- International School for Advances Studies (SISSA/ISAS), via Bonomea 265,
Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS National Simulation Center C/o SISSA, via Bonomea 265,
Trieste, Italy
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29
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Giambaşu GM, Lee TS, Scott WG, York DM. Mapping L1 ligase ribozyme conformational switch. J Mol Biol 2012; 423:106-22. [PMID: 22771572 DOI: 10.1016/j.jmb.2012.06.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/21/2012] [Accepted: 06/25/2012] [Indexed: 01/10/2023]
Abstract
L1 ligase (L1L) molecular switch is an in vitro optimized synthetic allosteric ribozyme that catalyzes the regioselective formation of a 5'-to-3' phosphodiester bond, a reaction for which there is no known naturally occurring RNA catalyst. L1L serves as a proof of principle that RNA can catalyze a critical reaction for prebiotic RNA self-replication according to the RNA world hypothesis. L1L crystal structure captures two distinct conformations that differ by a reorientation of one of the stems by around 80Å and are presumed to correspond to the active and inactive state, respectively. It is of great interest to understand the nature of these two states in solution and the pathway for their interconversion. In this study, we use explicit solvent molecular simulation together with a novel enhanced sampling method that utilizes concepts from network theory to map out the conformational transition between active and inactive states of L1L. We find that the overall switching mechanism can be described as a three-state/two-step process. The first step involves a large-amplitude swing that reorients stem C. The second step involves the allosteric activation of the catalytic site through distant contacts with stem C. Using a conformational space network representation of the L1L switch transition, it is shown that the connection between the three states follows different topographical patterns: the stem C swing step passes through a narrow region of the conformational space network, whereas the allosteric activation step covers a much wider region and a more diverse set of pathways through the network.
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Affiliation(s)
- George M Giambaşu
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: setup and analysis. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.10. [PMID: 18428869 DOI: 10.1002/0471142700.nc0710s06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories.
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