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Wojdyla Z, Maldonado-Domínguez M, Bharadwaz P, Culka M, Srnec M. Elucidation of factors shaping reactivity of 5'-deoxyadenosyl - a prominent organic radical in biology. Phys Chem Chem Phys 2024. [PMID: 39041228 DOI: 10.1039/d4cp01725k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
This study investigates the factors modulating the reactivity of 5'-deoxyadenosyl (5'dAdo˙) radical, a potent hydrogen atom abstractor that forms in the active sites of radical SAM enzymes and that otherwise undergoes a rapid self-decay in aqueous solution. Here, we compare hydrogen atom abstraction (HAA) reactions between native substrates of radical SAM enzymes and 5'dAdo˙ in aqueous solution and in two enzymatic microenvironments. With that we reveal that HAA efficiency of 5'dAdo˙ is due to (i) the in situ formation of 5'dAdo˙ in a pre-ordered complex with a substrate, which attenuates the unfavorable effect of substrate:5'dAdo˙ complex formation, and (ii) the prevention of the conformational changes associated with self-decay by a tight active-site cavity. The enzymatic cavity, however, does not have a strong effect on the HAA activity of 5'dAdo˙. Thus, we performed an analysis of in-water HAA performed by 5'dAdo˙ based on a three-component thermodynamic model incorporating the diagonal effect of the free energy of reaction, and the off-diagonal effect of asynchronicity and frustration. To this aim, we took advantage of the straightforward relationship between the off-diagonal thermodynamic effects and the electronic-structure descriptor - the redistribution of charge between the reactants during the reaction. It allows to access HAA-competent redox and acidobasic properties of 5'dAdo˙ that are otherwise unavailable due to its instability upon one-electron reduction and protonation. The results show that all reactions feature a favourable thermodynamic driving force and tunneling, the latter of which lowers systematically barriers by ∼2 kcal mol-1. In addition, most of the reactions experience a favourable off-diagonal thermodynamic contribution. In HAA reactions, 5'dAdo˙ acts as a weak oxidant as well as a base, also 5'dAdo˙-promoted HAA reactions proceed with a quite low degree of asynchronicity of proton and electron transfer. Finally, the study elucidates the crucial and dual role of asynchronicity. It directly lowers the barrier as a part of the off-diagonal thermodynamic contribution, but also indirectly increases the non-thermodynamic part of the barrier by presumably controlling the adiabatic coupling between proton and electron transfer. The latter signals that the reaction proceeds as a hydrogen atom transfer rather than a proton-coupled electron transfer.
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Affiliation(s)
- Zuzanna Wojdyla
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
| | - Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
| | - Priyam Bharadwaz
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
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Kisgeropoulos E, Bharadwaj VS, Ledinina A, Lubner CE, Mulder DW, Smolinski SL, Boehm M, Gutekunst K, King PW, Svedruzic D. Structural and biophysical properties of a [4Fe4S] ferredoxin-like protein from Synechocystis sp. PCC 6803 with a unique two domain structure. J Inorg Biochem 2024; 251:112428. [PMID: 38008043 DOI: 10.1016/j.jinorgbio.2023.112428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 11/28/2023]
Abstract
Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron‑sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2×[4Fe4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 ± 9 mV and - 516 ± 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.
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Affiliation(s)
- Effie Kisgeropoulos
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Anastasia Ledinina
- Department of Molecular and Structural Biochemistry, North Carolina State University, USA
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Sharon L Smolinski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Marko Boehm
- Department of Biology, Botanical Institute, Christian-Albrechts-University, Kiel, Germany; Department of Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Kirstin Gutekunst
- Department of Biology, Botanical Institute, Christian-Albrechts-University, Kiel, Germany; Department of Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Drazenka Svedruzic
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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Du Z, Zhou X, Lai Y, Xu J, Zhang Y, Zhou S, Feng Z, Yu L, Tang Y, Wang W, Yu L, Tian C, Ran T, Chen H, Guddat LW, Liu F, Gao Y, Rao Z, Gong H. Structure of the human respiratory complex II. Proc Natl Acad Sci U S A 2023; 120:e2216713120. [PMID: 37098072 PMCID: PMC10161127 DOI: 10.1073/pnas.2216713120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/10/2023] [Indexed: 04/26/2023] Open
Abstract
Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been shown to cause mitochondrial disease and some types of cancers. However, the structure of this complex is yet to be resolved, hindering a comprehensive understanding of the functional aspects of this molecular machine. Here, we have determined the structure of human complex II in the presence of ubiquinone at 2.86 Å resolution by cryoelectron microscopy, showing it comprises two water-soluble subunits, SDHA and SDHB, and two membrane-spanning subunits, SDHC and SDHD. This structure allows us to propose a route for electron transfer. In addition, clinically relevant mutations are mapped onto the structure. This mapping provides a molecular understanding to explain why these variants have the potential to produce disease.
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Affiliation(s)
- Zhanqiang Du
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Xiaoting Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Jinxu Xu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Ziyan Feng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Long Yu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
| | - Weiwei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Ting Ran
- Innovative Center For Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Hongming Chen
- Innovative Center For Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Fengjiang Liu
- Innovative Center For Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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5
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Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation. Sci Rep 2023; 13:4082. [PMID: 36906658 PMCID: PMC10008544 DOI: 10.1038/s41598-023-30310-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 (T7RdhA) with potential for catalyzing the degradation of per- and polyfluoroalkyl substances (PFASs). AF2 models and experiments identified T7RdhA as a corrinoid iron-sulfur protein (CoFeSP) which uses a norpseudo-cobalamin (BVQ) cofactor and two Fe4S4 iron-sulfur clusters for catalysis. Docking and molecular dynamics simulations suggest that T7RdhA uses perfluorooctanoic acetate (PFOA) as a substrate, supporting the reported defluorination activity of its homolog, A6RdhA. We showed that AF2 provides processual (dynamic) predictions for the binding pockets of ligands (cofactors and/or substrates). Because the pLDDT scores provided by AF2 reflect the protein native states in complex with ligands as the evolutionary constraints, the Evoformer network of AF2 predicts protein structures and residue flexibility in complex with the ligands, i.e., in their native states. Therefore, an apo-protein predicted by AF2 is actually a holo-protein awaiting ligands.
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Mansilla S, Tórtora V, Pignataro F, Sastre S, Castro I, Chiribao ML, Robello C, Zeida A, Santos J, Castro L. Redox sensitive human mitochondrial aconitase and its interaction with frataxin: In vitro and in silico studies confirm that it takes two to tango. Free Radic Biol Med 2023; 197:71-84. [PMID: 36738801 DOI: 10.1016/j.freeradbiomed.2023.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/11/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Mitochondrial aconitase (ACO2) has been postulated as a redox sensor in the tricarboxylic acid cycle. Its high sensitivity towards reactive oxygen and nitrogen species is due to its particularly labile [4Fe-4S]2+ prosthetic group which yields an inactive [3Fe-4S]+ cluster upon oxidation. Moreover, ACO2 was found as a main oxidant target during aging and in pathologies where mitochondrial dysfunction is implied. Herein, we report the expression and characterization of recombinant human ACO2 and its interaction with frataxin (FXN), a protein that participates in the de novo biosynthesis of Fe-S clusters. A high yield of pure ACO2 (≥99%, 22 ± 2 U/mg) was obtained and kinetic parameters for citrate, isocitrate, and cis-aconitate were determined. Superoxide, carbonate radical, peroxynitrite, and hydrogen peroxide reacted with ACO2 with second-order rate constants of 108, 108, 105, and 102 M-1 s-1, respectively. Temperature-induced unfolding assessed by tryptophan fluorescence of ACO2 resulted in apparent melting temperatures of 51.1 ± 0.5 and 43.6 ± 0.2 °C for [4Fe-4S]2+ and [3Fe-4S]+ states of ACO2, sustaining lower thermal stability upon cluster oxidation. Differences in protein dynamics produced by the Fe-S cluster redox state were addressed by molecular dynamics simulations. Reactivation of [3Fe-4S]+-ACO2 by FXN was verified by activation assays and direct iron-dependent interaction was confirmed by protein-protein interaction ELISA and fluorescence spectroscopic assays. Multimer modeling and protein-protein docking predicted an ACO2-FXN complex where the metal ion binding region of FXN approaches the [3Fe-4S]+ cluster, supporting that FXN is a partner for reactivation of ACO2 upon oxidative cluster inactivation.
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Affiliation(s)
- Santiago Mansilla
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Verónica Tórtora
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Educación Médica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Florencia Pignataro
- Instituto de Biociencias, Biotecnología y Biología traslacional, Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Sastre
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Biofísica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ignacio Castro
- Instituto de Biociencias, Biotecnología y Biología traslacional, Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ma Laura Chiribao
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Laboratorio de Interacciones Hospedero-Patógeno, Institut Pasteur de Montevideo, Uruguay
| | - Carlos Robello
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Laboratorio de Interacciones Hospedero-Patógeno, Institut Pasteur de Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología traslacional, Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Laura Castro
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Pecourneau J, Losantos R, Delova A, Bernhard Y, Parant S, Mourer M, Monari A, Pasc A. Biomimetic Photo-Switches Softening Model Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15642-15655. [PMID: 36469419 DOI: 10.1021/acs.langmuir.2c02425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We report the synthesis and characterization of a novel photo-switch based on biomimetic cyclocurcumin analogous and interacting with the lipid bilayer, which can be used in the framework of oxygen-independent light-induced therapy. More specifically, by using molecular dynamics simulations and free energy techniques, we show that the inclusion of hydrophobic substituents is needed to allow insertion in the lipid membrane. After having confirmed experimentally that the substituents do not preclude the efficient photoisomerization, we show through UV-vis and dynamic light scattering measurements together with compression isotherms that the chromophore is internalized in both lipid vesicles and monomolecular film, respectively, inducing their fluidification. The irradiation of the chromophore-loaded lipid aggregates modifies their properties due to the different organization of the two diastereoisomers, E and Z. In particular, a competition between a fast structural reorganization and a slower expulsion of the chromophore after isomerization can be observed in the kinetic profiles recorded during E to Z photoisomerization. This report paves the way for future investigations in the optimization of biomimetic photoswitches potentially useful in modern light-induced therapeutic strategies.
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Affiliation(s)
| | - Raúl Losantos
- Université de Lorraine and CNRS, L2CM UMR 7053, F-5400Nancy, France
- Université de Lorraine, CNRS, LPCT UMR 7019, F-54000Nancy, France
- Université Paris Cité and CNRS, ITODYS, F-75006Paris, France
- Department of Chemistry, CISQ, Universidad de La Rioja, 26006Logroño, Spain
| | | | - Yann Bernhard
- Université de Lorraine and CNRS, L2CM UMR 7053, F-5400Nancy, France
| | - Stéphane Parant
- Université de Lorraine and CNRS, L2CM UMR 7053, F-5400Nancy, France
| | - Maxime Mourer
- Université de Lorraine and CNRS, L2CM UMR 7053, F-5400Nancy, France
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, F-54000Nancy, France
- Université Paris Cité and CNRS, ITODYS, F-75006Paris, France
| | - Andreea Pasc
- Université de Lorraine and CNRS, L2CM UMR 7053, F-5400Nancy, France
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Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms232415913. [PMID: 36555561 PMCID: PMC9782105 DOI: 10.3390/ijms232415913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
"Plant-type" ferredoxins (Fds) in the thylakoid membranes of plants, algae, and cyanobacteria possess a single [2Fe-2S] cluster in active sites and mediate light-induced electron transfer from Photosystem I reaction centers to various Fd-dependent enzymes. Structural knowledge of plant-type Fds is relatively limited to static structures, and the detailed behavior of oxidized and reduced Fds has not been fully elucidated. It is important that the investigations of the effects of active-center reduction on the structures and dynamics for elucidating electron-transfer mechanisms. In this study, model systems of oxidized and reduced Fds were constructed from the high-resolution crystal structure of Chlamydomonas reinhardtii Fd1, and three 200 ns molecular dynamics simulations were performed for each system. The force field parameters of the oxidized and reduced active centers were independently obtained using quantum chemical calculations. There were no substantial differences in the global conformations of the oxidized and reduced forms. In contrast, active-center reduction affected the hydrogen-bond network and compactness of the surrounding residues, leading to the increased flexibility of the side chain of Phe61, which is essential for the interaction between Fd and the target protein. These computational results will provide insight into the electron-transfer mechanisms in the Fds.
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9
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Hargrove TY, Lamb DC, Smith JA, Wawrzak Z, Kelly SL, Lepesheva GI. Unravelling the role of transient redox partner complexes in P450 electron transfer mechanics. Sci Rep 2022; 12:16232. [PMID: 36171457 PMCID: PMC9519919 DOI: 10.1038/s41598-022-20671-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/16/2022] [Indexed: 01/05/2023] Open
Abstract
The molecular evolution of cytochromes P450 and associated redox-driven oxidative catalysis remains a mystery in biology. It is widely believed that sterol 14α-demethylase (CYP51), an essential enzyme of sterol biosynthesis, is the ancestor of the whole P450 superfamily given its conservation across species in different biological kingdoms. Herein we have utilized X-ray crystallography, molecular dynamics simulations, phylogenetics and electron transfer measurements to interrogate the nature of P450-redox partner binding using the naturally occurring fusion protein, CYP51-ferredoxin found in the sterol-producing bacterium Methylococcus capsulatus. Our data advocates that the electron transfer mechanics in the M. capsulatus CYP51-ferredoxin fusion protein involves an ensemble of ferredoxin molecules in various orientations and the interactions are transient. Close proximity of ferredoxin, however, is required to complete the substrate-induced large-scale structural switch in the P450 domain that enables proton-coupled electron transfer and subsequent oxygen scission and catalysis. These results have fundamental implications regarding the early evolution of electron transfer proteins and for the redox reactions in the early steps of sterol biosynthesis. They also shed new light on redox protein mechanics and the subsequent diversification of the P450 electron transfer machinery in nature.
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Affiliation(s)
- Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - David C Lamb
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - Jarrod A Smith
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, IL, 60439, USA
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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Trindade IB, Coelho A, Cantini F, Piccioli M, Louro RO. NMR of paramagnetic metalloproteins in solution: Ubi venire, quo vadis? J Inorg Biochem 2022; 234:111871. [DOI: 10.1016/j.jinorgbio.2022.111871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
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11
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Hanževački M, Croft AK, Jäger CM. Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. J Chem Inf Model 2022; 62:3401-3414. [PMID: 35771966 PMCID: PMC9326890 DOI: 10.1021/acs.jcim.2c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.
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Affiliation(s)
- Marko Hanževački
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
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12
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Bignon E, Marazzi M, Grandemange S, Monari A. Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer. Chem Sci 2022; 13:6098-6105. [PMID: 35685814 PMCID: PMC9132136 DOI: 10.1039/d2sc00108j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022] Open
Abstract
The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms. Among the complex pathways induced by the viral infection, autophagy is particularly crucial and is strongly influenced by the action of the non-structural protein 6 (Nsp6) interacting with the endoplasmic reticulum membrane. Importantly, differently from other non-structural proteins, Nsp6 is mutated in the recently emerged Omicron variant, suggesting a possible different role of autophagy. In this contribution we explore, for the first time, the structural properties of Nsp6 thanks to long-timescale molecular dynamics simulations and machine learning analysis, identifying the interaction patterns with the lipid membrane. We also show how the mutation brought by the Omicron variant may indeed modify some of the specific interactions, and more particularly help anchor the viral protein to the lipid bilayer interface. The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms.![]()
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Affiliation(s)
| | - Marco Marazzi
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering and Chemical Research Institute "Andres M. del Rio" (IQAR), Universidad de Alcalá 28805 Alcalá de Hénares Spain
| | | | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS F-75006 Paris France
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13
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Ali F, Shafaa MW, Amin M. Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I. BIOLOGY 2022; 11:biology11030362. [PMID: 35336736 PMCID: PMC8945787 DOI: 10.3390/biology11030362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022]
Abstract
Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron-sulfur cluster FX, which is followed by two terminal iron-sulfur clusters FA and FB. Experiments have shown that FX has lower oxidation potential than FA and FB, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint Em potentials of the FX, FA and FB clusters. Our calculations show that FX has the lowest oxidation potential compared to FA and FB due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for FX compared to FA and FB. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for FX compared to both FA and FB. These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.
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Affiliation(s)
- Fedaa Ali
- Medical Biophysics Division, Department of Physics, Faculty of Science, Helwan University, Cairo 11795, Egypt; (F.A.); (M.W.S.)
- Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Medhat W. Shafaa
- Medical Biophysics Division, Department of Physics, Faculty of Science, Helwan University, Cairo 11795, Egypt; (F.A.); (M.W.S.)
| | - Muhamed Amin
- Department of Sciences, University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
- Universiteit Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9718 BG Groningen, The Netherlands
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Correspondence:
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14
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Gaughan SJH, Hirst JD, Croft AK, Jäger CM. Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis. J Chem Inf Model 2022; 62:591-601. [PMID: 35045248 DOI: 10.1021/acs.jcim.1c00791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active-site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Oriented electric fields in enzymatic active sites can be significantly strong, and understanding the extent of their effect on iron-sulfur cluster reactivity can inform first steps toward rationally engineering their reactivity. An extensive systematic density functional theory-based screening approach using OPBE/TZP has afforded a simple electric field-effect representation. The results demonstrate that the orientation of an external electric field of strength 28.8 MV cm-1 at the center of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol-1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken-symmetry state, which further has implications on the directionality of initiated electron-transfer reactions. These insights open the path for manipulating the enzymatic redox reactivity of iron-sulfur cluster-containing enzymes by rationally engineering oriented electric fields within the enzymes.
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Affiliation(s)
- Samuel J H Gaughan
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.,Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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15
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Mejuto-Zaera C, Tzeli D, Williams-Young D, Tubman NM, Matoušek M, Brabec J, Veis L, Xantheas SS, de Jong WA. The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron-Sulfur Cubanes. J Chem Theory Comput 2022; 18:687-702. [PMID: 35034448 DOI: 10.1021/acs.jctc.1c00830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Iron-sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. To provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III)4S4(SMe)4]-2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.
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Affiliation(s)
- Carlos Mejuto-Zaera
- University of California, Berkeley, California 94720, United States.,Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 15784, Greece.,Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
| | - David Williams-Young
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Norm M Tubman
- Quantum Artificial Intelligence Lab. (QuAIL), Exploration Technology Directorate, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Mikuláš Matoušek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Jiri Brabec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Sotiris S Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98185, United States
| | - Wibe A de Jong
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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16
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Hognon C, Bignon E, Harle G, Touche N, Grandemange S, Monari A. The Iron Maiden. Cytosolic Aconitase/IRP1 Conformational Transition in the Regulation of Ferritin Translation and Iron Hemostasis. Biomolecules 2021; 11:biom11091329. [PMID: 34572542 PMCID: PMC8469783 DOI: 10.3390/biom11091329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/29/2021] [Accepted: 09/07/2021] [Indexed: 01/16/2023] Open
Abstract
Maintaining iron homeostasis is fundamental for almost all living beings, and its deregulation correlates with severe and debilitating pathologies. The process is made more complicated by the omnipresence of iron and by its role as a fundamental component of a number of crucial metallo proteins. The response to modifications in the amount of the free-iron pool is performed via the inhibition of ferritin translation by sequestering consensus messenger RNA (mRNA) sequences. In turn, this is regulated by the iron-sensitive conformational equilibrium between cytosolic aconitase and IRP1, mediated by the presence of an iron-sulfur cluster. In this contribution, we analyze by full-atom molecular dynamics simulation, the factors leading to both the interaction with mRNA and the conformational transition. Furthermore, the role of the iron-sulfur cluster in driving the conformational transition is assessed by obtaining the related free energy profile via enhanced sampling molecular dynamics simulations.
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Affiliation(s)
- Cécilia Hognon
- Université de Lorraine and CNRS, UMR 7019 LPCT, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Emmanuelle Bignon
- Université de Lorraine and CNRS, UMR 7019 LPCT, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Guillaume Harle
- Université de Lorraine and CNRS, UMR 7039 CRAN, F-54000 Nancy, France; (G.H.); (N.T.)
| | - Nadège Touche
- Université de Lorraine and CNRS, UMR 7039 CRAN, F-54000 Nancy, France; (G.H.); (N.T.)
| | - Stéphanie Grandemange
- Université de Lorraine and CNRS, UMR 7039 CRAN, F-54000 Nancy, France; (G.H.); (N.T.)
- Correspondence: (S.G.); (A.M.)
| | - Antonio Monari
- Université de Lorraine and CNRS, UMR 7019 LPCT, F-54000 Nancy, France; (C.H.); (E.B.)
- Université de Paris and CNRS, ITODYS, F-75006 Paris, France
- Correspondence: (S.G.); (A.M.)
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17
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Shao Y, de Groot HJM, Buda F. Two-Channel Model for Electron Transfer in a Dye-Catalyst-Dye Supramolecular Complex for Photocatalytic Water Splitting. CHEMSUSCHEM 2021; 14:3155-3162. [PMID: 34097820 PMCID: PMC8453919 DOI: 10.1002/cssc.202100846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/24/2021] [Indexed: 05/04/2023]
Abstract
To improve the performance of dye-sensitized photoelectrochemical cell (DS-PEC) devices for splitting water, the tailoring of the photocatalytic four-photon water oxidation half-reaction represents a principle challenge of fundamental significance. In this study, a Ru-based water oxidation catalyst (WOC) covalently bound to two 2,6-diethoxy-1,4,5,8-diimide-naphthalene (NDI) dye functionalities provides comparable driving forces and channels for electron transfer. Constrained ab initio molecular dynamics simulations are performed to investigate the photocatalytic cycle of this two-channel model for photocatalytic water splitting. The introduction of a second light-harvesting dye in the Ru-based dye-WOC-dye supramolecular complex enables two separate parallel electron-transfer channels, leading to a five-step catalytic cycle with three intermediates and two doubly oxidized states. The total spin S=1 is conserved during the catalytic process and the system with opposite spin on the oxidized NDI proceeds from the Ru=O intermediate to the final Ru-O2 intermediate with a triplet molecular 3 O2 ligand that is eventually released into the environment. The in-depth insight into the proposed photocatalytic cycle of the two-channel model provides a strategy for the development of novel high-efficiency supramolecular complexes for DS-PEC devices with buildup and conservation of spin multiplicity along the reaction coordinate as a design principle.
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Affiliation(s)
- Yang Shao
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
| | - Huub J. M. de Groot
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
| | - Francesco Buda
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
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18
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Bím D, Alonso-Gil S, Srnec M. From Synthetic to Biological Fe 4 S 4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes. Chempluschem 2020; 85:2534-2541. [PMID: 33245201 DOI: 10.1002/cplu.202000663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Indexed: 11/10/2022]
Abstract
By employing the computational protocol for calculation of reduction potentials of the Fe4 S4 -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe4 S4 , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.
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Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
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19
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da Silva TU, Pougy KDC, Albuquerque MG, da Silva Lima CH, Machado SDP. Development of parameters compatible with the CHARMM36 force field for [Fe 4S 4] 2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019. J Biomol Struct Dyn 2020; 40:3481-3491. [PMID: 33183173 DOI: 10.1080/07391102.2020.1847687] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe4S4]2+ that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe4S4]2+ through the CHARMM36 force field.
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20
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Trindade IB, Invernici M, Cantini F, Louro RO, Piccioli M. PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems. FEBS J 2020; 288:3010-3023. [PMID: 33124176 DOI: 10.1111/febs.15615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/10/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023]
Abstract
Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their physiological role. For those metalloproteins containing paramagnetic states, the enhanced relaxation caused by the unpaired electrons often makes signal detection unfeasible near the metal center, precluding adequate structural characterization right where it is more biochemically relevant. Here, we report a protein structure determination by NMR where two different sets of restraints, one containing Nuclear Overhauser Enhancements (NOEs) and another containing Paramagnetic Relaxation Enhancements (PREs), are used separately and eventually together. The protein PioC from Rhodopseudomonas palustris TIE-1 is a High Potential Iron-Sulfur Protein (HiPIP) where the [4Fe-4S] cluster is paramagnetic in both oxidation states at room temperature providing the source of PREs used as alternative distance restraints. Comparison of the family of structures obtained using NOEs only, PREs only, and the combination of both reveals that the pairwise root-mean-square deviation (RMSD) between them is similar and comparable with the precision within each family. This demonstrates that, under favorable conditions in terms of protein size and paramagnetic effects, PREs can efficiently complement and eventually replace NOEs for the structural characterization of small paramagnetic metalloproteins and de novo-designed metalloproteins by NMR. DATABASES: The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).
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Affiliation(s)
- Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Michele Invernici
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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21
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Kaiser J, Castellano M, Gnandt D, Koslowski T. Monte Carlo simulation and thermodynamic integration applied to protein charge transfer. J Comput Chem 2020; 41:1105-1115. [PMID: 31981372 DOI: 10.1002/jcc.26155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/29/2019] [Accepted: 01/02/2020] [Indexed: 11/09/2022]
Abstract
We introduce a combination of Monte Carlo simulation and thermodynamic integration methods to address a model problem in free energy computations, electron transfer in proteins. The feasibility of this approach is tested using the ferredoxin protein from Clostridium acidurici. The results are compared to numerical solutions of the Poisson-Boltzmann equation and data from recent molecular dynamics simulations on charge transfer in a protein complex, the NrfHA nitrite reductase of Desulfovibrio vulgaris. Despite the conceptual and computational simplicity of the Monte Carlo approach, the data agree well with those obtained by other methods. A link to experiments is established via the cytochrome subunit of the bacterial photosynthetic reaction center of Rhodopseudomonas viridis.
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Affiliation(s)
- Jan Kaiser
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
| | - Mike Castellano
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
| | - David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany
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22
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Teo RD, Migliore A, Beratan DN. Mutation effects on charge transport through the p58c iron-sulfur protein. Chem Sci 2020; 11:7076-7085. [PMID: 33250976 PMCID: PMC7690218 DOI: 10.1039/d0sc02245d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/16/2020] [Indexed: 12/25/2022] Open
Abstract
Growing experimental evidence indicates that iron–sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [Fe4S4] clusters, mediated by proteins and DNA, may convey signals to coordinate enzyme action. Human primase is a well studied [Fe4S4] protein, and its p58c domain (which contains an [Fe4S4] cluster) plays a role in the initiation of DNA replication. The Y345C mutation in p58c is linked to gastric tumors and may influence the protein-mediated charge transport. The complexity of protein–DNA systems, and the intricate electronic structure of [Fe4S4] clusters, have impeded progress into understanding functional charge transport in these systems. In this study, we built force fields to describe the high potential [Fe4S4] cluster in both oxidation states. The parameterization is compatible with AMBER force fields and enabled well-balanced molecular dynamics simulations of the p58c–RNA/DNA complex relevant to the initiation of DNA replication. Using the molecular mechanics Poisson–Boltzmann and surface area solvation method on the molecular dynamics trajectories, we find that the p58c mutation induces a modest change in the p58c–duplex binding free energy in agreement with recent experiments. Through kinetic modeling and analysis, we identify key features of the main charge transport pathways in p58c. In particular, we find that the Y345C mutation partially changes the composition and frequency of the most efficient (and potentially relevant to the biological function) charge transport pathways between the [Fe4S4] cluster and the duplex. Moreover, our approach sets the stage for a deeper understanding of functional charge transfer in [Fe4S4] protein–DNA complexes. Functional electron transfer between the [Fe4S4] cluster and the nucleic acid is impacted by a Y345C mutation in the p58c subunit of human primase.![]()
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ;
| | - Agostino Migliore
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ;
| | - David N Beratan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ; .,Department of Physics , Duke University , Durham , North Carolina 27708 , USA.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , USA
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23
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Suess CJ, Martins FL, Croft AK, Jäger CM. Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE. J Chem Inf Model 2019; 59:5111-5125. [PMID: 31730347 DOI: 10.1021/acs.jcim.9b00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Experimental assessment of catalytic reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates and sensitivity of cofactors such as iron-sulfur clusters. Here, we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radical S-adenosylmethione enzyme 7-carboxy-7-deazaguanine synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg2+, Ca2+, or Na+. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semiempirical methods. The impact of intermolecular interactions on RSE was clearly established, and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates as candidates for catalytic turnover by QueE.
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Affiliation(s)
- Christian J Suess
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Floriane L Martins
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna K Croft
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
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24
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Sarre A, Stelter M, Rollo F, De Bonis S, Seck A, Hognon C, Ravanat JL, Monari A, Dehez F, Moe E, Timmins J. The three Endonuclease III variants of Deinococcus radiodurans possess distinct and complementary DNA repair activities. DNA Repair (Amst) 2019; 78:45-59. [DOI: 10.1016/j.dnarep.2019.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/26/2022]
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25
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Carrillo-Campos J, Riveros-Rosas H, Rodríguez-Sotres R, Muñoz-Clares RA. Bona fide choline monoxygenases evolved in Amaranthaceae plants from oxygenases of unknown function: Evidence from phylogenetics, homology modeling and docking studies. PLoS One 2018; 13:e0204711. [PMID: 30256846 PMCID: PMC6157903 DOI: 10.1371/journal.pone.0204711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/12/2018] [Indexed: 12/25/2022] Open
Abstract
Few land plants can synthesize and accumulate the osmoprotectant glycine betaine (GB) even though this metabolic trait has major adaptive importance given the prevalence of drought, hypersaline soils or cold. GB is synthesized from choline in two reactions catalyzed by choline monooxygenases (CMOs) and enzymes of the family 10 of aldehyde dehydrogenases (ALDH10s) that gained betaine aldehyde dehydrogenase activity (BADH). Homolog genes encoding CMO and ALDH10 enzymes are present in all known land plant genomes, but since GB-non-accumulators plants lack the BADH-type ALDH10 isozyme, they would be expected to also lack the CMO activity to avoid accumulation of the toxic betaine aldehyde. To explore CMOs substrate specificity, we performed amino acid sequence alignments, phylogenetic analysis, homology modeling and docking simulations. We found that plant CMOs form a monophyletic subfamily within the Rieske/mononuclear non-heme oxygenases family with two clades: CMO1 and CMO2, the latter diverging from CMO1 after gene duplication. CMO1 enzymes are present in all plants; CMO2s only in the Amaranthaceae high-GB-accumulators plants. CMO2s, and particularly their mononuclear non-heme iron domain where the active site is located, evolved at a faster rate than CMO1s, which suggests positive selection. The homology model and docking simulations of the spinach CMO2 enzyme showed at the active site three aromatic residues forming a box with which the trimethylammonium group of choline could interact through cation-π interactions, and a glutamate, which also may interact with the trimethylammonium group through a charge-charge interaction. The aromatic box and the carboxylate have been shown to be critical for choline binding in other proteins. Interestingly, these residues are conserved in CMO2 proteins but not in CMO1 proteins, where two of these aromatic residues are leucine and the glutamate is asparagine. These findings reinforce our proposal that the CMO1s physiological substrate is not choline but a still unknown metabolite.
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Affiliation(s)
- Javier Carrillo-Campos
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosario A. Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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26
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Na S, Jurkovic S, Friedrich T, Koslowski T. Charge transfer through a fragment of the respiratory complex I and its regulation: an atomistic simulation approach. Phys Chem Chem Phys 2018; 20:20023-20032. [PMID: 30022212 DOI: 10.1039/c8cp02420k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We simulate electron transfer within a fragment of the NADH:ubiquinone oxidoreductase (respiratory complex I) of the hyperthermophilic bacterium Aquifex aeolicus. We apply molecular dynamics simulations, thermodynamic integration, and a thermodynamic network least squares analysis to compute two key parameters of Marcus' theory of charge transfer, the thermodynamic driving force and the reorganization energy. Intramolecular contributions to the Gibbs free energy differences of electron and hydrogen transfer processes, ΔG, are accessed by calibrating against experimental redox titration data. This approach permits the computation of the interactions between the species NAD+, FMNH2, N1a-, and N3-, and the construction of a free energy surface for the flow of electrons within the fragment. We find NAD+ to be a strong candidate for the regulation of charge transfer.
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Affiliation(s)
- Sehee Na
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße23a, 79104 Freiburg im Breisgau, Germany.
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27
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Cherepanov DA, Milanovsky GE, Gopta OA, Balasubramanian R, Bryant DA, Semenov AY, Golbeck JH. Electron–Phonon Coupling in Cyanobacterial Photosystem I. J Phys Chem B 2018; 122:7943-7955. [DOI: 10.1021/acs.jpcb.8b03906] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitry A. Cherepanov
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 117977 Moscow, Russia
| | - Georgy E. Milanovsky
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
| | - Oksana A. Gopta
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Ramakrishnan Balasubramanian
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
- Department of Chemistry and Biochemistry, Montana State University, 103 Chemistry and Biochemistry Building, PO Box 173400, Bozeman, Montana 59717, United States
| | - Alexey Yu. Semenov
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 117977 Moscow, Russia
| | - John H. Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
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28
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Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Nature 2018; 557:123-126. [PMID: 29695868 PMCID: PMC6004266 DOI: 10.1038/s41586-018-0061-y] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/20/2018] [Indexed: 12/31/2022]
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29
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Stüble P, Peschke S, Johrendt D, Röhr C. Na7[Fe2S6], Na2[FeS2] and Na2[FeSe2]: New ‘reduced’ sodium chalcogenido ferrates. J SOLID STATE CHEM 2018. [DOI: 10.1016/j.jssc.2017.10.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Dourado DFAR, Swart M, Carvalho ATP. Why the Flavin Adenine Dinucleotide (FAD) Cofactor Needs To Be Covalently Linked to Complex II of the Electron-Transport Chain for the Conversion of FADH 2 into FAD. Chemistry 2017; 24:5246-5252. [PMID: 29124817 PMCID: PMC5969107 DOI: 10.1002/chem.201704622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/07/2017] [Indexed: 11/10/2022]
Abstract
A covalently bound flavin cofactor is predominant in the succinate‐ubiquinone oxidoreductase (SQR; Complex II), an essential component of aerobic electron transport, and in the menaquinol‐fumarate oxidoreductase (QFR), the anaerobic counterpart, although it is only present in approximately 10 % of the known flavoenzymes. This work investigates the role of this 8α‐N3‐histidyl linkage between the flavin adenine dinucleotide (FAD) cofactor and the respiratory Complex II. After parameterization with DFT calculations, classical molecular‐dynamics simulations and quantum‐mechanics calculations for Complex II:FAD and Complex II:FADH2, with and without the covalent bond, were performed. It was observed that the covalent bond is essential for the active‐center arrangement of the FADH2/FAD cofactor. Removal of this bond causes a displacement of the isoalloxazine group, which influences interactions with the protein, flavin solvation, and possible proton‐transfer pathways. Specifically, for the noncovalently bound FADH2 cofactor, the N1 atom moves away from the His‐A365 and His‐A254 residues and the N5 atom moves away from the glutamine‐62A residue. Both of the histidine and glutamine residues interact with a chain of water molecules that cross the enzyme, which is most likely involved in proton transfer. Breaking this chain of water molecules could thereby compromise proton transfer across the two active sites of Complex II.
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Affiliation(s)
- Daniel F A R Dourado
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, UK.,Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, Northern Ireland, UK
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, 17003, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Alexandra T P Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
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31
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Schwarz M, Stüble P, Röhr C. Rubidium chalcogenido diferrates(III) containing dimers [Fe2
Q
6]6− of edge-sharing tetrahedra (Q=O, S, Se). ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2017. [DOI: 10.1515/znb-2017-0076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The two isotypic rubidium chalcogenido diferrates Rb12[Fe2
Q
6](Q
2)3 (Q=S/Se), which both form needles with green-metallic lustre, were synthesized from Rb2S, elemental iron, rubidium and sulfur (Q=S) or from the pure elements (Q=Se) at maximum temperatures of 500–800°C. Their triclinic crystal structures were determined by means of X-ray single crystal data (space group P1̅, a=863.960(10)/903.2(3), b=942.790(10)/982.1(3), c=1182.70(2)/1227.4(4) pm, α=77.4740(10)/77.262(6), β=71.5250(10)/71.462(6), γ=63.7560(10)/63.462(5)°, Z=1, R1=0.0308/0.0658 for Q=S/Se). The structures contain isolated dinuclear anions [FeIII
2
Q
6]6− composed of two edge-sharing [FeQ
4] tetrahedra (dFe
−Q
=223.4–232.3/236.2–244.8 pm), which are also found in the two polymorphs of the pure alkali diferrates Rb6[Fe2
Q
6]. The diferrate ions are arranged in layers running in the a/b plane around z=0. Inbetween (around
z
≈
1
2
$z \approx {1 \over 2}$
), two crystallographically different disulfide/diselenide ions
Q
2
2
−
$Q_2^{2 - }$
(dQ
−Q
=211.1–213.4/237.9–241.1 pm), which are arranged in slightly puckered 36 nets, are intercalated. The intra-anionic distances and angles, the Rb coordination numbers and the molar volumes of these two ‘double-salts’ are in accordance with their corresponding reference compounds, Rb6[Fe2
Q
6] and Rb2
Q
2. In addition, the two polymorphs of Rb6[Fe2Se6], which are both isotypic with the sulfido analogous (Cs6[Ga2Se6]-type, monoclinic, space group P21
/c, a=827.84(5), b=1329.51(7), c=1074.10(6) pm, β=127.130(5)°, R1=0.0443 and Ba6[Al2Sb6]-type, orthorhombic, space group Cmce, a=1963.70(3), b=718.98(3), c=1348.40(7) pm, R1=0.0264) were prepared and characterized to complete the series of alkali diferrates(III) with oxido, sulfido and selenido ligands. The electronic band structures of the three Rb salts Rb6[Fe2
Q
6], which have been calculated within the GGA+U approach applying an AFM spin ordering in the dimers and appropriate Hubbard parameters, allow a comparison of the chemical bonding characteristics (e.g. covalency) and the magnetic properties (magnetic moments) within the series of chalcogenido ligands. An analysis of the spin densities enables a comparative consideration of the mechanisms crucial for the magnetic ordering in chalcogenido ferrates. Ultimately, the electronic structure of the new compound Rb12[Fe2S6](S2)3 nicely compares with those of the S2-free reference compound Rb6[Fe2S6].
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Affiliation(s)
- Michael Schwarz
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstraße 21 , D-79104 Freiburg , Germany
| | - Pirmin Stüble
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstraße 21 , D-79104 Freiburg , Germany
| | - Caroline Röhr
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstraße 21 , D-79104 Freiburg , Germany
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32
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Wang R, Ozhgibesov M, Hirao H. Partial hessian fitting for determining force constant parameters in molecular mechanics. J Comput Chem 2016; 37:2349-59. [DOI: 10.1002/jcc.24457] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Ruixing Wang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University21 Nanyang Link637371 Singapore
| | - Mikhail Ozhgibesov
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University21 Nanyang Link637371 Singapore
| | - Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University21 Nanyang Link637371 Singapore
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