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Wiedemann HTA, Ruloff S, Richter R, Zollitsch CW, Kay CWM. Towards high performance dielectric microwave resonators for X-band EPR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 354:107519. [PMID: 37541024 DOI: 10.1016/j.jmr.2023.107519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 08/06/2023]
Abstract
Microwave (MW) resonators in Electron Paramagnetic Resonance (EPR) spectroscopy concentrate the MW magnetic field (B1) at the sample and separate the MW electric field from the sample. There are numerous experimental methods in EPR spectroscopy which all impose different requirements on MW resonators (e.g. high or low quality factor, MW conversion, and B1-field homogeneity). Although commercial spectrometers offer standardized MW resonators for a broad application range, newly emerging and highly-specialized research fields push these spectrometers to or beyond their sensitivity limits. Optimizing the MW resonator offers one direct approach to improve the sensitivity. Here we present three low-cost optimization approaches for a commercially available X-band (9-10 GHz) MW resonator for three experimental purposes (continuous-wave (CW), transient and pulse EPR). We obtain enhanced MW conversion factors for all three optimized resonators and higher quality factors for two optimized resonators. The latter is important for CW and transient EPR. Furthermore, we fabricated a resonator which features an extended area of homogeneous B1-field and, hence, improved pulse EPR performance. Our results demonstrate that small changes to a commercial MW resonator can enhance its performance in general or for specific applications.
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Affiliation(s)
- Haakon T A Wiedemann
- Department of Chemistry, Saarland University, Saarbrücken 66123, Saarland, Germany.
| | - Stefan Ruloff
- Department of Chemistry, Saarland University, Saarbrücken 66123, Saarland, Germany
| | - Rudolf Richter
- Department of Chemistry, Saarland University, Saarbrücken 66123, Saarland, Germany
| | - Christoph W Zollitsch
- Department of Chemistry, Saarland University, Saarbrücken 66123, Saarland, Germany; London Centre of Nanotechnology, University College London, London WC1H 0AH, United Kingdom; Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Christopher W M Kay
- Department of Chemistry, Saarland University, Saarbrücken 66123, Saarland, Germany; London Centre of Nanotechnology, University College London, London WC1H 0AH, United Kingdom
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2
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Experimental guidelines for trapping paramagnetic reaction intermediates in radical S-adenosylmethionine enzymes. Methods Enzymol 2022; 666:451-468. [DOI: 10.1016/bs.mie.2022.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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3
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Balo AR, Tao L, Britt RD. Characterizing SPASM/twitch Domain-Containing Radical SAM Enzymes by EPR Spectroscopy. APPLIED MAGNETIC RESONANCE 2021; 53:809-820. [PMID: 35509369 PMCID: PMC9012708 DOI: 10.1007/s00723-021-01406-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 06/14/2023]
Abstract
Owing to their importance, diversity and abundance of generated paramagnetic species, radical S-adenosylmethionine (rSAM) enzymes have become popular targets for electron paramagnetic resonance (EPR) spectroscopic studies. In contrast to prototypic single-domain and thus single-[4Fe-4S]-containing rSAM enzymes, there is a large subfamily of rSAM enzymes with multiple domains and one or two additional iron-sulfur cluster(s) called the SPASM/twitch domain-containing rSAM enzymes. EPR spectroscopy is a powerful tool that allows for the observation of the iron-sulfur clusters as well as potentially trappable paramagnetic reaction intermediates. Here, we review continuous-wave and pulse EPR spectroscopic studies of SPASM/twitch domain-containing rSAM enzymes. Among these enzymes, we will review in greater depth four well-studied enzymes, BtrN, MoaA, PqqE, and SuiB. Towards establishing a functional consensus of the additional architecture in these enzymes, we describe the commonalities between these enzymes as observed by EPR spectroscopy.
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Affiliation(s)
- Aidin R. Balo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - R. David Britt
- Department of Chemistry, University of California, Davis, CA 95616 USA
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4
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Electron paramagnetic resonance spectroscopy on G-protein-coupled receptors: Adopting strategies from related model systems. Curr Opin Struct Biol 2021; 69:177-186. [PMID: 34304006 DOI: 10.1016/j.sbi.2021.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/23/2022]
Abstract
Membrane proteins, including ion channels, transporters and G-protein-coupled receptors (GPCRs), play a significant role in various physiological processes. Many of these proteins are difficult to express in large quantities, imposing crucial experimental restrictions. Nevertheless, there is now a wide variety of studies available utilizing electron paramagnetic resonance (EPR) spectroscopic techniques that expand experimental accessibility by using relatively small quantities of protein. Here, we give an overview starting from basic strategies in EPR on membrane proteins with a focus on GPCRs, while emphasizing several applications from recent years. We highlight how the arsenal of EPR-based techniques may provide significant further contributions to understanding the complex molecular machinery and energetic phenomena responsible for seamless workflow in essential biological processes.
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5
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Pu T, Mei Z, Zhang W, Liang WJ, Zhou X, Liang J, Deng Z, Wang Z. An in vitro DNA phosphorothioate modification reaction. Mol Microbiol 2019; 113:452-463. [PMID: 31749226 DOI: 10.1111/mmi.14430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/10/2019] [Accepted: 11/17/2019] [Indexed: 12/25/2022]
Abstract
Phosphorothioation (PT) involves the replacement of a nonbridging phosphate oxygen on the DNA backbone with sulfur. In bacteria, the procedure is both sequence- and stereo-specific. We reconstituted the PT reaction using purified DndCDE from Salmonella enterica and IscS from Escherichia coli. We determined that the in vitro process of PT was oxygen sensitive. Only one strand on a double-stranded (ds) DNA substrate was modified in the reaction. The modification was dominant between G and A in the GAAC/GTTC conserved sequence. The modification between G and T required the presence of PT between G and A on the opposite strand. Cysteine, S-adenosyl methionine (SAM) and the formation of an iron-sulfur cluster in DndCDE (DndCDE-FeS) were essential for the process. Results from SAM cleavage reactions support the supposition that PT is a radical SAM reaction. Adenosine triphosphate (ATP) promoted the reaction but was not essential. The data and conclusions presented suggest that the PT reaction in bacteria involves three steps. The first step is the binding of DndCDE-FeS to DNA and searching for the modification sequence, possibly with the help of ATP. Cysteine locks DndCDE-FeS to the modification site with an appropriate protein conformation. SAM triggers the radical SAM reaction to complete the oxygen-sulfur swapping.
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Affiliation(s)
- Tianning Pu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhiling Mei
- Shanghai Thinkgene Biotech CO., LTD, Shanghai, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wei-Jun Liang
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Xiufen Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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6
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Yuan Y, Zallot R, Grove TL, Payan DJ, Martin-Verstraete I, Šepić S, Balamkundu S, Neelakandan R, Gadi VK, Liu CF, Swairjo MA, Dedon PC, Almo SC, Gerlt JA, de Crécy-Lagard V. Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. Proc Natl Acad Sci U S A 2019; 116:19126-19135. [PMID: 31481610 PMCID: PMC6754566 DOI: 10.1073/pnas.1909604116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Queuosine (Q) is a complex tRNA modification widespread in eukaryotes and bacteria that contributes to the efficiency and accuracy of protein synthesis. Eukaryotes are not capable of Q synthesis and rely on salvage of the queuine base (q) as a Q precursor. While many bacteria are capable of Q de novo synthesis, salvage of the prokaryotic Q precursors preQ0 and preQ1 also occurs. With the exception of Escherichia coli YhhQ, shown to transport preQ0 and preQ1, the enzymes and transporters involved in Q salvage and recycling have not been well described. We discovered and characterized 2 Q salvage pathways present in many pathogenic and commensal bacteria. The first, found in the intracellular pathogen Chlamydia trachomatis, uses YhhQ and tRNA guanine transglycosylase (TGT) homologs that have changed substrate specificities to directly salvage q, mimicking the eukaryotic pathway. The second, found in bacteria from the gut flora such as Clostridioides difficile, salvages preQ1 from q through an unprecedented reaction catalyzed by a newly defined subgroup of the radical-SAM enzyme family. The source of q can be external through transport by members of the energy-coupling factor (ECF) family or internal through hydrolysis of Q by a dedicated nucleosidase. This work reinforces the concept that hosts and members of their associated microbiota compete for the salvage of Q precursors micronutrients.
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Affiliation(s)
- Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Rémi Zallot
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Daniel J Payan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Isabelle Martin-Verstraete
- Laboratoire de Pathogénèse des Bactéries Anaérobies, Institut Pasteur et Université de Paris, F-75015 Paris, France
| | - Sara Šepić
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Vinod K Gadi
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Chuan-Fa Liu
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182
- The Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
- Department of Biological Engineering and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611;
- University of Florida Genetics Institute, Gainesville, FL 32610
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7
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Jeschke G. Quo vadis EPR? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:36-41. [PMID: 31345773 DOI: 10.1016/j.jmr.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/21/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Complexity of paramagnetic catalysts and materials increases, and the same applies to systems targeted by integrative structural biology. Hence, EPR spectroscopists must find ways to enhance information content of their data. I argue that a third major wave of method development in EPR spectroscopy, which is triggered by recent advances in digital electronics and computing, can achieve this. Transfer of NMR methods to EPR will go on, but part of the new EPR methodology will depend on completely new concepts.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zurich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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8
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Zhu W, Martins AM, Klinman JP. Methods for Expression, Purification, and Characterization of PqqE, a Radical SAM Enzyme in the PQQ Biosynthetic Pathway. Methods Enzymol 2019; 606:389-420. [PMID: 30097100 DOI: 10.1016/bs.mie.2018.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PqqE is the first enzyme in the biosynthetic pathway of the redox cofactor pyrroloquinoline quinone (PQQ), catalyzing the formation of a carbon-carbon bond in the precursor peptide PqqA. PqqE is a radical S-adenosyl-l-methionine (SAM) (RS) enzyme, a family of enzymes that use the reductive cleavage of a [4Fe-4S] cluster-bound SAM molecule to generate a 5'-deoxyadenosyl radical. This radical is then used to initiate an array of reactions that otherwise would be unlikely to occur. PqqE is a founding member of a subset family of RS enzymes that, additionally to the SAM [4Fe-4S] cluster, have a SPASM domain containing additional, auxiliary Fe-S clusters. Most radical SAM enzymes are highly sensitive to oxygen, which destroys their Fe-S clusters. This can pose several limitations when working with these enzymes, since most of the work has to be done under anaerobic conditions. Here, we summarize the methods developed in our lab for the expression and purification of PqqE. We also highlight the several methods we have used for the characterization of the enzyme.
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Affiliation(s)
- Wen Zhu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States; Department of Chemistry, University of California, Berkeley, CA, United States
| | - Ana M Martins
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States
| | - Judith P Klinman
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States; Department of Chemistry, University of California, Berkeley, CA, United States; Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States.
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9
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Degner A, Carlsson H, Karlsson I, Eriksson J, Pujari SS, Tretyakova NY, Törnqvist M. Discovery of Novel N-(4-Hydroxybenzyl)valine Hemoglobin Adducts in Human Blood. Chem Res Toxicol 2018; 31:1305-1314. [PMID: 30375232 DOI: 10.1021/acs.chemrestox.8b00173] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Humans are exposed to a wide range of electrophilic compounds present in our diet and environment or formed endogenously as part of normal physiological processes. These electrophiles can modify nucleophilic sites of proteins and DNA to form covalent adducts. Recently, powerful untargeted adductomic approaches have been developed for systematic screening of these adducts in human blood. Our earlier untargeted adductomics study detected 19 unknown adducts to N-terminal valine in hemoglobin (Hb) in human blood. We now describe a full characterization of one of these adducts, which corresponds to the addition of a 4-hydroxybenzyl (4-OHBn) group to N-terminal valine in Hb to form N(4-hydroxybenzyl)valine (4-OHBn-Val). The adduct structure was determined by comparison of its accurate mass, HPLC retention time, and MS/MS fragmentation to that of authentic standards prepared by chemical synthesis. Average 4-OHBn-Val adduct concentrations in 12 human blood samples were estimated to 380 ± 160 pmol/g Hb. Two possible routes of 4-OHBnVal adduct formation are proposed using two different precursor electrophiles: 4-quinone methide (4-QM) and 4-hydroxybenzaldehyde (4-OHBA). We found that 4-QM reacts rapidly with valine to form the 4-OHBn-Val adduct; however, the quinone methide is unstable under physiological conditions due to hydrolysis. It was shown that 4-OHBA forms reversible Schiff base adducts with valine, which can be stabilized via reduction in blood generating the 4-OHBn-Val adduct. In addition, trace amounts of isomeric 2-hydroxybenzyl-valine (2-OHBn-Val) adducts were detected in 12 human blood samples (estimated mean adduct level, 5.0 ± 1.4 pmol/g Hb). Further studies are needed to quantify the contributions from identified possible precursor electrophiles to the observed hydroxybenzyl adducts in humans.
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Affiliation(s)
- Amanda Degner
- Department of Medicinal Chemistry and the Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Henrik Carlsson
- Department of Environmental Science and Analytical Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Isabella Karlsson
- Department of Environmental Science and Analytical Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Johan Eriksson
- Department of Environmental Science and Analytical Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Suresh S Pujari
- Department of Medicinal Chemistry and the Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Margareta Törnqvist
- Department of Environmental Science and Analytical Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
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10
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Chalyavi F, Hogle DG, Tucker MJ. Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics. J Phys Chem B 2017; 121:6380-6389. [DOI: 10.1021/acs.jpcb.7b04999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - David G. Hogle
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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11
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Heidinger L, Kneuttinger AC, Kashiwazaki G, Weber S, Carell T, Schleicher E. Direct observation of a deoxyadenosyl radical in an active enzyme environment. FEBS Lett 2016; 590:4489-4494. [PMID: 27878994 DOI: 10.1002/1873-3468.12498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/11/2022]
Abstract
5'-deoxyadenosyl radicals have been proposed as the first common intermediate in the molecular reaction mechanism of the family of radical S-adenosyl-l-methionine (SAM) enzymes. However, this radical species has not yet been directly observed in a catalytically active enzyme environment. In a reduced and SAM-containing C140A mutant of the spore photoproduct lyase from Geobacillus thermodenitrificans, a mutant with altered catalytic activity, we were able to identify an organic radical with pronounced hyperfine structure using electron paramagnetic resonance spectroscopy. Guided by quantum-chemical computations at the density functional theory level of theory, this radical could be tentatively assigned to a deoxyadenosyl radical, which provides first experimental evidence for this intermediate in the reaction mechanism of radical SAM enzymes.
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Affiliation(s)
- Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Andrea C Kneuttinger
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
| | - Gengo Kashiwazaki
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Thomas Carell
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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12
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Suess DLM, Kuchenreuther JM, De La Paz L, Swartz JR, Britt RD. Biosynthesis of the [FeFe] Hydrogenase H Cluster: A Central Role for the Radical SAM Enzyme HydG. Inorg Chem 2016; 55:478-87. [PMID: 26703931 PMCID: PMC4780679 DOI: 10.1021/acs.inorgchem.5b02274] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hydrogenase enzymes catalyze the rapid and reversible interconversion of H2 with protons and electrons. The active site of the [FeFe] hydrogenase is the H cluster, which consists of a [4Fe-4S]H subcluster linked to an organometallic [2Fe]H subcluster. Understanding the biosynthesis and catalytic mechanism of this structurally unusual active site will aid in the development of synthetic and biological hydrogenase catalysts for applications in solar fuel generation. The [2Fe]H subcluster is synthesized and inserted by three maturase enzymes-HydE, HydF, and HydG-in a complex process that involves inorganic, organometallic, and organic radical chemistry. HydG is a member of the radical S-adenosyl-l-methionine (SAM) family of enzymes and is thought to play a prominent role in [2Fe]H subcluster biosynthesis by converting inorganic Fe(2+), l-cysteine (Cys), and l-tyrosine (Tyr) into an organometallic [(Cys)Fe(CO)2(CN)](-) intermediate that is eventually incorporated into the [2Fe]H subcluster. In this Forum Article, the mechanism of [2Fe]H subcluster biosynthesis is discussed with a focus on how this key [(Cys)Fe(CO)2(CN)](-) species is formed. Particular attention is given to the initial metallocluster composition of HydG, the modes of substrate binding (Fe(2+), Cys, Tyr, and SAM), the mechanism of SAM-mediated Tyr cleavage to CO and CN(-), and the identification of the final organometallic products of the reaction.
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Affiliation(s)
- Daniel L. M. Suess
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Jon M. Kuchenreuther
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Liliana De La Paz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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13
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Angamuthu R, Chen CS, Cochrane TR, Gray DL, Schilter D, Ulloa OA, Rauchfuss TB. N-Substituted Derivatives of the Azadithiolate Cofactor from the [FeFe] Hydrogenases: Stability and Complexation. Inorg Chem 2015; 54:5717-24. [PMID: 26000618 PMCID: PMC4475577 DOI: 10.1021/acs.inorgchem.5b00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experiments are described that probe the stability of N-substituted derivatives of the azadithiolate cofactor recently confirmed in the [FeFe] hydrogenases (Berggren, G., et al. Nature 2013, 499, 66). Acid-catalyzed hydrolysis of bis(thioester) BnN(CH2SAc)2 gives [BnNCH2SCH2]2 rather than azadithiol BnN(CH2SH)2. Treatment of BnN(CH2SAc)2 with NaO(t)Bu generates BnN(CH2SNa)2, which was trapped with NiCl2(diphos) (diphos = 1,2-C2H4(PR2)2; R = Ph (dppe) and Cy (dcpe)) to give fully characterized complexes Ni[(SCH2)2NBn](diphos). The related N-aryl derivative Ni[(SCH2)2NC6H4Cl](diphos) was prepared analogously from 4-ClC6H4N(CH2SAc)2, NaO(t)Bu, and NiCl2(dppe). Crystallographic analysis confirmed that these rare nonbridging [adt(R)](2-) complexes feature distorted square planar Ni centers. The analogue Pd[(SCH2)2NBn](dppe) was also prepared. (31)P NMR analysis indicates that Ni[(SCH2)2NBn](dppe) has basicity comparable to typical amines. As shown by cyclic voltammetry, the couple [M[(SCH2)2NBn](dppe)](+/0) is reversible near -2.0 V versus Fc(+/0). The wave shifts to -1.78 V upon N-protonation. In the presence of CF3CO2H, Ni[(SCH2)2NBn](dppe) catalyzes hydrogen evolution at rate of 22 s(-1) in the acid-independent regime, at room temperature in CH2Cl2 solution. In contrast to the instability of RN(CH2SH)2 (R = alkyl, aryl), the dithiol of tosylamide TsN(CH2SH)2 proved sufficiently stable to allow full characterization. This dithiol reacts with Fe3(CO)12 and, in the presence of base, NiCl2(dppe) to give Fe2[(SCH2)2NTs](CO)6 and Ni[(SCH2)2NTs](dppe), respectively.
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Affiliation(s)
| | - Chi-Shian Chen
- School of Chemical Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Tyler R. Cochrane
- School of Chemical Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Danielle L. Gray
- School of Chemical Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - David Schilter
- School of Chemical Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Olbelina A. Ulloa
- School of Chemical Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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14
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Affiliation(s)
- Perry Allen Frey
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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15
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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16
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Salamone M, Mangiacapra L, Bietti M. Kinetic Solvent Effects on the Reactions of the Cumyloxyl Radical with Tertiary Amides. Control over the Hydrogen Atom Transfer Reactivity and Selectivity through Solvent Polarity and Hydrogen Bonding. J Org Chem 2015; 80:1149-54. [DOI: 10.1021/jo5026767] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michela Salamone
- Dipartimento
di Scienze e
Tecnologie Chimiche, Università “Tor Vergata”, Via
della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Livia Mangiacapra
- Dipartimento
di Scienze e
Tecnologie Chimiche, Università “Tor Vergata”, Via
della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Massimo Bietti
- Dipartimento
di Scienze e
Tecnologie Chimiche, Università “Tor Vergata”, Via
della Ricerca Scientifica 1, I-00133 Rome, Italy
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17
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Gaffney BJ. Connecting lipoxygenase function to structure by electron paramagnetic resonance. Acc Chem Res 2014; 47:3588-95. [PMID: 25341190 PMCID: PMC4270396 DOI: 10.1021/ar500290r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Indexed: 01/09/2023]
Abstract
CONSPECTUS: Lipoxygenase enzymes insert oxygen in a polyunsaturated lipid, yielding a hydroperoxide product. When the acyl chain is arachidonate, with three cis-pentadiene units, 12 positionally and stereochemically different products might result. The plant lipids, linoleate and linolenate, have, respectively, four and eight potential oxygen insertion sites. The puzzle of how specificity is achieved in these reactions grows as more and more protein structures confirm the conservation of a lipoxygenase protein fold in plants, animals, and bacteria. Lipoxygenases are large enough (60-100 kDa) that they provide a protein shell completely surrounding an active site cavity that has the shape of a long acyl chain and contains a catalytic metal (usually iron). This Account summarizes electron paramagnetic resonance (EPR) spectroscopic, and other, experiments designed to bridge the gap between lipid-lipoxygenase interactions in solution and crystal structures. Experiments with spin-labeled lipids give a picture of bound lipids tethered to protein by an acyl chain, but with a polar end emerging from the cavity to solvent exposure, where the headgroup is highly flexible. The location of a spin on the polar end of a lysolecithin was determined by pulsed, dipolar EPR measurements, by representing the protein structure as a five-point grid of spin-labels with coordinates derived from 10 distance determinations between spin pairs. Distances from the lipid spin to each grid site completed a six-point representation of the enzyme with a bound lipid. Insight into the dynamics that allow substrate/product to enter/exit the cavity was obtained with a different set of spin-labeled protein mutants. Once substrate enters the cavity, the rate-limiting step of catalysis involves redox cycling at the metal center. Here, a mononuclear iron cycles between ferric and ferrous (high-spin) forms. Two helices provide pairs of side-chain ligands to the iron, resulting in characteristic EPR signals. Quantitative comparison of EPR spectra of plant and bacterial lipoxygenases has suggested conservation of a unique geometry of lipoxygenase iron centers. High frequency (94 GHz) EPR is consistent with a similar metal center in a manganese version of lipoxygenase. Overall, established and emerging EPR experiments have been developed and applied to the lipoxygenase family of enzymes to elucidate changes in the solution structures that are related to function.
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Affiliation(s)
- Betty J. Gaffney
- Department
of Biological
Science, Florida State University, Tallahassee, Florida 32306-4295, United States
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18
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Mehta AP, Abdelwahed SH, Mahanta N, Fedoseyenko D, Philmus B, Cooper LE, Liu Y, Jhulki I, Ealick SE, Begley TP. Radical S-adenosylmethionine (SAM) enzymes in cofactor biosynthesis: a treasure trove of complex organic radical rearrangement reactions. J Biol Chem 2014; 290:3980-6. [PMID: 25477515 DOI: 10.1074/jbc.r114.623793] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this minireview, we describe the radical S-adenosylmethionine enzymes involved in the biosynthesis of thiamin, menaquinone, molybdopterin, coenzyme F420, and heme. Our focus is on the remarkably complex organic rearrangements involved, many of which have no precedent in organic or biological chemistry.
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Affiliation(s)
- Angad P Mehta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Sameh H Abdelwahed
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Nilkamal Mahanta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Dmytro Fedoseyenko
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Benjamin Philmus
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Lisa E Cooper
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Yiquan Liu
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Isita Jhulki
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Steven E Ealick
- the Department of Chemistry, Cornell University, Ithaca, New York 14850
| | - Tadhg P Begley
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
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