1
|
Kurle-Tucholski P, Wiebeler C, Köhler L, Qin R, Zhao Z, Šimėnas M, Pöppl A, Matysik J. Red Shift in the Absorption Spectrum of Phototropin LOV1 upon the Formation of a Semiquinone Radical: Reconstructing the Orbital Architecture. J Phys Chem B 2024; 128:4344-4353. [PMID: 38688080 PMCID: PMC11089501 DOI: 10.1021/acs.jpcb.4c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/22/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Flavin mononucleotide (FMN) is a ubiquitous blue-light pigment due to its ability to drive one- and two-electron transfer reactions. In both light-oxygen-voltage (LOV) domains of phototropin from the green algae Chlamydomonas reinhardtii, FMN is noncovalently bound. In the LOV1 cysteine-to-serine mutant (C57S), light-induced electron transfer from a nearby tryptophan occurs, and a transient spin-correlated radical pair (SCRP) is formed. Within this photocycle, nuclear hyperpolarization is created by the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect. In a side reaction, a stable protonated semiquinone radical (FMNH·) forms undergoing a significant bathochromic shift of the first electronic transition from 445 to 591 nm. The incorporation of phototropin LOV1-C57S into an amorphous trehalose matrix, stabilizing the radical, allows for application of various magnetic resonance experiments at ambient temperatures, which are combined with quantum-chemical calculations. As a result, the bathochromic shift of the first absorption band is explained by lifting the degeneracy of the molecular orbital energy levels for electrons with alpha and beta spins in FMNH· due to the additional electron.
Collapse
Affiliation(s)
- Patrick Kurle-Tucholski
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Christian Wiebeler
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
- Institut
für Physik, Universität Augsburg, Universitätsstraße 1, D-86159 Augsburg, Germany
| | - Lisa Köhler
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Ruonan Qin
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Ziyue Zhao
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Mantas Šimėnas
- Faculty
of Physics, Vilnius University, Sauletekio 3, LT-10257 Vilnius, Lithuania
| | - Andreas Pöppl
- Felix
Bloch Institute for Solid State Physics, Universität Leipzig, Linnéstraße 5, D-04103, Leipzig, Germany
| | - Jörg Matysik
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| |
Collapse
|
2
|
González-Viegas M, Kar RK, Miller AF, Mroginski MA. Non-covalent interactions that tune the reactivities of the flavins in bifurcating electron transferring flavoprotein. J Biol Chem 2023:104762. [PMID: 37119850 DOI: 10.1016/j.jbc.2023.104762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/01/2023] Open
Abstract
Bifurcating electron transferring flavoproteins (Bf-ETFs) tune chemically identical flavins to two contrasting roles. To understand how, we used hybrid quantum mechanical molecular mechanical calculations to characterize non-covalent interactions applied to each flavin by the protein. Our computations replicated the differences between the reactivities of the flavins: the electron transferring flavin (ETflavin) was calculated to stabilize anionic semiquinone (ASQ) as needed to execute its single-electron transfers, whereas the Bf flavin (Bfflavin) was found to disfavor the ASQ state more than does free flavin and to be less susceptible to reduction. The stability of ETflavin ASQ was attributed in part to H-bond donation to the flavin O2 from a nearby His side chain, via comparison of models employing different tautomers of His. This H-bond between O2 and the ET site was uniquely strong in the ASQ state, whereas reduction of ETflavin to the anionic hydroquinone (AHQ) was associated with side chain reorientation, backbone displacement and reorganization of its H-bond network including a Tyr from the other domain and subunit of the ETF. The Bf site was less responsive overall, but formation of the Bfflavin AHQ allowed a nearby Arg side chain to adopt an alternative rotamer that can H-bond to the Bfflavin O4. This would stabilize the anionic Bfflavin and rationalize effects of mutation at this position. Thus, our computations provide insights on states and conformations that have not been possible to characterize experimentally, offering explanations for observed residue conservation and raising possibilities that can now be tested.
Collapse
Affiliation(s)
- María González-Viegas
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Rajiv K Kar
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany
| | - Anne-Frances Miller
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Chemistry, University of Kentucky, Lexington KY, U.S.A..
| | | |
Collapse
|
3
|
Understanding flavin electronic structure and spectra. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
4
|
Kar RK, Chasen S, Mroginski MA, Miller AF. Tuning the Quantum Chemical Properties of Flavins via Modification at C8. J Phys Chem B 2021; 125:12654-12669. [PMID: 34784473 DOI: 10.1021/acs.jpcb.1c07306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavins are central to countless enzymes but display different reactivities depending on their environments. This is understood to reflect modulation of the flavin electronic structure. To understand changes in orbital natures, energies, and correlation over the ring system, we begin by comparing seven flavin variants differing at C8, exploiting their different electronic spectra to validate quantum chemical calculations. Ground state calculations replicate a Hammett trend and reveal the significance of the flavin π-system. Comparison of higher-level theories establishes CC2 and ACD(2) as methods of choice for characterization of electronic transitions. Charge transfer character and electron correlation prove responsive to the identity of the substituent at C8. Indeed, bond length alternation analysis demonstrates extensive conjugation and delocalization from the C8 position throughout the ring system. Moreover, we succeed in replicating a particularly challenging UV/Vis spectrum by implementing hybrid QM/MM in explicit solvents. Our calculations reveal that the presence of nonbonding lone pairs correlates with the change in the UV/Vis spectrum observed when the 8-methyl is replaced by NH2, OH, or SH. Thus, our computations offer routes to understanding the spectra of flavins with different modifications. This is a first step toward understanding how the same is accomplished by different binding environments.
Collapse
Affiliation(s)
- Rajiv K Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Sam Chasen
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Maria-Andrea Mroginski
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Anne-Frances Miller
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.,Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| |
Collapse
|
5
|
Onchoke KK. 13C NMR chemical shift assignments of nitrated benzo[a]pyrenes based on two-dimensional techniques and DFT/GIAO calculations. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
6
|
Kar RK, Borin VA, Ding Y, Matysik J, Schapiro I. Spectroscopic Properties of Lumiflavin: A Quantum Chemical Study. Photochem Photobiol 2018; 95:662-674. [DOI: 10.1111/php.13023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/05/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Rajiv Kumar Kar
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry Hebrew University of Jerusalem Jerusalem Israel
| | - Veniamin A. Borin
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry Hebrew University of Jerusalem Jerusalem Israel
| | - Yonghong Ding
- Institute of Analytical Chemistry University of Leipzig Leipzig Germany
| | - Jörg Matysik
- Institute of Analytical Chemistry University of Leipzig Leipzig Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry Hebrew University of Jerusalem Jerusalem Israel
| |
Collapse
|
7
|
Miller AF. Solid-state NMR of flavins and flavoproteins. Methods Mol Biol 2014; 1146:307-40. [PMID: 24764096 DOI: 10.1007/978-1-4939-0452-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Why apply solid-state NMR (SSNMR) to flavins and flavoproteins? NMR provides information on an atom-specific basis about chemical functionality, structure, proximity to other groups, and dynamics of the system. Thus, it has become indispensable to the study of chemicals, materials, catalysts, and biomolecules. It is no surprise then that NMR has a great deal to offer in the study of flavins and flavoenzymes. In general, their catalytic or electron-transfer activity resides essentially in the flavin, a molecule eminently accessible by NMR. However, the specific reactivity displayed depends on a host of subtle interactions whereby the protein biases and reshapes the flavin's propensities to activate it for one reaction while suppressing other aspects of this cofactor's prodigious repertoire (Massey et al., J Biol Chem 244:3999-4006, 1969; Müller, Z Naturforsch 27B:1023-1026, 1972; Joosten and van Berkel, Curr Opin Struct Biol 11:195-202, 2007). Thus, we are fascinated to learn about how the flavin cofactor of one enzyme is, and is not, like the flavin cofactor of another. In what follows, we describe how the capabilities of SSNMR can help and are beginning to bear fruit in this exciting endeavor.
Collapse
Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, 505 Rose St, Lexington, KY, 40506-0055, USA,
| |
Collapse
|
8
|
Raju G, Singh S, Mutter AC, Everson BH, Cerda JF, Koder RL. An extended scope synthesis of an artificial safranine cofactor. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Abstract
(1)H-, (11)B-, (13)C-, (15)N-, (17)O-, (19)F-, and (31)P-NMR chemical shifts of flavocoenzymes and derivatives of it, as well as of alloxazines and isoalloxazinium salts, from NMR experiments performed under various experimental conditions (e.g., dependence of the chemical shifts on temperature, concentration, solvent polarity, and pH) are reported. Also solid-state (13)C- and (15)N-NMR experiments are described revealing the anisotropic values of corresponding chemical shifts. These data, in combination with a number of coupling constants, led to a detailed description of the electronic structure of oxidized and reduced flavins. The data also demonstrate that the structure of oxidized flavin can assume a configuration deviating from coplanarity, depending on substitutions in the isoalloxazine ring, while that of reduced flavin exhibits several configurations, from almost planar to quite bended. The complexes formed between oxidized flavin and metal ions or organic molecules revealed three coordination sites with metal ions (depending on the chemical nature of the ion), and specific interactions between the pyrimidine moiety of flavin and organic molecules, mimicking specific interactions between apoflavoproteins and their coenzymes. Most NMR studies on flavoproteins were performed using (13)C- and (15)N-substituted coenzymes, either specifically enriched in the pterin moiety of flavin or uniformly labeled flavins. The chemical shifts of free flavins are used as a guide in the interpretation of the chemical shifts observed in flavoproteins. Although the hydrogen-bonding pattern in oxidized and reduced flavoproteins varies considerably, no correlation is obvious between these patterns and the corresponding redox potentials. In all reduced flavoproteins the N(1)H group of the flavocoenzyme is deprotonated, an exception is thioredoxin reductase. Three-dimensional structures of only a few flavoproteins, mostly belonging to the family of flavodoxins, have been solved. Also the kinetics of unfolding and refolding of flavodoxins has been investigated by NMR techniques. In addition, (31)P-NMR data of all so far studied flavoproteins and some (19)F-NMR spectra are discussed.
Collapse
Affiliation(s)
- Franz Müller
- , Wylstrasse 13, CH-6052, Hergiswil, Switzerland,
| |
Collapse
|
10
|
Cui D, Koder RL, Dutton PL, Miller AF. 15N solid-state NMR as a probe of flavin H-bonding. J Phys Chem B 2011; 115:7788-98. [PMID: 21619002 DOI: 10.1021/jp202138d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flavins mediate a wide variety of chemical reactions in biology. To learn how one cofactor can be made to execute different reactions in different enzymes, we are developing solid-state NMR (SSNMR) to probe the flavin electronic structure, via the (15)N chemical shift tensor principal values (δ(ii)). We find that SSNMR has superior responsiveness to H-bonds, compared to solution NMR. H-bonding to a model of the flavodoxin active site produced an increase of 10 ppm in the δ(11) of N5, although none of the H-bonds directly engage N5, and solution NMR detected only a 4 ppm increase in the isotropic chemical shift (δ(iso)). Moreover SSNMR responded differently to different H-bonding environments, as H-bonding with water caused δ(11) to decrease by 6 ppm, whereas δ(iso) increased by less than 1 ppm. Our density functional theoretical (DFT) calculations reproduce the observations, validating the use of computed electronic structures to understand how H-bonds modulate the flavin's reactivity.
Collapse
Affiliation(s)
- Dongtao Cui
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | | | | | | |
Collapse
|
11
|
Cerda JF, Koder RL, Lichtenstein BR, Moser CM, Miller AF, Dutton PL. Hydrogen bond-free flavin redox properties: managing flavins in extreme aprotic solvents. Org Biomol Chem 2008; 6:2204-12. [PMID: 18528583 DOI: 10.1039/b801952e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a simple, single step reaction that transforms riboflavin, which is insoluble in benzene, to tetraphenylacetyl riboflavin (TPARF), which is soluble in this solvent to over 250 mM. Electrochemical analysis of TPARF both alone and in complexes with two benzene-soluble flavin receptors: dibenzylamidopyridine (DBAP) and monobenzylamidopyridine (MBAP), prove that this model system behaves similarly to other previously studied flavin model systems which were soluble only in more polar solvents such as dichloromethane. Binding titrations in both benzene and dichloromethane show that the association constants of TPARF with its ligands are over an order of magnitude higher in benzene than dichloromethane, a consequence of the fact that benzene does not compete for H-bonds, but dichloromethane does. The alteration induced in the visible spectrum of TPARF in benzene upon the addition of DBAP is very similar to the difference produced by transfer to dichloromethane, further indicating that the flavin head group engages in a similar degree of hydrogen bonding with dichloromethane as with its ligands. This work underlines the importance of using a truly nonpolar solvent for the analysis of the effects of hydrogen bonding on the energetics of any biomimetic host-guest model system.
Collapse
Affiliation(s)
- Jose F Cerda
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, The University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | | |
Collapse
|
12
|
Koder RL, Lichtenstein BR, Cerda JF, Miller AF, Dutton PL. A Flavin Analogue with Improved Solubility in Organic Solvents. Tetrahedron Lett 2007; 48:5517-5520. [PMID: 19568318 PMCID: PMC2702786 DOI: 10.1016/j.tetlet.2007.05.165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the synthesis and initial electrochemical characterization of a benzene-soluble flavin analogue: N(10)-2,2-dibenzylethyl-7,8-dimethylisoalloxazine (DBF, 1). This analogue, which has an unmodified flavin headgroup, is intended for use in the spectroscopic examination of the electronic effects of flavin hydrogen bonding in simple model systems in aprotic, non-hydrogen bonding solvents. With future spectroscopic studies in mind, we have developed a synthetic route which allows the incorporation of isotopic labels using inexpensive starting materials.
Collapse
Affiliation(s)
- Ronald L. Koder
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, the University of Pennsylvania, Philadelphia, PA, 19104
- Department of Physics, The City College of New York, New York, NY 10031
| | - Bruce R. Lichtenstein
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, the University of Pennsylvania, Philadelphia, PA, 19104
| | - Jose F. Cerda
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, the University of Pennsylvania, Philadelphia, PA, 19104
| | - Anne-Frances Miller
- The University of Kentucky Department of Chemistry, Lexington, KY 40506-0055
| | - P. Leslie Dutton
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, the University of Pennsylvania, Philadelphia, PA, 19104
| |
Collapse
|
13
|
Koder RL, Walsh JD, Pometun MS, Dutton PL, Wittebort RJ, Miller AF. 15N solid-state NMR provides a sensitive probe of oxidized flavin reactive sites. J Am Chem Soc 2006; 128:15200-8. [PMID: 17117871 PMCID: PMC5993988 DOI: 10.1021/ja0648817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Flavins are central to the reactivity of a wide variety of enzymes and electron transport proteins. There is great interest in understanding the basis for the different reactivities displayed by flavins in different protein contexts. We propose solid-state nuclear magnetic resonance (SS-NMR) as a tool for directly observing reactive positions of the flavin ring and thereby obtaining information on their frontier orbitals. We now report the SS-NMR signals of the redox-active nitrogens N1 and N5, as well as that of N3. The chemical shift tensor of N5 is over 720 ppm wide, in accordance with the predictions of theory and our calculations. The signal of N3 can be distinguished on the basis of coupling to 1H absent for N1 and N5, as well as the shift tensor span of only 170 ppm, consistent with N3's lower aromaticity and lack of a nonbonding lone pair. The isotropic shifts and spans of N5 and N1 reflect two opposite extremes of the chemical shift range for "pyridine-type" N's, consistent with their electrophilic and nucleophilic chemical reactivities, respectively. Upon flavin reduction, N5's chemical shift tensor contracts dramatically to a span of less than 110 ppm, and the isotropic chemical shift changes by approximately 300 ppm. Both are consistent with loss of N5's nonbonding lone pair and decreased aromaticity, and illustrate the responsiveness of the 15N chemical shift principal values to electronic structure. Thus. 15N chemical shift principal values promise to be valuable tools for understanding electronic differences that underlie variations in flavin reactivity, as well as the reactivities of other heterocyclic cofactors.
Collapse
Affiliation(s)
- Ronald L. Koder
- Department of Chemistry, University of Kentucky, Lexington KY 40506-0055
- Department of Biochemistry and Biophysics, The Johnson Research Foundation, University of Pennsylvania, Philadelphia, PA 19104
| | - Joseph D. Walsh
- Department of Chemistry, University of Kentucky, Lexington KY 40506-0055
| | - Maxim S. Pometun
- Department of Chemistry, University of Louisville, Louisville KY 40292
| | - P. Leslie Dutton
- Department of Biochemistry and Biophysics, The Johnson Research Foundation, University of Pennsylvania, Philadelphia, PA 19104
| | | | | |
Collapse
|
14
|
Mothana B, Ban F, Boyd * R, Thompson A, Hadden C. The effect of electron-withdrawing groups on15N and13C chemical shifts: a density functional study on a series of pyrroles. Mol Phys 2005. [DOI: 10.1080/00268970412331333519] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
15
|
|