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Initial excited state structural dynamics of lumiflavin upon ultraviolet excitation. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Werther T, Wahlefeld S, Salewski J, Kuhlmann U, Zebger I, Hildebrandt P, Dobbek H. Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase. Nat Commun 2017. [PMCID: PMC5519977 DOI: 10.1038/ncomms16084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
How an enzyme activates its substrate for turnover is fundamental for catalysis but incompletely understood on a structural level. With redox enzymes one typically analyses structures of enzyme–substrate complexes in the unreactive oxidation state of the cofactor, assuming that the interaction between enzyme and substrate is independent of the cofactors oxidation state. Here, we investigate the Michaelis complex of the flavoenzyme xenobiotic reductase A with the reactive reduced cofactor bound to its substrates by X-ray crystallography and resonance Raman spectroscopy and compare it to the non-reactive oxidized Michaelis complex mimics. We find that substrates bind in different orientations to the oxidized and reduced flavin, in both cases flattening its structure. But only authentic Michaelis complexes display an unexpected rich vibrational band pattern uncovering a strong donor–acceptor complex between reduced flavin and substrate. This interaction likely activates the catalytic ground state of the reduced flavin, accelerating the reaction within a compressed cofactor–substrate complex. Due to their transient nature, enzyme-substrate complexes are difficult to characterize structurally. Here, the authors capture the reactive reduced form of xenobiotic reductase A bound to its substrate and show that the oxidation state of the flavin cofactor affects the interaction of the substrate with the enzyme.
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Abstract
The reduction and oxidation of the flavin system is an important electron transfer reaction in biological systems. Several reaction pathways exist to connect oxidized to fully reduced riboflavin, each with unique intermediates including a semi-quinone radical. By performing surface-enhanced Raman scattering (SERS) with simultaneous electrochemical detection of riboflavin at different pH values, we are able to correlate reversible changes in spectral features to the current changes observed in the cyclic voltammetry. Multivariate curve resolution analysis of the SERS spectra indicates that three distinct components were present at the SERS electrode at each pH during the potential sweep. To verify and better understand the variations in Raman bands across the voltammogram, density functional theory (DFT) calculations were performed to model the effect of pH and oxidation state on the riboflavin Raman spectrum. The calculated spectra show qualitative agreement with the species identified in the chemometric analysis. This combination of results indicates the presence of the oxidized, semi-quinone, and reduced forms of riboflavin and provides insight into the mechanism of the flavin redox system.
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Affiliation(s)
- Matthew R Bailey
- University of Notre Dame, Department of Chemistry and Biochemistry, Notre Dame, IN 46556, USA.
| | - Zachary D Schultz
- University of Notre Dame, Department of Chemistry and Biochemistry, Notre Dame, IN 46556, USA.
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Li J, Kitagawa T. Resonance Raman spectroscopy. Methods Mol Biol 2014; 1146:377-400. [PMID: 24764099 DOI: 10.1007/978-1-4939-0452-5_15] [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
Flavin is a general name given to molecules having the heteroaromatic ring system of 7,8-dimethylisoalloxazine but practically means riboflavin (Rfl), flavin adenine dinucleotide (FAD), and flavin mononucleotide (FMN) in biological systems, whose structures are illustrated in Fig. 1, together with the atomic numbering scheme and ring numbering of the isoalloxazine moiety. As the isoalloxazine skeleton cannot be synthesized in human cells, it is obtained from diet as Rfl (vitamin B2). FAD and FMN can act as cofactors in flavoenzymes but Rfl does not. Most flavoenzymes catalyze redox reactions of substrates (Miura, Chem Rec 1:183-194, 2001). When O2 serves as the oxidant in the oxidation half cycle of an enzymic reaction, the enzyme is called "flavo-oxidase" but when others do, the enzyme is called "flavo-dehydrogenase." The difference between the two types of oxidative catalysis arises from delicate differences in the π-electron distributions in the isoalloxazine ring, which can be revealed by Raman spectroscopy (Miura, Chem Rec 1:183-194, 2001). Since a flavin is an extremely versatile molecule, the scientific field including chemistry, biochemistry, and enzymology is collectively called "flavonology." It was found recently, however, that the flavin also acts as a chromophore to initiate light-induced DNA repair and signal transductions (Sancar, Chem Rev 103:2203-2237, 2003).
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Affiliation(s)
- Jiang Li
- Graduate School of Life Science, University of Hyogo, Kamigori-cho, Aku-gum, 678-1297, Hyogo, Japan
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6
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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.
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Affiliation(s)
- Franz Müller
- , Wylstrasse 13, CH-6052, Hergiswil, Switzerland,
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Haigney A, Lukacs A, Brust R, Zhao RK, Towrie M, Greetham GM, Clark I, Illarionov B, Bacher A, Kim RR, Fischer M, Meech SR, Tonge PJ. Vibrational assignment of the ultrafast infrared spectrum of the photoactivatable flavoprotein AppA. J Phys Chem B 2012; 116:10722-9. [PMID: 22871066 DOI: 10.1021/jp305220m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The blue light using flavin (BLUF) domain proteins, such as the transcriptional antirepressor AppA, are a novel class of photosensors that bind flavin noncovalently in order to sense and respond to high-intensity blue (450 nm) light. Importantly, the noncovalently bound flavin chromophore is unable to undergo large-scale structural change upon light absorption, and thus there is significant interest in understanding how the BLUF protein matrix senses and responds to flavin photoexcitation. Light absorption is proposed to result in alterations in the hydrogen-bonding network that surrounds the flavin chromophore on an ultrafast time scale, and the structural changes caused by photoexcitation are being probed by vibrational spectroscopy. Here we report ultrafast time-resolved infrared spectra of the AppA BLUF domain (AppA(BLUF)) reconstituted with isotopes of FAD, specifically [U-(13)C(17)]-FAD, [xylene-(13)C(8)]-FAD, [U-(15)N(4)]-FAD, and [4-(18)O(1)]-FAD both in solution and bound to AppA(BLUF). This allows for unambiguous assignment of ground- and excited-state modes arising directly from the flavin. Studies of model compounds and DFT calculations of the ground-state vibrational spectra reveal the sensitivity of these modes to their environment, indicating they can be used as probes of structural dynamics.
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Affiliation(s)
- Allison Haigney
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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Theoretical analyses of photoinduced electron transfer in medium chain acyl-CoA dehydrogenase: Electron transfer in the normal region. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rieff B, Bauer S, Mathias G, Tavan P. DFT/MM description of flavin IR spectra in BLUF domains. J Phys Chem B 2011; 115:11239-53. [PMID: 21888341 DOI: 10.1021/jp2043637] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A class of photoreceptors occurring in various organisms consists of domains that are blue light sensing using flavin (BLUF). The vibrational spectra of the flavin chromophore are spectroscopically well characterized for the dark-adapted resting states and for the light-adapted signaling states of BLUF domains in solution. Here we present a theoretical analysis of such spectra by applying density functional theory (DFT) to the flavin embedded in molecular mechanics (MM) models of its protein and solvent environment. By DFT/MM we calculate flavin spectra for seven different X-ray and NMR structures of BLUF domains occurring in the transcriptional antirepressor AppA and in the blue light receptor B (BlrB) of the purple bacterium Rb. Sphaeroides as well as in the phototaxis photoreceptor Slr1694 of the cyanobacterium Synechocystis. By considering the dynamical stabilities of associated all-atom simulation models and by comparing calculated with observed vibrational spectra, we show that two of the considered structures (both AppA) are obviously erroneous and that specific features of two further crystal structures (BlrB and Slr1694) cannot represent the states of the respective BLUF domains in solution. Thereby, the conformational transitions elicited by solvation are identified. In this context we demonstrate how hydrogen bonds of varying strengths can tune in BLUF domains the C═O stretching frequencies of the flavin chromophore. Furthermore we show that the DFT/MM spectra of the flavin calculated for two different AppA BLUF conformations, which are called Trp(in) and Met(in), fit very well to the spectroscopic data observed for the dark and light states, respectively, if (i) polarized MM force fields, which are calculated by an iterative DFT/MM procedure, are employed for the flavin binding pockets and (ii) the calculated frequencies are properly scaled. Although the associated analysis indicates that the Trp(in) conformation belongs to the dark state, no clear light vs dark distinction emerges for the Met(in) conformation. In this connection, a number of methodological issues relevant for such complex computations are thoroughly discussed showing, in particular, why our current descriptions could not decide the light vs dark question for Met(in).
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Affiliation(s)
- Benjamin Rieff
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
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Rieff B, Bauer S, Mathias G, Tavan P. IR Spectra of Flavins in Solution: DFT/MM Description of Redox Effects. J Phys Chem B 2011; 115:2117-23. [DOI: 10.1021/jp111334z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Benjamin Rieff
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - Sebastian Bauer
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - Gerald Mathias
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
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11
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Rieff B, Mathias G, Bauer S, Tavan P. Density Functional Theory Combined with Molecular Mechanics: The Infrared Spectra of Flavin in Solution†. Photochem Photobiol 2010; 87:511-23. [DOI: 10.1111/j.1751-1097.2010.00866.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Eisenberg AS, Schelvis JPM. Contributions of the 8-methyl group to the vibrational normal modes of flavin mononucleotide and its 5-methyl semiquinone radical. J Phys Chem A 2008; 112:6179-89. [PMID: 18547041 DOI: 10.1021/jp711832g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Resonance Raman spectroscopy is a powerful tool to investigate flavins and flavoproteins, and a good understanding of the flavin vibrational normal modes is essential for the interpretation of the Raman spectra. Isotopic labeling is the most effective tool for the assignment of vibrational normal modes, but such studies have been limited to labeling of rings II and III of the flavin isoalloxazine ring. In this paper, we report the resonance and pre-resonance Raman spectra of flavin mononucleotide (FMN) and its N5-methyl neutral radical semiquinone (5-CH 3FMN(*)), of which the 8-methyl group of ring I has been deuterated. The experiments indicate that the Raman bands in the low-frequency region are the most sensitive to 8-methyl deuteration. Density functional theory (DFT) calculations have been performed on lumiflavin to predict the isotope shifts, which are used to assign the calculated normal modes to the Raman bands of FMN. A first assignment of the low-frequency Raman bands on the basis of isotope shifts is proposed. Partial deuteration of the 8-methyl group reveals that the changes in the Raman spectra do not always occur gradually. These observations are reproduced by the DFT calculations, which provide detailed insight into the underlying modifications of the normal modes that are responsible for the changes in the Raman spectra. Two types of isotopic shift patterns are observed: either the frequency of the normal mode but not its composition changes or the composition of the normal mode changes, which then appears at a new frequency. The DFT calculations also reveal that the effect of H/D-exchange in the 8-methyl group on the composition of the vibrational normal modes is affected by the position of the exchanged hydrogen, i.e., whether it is in or out of the isoalloxazine plane.
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Affiliation(s)
- Azaria S Eisenberg
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
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Masuda S, Hasegawa K, Ono TA. Light-induced structural changes of apoprotein and chromophore in the sensor of blue light using FAD (BLUF) domain of AppA for a signaling state. Biochemistry 2005; 44:1215-24. [PMID: 15667215 DOI: 10.1021/bi047876t] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AppA is a new class blue-light receptor controlling photosynthesis gene expression in the purple bacterium Rhodobacter sphaeroides and retains a characteristic flavin adenine dinucleotide (FAD)-binding domain named the "sensor of blue light using FAD" (BLUF). AppA functions as an antirepressor controlling transcription of photosynthesis genes through the direct association with a transcriptional repressor PpsR in a blue-light-dependent manner [Masuda and Bauer (2002) Cell 110, 613-623]. Illumination of AppA induces a red shift in the UV-visible absorption of FAD, which results in a signaling state of AppA. Light-induced Fourier transform infrared (FTIR) difference spectrum of the AppA BLUF domain showed relatively simple features, which were mainly composed of two sets of derivative-shaped sharp bands at 1709(-)/1695(+) and 1632(+)/1619(-) cm(-)(1). We have developed an in vitro reconstitution method, by which a fully functional BLUF domain was reconstituted from free FAD and an apoprotein for the BLUF domain of AppA. An AppA BLUF domain that consisted of an apoprotein isotopically labeled with (13)C and unlabeled FAD was constituted using this method, and hydrated and deuterated samples were applied to FTIR spectroscopic analyses. When the spectra for the reconstituted domain were compared with those for uniformly (15)N- and (13)C-labeled or deuterated domains as well as for the unlabeled domain, the IR bands responsible for the light-induced changes in the FAD chromophore and apoprotein were identified. Unexpectedly, the light-induced spectrum of the unlabeled BLUF domain of AppA was predominantly composed of multiple apoprotein bands, while a C(4)=O stretching of an isoalloxazine ring was the only band exclusively assigned to FAD. The results showed that relatively large structural changes occur in the protein backbone of the BLUF domain of AppA upon illumination. These changes were discussed in relation to the mechanistic role of the BLUF domain in the process of blue-light perception by AppA.
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Affiliation(s)
- Shinji Masuda
- Laboratory for Photobiology (1), RIKEN Photodynamics Research Center, The Institute of Physical and Chemical Research, 519-1399, Aoba, Sendai 980-0845, Japan
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Masuda S, Hasegawa K, Ishii A, Ono TA. Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of synechocystis sp. PCC6803. Biochemistry 2004; 43:5304-13. [PMID: 15122896 DOI: 10.1021/bi049836v] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sensor of blue-light using FAD (BLUF) domain is the flavin-binding fold categorized to a new class of blue-light sensing domain found in AppA from Rhodobacter sphaeroides and PAC from Euglena gracilis, but little is known concerning the mechanism of blue-light perception. An open reading frame slr1694 in a cyanobacterium Synechocystis sp. PCC6803 encodes a protein possessing the BLUF domain. Here, a full-length Slr1694 protein retaining FAD was expressed and purified and found to be present as an oligomeric form (trimer or tetramer). Using the purified Slr1694, spectroscopic properties of Slr1694 were characterized. Slr1694 was found to show the same red-shift of flavin absorption and quenching of flavin fluorescence by illumination as those of AppA. These changes reversed in the dark although the rate of dark state regeneration was much faster in Slr1694 than AppA, indicating that Slr1694 is a blue-light receptor based on BLUF with the similar photocycle to that of AppA. The dark decay in D(2)O was nearly four times slower than in H(2)O. Light-induced Fourier transform infrared (FTIR) difference spectroscopy was applied to examine the light-induced structure change of a chromophore and apo-protein with deuteration and universal (13)C and (15)N isotope labeling. The FTIR results indicate that light excitation induced distinct changes in the amide I modes of peptide backbone but relatively limited changes in flavin chromophore. Light excitation predominantly weakened the C(4)=O and C(2)=O bonding and strengthened the N1C10a and/or C4aN5 bonding, indicating formational changes of the isoalloxazine ring II and III of FAD but little formational change in the isoalloxazine ring I. The photocycle of the BLUF is unique in the sense that light excitation leads to the structural rearrangements of the protein moieties coupled with a minimum formational change of the chromophore.
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Affiliation(s)
- Shinji Masuda
- Laboratory for Photo-Biology (1), RIKEN Photodynamics Research Center, The Institute of Physical and Chemical Research, 519-1399 Aoba, Aramaki, Aoba, Sendai 980-0845, Japan
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Wille G, Ritter M, Friedemann R, Mäntele W, Hübner G. Redox-triggered FTIR difference spectra of FAD in aqueous solution and bound to flavoproteins. Biochemistry 2004; 42:14814-21. [PMID: 14674755 DOI: 10.1021/bi035219f] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavin adenine dinucleotide (FAD) and three different flavoproteins in aqueous solution were subjected to redox-triggered Fourier transform infrared difference spectroscopy. The acquired vibrational spectra show a great number of positive and negative peaks, pertaining to the oxidized and reduced state of the molecule, respectively. Density functional theory calculations on the B3LYP/6-31G(d) level were employed to assign several of the observed bands to vibrational modes of the isoalloxazine moiety of the flavin cofactor in both its oxidized and, for the first time, its reduced state. Prominent modes measured for oxidized FAD include nu(C(4)=O) and nu(C(2)=O) at 1716 and 1674 cm(-1), respectively, nu(C(4a)=N(5)) at 1580 cm(-1), and nu(C(10a)=N(1)) at 1548 cm(-1). Measured modes of the reduced form of FAD include nu(C(2)=O) at 1692 cm(-1), nu(C(4)=O) at 1634 cm(-1), and nu(C(4a)=C(10a)) at 1600 cm(-1). While the overall shape of the enzyme spectra is similar to the shape of the spectrum of free FAD, there are numerous differences in detail. In particular, the nu(C=N) modes of the flavin exhibit frequency shifts in the protein-bound form, most prominently for pyruvate oxidase where nu(C(10a)=N(1)) downshifts by 14 cm(-1) to 1534 cm(-1). The significance of this shift and a possible explanation in connection with the bent conformation of the flavin cofactor in this enzyme are discussed.
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Affiliation(s)
- Georg Wille
- Institut für Biochemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
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Abstract
Acyl-CoA dehydrogenases constitute a family of flavoproteins that catalyze the alpha,beta-dehydrogenation of fatty acid acyl-CoA conjugates. While they differ widely in their specificity, they share the same basic chemical mechanism of alpha,beta-dehydrogenation. Medium chain acyl-CoA dehydrogenase is probably the best-studied member of the class and serves as a model for the study of catalytic mechanisms. Based on medium chain acyl-CoA dehydrogenase we discuss the main factors that bring about catalysis, promote specificity and determine the selective transfer of electrons to electron transferring flavoprotein. The mechanism of alpha,beta-dehydrogenation is viewed as a process in which the substrate alphaC-H and betaC-H bonds are ruptured concertedly, the first hydrogen being removed by the active center base Glu376-COO- as an H+, the second being transferred as a hydride to the flavin N(5) position. Hereby the pKa of the substrate alphaC-H is lowered from > 20 to approximately 8 by the effect of specific hydrogen bonds. Concomitantly, the pKa of Glu376-COO- is also raised to 8-9 due to the decrease in polarity brought about by substrate binding. The kinetic sequence of medium chain acyl-CoA dehydrogenase is rather complex and involves several intermediates. A prominent one is the molecular complex of reduced enzyme with the enoyl-CoA product that is characterized by an intense charge transfer absorption and serves as the point of transfer of electrons to the electron transferring flavoprotein. These views are also discussed in the context of the accompanying paper on the three-dimensional properties of acyl-CoA dehydrogenases.
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Affiliation(s)
- Sandro Ghisla
- Department of Biology, University of Konstanz, Germany.
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He M, Burghardt TP, Vockley J. A novel approach to the characterization of substrate specificity in short/branched chain Acyl-CoA dehydrogenase. J Biol Chem 2003; 278:37974-86. [PMID: 12855692 DOI: 10.1074/jbc.m306882200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rat and human short/branched chain acyl-CoA dehydrogenases exhibit key differences in substrate specificity despite an overall amino acid identity of 85% between them. Rat short/branched chain acyl-CoA dehydrogenases (SBCAD) are more active toward substrates with longer carbon side chains than human SBCAD, whereas the human enzyme utilizes substrates with longer primary carbon chains. The mechanism underlying this difference in substrate specificity was investigated with a novel surface plasmon resonance assay combined with absorbance and circular dichroism spectroscopy, and kinetics analysis of wild type SBCADs and mutants with altered amino acid residues in the substrate binding pocket. Results show that a relatively few amino acid residues are critical for determining the difference in substrate specificity seen between the human and rat enzymes and that alteration of these residues influences different portions of the enzyme mechanism. Molecular modeling of the SBCAD structure suggests that position 104 at the bottom of the substrate binding pocket is important in determining the length of the primary carbon chain that can be accommodated. Conformational changes caused by alteration of residues at positions 105 and 177 directly affect the rate of electron transfer in the dehydrogenation reactions, and are likely transmitted from the bottom of the substrate binding pocket to beta-sheet 3. Differences between the rat and human enzyme at positions 383, 222, and 220 alter substrate specificity without affecting substrate binding. Modeling predicts that these residues combine to determine the distance between the flavin ring of FAD and the catalytic base, without changing the opening of the substrate binding pocket.
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Affiliation(s)
- Miao He
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota 55905, USA
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Kapetanaki S, Chouchane S, Girotto S, Yu S, Magliozzo RS, Schelvis JPM. Conformational differences in Mycobacterium tuberculosis catalase-peroxidase KatG and its S315T mutant revealed by resonance Raman spectroscopy. Biochemistry 2003; 42:3835-45. [PMID: 12667074 DOI: 10.1021/bi026992y] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
KatG from Mycobacterium tuberculosis is a heme-containing catalase-peroxidase, which belongs to the class I peroxidases and is important for activation of the prodrug isoniazid (INH), a front-line antituberculosis drug. In many clinical isolates, resistance to INH has been linked to mutations on the katG gene, and the most prevalent mutation, S315T, suggests that modification of the heme pocket has occurred. Electronic absorption and resonance Raman spectra of ferric wild-type (WT) KatG and its INH-resistant mutant KatG(S315T) at different pH values and their complexes with INH and benzohydroxamic acid (BHA) are reported. At neutral pH, a quantum mechanically mixed spin state (QS) is revealed, which coexists with five-coordinate and six-coordinate high-spin hemes in WT KatG. The QS heme is the major species in KatG(S315T). Addition of either INH or BHA to KatG induces only minor changes in the resonance Raman spectra, indicating that both compounds do not directly interact with the heme iron. New vibrational modes are observed at 430, 473, and 521 cm(-1), and these modes are indicative of a change in conformation in the KatG heme pocket. The intensity of these modes and the relative population of the QS heme are stable in KatG(S315T) but not in the WT enzyme. This indicates that there are differences in heme pocket stability between WT KatG and KatG(S315T). We will discuss the stabilization of the QS heme and propose a model for the inhibition of INH oxidation by KatG(S315T).
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Affiliation(s)
- Sofia Kapetanaki
- Department of Chemistry, New York University, 31 Washington Place, Room 1001, New York, New York 10003, USA
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Ataka K, Hegemann P, Heberle J. Vibrational spectroscopy of an algal Phot-LOV1 domain probes the molecular changes associated with blue-light reception. Biophys J 2003; 84:466-74. [PMID: 12524299 PMCID: PMC1302627 DOI: 10.1016/s0006-3495(03)74866-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The LOV1 domain of the blue light Phot1-receptor (phototropin homolog) from Chlamydomonas reinhardtii has been studied by vibrational spectroscopy. The FMN modes of the dark state of LOV1 were identified by preresonance Raman spectroscopy and assigned to molecular vibrations. By comparing the blue-light-induced FTIR difference spectrum with the preresonance Raman spectrum, most of the differences are due to FMN modes. Thus, we exclude large backbone changes of the protein that might occur during the phototransformation of the dark state LOV1-447 into the putative signaling state LOV1-390. Still, the presence of smaller amide difference bands cannot be excluded but may be masked by overlapping FMN modes. The band at 2567 cm(-1) is assigned to the S-H stretching vibration of C57, the residue that forms the transient thio-adduct with the chromophore FMN. The occurrence of this band is evidence that C57 is protonated in the dark state of LOV1. This result challenges conclusions from the homologous LOV2 domain from oat that the thiolate of the corresponding cysteine is the reactive species.
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Affiliation(s)
- K Ataka
- Forschungszentrum Jülich, IBI-2: Structural Biology, Germany
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20
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Römisch W, Eisenreich W, Richter G, Bacher A. Rapid one-pot synthesis of riboflavin isotopomers. J Org Chem 2002; 67:8890-4. [PMID: 12467404 DOI: 10.1021/jo026105x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flavocoenzymes labeled with stable isotopes are important reagents for the study of flavoproteins using isotope-sensitive methods such as NMR, ENDOR, infrared, and Raman spectroscopy. We describe highly versatile one-pot methods for the preparation of riboflavin isotopomers labeled with (13)C in every desired position of the xylene moiety. The starting materials are commercially available (13)C-labeled glucose samples, which are converted into riboflavin using enzymes of the oxidative pentose phosphate pathway in combination with recombinant enzymes of the riboflavin biosynthetic pathway. The overall reaction comprises six enzyme-catalyzed reaction steps for the synthesis of the vitamin and two auxiliary enzymes for in situ recycling of cofactors. The overall yields of riboflavin based on isotope-labeled glucose are 35-50%.
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Affiliation(s)
- Werner Römisch
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
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21
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Miura R. Versatility and specificity in flavoenzymes: control mechanisms of flavin reactivity. CHEM REC 2002; 1:183-94. [PMID: 11895118 DOI: 10.1002/tcr.1007] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Flavoenzymes are characterized by their remarkable versatility and strict specificity. The former can be grasped when flavoenzymes are treated as a whole, while the latter refers to each flavoenzyme in which the broad versatility of flavin is specifically controlled. The versatility stems from the variety of the redox, ionic, and electronic states that the flavin ring system can adopt. Versatility of flavoenzymes is reflected in their classification, which has generally been based on substrates and reactions catalyzed. A different classification is presented according to the number of electrons transferred in the reductive and oxidative half reactions. Specificity of each flavoenzyme is understood in terms of the regulatory mechanism of the broad reactive potentiality of flavin. The elements of this regulatory mechanism include hydrogen-bonding network, electrostatic effect, charge-transfer interaction, positioning between a substrate/ligand and flavin, and modulation of resonance hybridization, each of which is explained with relevant examples provided mainly by studies from the author's group.
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Affiliation(s)
- R Miura
- Department of Biochemistry, Kumamoto University School of Medicine, Japan.
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Pollegioni L, Porrini D, Molla G, Pilone MS. Redox potentials and their pH dependence of D-amino-acid oxidase of Rhodotorula gracilis and Trigonopsis variabilis. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:6624-32. [PMID: 11054115 DOI: 10.1046/j.1432-1327.2000.01757.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The redox potentials and pH characteristics of D-amino-acid oxidase (EC 1.4.3.3; DAAO) from the yeast Rhodotorula gracilis and Trigonopsis variabilis were measured in the pH range 6.5-8.5 at 15 degrees C. In the free enzyme form, the anionic red semiquinone is quantitatively formed in both DAAOs, indicating that a two single-electron transfer mechanism is active. The semiquinone species is also thermodynamically stable, as indicated by the large separation of the single-electron transfer potentials. The first electron potential is pH-independent, while the second electron transfer is pH-dependent exhibiting a approximately -60 mV/pH unit slope, consistent with a one-electron/one-proton transfer. In the presence of the substrate analogue benzoate, the two-electron transfer is the thermodynamically favoured process for both DAAOs, with only a quantitative difference in the stabilization of the anionic semiquinone. Clearly binding of the substrate (or substrate analogue) modulates the redox properties of the two enzymes. In both cases, in the presence and absence of benzoate, the slope of Em vs. pH (-30 mV/pH unit) corresponds to an overall two-electron/one-proton transfer in the reduction to yield the anionic reduced flavin. This behaviour is similar to that reported for DAAO from pig kidney. The differences in potentials and the stability of the semiquinone intermediate measured for the three DAAOs probably stem from different isoalloxazine environments. In the case of R. gracilis DAAO, the low stability of the semiquinone form in the DAAO-benzoate complex can be explained by the shift in position of the side chain of Arg285 following substrate analogue binding.
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Affiliation(s)
- L Pollegioni
- Department of Structural and Functional Biology, University of Insubria, Varese, Italy
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