1
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Min J, Ali F, Brooks BR, Bruce BD, Amin M. Predicting Iron-Sulfur Cluster Redox Potentials: A Simple Model Derived from Protein Structures. ACS OMEGA 2025; 10:15790-15798. [PMID: 40291006 PMCID: PMC12019745 DOI: 10.1021/acsomega.5c01976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 04/02/2025] [Accepted: 04/04/2025] [Indexed: 04/30/2025]
Abstract
Iron-sulfur (Fe-S) clusters are critical cofactors in metalloproteins, essential for cellular processes such as energy production, DNA repair, enzymatic catalysis, and metabolic regulation. While Fe-S cluster functions are intimately linked to their redox properties, their precise roles in many proteins remain unclear. In this study, we present a regression model based on experimental redox potential (E m ) data, utilizing only two features: the Fe-S cluster's total charge and the Fe atoms' average valence. This model achieves a high correlation with experimental data (R 2 = 0.82) and an average prediction error of 0.12 V. Applying this model across the Protein Data Bank, we predict E m values for all cataloged Fe-S clusters, uncovering redox potential trends across diverse cluster classes. The computed redox potentials showed strong agreement with experimental values, achieving an overall accuracy of 88%. This streamlined, computationally accessible approach enhances the annotation and mechanistic understanding of Fe-S proteins, offering new insights into the redox variability of electron transport proteins. Our model holds promise for advancing studies of metalloprotein function and facilitating the design of bioinspired redox systems.
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Affiliation(s)
- Jiyeon Min
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
- Biophysics
Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Fidaa Ali
- Bredesen
Center for Interdisciplinary Research and Graduate Education, Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996, United States
| | - Bernard R. Brooks
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Barry D. Bruce
- Bredesen
Center for Interdisciplinary Research and Graduate Education, Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996 United States
| | - Muhamed Amin
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
- Department
of Sciences, University College Groningen, University of Groningen, 9718 BG, Groningen, The Netherlands
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2
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Landry L, Li P. Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals. J Phys Chem B 2024; 128:10329-10338. [PMID: 39395013 DOI: 10.1021/acs.jpcb.4c03219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2024]
Abstract
Metalloproteins widely exist in biology, playing pivotal roles in diverse life processes. Meanwhile, molecular dynamics (MD) simulations based on classical force fields has emerged as an important tool in scientific research. Partial charges are critical parameters within classical force fields and usually derived from quantum mechanical (QM) calculations. However, QM calculations are often time-consuming and prone to basis set dependence. Alternatively, fluctuating charge (FQ) models offer another avenue for partial charge derivation, which has significant speed advantages and can be used for large-scale screening. Building upon our previous work, which introduced an FQ model for zinc-containing complexes, herein we extend this model to include additional 3d transition metals which are important to the life sciences, namely chromium, manganese, iron, cobalt, and nickel. Employing CM5 charges as target for parametrization, our FQ model accurately reproduces partial charges for 3d metal complexes featuring biologically relevant ligands. Furthermore, by using atomic charges derived by our FQ model, MD simulations have been performed. These charges showed excellent performance in simulating proteomic metal sites housing multiple metal ions, specifically, a metalloprotein containing an iron-sulfur cluster and another containing a dimanganese metal site, showcasing comparable performance to those of RESP charges. We anticipate that our study can accelerate the parametrization of atomic charges for metalloproteins featuring 3d transition metals, thereby facilitating simulations of relevant systems.
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Affiliation(s)
- Luke Landry
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Pengfei Li
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
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3
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Syed K. Ferredoxins: Functions, Evolution, Potential Applications, and Challenges of Subtype Classification. Curr Issues Mol Biol 2024; 46:9659-9673. [PMID: 39329926 PMCID: PMC11430716 DOI: 10.3390/cimb46090574] [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: 08/03/2024] [Revised: 08/27/2024] [Accepted: 08/31/2024] [Indexed: 09/28/2024] Open
Abstract
Ferredoxins are proteins found in all biological kingdoms and are involved in essential biological processes including photosynthesis, lipid metabolism, and biogeochemical cycles. Ferredoxins are classified into different groups based on the iron-sulfur (Fe-S) clusters that they contain. A new subtype classification and nomenclature system, based on the spacing between amino acids in the Fe-S binding motif, has been proposed in order to better understand ferredoxins' biological diversity and evolutionary linkage across different organisms. This new classification system has revealed an unparalleled diversity between ferredoxins and has helped identify evolutionarily linked ferredoxins between species. The current review provides the latest insights into ferredoxin functions and evolution, and the new subtype classification, outlining their potential biotechnological applications and the future challenges in streamlining the process.
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Affiliation(s)
- Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa, Empangeni 3886, South Africa
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4
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Jafari S, Ryde U, Irani M. Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods. Sci Rep 2023; 13:10832. [PMID: 37402767 PMCID: PMC10319735 DOI: 10.1038/s41598-023-37755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
[4Fe-4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe-Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe-4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r2SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O.Box 66175-416, Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O.Box 124, 221 00, Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O.Box 66175-416, Sanandaj, Iran.
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5
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Kanda T, Saito K, Ishikita H. Mechanism of Mixed-Valence Fe 2.5+···Fe 2.5+ Formation in Fe 4S 4 Clusters in the Ferredoxin Binding Motif. J Phys Chem B 2022; 126:3059-3066. [PMID: 35435680 PMCID: PMC9059760 DOI: 10.1021/acs.jpcb.2c01320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most low-potential Fe4S4 clusters exist in the conserved binding sequence CxxCxxC (CnCn+3Cn+6). Fe(II) and Fe(III) at the first (Cn) and third (Cn+6) cysteine ligand sites form a mixed-valence Fe2.5+···Fe2.5+ pair in the reduced Fe(II)3Fe(III) cluster. Here, we investigate the mechanism of how the conserved protein environment induces mixed-valence pair formation in the Fe4S4 clusters, FX, FA, and FB in photosystem I, using a quantum mechanical/molecular mechanical approach. Exchange coupling between Fe sites is predominantly determined by the shape of the Fe4S4 cluster, which is stabilized by the preorganized protein electrostatic environment. The backbone NH and CO groups in the conserved CxxCxxC and adjacent helix regions orient along the FeCn···FeC(n+6) axis, generating an electric field and stabilizing the FeCn(II)FeC(n+6)(III) state in FA and FB. The overlap of the d orbitals via -S- (superexchange) is observed for the single FeCn(II)···FeC(n+6)(III) pair, leading to the formation of the mixed-valence Fe2.5+···Fe2.5+ pair. In contrast, several superexchange Fe(II)···Fe(III) pairs are observed in FX due to the highly symmetric pair of the CDGPGRGGTC sequences. This is likely the origin of FX serving as an electron acceptor in the two electron transfer branches.
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Affiliation(s)
- Tomoki Kanda
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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6
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Jafari S, Tavares Santos YA, Bergmann J, Irani M, Ryde U. Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins. Inorg Chem 2022; 61:5991-6007. [PMID: 35403427 PMCID: PMC9044450 DOI: 10.1021/acs.inorgchem.1c03422] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Redox potentials
have been calculated for 12 different iron–sulfur
sites of 6 different types with 1–4 iron ions. Structures were
optimized with combined quantum mechanical and molecular mechanical
(QM/MM) methods, and the redox potentials were calculated using the
QM/MM energies, single-point QM methods in a continuum solvent or
by QM/MM thermodynamic cycle perturbations. We show that the best
results are obtained with a large QM system (∼300 atoms, but
a smaller QM system, ∼150 atoms, can be used for the QM/MM
geometry optimization) and a large value of the dielectric constant
(80). For absolute redox potentials, the B3LYP density functional
method gives better results than TPSS, and the results are improved
with a larger basis set. However, for relative redox potentials, the
opposite is true. The results are insensitive to the force field (charges
of the surroundings) used for the QM/MM calculations or whether the
protein and solvent outside the QM system are relaxed or kept fixed
at the crystal structure. With the best approach for relative potentials,
mean absolute and maximum deviations of 0.17 and 0.44 V, respectively,
are obtained after removing a systematic error of −0.55 V.
Such an approach can be used to identify the correct oxidation states
involved in a certain redox reaction. We
have studied redox potentials of 12 iron−sulfur
sites of 6 types with 1−4 iron ions. Structures were optimized
with combined quantum mechanical and molecular mechanical (QM/MM)
methods, and the redox potentials were calculated with QM/MM, QM calculations
in a continuum solvent or by QM/MM thermodynamic cycle perturbations.
The best results are obtained with the second approach using ∼300
atoms in the QM model and a large dielectric constant.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran.,Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Yakini A Tavares Santos
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Justin Bergmann
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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7
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Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming. Molecules 2021; 26:molecules26206129. [PMID: 34684710 PMCID: PMC8538827 DOI: 10.3390/molecules26206129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
The effect of hydrogen bonds around the active site of Anabaena [2Fe-2S] ferredoxin (Fd) on a vertical ionization potential of the reduced state (IP(red)) is examined based on the density functional theory (DFT) calculations. The results indicate that a single hydrogen bond increases the relative stability of the reduced state, and shifts IP(red) to a reductive side by 0.31–0.33 eV, regardless of the attached sulfur atoms. In addition, the IP(red) value can be changed by the number of hydrogen bonds around the active site. The results also suggest that the redox potential of [2Fe-2S] Fd is controlled by the number of hydrogen bonds because IP(red) is considered to be a major factor in the redox potential. Furthermore, there is a possibility that the redox potentials of artificial iron-sulfur clusters can be finely controlled by the number of the hydrogen bonds attached to the sulfur atoms of the cluster.
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8
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Kanda T, Saito K, Ishikita H. Electron Acceptor-Donor Iron Sites in the Iron-Sulfur Cluster of Photosynthetic Electron-Transfer Pathways. J Phys Chem Lett 2021; 12:7431-7438. [PMID: 34338530 DOI: 10.1021/acs.jpclett.1c01896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In photosystem I, two electron-transfer pathways via quinones (A1A and A1B) are merged at the iron-sulfur Fe4S4 cluster FX into a single pathway toward the other two Fe4S4 clusters FA and FB. Using a quantum mechanical/molecular mechanical approach, we identify the redox-active Fe sites in the clusters. In FA and FB, the Fe site, which does not belong to the CxxCxxCxxxCP motif, serves as an electron acceptor/donor. FX has two independent electron acceptor Fe sites for A- and B-branch electron transfers, depending on the Asp-B575 protonation state, which causes the A1A-to-FX electron transfer to be uphill and the A1B-to-FX electron transfer to be downhill. The two asymmetric electron-transfer pathways from A1 to FX and the separation of the electron acceptor and donor Fe sites are likely associated with the specific role of FX in merging the two electron transfer pathways into the single pathway.
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Affiliation(s)
- Tomoki Kanda
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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9
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Li B, Steindel P, Haddad N, Elliott SJ. Maximizing (Electro)catalytic CO 2 Reduction with a Ferredoxin-Based Reduction Potential Gradient. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Bin Li
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Phillip Steindel
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Narmien Haddad
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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10
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Miyagawa K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Okumura M, Yamaguchi K. Theory of chemical bonds in metalloenzymes XXIV electronic and spin structures of FeMoco and Fe-S clusters by classical and quantum computing. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1760388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Koichi Miyagawa
- The Institute for Scientific and Industrial Research, Osaka University, Ibaraki, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Japan
| | - Hiroshi Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
| | - Takashi Kawakami
- Graduate School of Science, Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
| | | | - Kizashi Yamaguchi
- The Institute for Scientific and Industrial Research, Osaka University, Ibaraki, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- Institute for Nanoscience Design, Osaka University, Toyonaka, Japan
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11
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Miyagawa K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Okumura M, Yamaguchi K. UNO(ULO) active space for multireference calculations on classical and quantum computers. Revisit to the iron-sulfur complexes. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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The competition between chemistry and biology in assembling iron-sulfur derivatives. Molecular structures and electrochemistry. Part IV. {[Fe3S4](SγCys)3} proteins. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Trasviña-Arenas CH, Lopez-Castillo LM, Sanchez-Sandoval E, Brieba LG. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY. FEBS J 2016; 283:521-40. [PMID: 26613369 DOI: 10.1111/febs.13608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 11/15/2015] [Accepted: 11/24/2015] [Indexed: 01/31/2023]
Abstract
7,8-Dihydro-8-deoxyguanine (8oG) is one of the most common oxidative lesions in DNA. DNA polymerases misincorporate an adenine across from this lesion. Thus, 8oG is a highly mutagenic lesion responsible for G:C→T:A transversions. MutY is an adenine glycosylase, part of the base excision repair pathway that removes adenines, when mispaired with 8oG or guanine. Its catalytic domain includes a [4Fe-4S] cluster motif coordinated by cysteinyl ligands. When this cluster is absent, MutY activity is depleted and several studies concluded that the [4Fe-4S] cluster motif is an indispensable component for DNA binding, substrate recognition and enzymatic activity. In the present study, we identified 46 MutY homologues that lack the canonical cysteinyl ligands, suggesting an absence of the [4Fe-4S] cluster. A phylogenetic analysis groups these novel MutYs into two different clades. One clade is exclusive of the order Lactobacillales and another clade has a mixed composition of anaerobic and microaerophilic bacteria and species from the protozoan genus Entamoeba. Structural modeling and sequence analysis suggests that the loss of the [4Fe-4S] cluster is compensated by a convergent solution in which bulky amino acids substitute the [4Fe-4S] cluster. We functionally characterized MutYs from Lactobacillus brevis and Entamoeba histolytica as representative members from each clade and found that both enzymes are active adenine glycosylases. Furthermore, chimeric glycosylases, in which the [4Fe-4S] cluster of Escherichia coli MutY is replaced by the corresponding amino acids of LbY and EhY, are also active. Our data indicates that the [4Fe-4S] cluster plays a structural role in MutYs and evidences the existence of alternative functional solutions in nature.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Laura M Lopez-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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15
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Blachly PG, Sandala GM, Giammona D, Liu T, Bashford D, McCammon JA, Noodleman L. Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput 2014; 10:3871-3884. [PMID: 25221444 PMCID: PMC4159220 DOI: 10.1021/ct5005214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 12/31/2022]
Abstract
With current therapies becoming less efficacious due to increased drug resistance, new inhibitors of both bacterial and malarial targets are desperately needed. The recently discovered methylerythritol phosphate (MEP) pathway for isoprenoid synthesis provides novel targets for the development of such drugs. Particular attention has focused on the IspH protein, the final enzyme in the MEP pathway, which uses its [4Fe-4S] cluster to catalyze the formation of the isoprenoid precursors IPP and DMAPP from HMBPP. IspH catalysis is achieved via a 2e-/2H+ reductive dehydroxylation of HMBPP; the mechanism by which catalysis is achieved, however, is highly controversial. The work presented herein provides the first step in assessing different routes to catalysis by using computational methods. By performing broken-symmetry density functional theory (BS-DFT) calculations that employ both the conductor-like screening solvation model (DFT/COSMO) and a finite-difference Poisson-Boltzmann self-consistent reaction field methodology (DFT/SCRF), we evaluate geometries, energies, and Mössbauer signatures of the different protonation states that may exist in the oxidized state of the IspH catalytic cycle. From DFT/SCRF computations performed on the oxidized state, we find a state where the substrate, HMBPP, coordinates the apical iron in the [4Fe-4S] cluster as an alcohol group (ROH) to be one of two, isoenergetic, lowest-energy states. In this state, the HMBPP pyrophosphate moiety and an adjacent glutamate residue (E126) are both fully deprotonated, making the active site highly anionic. Our findings that this low-energy state also matches the experimental geometry of the active site and that its computed isomer shifts agree with experiment validate the use of the DFT/SCRF method to assess relative energies along the IspH reaction pathway. Additional studies of IspH catalytic intermediates are currently being pursued.
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Affiliation(s)
- Patrick G. Blachly
- Department
of Chemistry and Biochemistry, University
of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093-0365, United States
| | - Gregory M. Sandala
- Department
of Chemistry and Biochemistry, Mount Allison
University, 63C York
Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Debra
Ann Giammona
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, 262
Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Tiqing Liu
- Skaggs School of Pharmacy and Pharmaceutical
Sciences, Howard Hughes Medical
Institute, and Department of Pharmacology, University
of California San Diego, La Jolla, California 92093-0365, United States
| | - Donald Bashford
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, 262
Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093-0365, United States
- Skaggs School of Pharmacy and Pharmaceutical
Sciences, Howard Hughes Medical
Institute, and Department of Pharmacology, University
of California San Diego, La Jolla, California 92093-0365, United States
| | - Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, TPC15, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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16
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17
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Sobolev OV. Detection of alternative conformations: Shift_plotand AC_predictionprograms. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889812052065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Increased mobility of poorly ordered atoms compared to well ordered ones in unrestrained refinement was adopted as the basis for the development of a method for predicting alternative conformations. Two programs for the analysis of atomic mobility are presented.Shift_plotmay be useful for visual analysis of magnitudes of atomic shifts in refinement.AC_predictionimplements automatic decision-making procedures based on atomic shift magnitudes in unrestrained refinement to highlight the specific residues that are likely to harbour alternative conformations and that hence require checkingviaelectron density maps.
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18
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Mitra D, George SJ, Guo Y, Kamali S, Keable S, Peters JW, Pelmenschikov V, Case DA, Cramer SP. Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses. J Am Chem Soc 2013; 135:2530-43. [PMID: 23282058 DOI: 10.1021/ja307027n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm(-1) decrease in Fe-S stretching frequencies with each added electron. The "oxidized" [4Fe-4S](2+) state spectrum is consistent with and extends previous resonance Raman spectra. For the "reduced" [4Fe-4S](1+) state in Fe protein, and for any "all-ferrous" [4Fe-4S](0) cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å(-1) indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.
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Affiliation(s)
- Devrani Mitra
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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19
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Mitra D, Pelmenschikov V, Guo Y, Case DA, Wang H, Dong W, Tan ML, Ichiye T, Jenney FE, Adams MWW, Yoda Y, Zhao J, Cramer SP. Dynamics of the [4Fe-4S] cluster in Pyrococcus furiosus D14C ferredoxin via nuclear resonance vibrational and resonance Raman spectroscopies, force field simulations, and density functional theory calculations. Biochemistry 2011; 50:5220-35. [PMID: 21500788 DOI: 10.1021/bi200046p] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal-mode assignments, we conducted NRVS with D14C ferredoxin samples with (36)S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains, (Ph(4)P)(2)[Fe(4)S(4)Cl(4)]. Several distinct regions of NRVS intensity are identified, ranging from "protein" and torsional modes below 100 cm(-1), through bending and breathing modes near 150 cm(-1), to strong bands from Fe-S stretching modes between 250 and ∼400 cm(-1). The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy. We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The (57)Fe partial vibrational densities of states for the oxidized samples were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low-frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe(4)S(4)](2+/+) redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.
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Affiliation(s)
- Devrani Mitra
- Department of Applied Science, University of California , Davis, CA 95616, USA
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20
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Crystal structures of the all-cysteinyl-coordinated D14C variant of Pyrococcus furiosus ferredoxin: [4Fe–4S] ↔ [3Fe–4S] cluster conversion. J Biol Inorg Chem 2011; 16:763-75. [DOI: 10.1007/s00775-011-0778-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 03/25/2011] [Indexed: 10/18/2022]
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21
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Niu S, Ichiye T. Insight into environmental effects on bonding and redox properties of [4Fe-4S] clusters in proteins. J Am Chem Soc 2009; 131:5724-5. [PMID: 19341280 DOI: 10.1021/ja900406j] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The large differences in redox potentials between the HiPIPs and ferredoxins are generally attributed to hydrogen bonds and electrostatic effects from the protein and solvent. Recent ligand K-edge X-ray absorption studies by Solomon and co-workers show that the Fe-S covalencies of [4Fe-4S] clusters in the two proteins differ considerably apparently because of hydrogen bonds from water, indicating electronic effects may be important. However, combined density function theory (DFT) and photoelectron spectroscopy studies by our group and Wang and co-workers indicate that hydrogen bonds tune the potential of [4Fe-4S] clusters by mainly electrostatics. The DFT studies here rationalize both results, namely that the observed change in the Fe-S covalency is due to differences in ligand conformation between the two proteins rather than hydrogen bonds. Moreover, the ligand conformation affects the calculated potentials by approximately 100 mV and, thus, is a heretofore unconsidered means of tuning the potential.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, DC 20057-1227, USA
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22
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Groysman S, Holm RH. Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites. Biochemistry 2009; 48:2310-20. [PMID: 19206188 PMCID: PMC2765533 DOI: 10.1021/bi900044e] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biomimetic inorganic chemistry has as its primary goal the synthesis of molecules that approach or achieve the structures, oxidation states, and electronic and reactivity features of native metal-containing sites of variant nuclearity. Comparison of properties of accurate analogues and these sites ideally provides insight into the influence of protein structure and environment on intrinsic properties as represented by the analogue. For polynuclear sites in particular, the goal provides a formidable challenge for, with the exception of iron-sulfur clusters, all such site structures have never been achieved and few have even been closely approximated by chemical synthesis. This account describes the current status of the synthetic analogue approach as applied to the mononuclear sites in certain molybdoenzymes and the polynuclear sites in hydrogenases, nitrogenase, and carbon monoxide dehydrogenases.
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Affiliation(s)
- Stanislav Groysman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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23
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Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and the homologous Escherichia coli ferredoxin. J Biol Inorg Chem 2009; 14:783-99. [PMID: 19290553 DOI: 10.1007/s00775-009-0492-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 02/26/2009] [Indexed: 10/21/2022]
Abstract
The crystal structures of the C57A and V13G molecular variants of Allochromatium vinosum 2[4Fe-4S] ferredoxin (AlvinFd) and that of the homologous ferredoxin from Escherichia coli (EcFd) have been determined at 1.05-, 1.48-, and 1.65-A resolution, respectively. The present structures combined with cyclic voltammetry studies establish clear effects of the degree of exposure of the cluster with the lowest reduction potential (cluster I) towards less negative reduction potentials (E degrees ). This is better illustrated by V13G AlvinFd (high exposure, E degrees = -594 mV) and EcFd (low exposure, E degrees = -675 mV). In C57A AlvinFd, the movement of the protein backbone, as a result of replacing the noncoordinating Cys57 by Ala, leads to a +50-mV upshift of the potential of the nearby cluster I, by removal of polar interactions involving the thiolate group and adjustment of the hydrogen-bond network involving the cluster atoms. In addition, the present structures and other previously reported accurate structures of this family of ferredoxins indicate that polar interactions of side chains and water molecules with cluster II sulfur atoms, which are absent in the environment of cluster I, are correlated to the approximately 180-250 mV difference between the reduction potentials of clusters I and II. These findings provide insight into the significant effects of subtle structural differences of the protein and solvent environment around the clusters of [4Fe-4S] ferredoxins on their electrochemical properties.
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24
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Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol 2009; 388:356-80. [PMID: 19265704 DOI: 10.1016/j.jmb.2009.02.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 11/24/2022]
Abstract
In metalloproteins, the protein environment modulates metal properties to achieve the required goal, which can be protein stabilization or function. The analysis of metal sites at the atomic level of detail provided by protein structures can thus be of benefit in functional and evolutionary studies of proteins. In this work, we propose a structural bioinformatics approach to the study of metalloproteins based on structural templates of metal sites that include the PDB coordinates of protein residues forming the first and the second coordination sphere of the metal. We have applied this approach to non-heme iron sites, which have been analyzed at various levels. Templates of sites located in different protein domains have been compared, showing that similar sites can be found in unrelated proteins as the result of convergent evolution. Templates of sites located in proteins of a large superfamily have been compared, showing possible mechanisms of divergent evolution of proteins to achieve different functions. Furthermore, template comparisons have been used to predict the function of uncharacterized proteins, showing that similarity searches focused on metal sites can be advantageously combined with typical whole-domain comparisons. Structural templates of metal sites, finally, may constitute the basis for a systematic classification of metalloproteins in databases.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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25
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Karcher A, Schele A, Hopfner KP. X-ray structure of the complete ABC enzyme ABCE1 from Pyrococcus abyssi. J Biol Chem 2007; 283:7962-71. [PMID: 18160405 DOI: 10.1074/jbc.m707347200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ATP binding cassette enzyme ABCE1 (also known as RNase-L (ribonuclease L) inhibitor, Pixie, and HP68), one of the evolutionary most sequence-conserved enzymes, functions in translation initiation, ribosome biogenesis, and human immunodeficiency virus capsid assembly. However, its structural mechanism and biochemical role in these processes have not been revealed. We determined the crystal structure of Pyrococcus abyssi ABCE1 in complex with Mg(2+) and ADP to 2.8A resolution. ABCE1 consists of four structural domains. Two nucleotide binding domains are arranged in a head-to-tail orientation by a hinge domain, suggesting that these domains undergo the characteristic tweezers-like powerstroke of ABC enzymes. In contrast to all other known ABC enzymes, ABCE1 has a N-terminal iron-sulfur-cluster (FeS) domain. The FeS domain contains two [4Fe-4S] clusters and is structurally highly related to bacterial-type ferredoxins. However, one cluster is coordinated by an unusual CX(4)CX(3/4)C triad. Surprisingly, intimate interactions of the FeS domain with the adenine and ribose binding Y-loop on nucleotide binding domain 1 suggest a linkage between FeS domain function and ATP-induced conformational control of the ABC tandem cassette. The structure substantially expands the functional architecture of ABC enzymes and raises the possibility that ABCE1 is a chemomechanical engine linked to a redox process.
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Affiliation(s)
- Annette Karcher
- Center for Integrated Protein Science and Center for Advanced Photonics at the Gene Center, Ludwig-Maximilians-University Munich, D-81377 Munich, Germany
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26
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Antonkine ML, Maes EM, Czernuszewicz RS, Breitenstein C, Bill E, Falzone CJ, Balasubramanian R, Lubner C, Bryant DA, Golbeck JH. Chemical rescue of a site-modified ligand to a [4Fe–4S] cluster in PsaC, a bacterial-like dicluster ferredoxin bound to Photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:712-24. [PMID: 17434441 DOI: 10.1016/j.bbabio.2007.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 01/21/2007] [Accepted: 02/02/2007] [Indexed: 10/23/2022]
Abstract
Chemical rescue of site-modified amino acids using externally supplied organic molecules represents a powerful method to investigate structure-function relationships in proteins. Here we provide definitive evidence that aryl and alkyl thiolates, reagents typically used for in vitro iron-sulfur cluster reconstitutions, serve as rescue ligands to a site-specifically modified [4Fe-4S](1+,2+) cluster in PsaC, a bacterial dicluster ferredoxin-like subunit of Photosystem I. PsaC binds two low-potential [4Fe-4S](1+,2+) clusters termed F(A) and F(B). In the C13G/C33S variant of PsaC, glycine has replaced cysteine at position 13 creating a protein that is missing one of the ligating amino acids to iron-sulfur cluster F(B). Using a variety of analytical techniques, including non-heme iron and acid-labile sulfur assays, and EPR, resonance Raman, and Mössbauer spectroscopies, we showed that the C13G/C33S variant of PsaC binds two [4Fe-4S](1+,2+) clusters, despite the absence of one of the biological ligands. (19)F NMR spectroscopy indicated that the external thiolate replaces cysteine 13 as a substitute ligand to the F(B) cluster. The finding that site-modified [4Fe-4S](1+,2+) clusters can be chemically rescued with external thiolates opens new opportunities for modulating their properties in proteins. In particular, it provides a mechanism to attach an additional electron transfer cofactor to the protein via a bound, external ligand.
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Affiliation(s)
- Mikhail L Antonkine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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27
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Villa A, Fan H, Wassenaar T, Mark AE. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field? J Phys Chem B 2007; 111:6015-25. [PMID: 17489626 DOI: 10.1021/jp068580v] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ significantly in regard to the nonbonded parameters for polar functional groups and their ability to reproduce the correct solvation and partitioning behavior of small molecular analogues of the amino acid side chains. Despite the differences in the force field parameters no major differences could be detected in a wide range of structural properties such as the root-mean-square deviation from the experimental structure, radii of gyration, solvent accessible surface, secondary structure, or hydrogen bond propensities on a 5 to 10 ns time scale. The small differences that were observed correlated primarily with the presence of charged residues as opposed to residues that differed most between the parameter sets. The work highlights the variation that can be observed in nanosecond simulations of protein systems and implications of this for force field validation, as well as for the analysis of protein simulations in general.
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Affiliation(s)
- Alessandra Villa
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
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28
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Giastas P, Pinotsis N, Efthymiou G, Wilmanns M, Kyritsis P, Moulis JM, Mavridis IM. The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values. J Biol Inorg Chem 2006; 11:445-58. [PMID: 16596388 DOI: 10.1007/s00775-006-0094-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
The structure of the 2[4Fe-4S] ferredoxin (PaFd) from Pseudomonas aeruginosa, which belongs to the Allochromatium vinosum (Alvin) subfamily, has been determined by X-ray crystallography at 1.32-A resolution, which is the highest up to now for a member of this subfamily of Fds. The main structural features of PaFd are similar to those of AlvinFd. However, the significantly higher resolution of the PaFd structure makes possible a reliable comparison with available high-resolution structures of [4Fe-4S]-containing Fds, in an effort to rationalize the unusual electrochemical properties of Alvin-like Fds. Three major factors contributing to the reduction potential values of [4Fe-4S]2+/+ clusters of Fds, namely, the surface accessibility of the clusters, the N-H...S hydrogen-bonding network, and the volume of the cavities hosting the clusters, are extensively discussed. The volume of the cavities is introduced in the present work for the first time, and can in part explain the very negative potential of cluster I of Alvin-like Fds.
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Affiliation(s)
- Petros Giastas
- Institute of Physical Chemistry, NCSR Demokritos, Aghia Paraskevi, 15310, PO Box 60228, Athens, Greece
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29
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Xiao Y, Koutmos M, Case DA, Coucouvanis D, Wang H, Cramer SP. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields. Dalton Trans 2006:2192-201. [PMID: 16673033 DOI: 10.1039/b513331a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies. The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT theory is shown to provide remarkable agreement with the experimental NRVS data. These results provide a reference point for the analysis of more complex Fe-S clusters in proteins.
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Affiliation(s)
- Yuming Xiao
- Department of Applied Science, University of California, Davis, CA 95616, USA
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30
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Shirakawa T, Takahashi Y, Wada K, Hirota J, Takao T, Ohmori D, Fukuyama K. Identification of variant molecules of Bacillus thermoproteolyticus ferredoxin: crystal structure reveals bound coenzyme A and an unexpected [3Fe-4S] cluster associated with a canonical [4Fe-4S] ligand motif. Biochemistry 2005; 44:12402-10. [PMID: 16156653 DOI: 10.1021/bi0508441] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During the purification of recombinant Bacillus thermoproteolyticus ferredoxin (BtFd) from Escherichia coli, we have noted that some Fe-S proteins were produced in relatively small amounts compared to the originally identified BtFd carrying a [4Fe-4S] cluster. These variants could be purified into three Fe-S protein components (designated as V-I, V-II, and V-III) by standard chromatography procedures. UV-vis and EPR spectroscopic analyses indicated that each of these variants accommodates a [3Fe-4S] cluster. From mass spectrometric and protein sequence analyses together with native and SDS gel electrophoresis, we established that V-I and V-II contain the polypeptide of BtFd associated with acyl carrier protein (ACP) and with coenzyme A (CoA), respectively, and that V-III is a BtFd dimer linked by a disulfide bond. The crystal structure of the BtFd-CoA complex (V-II) determined at 1.6 A resolution revealed that each of the four complexes in the crystallographic asymmetric unit possesses a [3Fe-4S] cluster that is coordinated by Cys(11), Cys(17), and Cys(61). The polypeptide chain of each complex is superimposable onto that of the original [4Fe-4S] BtFd except for the segment containing Cys(14), the fourth ligand to the [4Fe-4S] cluster of BtFd. In the variant molecules, the side chain of Cys(14) is rotated away to the molecular surface, forming a disulfide bond with the terminal sulfhydryl group of CoA. This covalent modification may have occurred in vivo, thereby preventing the assembly of the [4Fe-4S] cluster as observed previously for Desulfovibrio gigas ferredoxin. Possibilities concerning how the variant molecules are formed in the cell are discussed.
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Affiliation(s)
- Tadayoshi Shirakawa
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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31
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Walters MA, Roche CL, Rheingold AL, Kassel SW. N-H···S Hydrogen Bonds in a Ferredoxin Model. Inorg Chem 2005; 44:3777-9. [PMID: 15907101 DOI: 10.1021/ic048208z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Fe4S4 complex {(CH3)3NCH2CONH2}2[Fe4S4((tBuS)4] (1) was synthesized to replicate the ferredoxin active site with a subset of its N-H...S hydrogen bonds. The two cationic counterions mimic the polypeptide backbone of ferredoxin (Fd) as amide hydrogen-bond donors to sulfur atoms of the iron-sulfur cluster. X-ray crystallographic data show that the organic sulfur (Sgamma) of one tert-butylthiolate ligand and one inorganic sulfur of the cluster core serve as N-H...S hydrogen-bond acceptors. The cluster core of complex 1 is tetragonally elongated in contrast to that of Fd, which is tetragonally compressed. This is the first observation of an elongated [Fe4S4]2+ cluster core. Additionally, this is the first synthetic Fd model in which N-H...S hydrogen bonding to a cluster has been achieved.
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Affiliation(s)
- Marc A Walters
- Department of Chemistry, New York University, New York, New York 10003, USA.
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32
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Dey A, Glaser T, Couture MMJ, Eltis LD, Holm RH, Hedman B, Hodgson KO, Solomon EI. Ligand K-Edge X-ray Absorption Spectroscopy of [Fe4S4]1+,2+,3+ Clusters: Changes in Bonding and Electronic Relaxation upon Redox. J Am Chem Soc 2004; 126:8320-8. [PMID: 15225075 DOI: 10.1021/ja0484956] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfur K-edge X-ray absorption spectroscopy (XAS) is reported for [Fe(4)S(4)](1+,2+,3+) clusters. The results are quantitatively and qualitatively compared with DFT calculations. The change in covalency upon redox in both the [Fe(4)S(4)](1+/2+) (ferredoxin) and the [Fe(4)S(4)](2+/3+) (HiPIP) couple are much larger than that expected from just the change in number of 3d holes. Moreover, the change in the HiPIP couple is higher than that of the ferredoxin couple. These changes in electronic structure are analyzed using DFT calculations in terms of contributions from the nature of the redox active molecular orbital (RAMO) and electronic relaxation. The results indicate that the RAMO of HiPIP has 50% ligand character, and hence, the HiPIP redox couple involves limited electronic relaxation. Alternatively, the RAMO of the ferredoxin couple is metal-based, and the ferredoxin redox couple involves extensive electronic relaxation. The contributions of these RAMO differences to ET processes in the different proteins are discussed.
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Affiliation(s)
- Abhishek Dey
- Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, CA 94305, USA
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33
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Venkateswara Rao P, Holm RH. Synthetic Analogues of the Active Sites of Iron−Sulfur Proteins. Chem Rev 2004; 104:527-59. [PMID: 14871134 DOI: 10.1021/cr020615+] [Citation(s) in RCA: 430] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P Venkateswara Rao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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34
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Brookhaven National Laboratory, Building 725 A X9, Upton, New York 11973, USA
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35
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Fan H, Mark AE. Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins 2003; 53:111-20. [PMID: 12945054 DOI: 10.1002/prot.10496] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been evaluated. The proteins selected represent a mixture of secondary structure types including all alpha, all beta, and alpha/beta. The proteins selected do not contain cysteine-cysteine bridges. In addition, any crystallographic waters, metal ions, cofactors, or bound ligands were removed before the systems were simulated. The stability of the structures was evaluated by simulating, under identical conditions, each of the proteins for at least 5 ns in explicit solvent. It is found that not only do NMR-derived structures have, on average, higher internal strain than structures determined by X-ray crystallography but that a significant proportion of the structures are unstable and rapidly diverge in simulations.
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Affiliation(s)
- Hao Fan
- Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands
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36
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Fee JA, Castagnetto JM, Case DA, Noodleman L, Stout CD, Torres RA. The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters. J Biol Inorg Chem 2003; 8:519-526. [PMID: 12632271 DOI: 10.1007/s00775-003-0445-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Accepted: 01/23/2003] [Indexed: 11/25/2022]
Abstract
The geometry proposition that "four points not in a plane describe one and only one sphere" provides a novel tool for analyzing protein-induced distortions in [4Fe-4S] clusters. A geometrically perfect reference structure comprises interlaced, regular tetrahedra of Fe, S, and S gamma atoms having T(d) symmetry. Three circumspheres are defined by the three sets of four atoms, the circumcenters of which are unique points within the cluster. The structure is thus re-defined by the positions of the circumcenters in xyz space and the r, theta, phi of each atom on its respective sphere. Analysis of 12 high-resolution structures of protein-bound and small molecule [4Fe-4S](SR)(4) clusters revealed: (a) the circumcenters are generally non-coincident by approximately 0.01 to approximately 0.06 A; (b) the Fe radius, r(Fe), is nominally independent of core oxidation state, having values between 1.66 to 1.69 A, whereas r(S) and r(SG), which have ranges of 2.18-2.24 A and 3.87-3.94 A, respectively, both increase by as much as approximately 3% upon reduction from the 3+ to the 1+ core valence; (c) deviation of some atoms from the theta, phi of a perfect tetrahedron can be large, approximately 10 degrees, and sets of atoms can show patterns of motion on their spheres that result from changes in Fe-S bond lengths. Density functional theory calculations suggest that the [4Fe-4S] core itself requires rather little energy to distort (approximately 2 kcal/mol), whereas significantly more energy is required to distort the Sgamma shell (~4 kcal/mol) to that of cluster I in Clostridium acidurici ferredoxin.
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Affiliation(s)
- James A Fee
- Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA , 92037, USA.
- Division of Biology, Department of Molecular Biology and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA , 92093, USA.
| | - Jesus M Castagnetto
- Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA , 92037, USA
| | - David A Case
- Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA , 92037, USA
| | - Louis Noodleman
- Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA , 92037, USA
| | - C David Stout
- Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA , 92037, USA
| | - Rhonda A Torres
- Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA , 92037, USA
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