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Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
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Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
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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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Li Z, Guo S, Sun Q, Chan GKL. Electronic landscape of the P-cluster of nitrogenase as revealed through many-electron quantum wavefunction simulations. Nat Chem 2019; 11:1026-1033. [PMID: 31570817 DOI: 10.1038/s41557-019-0337-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/20/2019] [Indexed: 11/09/2022]
Abstract
The electronic structure of the nitrogenase metal cofactors is central to nitrogen fixation. However, the P-cluster and FeMo cofactor, each containing eight Fe atoms, have eluded detailed characterization of their electronic properties. We report on the low-energy electronic states of the P-cluster in three oxidation states through exhaustive many-electron wavefunction simulations enabled by new theoretical methods. The energy scales of orbital and spin excitations overlap, yielding a dense spectrum with features that we trace to the underlying atomic states and recouplings. The clusters exist in superpositions of spin configurations with non-classical spin correlations, complicating interpretation of magnetic spectroscopies, whereas the charges are mostly localized from reorganization of the cluster and its surroundings. On oxidation, the opening of the P-cluster substantially increases the density of states, which is intriguing given its proposed role in electron transfer. These results demonstrate that many-electron simulations stand to provide new insights into the electronic structure of the nitrogenase cofactors.
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Affiliation(s)
- Zhendong Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Sheng Guo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Qiming Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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Volbeda A, Mouesca JM, Darnault C, Roessler MM, Parkin A, Armstrong FA, Fontecilla-Camps JC. X-ray structural, functional and computational studies of the O 2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster. Chem Commun (Camb) 2018; 54:7175-7178. [PMID: 29888350 DOI: 10.1039/c8cc02896f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity. Computational studies on electron transfer help to explain how the structural and redox properties of the novel FeS cluster modulate the observed phenotype.
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Affiliation(s)
- A Volbeda
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France.
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Wodyński A, Kaupp M. Noncollinear Two-Component Quasirelativistic Description of Spin Interactions in Exchange-Coupled Systems. Mapping Generalized Broken-Symmetry States to Effective Spin Hamiltonians. J Chem Theory Comput 2018; 14:1267-1276. [PMID: 29376389 DOI: 10.1021/acs.jctc.7b01067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We provide a consistent mapping of noncollinear two-component quasirelativistic DFT energies with appropriate orientations of localized spinor quantization axes for multinuclear exchange-coupled transition-metal complexes onto an uncoupled anisotropic effective spin Hamiltonian. This provides access to the full exchange interaction tensor between the centers of spin-coupled systems in a consistent way. The proposed methodology may be best viewed as a generalized broken-symmetry density functional theory approach (gBS-DFT). While the calculations provided are limited to trinuclear systems ([M3O(OOCH)6(H2O)3]+, where M = Cr(III), Mn(III), Fe(III)) with C3 symmetry, the method provides a general framework that is extendable to arbitrary systems. It offers an alternative to previous approaches to single-ion zero-field splittings, and it provides access to the less often examined antisymmetric Dzyaloshinskii-Moriya exchange interaction. Spin-orbit coupling is included self-consistently. This will be of particular importance for complexes involving 4d or 5d transition metal centers or possibly also for f-block elements, where a perturbational treatment of spin-orbit coupling may not be valid anymore. While a comparison with experimental data was indirect due to simplifications in the chosen model structures, the agreement obtained indicates the essential soundness of the presented approach.
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Affiliation(s)
- Artur Wodyński
- Institut für Chemie, Theoretische Chemie/Quantenchemie , Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135 , D-10623 Berlin , Germany.,National Centre for Nuclear Research , Andrzeja Sołtana 7 , 05-400 Otwock-Świerk , Poland
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie , Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135 , D-10623 Berlin , Germany
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Kamnev AA, Tugarova AV. Sample treatment in Mössbauer spectroscopy for protein-related analyses: Nondestructive possibilities to look inside metal-containing biosystems. Talanta 2017; 174:819-837. [PMID: 28738659 DOI: 10.1016/j.talanta.2017.06.057] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/01/2017] [Accepted: 06/19/2017] [Indexed: 01/07/2023]
Abstract
In this review, the unique possibilities are considered of the 57Fe transmission (TMS) and 57Co emission (EMS) variants of Mössbauer (nuclear γ-resonance) spectroscopy as nondestructive techniques with minimal sample preparation/treatment and a significant analytical potential, with a focus on the analysis of cation-binding sites in metalloproteins. The techniques are shown to provide unique structural and quantitative information on the coordination microenvironment, the chemical state and transformations of the Mössbauer nuclides in sophisticated metal-containing proteins, including those within complicated supramolecular structures, and in microbial cells or tissues. Recent representative examples of analyses of Fe-containing proteins by 57Fe TMS are briefly discussed, along with the newly emerging data on using 57Co EMS for probing the structural organisation of 57Co-doped cation-binding sites in sophisticated biocomplexes including metalloenzymes. Finally, some rare or exotic applications of Mössbauer spectroscopy (including the synchrotron-based methodology) in protein-related studies are outlined.
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Affiliation(s)
- Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia.
| | - Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia
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Abstract
The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.
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Affiliation(s)
- Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University , SE-106 91 Stockholm, Sweden
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Quantum chemical approaches to [NiFe] hydrogenase. Essays Biochem 2017; 61:293-303. [PMID: 28487405 DOI: 10.1042/ebc20160079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
Abstract
The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes.
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