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Terranova U. Residues surrounding the active centre of carbon monoxide dehydrogenase are key in converting [Formula: see text] to CO. J Biol Inorg Chem 2021; 26:617-624. [PMID: 34255144 DOI: 10.1007/s00775-021-01878-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/17/2021] [Indexed: 10/20/2022]
Abstract
The enzyme carbon monoxide dehydrogenase is capable of efficiently converting [Formula: see text] to CO and, therefore, can enable an affordable [Formula: see text] recycling strategy. The reduction of [Formula: see text] occurs at a peculiar nickel-iron-sulfur cluster, following a mechanism that remains little understood. In this study, we have used ab initio molecular dynamics simulations to explore the free energy landscape of the reaction. We predict the existence of a COOH ligand that strongly interacts with the surrounding protein residues and favours a mechanism where a [Formula: see text] molecule is eliminated before CO. We have taken advantages of the insights offered by our simulations to revisit the catalytic mechanism and the role of the residues surrounding the active centre in particular, thus assisting in the design of inorganic catalysts that mimic the enzyme.
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Affiliation(s)
- Umberto Terranova
- Faculty of Medicine and Health Sciences, Crewe Campus, University of Buckingham, Crewe, CW1 5DU, UK.
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2
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Siemer N, Lüken A, Zalibera M, Frenzel J, Muñoz-Santiburcio D, Savitsky A, Lubitz W, Muhler M, Marx D, Strunk J. Atomic-Scale Explanation of O2 Activation at the Au–TiO2 Interface. J Am Chem Soc 2018; 140:18082-18092. [DOI: 10.1021/jacs.8b10929] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Niklas Siemer
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Alexander Lüken
- Lehrstuhl für Technische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Michal Zalibera
- Max-Planck-Institut für Chemische Energiekonversion, 45470 Mülheim/Ruhr, Germany
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, SK-812 37 Bratislava, Slovakia
| | - Johannes Frenzel
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | | | - Anton Savitsky
- Fakultät Physik, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, 45470 Mülheim/Ruhr, Germany
| | - Martin Muhler
- Lehrstuhl für Technische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jennifer Strunk
- Leibniz-Institut für Katalyse e.V. an der Universität Rostock, 18059 Rostock, Germany
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3
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The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease. J Biol Inorg Chem 2018; 23:599-612. [PMID: 29435647 PMCID: PMC6006223 DOI: 10.1007/s00775-018-1538-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 02/08/2023]
Abstract
NEET proteins comprise a new class of [2Fe-2S] cluster proteins. In human, three genes encode for NEET proteins: cisd1 encodes mitoNEET (mNT), cisd2 encodes the Nutrient-deprivation autophagy factor-1 (NAF-1) and cisd3 encodes MiNT (Miner2). These recently discovered proteins play key roles in many processes related to normal metabolism and disease. Indeed, NEET proteins are involved in iron, Fe-S, and reactive oxygen homeostasis in cells and play an important role in regulating apoptosis and autophagy. mNT and NAF-1 are homodimeric and reside on the outer mitochondrial membrane. NAF-1 also resides in the membranes of the ER associated mitochondrial membranes (MAM) and the ER. MiNT is a monomer with distinct asymmetry in the molecular surfaces surrounding the clusters. Unlike its paralogs mNT and NAF-1, it resides within the mitochondria. NAF-1 and mNT share similar backbone folds to the plant homodimeric NEET protein (At-NEET), while MiNT's backbone fold resembles a bacterial MiNT protein. Despite the variation of amino acid composition among these proteins, all NEET proteins retained their unique CDGSH domain harboring their unique 3Cys:1His [2Fe-2S] cluster coordination through evolution. The coordinating exposed His was shown to convey the lability to the NEET proteins' [2Fe-2S] clusters. In this minireview, we discuss the NEET fold and its structural elements. Special attention is given to the unique lability of the NEETs' [2Fe-2S] cluster and the implication of the latter to the NEET proteins' cellular and systemic function in health and disease.
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4
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Tsipis AC. RETRACTED: DFT challenge of intermetallic interactions: From metallophilicity and metallaromaticity to sextuple bonding. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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5
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Barborini M, Guidoni L. Geometries of low spin states of multi-centre transition metal complexes through extended broken symmetry variational Monte Carlo. J Chem Phys 2016; 145:124107. [DOI: 10.1063/1.4963015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matteo Barborini
- Dipartimento di Ingegneria, Scienze dell’Informazione e Matematica, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
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Barborini M. Neutral, Anionic, and Cationic Manganese Dimers through Density Functional Theory. J Phys Chem A 2016; 120:1716-26. [DOI: 10.1021/acs.jpca.5b12169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matteo Barborini
- S3 Research Center, CNR-NANO, Via Campi 213/a, 41125 Modena, Italy
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7
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Terranova U, de Leeuw NH. Aqueous Fe2S2 cluster: structure, magnetic coupling, and hydration behaviour from Hubbard U density functional theory. Phys Chem Chem Phys 2015; 16:13426-33. [PMID: 24881882 DOI: 10.1039/c4cp00984c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We present a DFT + U investigation of the all-ferrous Fe2S2 cluster in aqueous solution. We determine the value of U by tuning the geometry of the cluster in the gas-phase to that obtained by the highly accurate CCSD(T) method. When the optimised value of U is employed for the aqueous Fe2S2 cluster (Fe2S2(aq)), the resulting geometry agrees well with the X-ray diffraction structure, while the magnetic coupling is in line with the estimate from Mössbauer data. Molecular dynamics trajectories predict Fe2S2(aq) to be stable in water, regardless of the introduction of U. However, significant differences arise in the geometry, hydration, and exchange constant of the solvated clusters.
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Affiliation(s)
- Umberto Terranova
- Department of Chemistry, University College London, London, WC1H 0AJ, UK.
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Ali ME, Staemmler V, Marx D. Magnetostructural dynamics of Rieske versus ferredoxin iron-sulfur cofactors. Phys Chem Chem Phys 2015; 17:6289-96. [PMID: 25648433 DOI: 10.1039/c4cp05465b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The local chemical environment of the [2Fe-2S] cofactor hosted by ferredoxin and Rieske-type proteins is fundamentally different due to the presence of distinct ligands at the two iron centers in the case of Rieske proteins, whereas they are identical in ferredoxins. This renders Rieske [2Fe-2S] cores chemically asymmetric and results in more complex vibrational spectra as compared to ferredoxin. Likewise, one would expect other properties, for instance the dynamics of the magnetic exchange coupling constant J, to be also more complex. Applying ab initio molecular dynamics using our recently introduced spin-constrained two-determinant extended broken symmetry (CEBS) approach to Rieske and ferredoxin model complexes at 300 K, we extract the molecular fluctuations and the resulting magnetostructural cross-correlations involving the antiferromagnetic exchange interaction J(t). This analysis demonstrates that the details of the magnetostructural dynamics are indeed distinctly different for Rieske and ferredoxin cofactors, while the time averages of 〈J〉 are shown to be essentially identical. In particular, the frequency window between about 200 and 350 cm(-1), is a "fingerprint region" that allows one to distinguish chemically asymmetric from symmetric cofactors and thus Rieske proteins from ferredoxins.
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Affiliation(s)
- Md Ehesan Ali
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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The iron-sulfur core in Rieske proteins is not symmetric. J Biol Inorg Chem 2014; 19:1287-93. [PMID: 25151276 DOI: 10.1007/s00775-014-1185-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
At variance with ferredoxins, Rieske-type proteins contain a chemically asymmetric iron-sulfur cluster. Nevertheless, X-ray crystallography apparently finds their [2Fe-2S] cores to be structurally symmetric or very close to symmetric (i.e. the four iron-sulfur bonds in the [2Fe-2S] core are equidistant). Using a combination of advanced density-based approaches, including finite-temperature molecular dynamics to access thermal fluctuations and free-energy profiles, in conjunction with correlated wavefunction-based methods we clearly predict an asymmetric core structure. This reveals a fundamental and intrinsic difference within the iron-sulfur clusters hosted by Rieske proteins and ferredoxins and thus opens up a new dimension for the ongoing efforts in understanding the role of Rieske-type [2Fe-2S] cluster in electron transfer processes that occur in almost all biological systems.
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10
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Schöppach A, Gnandt D, Koslowski T. Charge transfer in strongly correlated systems: an exact diagonalization approach to model Hamiltonians. J Chem Phys 2014; 140:134101. [PMID: 24712774 DOI: 10.1063/1.4869520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study charge transfer in bridged di- and triruthenium complexes from a theoretical and computational point of view. Ab initio computations are interpreted from the perspective of a simple empirical Hamiltonian, a chemically specific Mott-Hubbard model of the complexes' π electron systems. This Hamiltonian is coupled to classical harmonic oscillators mimicking a polarizable dielectric environment. The model can be solved without further approximations in a valence bond picture using the method of exact diagonalization and permits the computation of charge transfer reaction rates in the framework of Marcus' theory. In comparison to the exact solution, the Hartree-Fock mean field theory overestimates both the activation barrier and the magnitude of charge-transfer excitations significantly. For triruthenium complexes, we are able to directly access the interruthenium antiferromagnetic coupling strengths.
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Affiliation(s)
- Andreas Schöppach
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, D-79104 Freiburg im Breisgau, Germany
| | - David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, D-79104 Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, D-79104 Freiburg im Breisgau, Germany
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11
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Fink K, Staemmler V. A modified CAS-CI approach for an efficient calculation of magnetic exchange coupling constants. Mol Phys 2013. [DOI: 10.1080/00268976.2013.804961] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Bovi D, Guidoni L. Magnetic coupling constants and vibrational frequencies by extended broken symmetry approach with hybrid functionals. J Chem Phys 2012; 137:114107. [DOI: 10.1063/1.4752398] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Ali ME, Nair NN, Staemmler V, Marx D. Constrained spin-density dynamics of an iron-sulfur complex: Ferredoxin cofactor. J Chem Phys 2012; 136:224101. [DOI: 10.1063/1.4722552] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Fiethen SA, Staemmler V, Nair NN, Ribas-Arino J, Schreiner E, Marx D. Revealing the magnetostructural dynamics of [2Fe-2S] ferredoxins from reduced-dimensionality analysis of antiferromagnetic exchange coupling fluctuations. J Phys Chem B 2010; 114:11612-9. [PMID: 20718446 DOI: 10.1021/jp1014912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metalloproteins are biomolecular hybrids composed of an "inorganic core" embedded in a "bioorganic matrix". Cofactors typically contain transition metal clusters with complex electronic structure whereas the protein host undergoes dynamics on many length and time scales. This renders computational studies of spectroscopic properties challenging, in particular, when magnetic interactions are involved. In the present study we introduce a simplified description of the antiferromagnetic exchange coupling J in reduced dimensionality which allows one to study magnetostructural dynamics of [2Fe-2S] type iron-sulfur proteins in their oxidized form by molecular dynamics. It is demonstrated that parametrization in terms of a 2D J-surface faithfully reproduces the rigorous results both in vacuo and in Anabaena ferredoxin. In particular, we present a parametrization which relies on a spin-projected density functional approach based on two Kohn-Sham determinants corrected for self-interaction via a self-consistent linear-response Hubbard-U technique. This yields an average J for Anabaena Fd in close agreement with experimental in vitro results without any specific adjustment or fitting. The analytical J-surface can be used for [2Fe-2S] proteins in their oxidized form in general and the idea can be extended to other metalloproteins as well as to other spectroscopic properties.
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Affiliation(s)
- S Annamaria Fiethen
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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