1
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Olivieri A, Nardi AN, D'Abramo M. Theoretical Insights into MutY Glycosylase DNA Repair Mechanism. Biochemistry 2024; 63:1991-1998. [PMID: 38990758 DOI: 10.1021/acs.biochem.4c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Maintaining the integrity of the genome is fundamental to living organisms. To this end, nature developed several mechanisms to find and promptly repair DNA lesions. Among them, base excision repair (BER) enzymes evolved to efficiently carry out this task. Notably, the mechanisms allowing these proteins to search for, detect, and fix DNA damage on a biologically relevant time scale still remain partially unclear. By taking MutY, a BER enzyme implied in the repair of the 8-oxoguanine-adenine mismatches, as a model system, we shed some light on the repair mechanism through a theoretical-computational approach. First, we estimated the effect of the oxidation state of the MutY iron-sulfur cluster on the protein-DNA binding. Then, the redox thermodynamics of both the protein cluster and DNA nucleobases are calculated. Finally, the charge migration kinetics along the double strand bound to the enzyme has been evaluated. The rationalization of our results indicates that the search for DNA lesions is essentially dictated by the redox chemistry of the species involved, i.e., the iron-sulfur redox cofactor and the DNA bound to the enzyme.
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Affiliation(s)
- Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
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2
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Grunwald L, Abbott DF, Mougel V. Gauging Iron-Sulfur Cubane Reactivity from Covalency: Trends with Oxidation State. JACS AU 2024; 4:1315-1322. [PMID: 38665672 PMCID: PMC11040707 DOI: 10.1021/jacsau.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge position provides a qualitative but convenient alternative to the traditional spectroscopic descriptors used to identify oxidation states in these systems, which we demonstrate by providing a calibration curve based on two analytic methods. Furthermore, high energy resolution fluorescence detected XAS (HERFD-XAS) at the S K-edge was used to measure Fe-S bond covalencies and record their variation with the average valence of the Fe atoms. While the Fe-S(thiolate) covalency evolves linearly, gaining 11 ± 0.4% per bond and hole, the Fe-S(μ3) covalency evolves asystematically, reflecting changes in the magnetic exchange mechanism. A strong discontinuity manifested for superoxidation to the all-ferric state, distinguishing its electronic structure and its potential (bio)chemical role from those of its redox congeners. We highlight the functional implications of these trends for the reactivity of iron-sulfur cubanes.
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Affiliation(s)
- Liam Grunwald
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Daniel F. Abbott
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Victor Mougel
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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3
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Li Z, Tan Y, Ding M, Tang L, Zeng F. Keto-Adamantane-Based Macrocycle Crystalline Supramolecular Assemblies Showing Selective Vapochromism to Tetrahydrofuran. Molecules 2024; 29:719. [PMID: 38338463 PMCID: PMC10856198 DOI: 10.3390/molecules29030719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
Here, we report the synthesis of adamantane-based macrocycle 2 by combining adamantane building blocks with π-donor 1,3-dimethoxy-benzene units. An unpredictable keto-adamantane-based macrocycle 3 was obtained by the oxidation of 2 using DDQ as an oxidant. Moreover, a new type of macrocyclic molecule-based CT cocrystal was prepared through exo-wall CT interactions between 3 and DDQ. The cocrystal material showed selective vapochromism behavior towards THF, specifically, among nine volatile organic solvents commonly used in the laboratory. Powder X-ray diffraction; UV-Vis diffuse reflectance spectroscopy; 1H NMR; and single crystal X-ray diffraction analyses revealed that color changes are attributed to the vapor-triggered decomplexation of cocrystals.
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Affiliation(s)
| | | | - Manhua Ding
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 415199, China; (Z.L.); (Y.T.); (L.T.)
| | | | - Fei Zeng
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 415199, China; (Z.L.); (Y.T.); (L.T.)
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4
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Sarhangi SM, Matyushov DV. Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin. J Phys Chem B 2022; 126:10360-10373. [PMID: 36459590 DOI: 10.1021/acs.jpcb.2c05258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, where it is determined by the protein-water dynamics, and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site.
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Affiliation(s)
- Setare Mostajabi Sarhangi
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
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5
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Salay LE, Blee AM, Raza MK, Gallagher KS, Chen H, Dorfeuille AJ, Barton JK, Chazin WJ. Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase. Biochemistry 2022; 61:1113-1123. [PMID: 35617695 DOI: 10.1021/acs.biochem.2c00100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA synthesis during replication begins with the generation of an ∼10-nucleotide primer by DNA primase. Primase contains a redox-active 4Fe-4S cluster in the C-terminal domain of the p58 subunit (p58C). The redox state of this 4Fe-4S cluster can be modulated via the transport of charge through the protein and the DNA substrate (redox switching); changes in the redox state of the cluster alter the ability of p58C to associate with its substrate. The efficiency of redox switching in p58C can be altered by mutating tyrosine residues that bridge the 4Fe-4S cluster and the nucleic acid binding site. Here, we report the effects of mutating bridging tyrosines to phenylalanines in yeast p58C. High-resolution crystal structures show that these mutations, even with six tyrosines simultaneously mutated, do not perturb the three-dimensional structure of the protein. In contrast, measurements of the electrochemical properties on DNA-modified electrodes of p58C containing multiple tyrosine to phenylalanine mutations reveal deficiencies in their ability to engage in DNA charge transport. Significantly, this loss of electrochemical activity correlates with decreased primase activity. While single-site mutants showed modest decreases in activity compared to that of the wild-type primase, the protein containing six mutations exhibited a 10-fold or greater decrease. Thus, many possible tyrosine-mediated pathways for charge transport in yeast p58C exist, but inhibiting these pathways together diminishes the ability of yeast primase to generate primers. These results support a model in which redox switching is essential for primase activity.
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Affiliation(s)
- Lauren E Salay
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Alexandra M Blee
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Md Kausar Raza
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kaitlyn S Gallagher
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Huiqing Chen
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Andrew J Dorfeuille
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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6
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Gaughan SJH, Hirst JD, Croft AK, Jäger CM. Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis. J Chem Inf Model 2022; 62:591-601. [PMID: 35045248 DOI: 10.1021/acs.jcim.1c00791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active-site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Oriented electric fields in enzymatic active sites can be significantly strong, and understanding the extent of their effect on iron-sulfur cluster reactivity can inform first steps toward rationally engineering their reactivity. An extensive systematic density functional theory-based screening approach using OPBE/TZP has afforded a simple electric field-effect representation. The results demonstrate that the orientation of an external electric field of strength 28.8 MV cm-1 at the center of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol-1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken-symmetry state, which further has implications on the directionality of initiated electron-transfer reactions. These insights open the path for manipulating the enzymatic redox reactivity of iron-sulfur cluster-containing enzymes by rationally engineering oriented electric fields within the enzymes.
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Affiliation(s)
- Samuel J H Gaughan
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.,Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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7
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So M, Stiban J, Ciesielski GL, Hovde SL, Kaguni LS. Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase. Front Genet 2021; 12:790521. [PMID: 34950192 PMCID: PMC8688847 DOI: 10.3389/fgene.2021.790521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Recent evidence suggests that iron-sulfur clusters (ISCs) in DNA replicative proteins sense DNA-mediated charge transfer to modulate nuclear DNA replication. In the mitochondrial DNA replisome, only the replicative DNA helicase (mtDNA helicase) from Drosophila melanogaster (Dm) has been shown to contain an ISC in its N-terminal, primase-like domain (NTD). In this report, we confirm the presence of the ISC and demonstrate the importance of a metal cofactor in the structural stability of the Dm mtDNA helicase. Further, we show that the NTD also serves a role in membrane binding. We demonstrate that the NTD binds to asolectin liposomes, which mimic phospholipid membranes, through electrostatic interactions. Notably, membrane binding is more specific with increasing cardiolipin content, which is characteristically high in the mitochondrial inner membrane (MIM). We suggest that the N-terminal domain of the mtDNA helicase interacts with the MIM to recruit mtDNA and initiate mtDNA replication. Furthermore, Dm NUBPL, the known ISC donor for respiratory complex I and a putative donor for Dm mtDNA helicase, was identified as a peripheral membrane protein that is likely to execute membrane-mediated ISC delivery to its target proteins.
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Affiliation(s)
- Minyoung So
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine
| | - Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland.,Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States
| | - Stacy L Hovde
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
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8
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Multiple hops move electrons from bacteria to rocks. Proc Natl Acad Sci U S A 2021; 118:2115620118. [PMID: 34625473 DOI: 10.1073/pnas.2115620118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
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9
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Ru X, Crane BR, Zhang P, Beratan DN. Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex? J Phys Chem B 2021; 125:7763-7773. [PMID: 34235935 DOI: 10.1021/acs.jpcb.1c05064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) complex (CcP:Cc) is used widely to study interprotein electron transfer (ET) mechanisms. Tryptophan 191 (Trp191) of CcP supports hole hopping charge recombination in the CcP:Cc complex. Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decrease. Theoretical analysis of these CcP:Cc complexes finds that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically to the Cc heme, and the structural disorder of the guest molecule in the binding pocket may contribute further to the lack of enzymatic activity. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine vs tryptophan oxidation accounts for the slower rate in the Tyr mutant. Thus, theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex. Favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in this protein-protein complex.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States
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10
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Pastore AJ, Teo RD, Montoya A, Burg MJ, Twahir UT, Bruner SD, Beratan DN, Angerhofer A. Oxalate decarboxylase uses electron hole hopping for catalysis. J Biol Chem 2021; 297:100857. [PMID: 34097877 PMCID: PMC8254039 DOI: 10.1016/j.jbc.2021.100857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 01/16/2023] Open
Abstract
The hexameric low-pH stress response enzyme oxalate decarboxylase catalyzes the decarboxylation of the oxalate mono-anion in the soil bacterium Bacillus subtilis. A single protein subunit contains two Mn-binding cupin domains, and catalysis depends on Mn(III) at the N-terminal site. The present study suggests a mechanistic function for the C-terminal Mn as an electron hole donor for the N-terminal Mn. The resulting spatial separation of the radical intermediates directs the chemistry toward decarboxylation of the substrate. A π-stacked tryptophan pair (W96/W274) links two neighboring protein subunits together, thus reducing the Mn-to-Mn distance from 25.9 Å (intrasubunit) to 21.5 Å (intersubunit). Here, we used theoretical analysis of electron hole-hopping paths through redox-active sites in the enzyme combined with site-directed mutagenesis and X-ray crystallography to demonstrate that this tryptophan pair supports effective electron hole hopping between the C-terminal Mn of one subunit and the N-terminal Mn of the other subunit through two short hops of ∼8.5 Å. Replacement of W96, W274, or both with phenylalanine led to a large reduction in catalytic efficiency, whereas replacement with tyrosine led to recovery of most of this activity. W96F and W96Y mutants share the wildtype tertiary structure. Two additional hole-hopping networks were identified leading from the Mn ions to the protein surface, potentially protecting the enzyme from high Mn oxidation states during turnover. Our findings strongly suggest that multistep hole-hopping transport between the two Mn ions is required for enzymatic function, adding to the growing examples of proteins that employ aromatic residues as hopping stations.
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Affiliation(s)
- Anthony J Pastore
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Alvaro Montoya
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Matthew J Burg
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Umar T Twahir
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina, USA.
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11
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Valdiviezo J, Clever C, Beall E, Pearse A, Bae Y, Zhang P, Achim C, Beratan DN, Waldeck DH. Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions. Biochemistry 2021; 60:1368-1378. [PMID: 33870693 DOI: 10.1021/acs.biochem.1c00072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even-odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA-electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G0, where G0 is the quantum of conductance, for 5 nm duplexes.
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Affiliation(s)
- Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Caleb Clever
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Edward Beall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Pearse
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yookyung Bae
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - David H Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Patwardhan A, Sarangi R, Ginovska B, Raugei S, Ragsdale SW. Nickel-Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer. J Am Chem Soc 2021; 143:5481-5496. [PMID: 33761259 DOI: 10.1021/jacs.1c01086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F430. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)-sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.
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Affiliation(s)
- Anjali Patwardhan
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48103, United States
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Simone Raugei
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48103, United States
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13
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Kubas A. How the Donor/Acceptor Spin States Affect the Electronic Couplings in Molecular Charge-Transfer Processes? J Chem Theory Comput 2021; 17:2917-2927. [PMID: 33830757 PMCID: PMC8154369 DOI: 10.1021/acs.jctc.1c00126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The electronic coupling
matrix element HAB is an essential ingredient
of most electron-transfer theories. HAB depends on the overlap between donor and
acceptor wave functions and is affected by the involved states’
spin. We classify the spin-state effects into three categories: orbital
occupation, spin-dependent electron density, and density delocalization.
The orbital occupancy reflects the diverse chemical nature and reactivity
of the spin states of interest. The effect of spin-dependent density
is related to a more compact electron density cloud at lower spin
states due to decreased exchange interactions between electrons. Density
delocalization is strongly connected with the covalency concept that
increases the spatial extent of the diabatic state’s electron
density in specific directions. We illustrate these effects with high-level ab initio calculations on model direct donor–acceptor
systems relevant to metal oxide materials and biological electron
transfer. Obtained results can be used to benchmark existing methods
for HAB calculations in complicated cases
such as spin-crossover materials or antiferromagnetically coupled
systems.
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Affiliation(s)
- A Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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14
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Teo RD, Du X, Vera HLT, Migliore A, Beratan DN. Correlation between Charge Transport and Base Excision Repair in the MutY-DNA Glycosylase. J Phys Chem B 2021; 125:17-23. [PMID: 33371674 DOI: 10.1021/acs.jpcb.0c08598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Experimental evidence suggests that DNA-mediated redox signaling between high-potential [Fe4S4] proteins is relevant to DNA replication and repair processes, and protein-mediated charge transfer (CT) between [Fe4S4] clusters and nucleic acids is a fundamental process of the signaling and repair mechanisms. We analyzed the dominant CT pathways in the base excision repair glycosylase MutY using molecular dynamics simulations and hole hopping pathway analysis. We find that the adenine nucleobase of the mismatched A·oxoG DNA base pair facilitates [Fe4S4]-DNA CT prior to adenine excision by MutY. We also find that the R153L mutation in MutY (linked to colorectal adenomatous polyposis) influences the dominant [Fe4S4]-DNA CT pathways and appreciably decreases their effective CT rates.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Xiaochen Du
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Héctor Luis Torres Vera
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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15
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Mi Y, Ma J, Liang W, Xiao C, Wu W, Zhou D, Yao J, Sun W, Sun J, Gao G, Chen X, Chruma JJ, Yang C. Guest-Binding-Induced Interhetero Hosts Charge Transfer Crystallization: Selective Coloration of Commonly Used Organic Solvents. J Am Chem Soc 2021; 143:1553-1561. [PMID: 33432813 DOI: 10.1021/jacs.0c11833] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Unprecedented interheteromacrocyclic hosts charge transfer (CT) crystals were generated by cooling organic solutions containing p-dimethoxybenzene-constituted pillar[5]arene (P5A) and p-benzoquinone-constituted pillar[5]quinone (P5Q). Despite the weak CT interaction known between p-dimethoxybenzene and p-benzoquinone and the lack of formation of CT complexes between P5A and P5Q in the solution phase, CT cocrystals between P5A and P5Q were formed with solvent molecules included into the hosts' cavities. Such a cocrystallization arises from an elegant synergy between the CT interaction and solvent-binding-promoted crystallization. The interhetero hosts CT crystals were studied by optical and electron microscopic techniques, X-ray powder diffraction, solid-state NMR, UV-vis, IR spectroscopic studies, and X-ray single-crystal studies. The solvent complexation was critical for formation of the supramolecular CT microcrystals. The CT absorption bands faded upon removing the solvent molecules under vacuum, but they could be recovered by reuptake of the solvent molecules. Intriguingly, the CT absorption bands and uptake kinetics are distinguishably different for various organic solvents, thus providing a unique way to distinguish between different commonly used chemicals.
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Affiliation(s)
- Yan Mi
- Key Laboratory of Green Chemistry & Technology, College of Chemistry, State Key Laboratory of Biotherapy, West China Medical Center, and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610064, People's Republic of China
| | - Jingyu Ma
- Key Laboratory of Green Chemistry & Technology, College of Chemistry, State Key Laboratory of Biotherapy, West China Medical Center, and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610064, People's Republic of China
| | - Wenting Liang
- Institute of Environmental Science, Department of Chemistry, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Chao Xiao
- Key Laboratory of Green Chemistry & Technology, College of Chemistry, State Key Laboratory of Biotherapy, West China Medical Center, and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610064, People's Republic of China
| | - Wanhua Wu
- Key Laboratory of Green Chemistry & Technology, College of Chemistry, State Key Laboratory of Biotherapy, West China Medical Center, and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610064, People's Republic of China
| | - Dayang Zhou
- Comprehensive Analysis Center, ISIR, Osaka University, Suita, Osaka 565-0871, Japan
| | - Jiabin Yao
- Key Laboratory of Green Chemistry & Technology, College of Chemistry, State Key Laboratory of Biotherapy, West China Medical Center, and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610064, People's Republic of China
| | - Wenjia Sun
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Junliang Sun
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Guowei Gao
- College of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Xiaochuan Chen
- College of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Jason J Chruma
- College of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China.,Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Cheng Yang
- Key Laboratory of Green Chemistry & Technology, College of Chemistry, State Key Laboratory of Biotherapy, West China Medical Center, and Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610064, People's Republic of China
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16
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Characterization of charge transfer excited states in [2Fe–2S] iron–sulfur clusters using conventional configuration interaction techniques. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02635-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractThe experimental UV–Vis spectra of the biologically relevant [2Fe–2S] iron–sulfur clusters feature typically three bands in the 300–800 nm range. Based on ground-state orbitals and using the one electron transition picture, these bands are said to be of charge transfer character. The key complication in the electronic structure calculations of these compounds are the antiferromagnetic coupling of the iron centers and high covalency of Fe–S bonds. Thus, the examples of the direct computations of electronically excited states of these systems are rare. Whereas low lying electronic excited states were subject of recent studies, higher energy states computed with many-body theories were never reported. In this work we present, for the first time, calculations of the electronic spectra of [Fe2S2](SMe)42−
biomimetic compound. We demonstrate that spin-averaged restricted open-shell Hartree–Fock orbitals are superior to high-spin orbitals and are convenient reference for subsequent configuration interaction calculations. Moreover, the use of conventional configuration interaction methods enabled us to study the nature of the excited states in details with the difference density maps. By systematic extension of the donor orbital space we show that key excitations in the 300–800 nm range are of Fe 3d ← (μ-S) character.
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17
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Onuchic JN, Rubtsov IV, Therien MJ. Tribute to David N. Beratan. J Phys Chem B 2020; 124:3437-3440. [DOI: 10.1021/acs.jpcb.0c02606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Jin Y, Ru X, Su NQ, Mei Y, Beratan DN, Zhang P, Yang W. Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections. J Phys Chem B 2020; 124:3428-3435. [PMID: 32272019 DOI: 10.1021/acs.jpcb.0c03112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier's wave function delocalization is regulated by the solvation induced localization and the quantum delocalization among the π stacked base pairs at any instant of time. Using a newly developed localized orbital scaling correction (LOSC) density functional theory method, we accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA. This approach can be used to diagnose the extent of delocalization in fluctuating DNA structures. Our studies indicate that the hole state tends to delocalize among 4 guanine-cytosine (GC) base pairs and among 3 adenine-thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. The relatively small delocalization in AT base pairs is caused by the weaker π-π interaction. This extent of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering coherent carrier transport in DNA.
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Affiliation(s)
- Ye Jin
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Neil Qiang Su
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yuncai Mei
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27705, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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19
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Teo RD, Migliore A, Beratan DN. Mutation effects on charge transport through the p58c iron-sulfur protein. Chem Sci 2020; 11:7076-7085. [PMID: 33250976 PMCID: PMC7690218 DOI: 10.1039/d0sc02245d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/16/2020] [Indexed: 12/25/2022] Open
Abstract
Growing experimental evidence indicates that iron–sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [Fe4S4] clusters, mediated by proteins and DNA, may convey signals to coordinate enzyme action. Human primase is a well studied [Fe4S4] protein, and its p58c domain (which contains an [Fe4S4] cluster) plays a role in the initiation of DNA replication. The Y345C mutation in p58c is linked to gastric tumors and may influence the protein-mediated charge transport. The complexity of protein–DNA systems, and the intricate electronic structure of [Fe4S4] clusters, have impeded progress into understanding functional charge transport in these systems. In this study, we built force fields to describe the high potential [Fe4S4] cluster in both oxidation states. The parameterization is compatible with AMBER force fields and enabled well-balanced molecular dynamics simulations of the p58c–RNA/DNA complex relevant to the initiation of DNA replication. Using the molecular mechanics Poisson–Boltzmann and surface area solvation method on the molecular dynamics trajectories, we find that the p58c mutation induces a modest change in the p58c–duplex binding free energy in agreement with recent experiments. Through kinetic modeling and analysis, we identify key features of the main charge transport pathways in p58c. In particular, we find that the Y345C mutation partially changes the composition and frequency of the most efficient (and potentially relevant to the biological function) charge transport pathways between the [Fe4S4] cluster and the duplex. Moreover, our approach sets the stage for a deeper understanding of functional charge transfer in [Fe4S4] protein–DNA complexes. Functional electron transfer between the [Fe4S4] cluster and the nucleic acid is impacted by a Y345C mutation in the p58c subunit of human primase.![]()
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ;
| | - Agostino Migliore
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ;
| | - David N Beratan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ; .,Department of Physics , Duke University , Durham , North Carolina 27708 , USA.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , USA
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20
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Paradisi A, Johnston EM, Tovborg M, Nicoll CR, Ciano L, Dowle A, McMaster J, Hancock Y, Davies GJ, Walton PH. Formation of a Copper(II)-Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by H 2O 2. J Am Chem Soc 2019; 141:18585-18599. [PMID: 31675221 PMCID: PMC7007232 DOI: 10.1021/jacs.9b09833] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 01/14/2023]
Abstract
Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen peroxide is high, but it is accompanied by rapid inactivation of the enzymes, presumably through protein oxidation. Herein, we use UV-vis, CD, XAS, EPR, VT/VH-MCD, and resonance Raman spectroscopies, augmented with mass spectrometry and DFT calculations, to show that the product of reaction of an AA9 LPMO with H2O2 at higher pHs is a singlet Cu(II)-tyrosyl radical species, which is inactive for the oxidation of saccharidic substrates. The Cu(II)-tyrosyl radical center entails the formation of significant Cu(II)-(●OTyr) overlap, which in turn requires that the plane of the d(x2-y2) SOMO of the Cu(II) is orientated toward the tyrosyl radical. We propose from the Marcus cross-relation that the active site tyrosine is part of a "hole-hopping" charge-transfer mechanism formed of a pathway of conserved tyrosine and tryptophan residues, which can protect the protein active site from inactivation during uncoupled turnover.
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Affiliation(s)
- Alessandro Paradisi
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Esther M. Johnston
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | | | - Callum R. Nicoll
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Luisa Ciano
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Adam Dowle
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Jonathan McMaster
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Y. Hancock
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
- York
Cross-Disciplinary Centre for Systems Analysis, University of York, Heslington,
York YO10 5GE, United Kingdom
| | - Gideon J. Davies
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Paul H. Walton
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
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21
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Teo RD, Smithwick ER, Migliore A. 2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport. Phys Chem Chem Phys 2019; 21:22869-22878. [PMID: 31599901 PMCID: PMC7050622 DOI: 10.1039/c9cp04805g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The non-biological 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2'F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2'F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs. Inserting these charge-transfer parameters into a kinetic model for charge conduction, we find similar conductive properties for DNA and 2'F-ANA. Moreover, we find that 2'F-ANA's enhanced chemical stability does not correspond to a reduction in the nucleobase π-stack structural flexibility relevant to both electronic couplings and reorganization free energies. Our results promote the use of 2'F-ANA in applications that can be based on charge transport, such as biosensing and chip technology, where its chemical stability and conductivity can advantageously combine.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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22
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Migliore A. How To Extract Quantitative Information on Electronic Transitions from the Density Functional Theory "Black Box". J Chem Theory Comput 2019; 15:4915-4923. [PMID: 31314526 DOI: 10.1021/acs.jctc.9b00518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electronic couplings and vertical excitation energies are crucial determinants of charge and excitation energy transfer rates in a broad variety of processes ranging from biological charge transfer to charge transport through inorganic materials, from molecular sensing to intracellular signaling. Density Functional Theory (DFT) is generally used to calculate these critical parameters, but the quality of the results is unpredictable because of the semiempirical nature of the available DFT approaches. This study identifies a small set of fundamental rules that enables accurate DFT computation of electronic couplings and vertical excitation energies in molecular complexes and materials. These rules are applied to predict efficient DFT approaches to coupling calculations. The result is an easy-to-use guide for reliable DFT descriptions of electronic transitions.
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Affiliation(s)
- Agostino Migliore
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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23
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Abstract
A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on the mean residence times of the transferring charge along these hopping pathways. The residence times are estimated by combining a kinetic model with well-known rate expressions for the charge-transfer steps in the pathways. We identify the most rapid hole hopping escape routes in cytochrome P450 monooxygenase, cytochrome c peroxidase, and benzylsuccinate synthase (BSS). This theoretical analysis supports the existence of hole hopping chains as a mechanism capable of providing hole escape from protein catalytic sites on biologically relevant timescales. Furthermore, we find that pathways involving the [4Fe4S] cluster as the terminal hole acceptor in BSS are accessible on the millisecond timescale, suggesting a potential protective role of redox-active cofactors for preventing protein oxidative damage.
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24
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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25
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Goodpaster JD. Theoretical Chemistry Answers Bimolecular Signaling Debate in [4Fe4S] Proteins. Chem 2019. [DOI: 10.1016/j.chempr.2018.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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