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Golczak A, Prukała D, Sikorska E, Gierszewski M, Cherkas V, Kwiatek D, Kubiak A, Varma N, Pędziński T, Murphree S, Cibulka R, Mrówczyńska L, Kolanowski JL, Sikorski M. Tetramethylalloxazines as efficient singlet oxygen photosensitizers and potential redox-sensitive agents. Sci Rep 2023; 13:13426. [PMID: 37591918 PMCID: PMC10435492 DOI: 10.1038/s41598-023-40536-4] [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: 06/23/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023] Open
Abstract
Tetramethylalloxazines (TMeAll) have been found to have a high quantum yield of singlet oxygen generation when used as photosensitizers. Their electronic structure and transition energies (S0 → Si, S0 → Ti, T1 → Ti) were calculated using DFT and TD-DFT methods and compared to experimental absorption spectra. Generally, TMeAll display an energy diagram similar to other derivatives belonging to the alloxazine class of compounds, namely π,π* transitions are accompanied by closely located n,π* transitions. Photophysical data such as quantum yields of fluorescence, fluorescence lifetimes, and nonradiative rate constants were also studied in methanol (MeOH), acetonitrile (ACN), and 1,2-dichloroethane (DCE). The transient absorption spectra were also analyzed. To assess cytotoxicity of new compounds, a hemolytic assay was performed using human red blood cells (RBC) in vitro. Subsequently, fluorescence lifetime imaging experiments (FLIM) were performed on RBC under physiological and oxidative stress conditions alone or in the presence of TMeAll allowing for pinpointing changes caused by those compounds on the intracellular environment of these cells.
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Affiliation(s)
- Anna Golczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Dorota Prukała
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Ewa Sikorska
- Poznań University of Economics and Business, Al. Niepodległości 10, 61-875, Poznan, Poland
| | - Mateusz Gierszewski
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614, Poznan, Poland
| | - Volodymyr Cherkas
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Dorota Kwiatek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Adam Kubiak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Naisargi Varma
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Tomasz Pędziński
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Shaun Murphree
- Department of Chemistry, Allegheny College, 520 N. Main Street, Meadville, PA, USA
| | - Radek Cibulka
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628, Prague 6, Czech Republic.
| | - Lucyna Mrówczyńska
- Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
| | - Jacek Lukasz Kolanowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Marek Sikorski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland.
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2
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Abstract
Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked in arms races with the hosts. Here, we discuss a simple functional logic to explain virus macroevolution that appears to define the course of virus evolution. A small core of virus hallmark genes that are responsible for genome replication apparently descended from primordial replicators, whereas most virus genes, starting with those encoding capsid proteins, were subsequently acquired from hosts. The oldest of these acquisitions antedate the last universal cellular ancestor (LUCA). Host gene capture followed two major routes: convergent recruitment of genes with functions that directly benefit virus reproduction and exaptation when host proteins are repurposed for unique virus functions. These forms of host protein recruitment by viruses result in different levels of similarity between virus and host homologs, with the exapted ones often changing beyond easy recognition.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Valerian V Dolja
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015 Paris, France.
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3
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Ghosh S, Puranik M. Initial Excited State Dynamics of Lumichrome upon Ultraviolet Excitation. Photochem Photobiol 2022; 98:1270-1283. [PMID: 35380739 DOI: 10.1111/php.13631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
Lumichrome (LC) is the major photodegradation product of biologically important flavin cofactors. Since LC serves as a structural comparison to the flavins; understanding excited states of LC is fundamentally important to establish a connection with photophysics of different flavins, such as lumiflavin (LF), riboflavin (RF), flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Herein, we deduce the initial excited state structural dynamics of LC using UV resonance Raman (UVRR) intensity analysis. The UVRR spectra at wavelengths across the 260 nm absorption band of LC were measured and resulting Raman excitation profiles and absorption spectrum were self consistently simulated using a time-dependent wave packet formalism to extract the initial excited state structural and solvent broadening parameters. These results are compared with those obtained for other flavins following UV excitations. We find that LC undergoes a very distinct instantaneous charge redistribution than flavins, which is attributed to the extended π-conjugation present in flavins but missing in LC. The homogeneous broadening linewidth of LC appears to be lower than that of LF, while the inhomogeneous broadening values are comparable, indicating greater solvent interaction with excited flavin on ultrafast timescale compared to LC, whereas on longer timescale these interactions are almost similar.
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Affiliation(s)
- Sudeb Ghosh
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411 008, India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411 008, India
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4
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Weidenbach K, Gutt M, Cassidy L, Chibani C, Schmitz RA. Small Proteins in Archaea, a Mainly Unexplored World. J Bacteriol 2022; 204:e0031321. [PMID: 34543104 PMCID: PMC8765429 DOI: 10.1128/jb.00313-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.
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Affiliation(s)
- Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Cynthia Chibani
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
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5
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van Galen C, Barnard DT, Stanley RJ. Stark Spectroscopy of Lumichrome: A Possible Candidate for Stand-Off Detection of Bacterial Quorum Sensing. J Phys Chem B 2020; 124:11835-11842. [PMID: 33325706 DOI: 10.1021/acs.jpcb.0c09498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Lumichrome (7,8-dimethylalloxazine, LC) is a natural photodegradation product and catabolite of flavin coenzymes. Although not a coenzyme itself, LC is used for biosignaling in plants and single-celled organisms, including quorum sensing in the formation of biofilms. The noninvasive detection of in vivo lumichrome would be useful for monitoring this signaling event. For molecules that undergo significant charge redistribution upon light excitation (e.g., intramolecular charge transfer), there are optical detection methods (e.g., second-harmonic generation) that would be well suited to this task. Here, we have used Stark spectroscopy to measure the extent and direction of charge redistribution in photoexcited LC. Stark and low-temperature absorption spectra were obtained at 77 K on LC in ethanol glasses and analyzed using the Liptay analysis to obtain the difference dipole moments and polarizabilities. These data were complemented by a computational analysis of the excited states using density functional theory (DFT) at the TD-B3LYP/6-311+G(2d,p) level of theory.
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Affiliation(s)
- Cornelius van Galen
- Department of Chemistry, Temple University, 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - David T Barnard
- Department of Chemistry, Temple University, 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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6
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Cauduro GP, Leal AL, Lopes TF, Marmitt M, Valiati VH. Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us? Int J Microbiol 2020; 2020:8831331. [PMID: 32908529 PMCID: PMC7474390 DOI: 10.1155/2020/8831331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/04/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022] Open
Abstract
Petroleum is the major energy matrix in the world whose refining generates chemical byproducts that may damage the environment. Among such waste, polycyclic aromatic hydrocarbons (PAH) are considered persistent pollutants. Sixteen of these are considered priority for remediation, and among them is benzo(a)pyrene. Amid remediation techniques, bioremediation stands out. The genus Burkholderia is amongst the microorganisms known for being capable of degrading persistent compounds; its strains are used as models to study such ability. High-throughput sequencing allows researchers to reach a wider knowledge about biodegradation by bacteria. Using transcripts and mRNA analysis, the genomic regions involved in this aptitude can be detected. To unravel these processes, we used the model B. vietnamiensis strain G4 in two experimental groups: one was exposed to benzo(a)pyrene and the other one (control) was not. Six transcriptomes were generated from each group aiming to compare gene expression and infer which genes are involved in degradation pathways. One hundred fifty-six genes were differentially expressed in the benzo(a)pyrene exposed group, from which 33% are involved in catalytic activity. Among these, the most significant genomic regions were phenylacetic acid degradation protein paaN, involved in the degradation of organic compounds to obtain energy; oxidoreductase FAD-binding subunit, related to the regulation of electrons within groups of dioxygenase enzymes with potential to cleave benzene rings; and dehydrogenase, described as accountable for phenol degradation. These data provide the basis for understanding the bioremediation of benzo(a)pyrene and the possible applications of this strain in polluted environments.
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Affiliation(s)
| | - Ana Lusia Leal
- Companhia Riograndense de Saneamento, Biology Laboratory, Triunfo, RS, Brazil
| | - Tiago Falcón Lopes
- Centro de Terapia Gênica, Centro de Pesquisa Experimental, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Marcela Marmitt
- Universidade do Vale do Rio dos Sinos, Biology Graduate Program, São Leopoldo, RS, Brazil
| | - Victor Hugo Valiati
- Universidade do Vale do Rio dos Sinos, Biology Graduate Program, São Leopoldo, RS, Brazil
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7
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Bourdeaux F, Kopp Y, Lautenschläger J, Gößner I, Besir H, Vabulas RM, Grininger M. Dodecin as carrier protein for immunizations and bioengineering applications. Sci Rep 2020; 10:13297. [PMID: 32764653 PMCID: PMC7414021 DOI: 10.1038/s41598-020-69990-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022] Open
Abstract
In bioengineering, scaffold proteins have been increasingly used to recruit molecules to parts of a cell, or to enhance the efficacy of biosynthetic or signalling pathways. For example, scaffolds can be used to make weak or non-immunogenic small molecules immunogenic by attaching them to the scaffold, in this role called carrier. Here, we present the dodecin from Mycobacterium tuberculosis (mtDod) as a new scaffold protein. MtDod is a homododecameric complex of spherical shape, high stability and robust assembly, which allows the attachment of cargo at its surface. We show that mtDod, either directly loaded with cargo or equipped with domains for non-covalent and covalent loading of cargo, can be produced recombinantly in high quantity and quality in Escherichia coli. Fusions of mtDod with proteins of up to four times the size of mtDod, e.g. with monomeric superfolder green fluorescent protein creating a 437 kDa large dodecamer, were successfully purified, showing mtDod's ability to function as recruitment hub. Further, mtDod equipped with SYNZIP and SpyCatcher domains for post-translational recruitment of cargo was prepared of which the mtDod/SpyCatcher system proved to be particularly useful. In a case study, we finally show that mtDod-peptide fusions allow producing antibodies against human heat shock proteins and the C-terminus of heat shock cognate 70 interacting protein (CHIP).
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Affiliation(s)
- Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Yannick Kopp
- Institute of Biophysical Chemistry, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Lauer Str. 15, 60438, Frankfurt am Main, Germany
| | - Julia Lautenschläger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Ines Gößner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Hüseyin Besir
- European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- PROGEN Biotechnik GmbH, 69123, Heidelberg, Germany
| | - R Martin Vabulas
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
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8
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Abstract
The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.
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9
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Duan HD, Mohamed-Raseek N, Miller AF. Spectroscopic evidence for direct flavin-flavin contact in a bifurcating electron transfer flavoprotein. J Biol Chem 2020; 295:12618-12634. [PMID: 32661195 DOI: 10.1074/jbc.ra120.013174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
A remarkable charge transfer (CT) band is described in the bifurcating electron transfer flavoprotein (Bf-ETF) from Rhodopseudomonas palustris (RpaETF). RpaETF contains two FADs that play contrasting roles in electron bifurcation. The Bf-FAD accepts electrons pairwise from NADH, directs one to a lower-reduction midpoint potential (E°) carrier, and the other to the higher-E° electron transfer FAD (ET-FAD). Previous work noted that a CT band at 726 nm formed when ET-FAD was reduced and Bf-FAD was oxidized, suggesting that both flavins participate. However, existing crystal structures place them too far apart to interact directly. We present biochemical experiments addressing this conundrum and elucidating the nature of this CT species. We observed that RpaETF missing either FAD lacked the 726 nm band. Site-directed mutagenesis near either FAD produced altered yields of the CT species, supporting involvement of both flavins. The residue substitutions did not alter the absorption maximum of the signal, ruling out contributions from residue orbitals. Instead, we propose that the residue identities modulate the population of a protein conformation that brings the ET-flavin and Bf-flavin into direct contact, explaining the 726 nm band based on a CT complex of reduced ET-FAD and oxidized Bf-FAD. This is corroborated by persistence of the 726 nm species during gentle protein denaturation and simple density functional theory calculations of flavin dimers. Although such a CT complex has been demonstrated for free flavins, this is the first observation of such, to our knowledge, in an enzyme. Thus, Bf-ETFs may optimize electron transfer efficiency by enabling direct flavin-flavin contact.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
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10
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Paithankar KS, Enderle M, Wirthensohn DC, Miller A, Schlesner M, Pfeiffer F, Rittner A, Grininger M, Oesterhelt D. Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation. Acta Crystallogr F Struct Biol Commun 2019; 75:576-585. [PMID: 31475924 PMCID: PMC6718144 DOI: 10.1107/s2053230x19010896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/04/2019] [Indexed: 12/15/2022] Open
Abstract
Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.
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Affiliation(s)
- Karthik Shivaji Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Mathias Enderle
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - David C. Wirthensohn
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Arthur Miller
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Schlesner
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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11
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Brisker-Klaiman D, Dreuw A. On the influence of dimerisation of lumiflavin in aqueous solution on its optical spectra – a quantum chemical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1616843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Daria Brisker-Klaiman
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
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12
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Krantz GP, Lucas K, Wunderlich EL, Hoang LT, Avci R, Siuzdak G, Fields MW. Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm. BIOFOULING 2019; 35:669-683. [PMID: 31402749 DOI: 10.1080/08927014.2019.1646731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 07/11/2019] [Accepted: 07/14/2019] [Indexed: 06/10/2023]
Abstract
Desulfovibrio alaskensis G20 biofilms were cultivated on 316 steel, 1018 steel, or borosilicate glass under steady-state conditions in electron-acceptor limiting (EAL) and electron-donor limiting (EDL) conditions with lactate and sulfate in a defined medium. Increased corrosion was observed on 1018 steel under EDL conditions compared to 316 steel, and biofilms on 1018 carbon steel under the EDL condition had at least twofold higher corrosion rates compared to the EAL condition. Protecting the 1018 metal coupon from biofilm colonization significantly reduced corrosion, suggesting that the corrosion mechanism was enhanced through attachment between the material and the biofilm. Metabolomic mass spectrometry analyses demonstrated an increase in a flavin-like molecule under the 1018 EDL condition and sulfonates under the 1018 EAL condition. These data indicate the importance of S-cycling under the EAL condition, and that the EDL is associated with increased biocorrosion via indirect extracellular electron transfer mediated by endogenously produced flavin-like molecules.
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Affiliation(s)
- Gregory P Krantz
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
| | - Kilean Lucas
- Image and Chemical Analysis Laboratory, Montana State University, Bozeman, USA
| | - Erica L- Wunderlich
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, USA
| | - Linh T Hoang
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, USA
| | - Recep Avci
- Image and Chemical Analysis Laboratory, Montana State University, Bozeman, USA
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, USA
- Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
- Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, USA
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13
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Atilho RM, Perkins KR, Breaker RR. Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity. RNA (NEW YORK, N.Y.) 2019; 25:23-34. [PMID: 30287481 PMCID: PMC6298564 DOI: 10.1261/rna.067975.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/02/2018] [Indexed: 05/10/2023]
Abstract
Many bacteria use flavin mononucleotide (FMN) riboswitches to control the expression of genes responsible for the biosynthesis and transport of this enzyme cofactor or its precursor, riboflavin. Rare variants of FMN riboswitches found in strains of Clostridium difficile and some other bacteria typically control the expression of proteins annotated as transporters, including multidrug efflux pumps. These RNAs no longer recognize FMN, and differ from the original riboswitch consensus sequence at nucleotide positions normally involved in binding of the ribityl and phosphate moieties of the cofactor. Representatives of one of the two variant subtypes were found to bind the FMN precursor riboflavin and the FMN degradation products lumiflavin and lumichrome. Although the biologically relevant ligand sensed by these variant FMN riboswitches remains uncertain, our findings suggest that many strains of C. difficile might use rare riboswitches to sense flavin degradation products and activate transporters for their detoxification.
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Affiliation(s)
- Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Kevin R Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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14
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Su Q, Vogt S, Nöll G. Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand-Apoprotein Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14738-14748. [PMID: 30005576 DOI: 10.1021/acs.langmuir.7b04347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work, the hybridization and dehybridization of ssDNA with 20 bases at gold coated sensor surfaces modified with complementary 20 bases capture probe ssDNA was investigated at 18 °C by quartz crystal microbalance measurements with dissipation monitoring (QCM-D). A sequence of 20 base pairs with a melting temperature of about 64 °C was chosen, since in many biosensor studies the target molecules are DNA or RNA oligomers of similar length. It turned out that at the applied experimental conditions the DNA hybridization was irreversible, and therefore the hybridization and dehybridization process could not be described by the Langmuir model of adsorption. Nevertheless, quantitative dehybridization could be achieved by rinsing the sensor surface thoroughly with pure water. When in contrast the hybridization of a target with only 10 bases complementary to the outermost 10 bases of the 20 bases capture probe was studied, binding and unbinding were reversible, and the hybridization/dehybridization process could be satisfactorily described by the Langmuir model. For the 10 base pair sequence, the melting temperature was about 36 °C. Apparently, for Langmuir behavior, it is important that the experiments are applied at a temperature sufficiently close to the melting temperature of the sequence under investigation to ensure that at least traces of the target molecules are unhybridized (i.e., there needs to be an equilibrium between hybridized and dehybridized target molecules). To validate the reliability of our experimental approach we also studied the reconstitution and disassembly of the flavoprotein dodecin at flavin-terminated DNA monolayers, as according to previous studies it is assumed that the apododecin-flavin system can be well described by the Langmuir model. As a result, this assumption could be verified. Using three different approaches, KD values were obtained that differ not more than by a factor of 4.
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Affiliation(s)
- Qiang Su
- Organic Chemistry, Chem. Biol. Dept., Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Stephan Vogt
- Organic Chemistry, Chem. Biol. Dept., Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Gilbert Nöll
- Organic Chemistry, Chem. Biol. Dept., Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
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Rudroff F. Whole-cell based synthetic enzyme cascades-light and shadow of a promising technology. Curr Opin Chem Biol 2018; 49:84-90. [PMID: 30458384 DOI: 10.1016/j.cbpa.2018.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023]
Abstract
Mimicking Nature by biocatalytic cascade reactions in a whole-cell environment is a revolutionary development in multistep synthesis for the production of bulk and fine chemicals. In the past decade, several proof of concept success stories demonstrated the power of those synthetic cascades and paved the road for future industrial applications. Although enzymes and their promiscuity are best suited to construct such artificial pathways, the complexity and the lack of understanding of the cellular machinery slowed down this progress significantly. In this review, recent achievements in the field of whole-cell biocatalysis are described, challenges and hidden traps that have to be overcome are depicted, and strategies are illustrated how to increase overall cascade productivity.
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Affiliation(s)
- Florian Rudroff
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 163-OC, 1060 Vienna, Austria.
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16
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Nöll T, Wenderhold-Reeb S, Bourdeaux F, Paululat T, Nöll G. Diffusion-Ordered NMR Spectroscopy of Guest Molecules in DNA Hydrogels and Related Matrices. ChemistrySelect 2018. [DOI: 10.1002/slct.201802364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tanja Nöll
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie; Universität Siegen, Fakultät IV; Department für Chemie und Biologie; Adolf-Reichwein-Strasse 2 57076 Siegen Germany
| | - Sabine Wenderhold-Reeb
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie; Universität Siegen, Fakultät IV; Department für Chemie und Biologie; Adolf-Reichwein-Strasse 2 57076 Siegen Germany
| | - Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences; Goethe University Frankfurt; Max-von-Laue-Str. 15 60438 Frankfurt am Main Germany
| | - Thomas Paululat
- Organische Chemie; Universität Siegen, Fakultät IV; Department für Chemie und Biologie; Adolf-Reichwein-Strasse 2 57076 Siegen Germany
| | - Gilbert Nöll
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie; Universität Siegen, Fakultät IV; Department für Chemie und Biologie; Adolf-Reichwein-Strasse 2 57076 Siegen Germany
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17
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Bourdeaux F, Hammer CA, Vogt S, Schweighöfer F, Nöll G, Wachtveitl J, Grininger M. Flavin Storage and Sequestration by Mycobacterium tuberculosis Dodecin. ACS Infect Dis 2018; 4:1082-1092. [PMID: 29608272 DOI: 10.1021/acsinfecdis.7b00237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dodecins are small flavin binding proteins occurring in archaea and bacteria. They are remarkable for binding dimers of flavins with their functional relevant aromatic isoalloxazine rings deeply covered. Bacterial dodecins are widely spread and found in a large variety of pathogens, among them Pseudomonas aeruginosa, Streptococcus pneumonia, Ralstonia solanacearum, and Mycobacterium tuberculosis ( M. tuberculosis). In this work, we seek to understand the function of dodecins from M. tuberculosis dodecin. We describe flavin binding in thermodynamic and kinetic properties and achieve mechanistic insight in dodecin function by applying spectroscopic and electrochemical methods. Intriguingly, we reveal a significant pH dependence in the affinity and specificity of flavin binding. Our data give insight in M. tuberculosis dodecin function and advance the current understanding of dodecins as flavin storage and sequestering proteins. We suggest that the dodecin in M. tuberculosis may specifically be important for flavin homeostasis during the elaborate lifestyle of this organism, which calls for the evaluation of this protein as drug target.
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Affiliation(s)
- Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Christopher A. Hammer
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Stephan Vogt
- Nöll Junior Research Group, Organic Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Felix Schweighöfer
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Gilbert Nöll
- Nöll Junior Research Group, Organic Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
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18
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Scheurer M, Brisker-Klaiman D, Dreuw A. Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg 2+-Promoted Proton Transfer. J Phys Chem B 2017; 121:10457-10466. [PMID: 29069901 DOI: 10.1021/acs.jpcb.7b08597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced biochemical reactions are ubiquitously governed by derivatives of flavin, which is a key player in a manifold of cellular redox reactions. The photoreactivity of flavins is also one of their greatest disadvantages as the molecules are sensitive to photodegradation. To prevent this unfavorable reaction, UV-light-exposed archaea bacteria, such as Halobacterium salinarum, manage the task of protecting flavin derivatives by dodecin, a protein which stores flavins and efficiently photoprotects them. In this study, we shed light on the photoprotection mechanism, i.e., the excited state quenching mechanism by dodecin using computational methodology. Molecular dynamics (MD) simulations unraveled the hydrogen bond network in the flavin binding pocket as a starting point for proton transfer upon preceding electron transfer. Using high-level ab initio quantum chemical methods, different proton transfer channels have been investigated and an energetically feasible Mg2+-promoted channel has been identified fully explaining previous experimental observations. This is the first extensive theoretical study of archaeal dodecin, furthering the understanding of its photocycle and manipulation.
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Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Daria Brisker-Klaiman
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
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Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel. Appl Environ Microbiol 2017; 83:AEM.03249-16. [PMID: 28314727 DOI: 10.1128/aem.03249-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/06/2017] [Indexed: 02/03/2023] Open
Abstract
Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have various degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons, while P. aeruginosa strain PAO1, a human pathogen, is less adapted and degrades jet fuel at a lower rate than does ATCC 33988. We investigated fuel-specific transcriptomic differences between these strains in order to ascertain the underlying mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat shock response, membrane proteins, efflux pumps, and several novel genes were upregulated in ATCC 33988. Overexpression of alk genes in PAO1 provided some improvement in growth, but it was not as robust as that of ATCC 33988, suggesting the role of other genes in adaptation. Expression of the function unknown gene PA5359 from ATCC 33988 in PAO1 increased the growth in fuel. Bioinformatic analysis revealed that PA5359 is a predicted lipoprotein with a conserved Yx(FWY)xxD motif, which is shared among bacterial adhesins. Overexpression of the putative resistance-nodulation-division (RND) efflux pump PA3521 to PA3523 increased the growth of the ATCC 33988 strain, suggesting a possible role in fuel tolerance. Interestingly, the PAO1 strain cannot utilize n-C8 and n-C10 The expression of green fluorescent protein (GFP) under the control of alkB promoters confirmed that alk gene promoter polymorphism affects the expression of alk genes. Promoter fusion assays further confirmed that the regulation of alk genes was different in the two strains. Protein sequence analysis showed low amino acid differences for many of the upregulated genes, further supporting transcriptional control as the main mechanism for enhanced adaptation.IMPORTANCE These results support that specific signal transduction, gene regulation, and coordination of multiple biological responses are required to improve the survival, growth, and metabolism of fuel in adapted strains. This study provides new insight into the mechanistic differences between strains and helpful information that may be applied in the improvement of bacterial strains for resistance to biotic and abiotic factors encountered during bioremediation and industrial biotechnological processes.
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20
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Vogt S, Wenderhold-Reeb S, Nöll G. Reversible assembly of protein-DNA nanostructures triggered by mediated electron transfer. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.02.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Sánchez CG, Su Q, Wenderhold-Reeb S, Nöll G. Nanomechanical properties of protein-DNA layers with different oligonucleotide tethers. RSC Adv 2016; 6:56467-56474. [PMID: 28066548 PMCID: PMC5171221 DOI: 10.1039/c6ra10090b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/05/2016] [Indexed: 12/23/2022] Open
Abstract
The length and flexibility of the oligonucleotide tethers strongly affect the viscoelastic properties of the resulting protein–DNA layers.
The multi-ligand binding flavoprotein dodecin is reconstituted on top of flavin-terminated oligonucleotide monolayers. A detailed quartz crystal microbalance with a dissipation monitoring (QCM-D) study showing how the length and flexibility of the oligonucleotide tethers influence the stability and the viscoelastic properties of the resulting DNA–protein layers is presented. Relatively dense protein layers can be obtained, if the length of the tethers is in the same range as the diameter of dodecin. When significantly longer tethers are used, less dense layers are formed. When rather short tethers are used, the reaching area of individual tethers is too low to capture single apododecin molecules cooperatively, and the formation of stable and dense protein layers is not possible. On top of the DNA–dodecin layers additional flavin–DNA ligands may be captured to form sandwich-type DNA–protein–DNA layers. Differences in the binding and unbinding behavior of flavin-dsDNA and flavin-ssDNA ligands are measured by QCM-D and surface plasmon fluorescence spectroscopy (SPFS). Both type of ligands show relatively low kon values, which might be explained by the structural rigidity of the binding pockets allowing a ligand to enter only when it approaches precisely in the right orientation. Apparently apododecin–flavin binding follows Fischer's classic lock-and-key binding model.
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Affiliation(s)
- Cristina Gutiérrez Sánchez
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
| | - Qiang Su
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
| | - Sabine Wenderhold-Reeb
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
| | - Gilbert Nöll
- Nöll Junior Research Group , Organic Chemistry , Chem. Biol. Dept. , Faculty IV , Siegen University , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany .
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22
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Gutiérrez Sánchez C, Su Q, Schönherr H, Grininger M, Nöll G. Multi-Ligand-Binding Flavoprotein Dodecin as a Key Element for Reversible Surface Modification in Nano-biotechnology. ACS NANO 2015; 9:3491-3500. [PMID: 25738566 DOI: 10.1021/nn506993s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper the multiple (re)programming of protein-DNA nanostructures comprising generation, deletion, and reprogramming on the same flavin-DNA-modified surface is introduced. This work is based on a systematic study of the binding affinity of the multi-ligand-binding flavoprotein dodecin on flavin-terminated DNA monolayers by surface plasmon resonance and quartz crystal microbalance with dissipation (QCM-D) measurements, surface plasmon fluorescence spectroscopy (SPFS), and dynamic AFM force spectroscopy. Depending on the flavin surface coverage, a single apododecin is captured by one or more surface-immobilized flavins. The corresponding complex binding and unbinding rate constants kon(QCM) = 7.7 × 10(3) M(-1)·s(-1) and koff(QCM) = 4.5 × 10(-3) s(-1) (Kd(QCM) = 580 nM) were determined by QCM and were found to be in agreement with values for koff determined by SPFS and force spectroscopy. Even though a single apododecin-flavin bond is relatively weak, stable dodecin monolayers were formed on flavin-DNA-modified surfaces at high flavin surface coverage due to multivalent interactions between apododecin bearing six binding pockets and the surface-bound flavin-DNA ligands. If bi- or multivalent flavin ligands are adsorbed on dodecin monolayers, stable sandwich-type surface-DNA-flavin-apododecin-flavin ligand arrays are obtained. Nevertheless, the apododecin flavin complex is easily and quantitatively disassembled by flavin reduction. Binding and release of apododecin are reversible processes, which can be carried out alternatingly several times to release one type of ligand by an external redox trigger and subsequently replace it with a different ligand. Hence the versatile concept of reprogrammable functional biointerfaces with the multi-ligand-binding flavoprotein dodecin is demonstrated.
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Affiliation(s)
| | | | | | - Martin Grininger
- ∥Goethe University Frankfurt, Riedberg Campus FMLS Building, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
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Jobichen C, Swaminathan K. Molecular replacement with a large number of molecules in the asymmetric unit. Acta Crystallogr F Struct Biol Commun 2014; 70:1296-302. [PMID: 25195913 PMCID: PMC4157440 DOI: 10.1107/s2053230x14014381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 06/18/2014] [Indexed: 11/11/2022] Open
Abstract
The exponential increase in protein structures deposited in the Protein Data Bank (PDB) has resulted in the elucidation of most, if not all, protein folds, thus making molecular replacement (MR) the most frequently used method for structure determination. A survey of the PDB shows that most of the structures determined by molecular replacement contain less than ten molecules in the asymmetric unit and that it is predominantly virus and ribosome structures that contain more than 20 molecules in the asymmetric unit. While the success of the MR method depends on several factors, such as the homology and the size of an input model, it is also a well known fact that this method can become significantly difficult in cases with a large number of molecules in the asymmetric unit, higher crystallographic symmetry and tight packing. In this paper, five representative structures containing 16-18 homomeric molecules in the asymmetric unit and the strategies that have been used to solve these structures are described. The difficulties faced and the lessons learned from these structure-determination efforts will be useful for selected and similar future situations with a large number of molecules in the asymmetric unit.
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Affiliation(s)
- Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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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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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Directed manipulation of a flavoprotein photocycle. Angew Chem Int Ed Engl 2013; 52:8463-6. [PMID: 23818044 DOI: 10.1002/anie.201302334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Heike Staudt
- Institut für Physikalische and Theoretische Chemie, Exzellenzcluster Makromolekulare Komplexe, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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26
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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Gerichtete Manipulation des Photozyklus eines Flavoproteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Yu Y, Heidel B, Parapugna TL, Wenderhold-Reeb S, Song B, Schönherr H, Grininger M, Nöll G. Das Flavoprotein Dodecin als redoxaktive Sonde für Elektronentransfer durch DNA. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Yu Y, Heidel B, Parapugna TL, Wenderhold-Reeb S, Song B, Schönherr H, Grininger M, Nöll G. The flavoprotein dodecin as a redox probe for electron transfer through DNA. Angew Chem Int Ed Engl 2013; 52:4950-3. [PMID: 23532984 PMCID: PMC3743158 DOI: 10.1002/anie.201208987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 11/18/2022]
Affiliation(s)
- Yaming Yu
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Björn Heidel
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Tamara Lourdes Parapugna
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Sabine Wenderhold-Reeb
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Bo Song
- Physikalische Chemie I, Universität Siegen, Fakultät IV, Department für Chemie und BiologieAdolf-Reichwein-Strasse 2, 57076 Siegen (Germany)
| | - Holger Schönherr
- Physikalische Chemie I, Universität Siegen, Fakultät IV, Department für Chemie und BiologieAdolf-Reichwein-Strasse 2, 57076 Siegen (Germany)
| | - Martin Grininger
- Institut für Organische Chemie und Chemische Biologie, Buchmann Institut für Molekulare Lebenswissenschaften, Cluster of Excellence “Macromolecular Complexes”, Goethe Universität FrankfurtMax-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany)
| | - Gilbert Nöll
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
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Metabolite damage and its repair or pre-emption. Nat Chem Biol 2013; 9:72-80. [PMID: 23334546 DOI: 10.1038/nchembio.1141] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 11/13/2012] [Indexed: 01/25/2023]
Abstract
It is increasingly evident that metabolites suffer various kinds of damage, that such damage happens in all organisms and that cells have dedicated systems for damage repair and containment. First, chemical biology is demonstrating that diverse metabolites are damaged by side reactions of 'promiscuous' enzymes or by spontaneous chemical reactions, that the products are useless or toxic and that the unchecked buildup of these products can be devastating. Second, genetic and genomic evidence from prokaryotes and eukaryotes is implicating a network of new, conserved enzymes that repair damaged metabolites or somehow pre-empt damage. Metabolite (that is, small-molecule) repair is analogous to macromolecule (DNA and protein) repair and seems from comparative genomic evidence to be equally widespread. Comparative genomics also implies that metabolite repair could be the function of many conserved protein families lacking known activities. How--and how well--cells deal with metabolite damage affects fields ranging from medical genetics to metabolic engineering.
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Staudt H, Oesterhelt D, Grininger M, Wachtveitl J. Ultrafast excited-state deactivation of flavins bound to dodecin. J Biol Chem 2012; 287:17637-17644. [PMID: 22451648 DOI: 10.1074/jbc.m111.331652] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dodecins, a group of flavin-binding proteins with a dodecameric quaternary structure, are able to incorporate two flavins within each of their six identical binding pockets building an aromatic tetrade with two tryptophan residues. Dodecin from the archaeal Halobacterium salinarum is a riboflavin storage device. We demonstrate that unwanted side reactions induced by reactive riboflavin species and degradation of riboflavin are avoided by ultrafast depopulation of the reactive excited state of riboflavin. Intriguingly, in this process, the staggered riboflavin dimers do not interact in ground and photoexcited states. Rather, within the tetrade assembly, each riboflavin is kept under the control of the respective adjacent tryptophan, which suggests that the stacked arrangement is a matter of optimizing the flavin load. We further identify an electron transfer in combination with a proton transfer as a central element of the effective excited state depopulation mechanism. Structural and functional comparisons of the archaeal dodecin with bacterial homologs reveal diverging evolution. Bacterial dodecins bind the flavin FMN instead of riboflavin and exhibit a clearly different binding pocket design with inverse incorporations of flavin dimers. The different adoption of flavin changes photochemical properties, making bacterial dodecin a comparably less efficient quencher of flavins. This supports a functional role different for bacterial and archaeal dodecins.
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Affiliation(s)
- Heike Staudt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Grininger
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
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31
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Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
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Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
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32
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Arockiasamy A, Aggarwal A, Savva CG, Holzenburg A, Sacchettini JC. Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium-binding site. Protein Sci 2011; 20:827-33. [PMID: 21370306 PMCID: PMC3125867 DOI: 10.1002/pro.607] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/01/2011] [Indexed: 01/07/2023]
Abstract
In eukaryotes, calcium-binding proteins play a pivotal role in diverse cellular processes, and recent findings suggest similar roles for bacterial proteins at different stages in their life cycle. Here, we report the crystal structure of calcium dodecin, Rv0379, from Mycobacterium tuberculosis with a dodecameric oligomeric assembly and a unique calcium-binding motif. Structure and sequence analysis were used to identify orthologs of Rv0379 with different ligand-binding specificity.
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Affiliation(s)
- Arulandu Arockiasamy
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTexas 77843-2128
| | - Anup Aggarwal
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTexas 77843-2128
| | - Christos G Savva
- Microscopy and Imaging Center and Department of Biology, Texas A&M University, Biological Sciences Building West, College StationTexas 77843-2257
| | - Andreas Holzenburg
- Microscopy and Imaging Center and Department of Biology, Texas A&M University, Biological Sciences Building West, College StationTexas 77843-2257
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTexas 77843-2128
- Center for Structural Biology, Institute of Biosciences and TechnologyHouston, Texas 77030
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33
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Liu F, Xiong J, Kumar S, Yang C, Ge S, Li S, Xia N, Swaminathan K. Structural and biophysical characterization of Mycobacterium tuberculosis dodecin Rv1498A. J Struct Biol 2011; 175:31-8. [PMID: 21539921 DOI: 10.1016/j.jsb.2011.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 10/18/2022]
Abstract
Dodecins (assembly of twelve monomers) are the smallest known flavoprotein with only 65-73 amino acids and are involved in binding and storage of flavins in archaea. Here we report the crystal structure of Rv1498A, a Mycobacterium tuberculosis dodecin. This bacterial dodecin structure is similar to that of other reported dodecins. Each monomer has a 3 stranded β-sheet and an α-helix perpendicular to it. This protein has polyextreme (halophilic and thermophilic) properties. Interestingly, positively and negatively charged residues aggregate separately and do not seem to contribute to thermophilic and halophilic stability. We have examined the interactions that stabilize the Rv1498A dodecamer by preparing selected point mutants that break salt bridges and hydrophobic contacts, thereby leading to collapse of the assembly.
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Affiliation(s)
- Fengxia Liu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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34
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Moyon NS, Mitra S. Fluorescence solvatochromism in lumichrome and excited-state tautomerization: a combined experimental and DFT study. J Phys Chem A 2011; 115:2456-64. [PMID: 21388154 DOI: 10.1021/jp1102687] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence solvatochromism of lumichrome (LC) was studied by steady-state and time-resolved fluorescence spectroscopy. The excited-state properties of LC do not show any correlation with solvent polarity, however, reasonably good correlation with solvent E(T)(30) parameter was observed. A quantitative estimation of contribution from different solvatochromic parameters, like solvent polarizability (π*), hydrogen bond donor (α), and hydrogen bond acceptor (β) ability of the solvent, was made using linear free energy relationship on the basis of Kamlet-Taft equation. The analysis reveals that hydrogen bond donating ability (acidity) of the solvent is the most important parameter that characterizes the excited-state behavior of lumichrome. Quantum mechanical calculations using density functional theory (DFT) were done to study the most stable structure and excited-state tautomerization process of LC toward the formation of isoalloxazines. Charge localization in the excited state and formation of hydrogen-bonded cluster through solvent hydrogen bond donation on the N10 atom of alloxazine moiety were predicted to be the key step toward this water-catalyzed tautomerization process.
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35
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Marchena M, Gil M, Martín C, Organero JA, Sanchez F, Douhal A. Stability and Photodynamics of Lumichrome Structures in Water at Different pHs and in Chemical and Biological Caging Media. J Phys Chem B 2011; 115:2424-35. [DOI: 10.1021/jp110134f] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Marchena
- Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Departamento de Quimica Fisica, Universidad de Castilla-La Mancha, Avenida Carlos III, S.N. 45071 Toledo, Spain
- Facultad de Quimica, Departamento de Quimica Fisica, Universidad de Sevilla, Calle Profesor Garcia Gonzalez, S.N. 41012 Sevilla, Spain
| | - Michał Gil
- Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Departamento de Quimica Fisica, Universidad de Castilla-La Mancha, Avenida Carlos III, S.N. 45071 Toledo, Spain
| | - Cristina Martín
- Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Departamento de Quimica Fisica, Universidad de Castilla-La Mancha, Avenida Carlos III, S.N. 45071 Toledo, Spain
| | - Juan Angel Organero
- Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Departamento de Quimica Fisica, Universidad de Castilla-La Mancha, Avenida Carlos III, S.N. 45071 Toledo, Spain
| | - Francisco Sanchez
- Facultad de Quimica, Departamento de Quimica Fisica, Universidad de Sevilla, Calle Profesor Garcia Gonzalez, S.N. 41012 Sevilla, Spain
| | - Abderrazzak Douhal
- Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Departamento de Quimica Fisica, Universidad de Castilla-La Mancha, Avenida Carlos III, S.N. 45071 Toledo, Spain
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36
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Zirak P, Penzkofer A, Mathes T, Hegemann P. Absorption and emission spectroscopic characterization of BLUF protein Slr1694 from Synechocystis sp. PCC6803 with roseoflavin cofactor. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 97:61-70. [DOI: 10.1016/j.jphotobiol.2009.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Revised: 07/08/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022]
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37
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Miskolczy Z, Biczók L, Görner H. Tautomerization of lumichrome promoted by supramolecular complex formation with cucurbit[7]uril. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2008.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Nöll G, Trawöger S, von Sanden-Flohe M, Dick B, Grininger M. Blue-Light-Triggered Photorelease of Active Chemicals Captured by the Flavoprotein Dodecin. Chembiochem 2009; 10:834-7. [DOI: 10.1002/cbic.200900014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Grininger M, Staudt H, Johansson P, Wachtveitl J, Oesterhelt D. Dodecin is the key player in flavin homeostasis of archaea. J Biol Chem 2009; 284:13068-76. [PMID: 19224924 DOI: 10.1074/jbc.m808063200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Flavins are employed to transform physical input into biological output signals. In this function, flavins catalyze a variety of light-induced reactions and redox processes. However, nature also provides flavoproteins with the ability to uncouple the mediation of signals. Such proteins are the riboflavin-binding proteins (RfBPs) with their function to store riboflavin for fast delivery of FMN and FAD. Here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin is an RfBP, and we reveal that riboflavin storage is not restricted to eukaryotes. However, the function of the prokaryotic RfBP dodecin seems to be adapted to the requirement of a monocellular organism. While in eukaryotes RfBPs are involved in trafficking riboflavin, and dodecin is responsible for the flavin homeostasis of the cell. Although only 68 amino acids in length, dodecin is of high functional versatility in neutralizing riboflavin to protect the cellular environment from uncontrolled flavin reactivity. Besides the predominant ultrafast quenching of excited states, dodecin prevents light-induced riboflavin reactivity by the selective degradation of riboflavin to lumichrome. Coordinated with the high affinity for lumichrome, the directed degradation reaction is neutral to the cellular environment and provides an alternative pathway for suppressing uncontrolled riboflavin reactivity. Intriguingly, the different structural and functional properties of a homologous bacterial dodecin suggest that dodecin has different roles in different kingdoms of life.
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Affiliation(s)
- Martin Grininger
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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40
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Mathes T, Vogl C, Stolz J, Hegemann P. In Vivo Generation of Flavoproteins with Modified Cofactors. J Mol Biol 2009; 385:1511-8. [DOI: 10.1016/j.jmb.2008.11.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 10/21/2022]
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41
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Vieira Ferreira LF, Costa AI, Ferreira Machado I, Botelho do Rego AM, Sikorska E, Sikorski M. Surface photochemistry: alloxazine within nanochannels of Na+ and H+ ZSM-5 zeolites. Phys Chem Chem Phys 2009; 11:5762-72. [DOI: 10.1039/b903013a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Electrochemical switching of the flavoprotein dodecin at gold surfaces modified by flavin-DNA hybrid linkers. Biointerphases 2008; 3:51-8. [DOI: 10.1116/1.2965134] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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43
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Vogl C, Grill S, Schilling O, Stülke J, Mack M, Stolz J. Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum. J Bacteriol 2007; 189:7367-75. [PMID: 17693491 PMCID: PMC2168442 DOI: 10.1128/jb.00590-07] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 08/03/2007] [Indexed: 01/12/2023] Open
Abstract
Riboflavin (vitamin B(2)) is the direct precursor of the flavin cofactors flavin mononucleotide and flavin adenine dinucleotide, essential components of cellular biochemistry. In this work we investigated the unrelated proteins YpaA from Bacillus subtilis and PnuX from Corynebacterium glutamicum for a role in riboflavin uptake. Based on the regulation of the corresponding genes by a riboswitch mechanism, both proteins have been predicted to be involved in flavin metabolism. Moreover, their primary structures suggested that these proteins integrate into the cytoplasmic membrane. We provide experimental evidence that YpaA is a plasma membrane protein with five transmembrane domains and a cytoplasmic C terminus. In B. subtilis, riboflavin uptake was increased when ypaA was overexpressed and abolished when ypaA was deleted. Riboflavin uptake activity and the abundance of the YpaA protein were also increased when riboflavin auxotrophic mutants were grown in limiting amounts of riboflavin. YpaA-mediated riboflavin uptake was sensitive to protonophors and reduced in the absence of glucose, demonstrating that the protein requires metabolic energy for substrate translocation. In addition, we demonstrate that PnuX from C. glutamicum also is a riboflavin transporter. Transport by PnuX was not energy dependent and had high apparent affinity for riboflavin (K(m) 11 microM). Roseoflavin, a toxic riboflavin analog, appears to be a substrate of PnuX and YpaA. We propose to designate the gene names ribU for ypaA and ribM for pnuX to reflect that the encoded proteins function in riboflavin uptake and that the genes have different phylogenetic origins.
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Affiliation(s)
- Christian Vogl
- Lehrstuhl für Ernährungsphysiologie, Technische Universität München, Am Forum 5, 85350, Freising-Weihenstephan, Germany
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Meissner B, Schleicher E, Weber S, Essen LO. The dodecin from Thermus thermophilus, a bifunctional cofactor storage protein. J Biol Chem 2007; 282:33142-54. [PMID: 17855371 DOI: 10.1074/jbc.m704951200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dodecins are so far the smallest known flavoproteins (68-71 amino acids) and are most likely involved in prokaryotic flavin storage. The dodecin monomers adopt a simple betaalphabetabeta-fold and assemble to hollow sphere-like dodecameric complexes. Flavin binding by the dodecin from Thermus thermophilus showed a 1:1 stoichiometry and apparent dissociation constants in the submicromolar to nanomolar range as characterized by isothermal titration calorimetry and fluorescence titrations. The x-ray structures of the flavin-prebound and FMN-reconstituted state of the T. thermophilus dodecin revealed binding of FMN dimers in a novel si-si- rather than the re-re- orientation of their isoalloxazine moieties as found before in an archaeal dodecin. Electron paramagnetic resonance studies demonstrated that upon reduction the excess electron is localized only on one flavin, thus making dodecin-bound flavins highly refractory to redox chemistry. Besides FMN dimers, trimers of coenzyme A are additionally bound to this eubacterial dodecin along the 3-fold symmetry face II of the dodecin complex. Therefore, dodecins can act as bifunctional cofactor storage proteins that sequester catalytic cofactors in prokaryotes very efficiently in an aggregated and unreactive state.
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Affiliation(s)
- Britta Meissner
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, Marburg, Germany
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45
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Grininger M, Seiler F, Zeth K, Oesterhelt D. Dodecin sequesters FAD in closed conformation from the aqueous solution. J Mol Biol 2006; 364:561-6. [PMID: 17027852 DOI: 10.1016/j.jmb.2006.08.083] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/25/2006] [Accepted: 08/28/2006] [Indexed: 10/24/2022]
Abstract
Both extensive theoretical calculations and experimental data obtained during several decades leave little doubt that flavin adenine dinucleotide (FAD) exists in an open as well as in a closed conformation in aqueous solution. However, the knowledge about the intramolecularly stacked complex of FAD is constructed on indirect methods while direct structural evidence is lacking. Recently, dodecin was reported as an unspecific flavin binding protein which exhibits the unique binding mode of incorporating stacked dimers of flavins into a single binding pocket. Here, we show that FAD is not bound in this manner, but in monomers of intramolecularly stacked conformation. As resulting from the dodecin ligand binding characteristic, this FAD stacked conformation suggests to be directly sequestered from the aqueous solution and thus to be the first X-ray structural view on a FAD solution-stacked form. Moreover, in extraordinary FAD binding, dodecin serves as a model for studying bound monomeric (FAD) versus bound dimeric (e.g. riboflavin) flavin properties.
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Affiliation(s)
- Martin Grininger
- Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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