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Du WGH, Götz AW, Noodleman L. Mössbauer Property Calculations on Fea33+∙∙∙H2O∙∙∙CuB2+ Dinuclear Center Models of the Resting Oxidized as-Isolated Cytochrome c Oxidase. Chemphyschem 2022; 23:e202100831. [PMID: 35142420 PMCID: PMC9054037 DOI: 10.1002/cphc.202100831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/03/2022] [Indexed: 11/24/2022]
Abstract
Mössbauer isomer shift and quadrupole splitting properties have been calculated using the OLYP‐D3(BJ) density functional method on previously obtained (W.‐G. Han Du, et al., Inorg Chem. 2020, 59, 8906–8915) geometry optimized Fea33+−H2O−CuB2+ dinuclear center (DNC) clusters of the resting oxidized (O state) “as‐isolated” cytochrome c oxidase (CcO). The calculated results are highly consistent with the available experimental observations. The calculations have also shown that the structural heterogeneities of the O state DNCs implicated by the Mössbauer experiments are likely consequences of various factors, particularly the variable positions of the central H2O molecule between the Fea33+ and CuB2+ sites in different DNCs, whether or not this central H2O molecule has H‐bonding interaction with another H2O molecule, the different spin states having similar energies for the Fea33+ sites, and whether the Fea33+ and CuB2+ sites are ferromagnetically or antiferromagnetically spin‐coupled.
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Affiliation(s)
- Wen-Ge Han Du
- The Scripps Research Institute, Integrative Structural and Computational Biology, UNITED STATES
| | | | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, Hz112, 10550 North Torrey Pines Road, 92037, La Jolla, UNITED STATES
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2
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Reinhardt CR, Li P, Kang G, Stubbe J, Drennan CL, Hammes-Schiffer S. Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase. J Am Chem Soc 2020; 142:13768-13778. [PMID: 32631052 DOI: 10.1021/jacs.0c04325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Catalysis is initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β and Y731α at the interface. Resolving the PCET pathway at the α/β interface has been a long-standing challenge due to the lack of structural data. Herein, molecular dynamics simulations based on a recently solved cryogenic-electron microscopy structure of an active α2β2 complex are performed to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Our free energy simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation with Y730 to enable collinear PCET with this residue. Y356 and Y731 exhibit hydrogen-bonding interactions with interfacial water molecules and, in some conformations, share a bridging water molecule, suggesting that the primary proton acceptor for PCET from Y356 and from Y731 is interfacial water. The conformational flexibility of Y731 and the hydrogen-bonding interactions of both Y731 and Y356 with interfacial water and hydrogen-bonded water chains appear critical for effective radical translocation along the PCET pathway. These simulations are consistent with biochemical and spectroscopic data and provide previously unattainable atomic-level insights into the fundamental mechanism of RNR.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven Connecticut 06520, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States
| | - Gyunghoon Kang
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
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Ryzhkova EP. Alternative enzymes as a special strategy for the adaptation of procaryotic organisms (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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McWilliams SF, Brennan-Wydra E, MacLeod KC, Holland PL. Density Functional Calculations for Prediction of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings in β-Diketiminate Complexes. ACS OMEGA 2017; 2:2594-2606. [PMID: 28691111 PMCID: PMC5494642 DOI: 10.1021/acsomega.7b00595] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 05/24/2017] [Indexed: 05/09/2023]
Abstract
The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together.
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Affiliation(s)
- Sean F McWilliams
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Emma Brennan-Wydra
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - K Cory MacLeod
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Patrick L Holland
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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Han Du WG, Noodleman L. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus. Inorg Chem 2015; 54:7272-90. [PMID: 26192749 PMCID: PMC4525772 DOI: 10.1021/acs.inorgchem.5b00700] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 12/22/2022]
Abstract
The Fea3(3+)···CuB(2+) dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt) is still not fully understood. When the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through X-ray irradiation. Several X-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent micelles, and whether the CcO's were chemically or radiolyticly reduced, the X-ray diffraction analysis of the crystals showed different Fea3(2+)···CuB(+) DNC structures. On the other hand, Mössbauer spectroscopic experiments on reduced and oxidized ba3 CcOs from Tt (Zimmermann et al., Proc. Natl. Acad. Sci. USA 1988, 85, 5779-5783) revealed multiple (57)Fea3(2+) and (57)Fea3(3+) components. Moreover, one of the (57)Fea3(3+) components observed at 4.2 K transformed from a proposed "low-spin" state to a different high-spin species when the temperature was increased above 190 K, whereas the other high-spin (57)Fea3(3+) component remained unchanged. In the current Article, in order to understand the heterogeneities of the DNC in both Mössbauer spectra and X-ray crystal structures, the spin crossover of one of the (57)Fea3(3+) components, and how the coordination and spin states of the Fea3(3+/2+) and Cu(2+/1+) sites relate to the heterogeneity of the DNC structures, we have applied density functional OLYP calculations to the DNC clusters established based on the different X-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the observed Mössbauer spectra and to spectral changes with temperature have been proposed. Our calculations also show that, in certain intermediate states, the His233 and His283 ligand side chains may dissociate from the CuB(+) site, and they may become potential proton loading sites during the catalytic cycle.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational
Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational
Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Čajan M, Trávníček Z. Impact of solvent models and van der Waals corrections on DFT geometric and 57Fe Mössbauer parameters of trans-[FeCl2(iPrOH)4]. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.08.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Luber S, Leung S, Herrmann C, Du WH, Noodleman L, Batista VS. EXAFS simulation refinement based on broken-symmetry DFT geometries for the Mn(IV)-Fe(III) center of class I RNR from Chlamydia trachomatis. Dalton Trans 2014; 43:576-83. [PMID: 24129440 PMCID: PMC3855085 DOI: 10.1039/c3dt51563j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides necessary for DNA biosynthesis. Unlike the conventional class Ia RNRs which use a diiron cofactor in their subunit R2, the active site of the RNR-R2 from Chlamydia trachomatis (Ct) contains a Mn/Fe cofactor. The detailed structure of the Mn/Fe core has yet to be established. In this paper we evaluate six different structural models of the Ct RNR active site in the Mn(iv)/Fe(iii) state by using Mössbauer parameter calculations and simulations of Mn/Fe extended X-ray absorption fine structure (EXAFS) spectroscopy, and we identify a structure similar to a previously proposed DFT-optimized model that shows quantitative agreement with both EXAFS and Mössbauer spectroscopic data.
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Affiliation(s)
- Sandra Luber
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| | - Sophie Leung
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| | - Carmen Herrmann
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| | - Wenge Han Du
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
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Du WGH, Noodleman L. Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus. Inorg Chem 2013; 52:14072-88. [PMID: 24262070 DOI: 10.1021/ic401858s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Parent A, Caux-Thang C, Signor L, Clémancey M, Sethu R, Blondin G, Maldivi P, Duarte V, Latour JM. Single Glutamate to Aspartate Mutation Makes Ferric Uptake Regulator (Fur) as Sensitive to H2O2as Peroxide Resistance Regulator (PerR). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Parent A, Caux-Thang C, Signor L, Clémancey M, Sethu R, Blondin G, Maldivi P, Duarte V, Latour JM. Single Glutamate to Aspartate Mutation Makes Ferric Uptake Regulator (Fur) as Sensitive to H2O2as Peroxide Resistance Regulator (PerR). Angew Chem Int Ed Engl 2013; 52:10339-43. [DOI: 10.1002/anie.201304021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/24/2013] [Indexed: 11/09/2022]
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12
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Wörsdörfer B, Conner DA, Yokoyama K, Livada J, Seyedsayamdost M, Jiang W, Silakov A, Stubbe J, Bollinger JM, Krebs C. Function of the diiron cluster of Escherichia coli class Ia ribonucleotide reductase in proton-coupled electron transfer. J Am Chem Soc 2013; 135:8585-93. [PMID: 23676140 PMCID: PMC3869997 DOI: 10.1021/ja401342s] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The class Ia ribonucleotide reductase (RNR) from Escherichia coli employs a free-radical mechanism, which involves bidirectional translocation of a radical equivalent or "hole" over a distance of ~35 Å from the stable diferric/tyrosyl-radical (Y122(•)) cofactor in the β subunit to cysteine 439 (C439) in the active site of the α subunit. This long-range, intersubunit electron transfer occurs by a multistep "hopping" mechanism via formation of transient amino acid radicals along a specific pathway and is thought to be conformationally gated and coupled to local proton transfers. Whereas constituent amino acids of the hopping pathway have been identified, details of the proton-transfer steps and conformational gating within the β sununit have remained obscure; specific proton couples have been proposed, but no direct evidence has been provided. In the key first step, the reduction of Y122(•) by the first residue in the hopping pathway, a water ligand to Fe1 of the diferric cluster was suggested to donate a proton to yield the neutral Y122. Here we show that forward radical translocation is associated with perturbation of the Mössbauer spectrum of the diferric cluster, especially the quadrupole doublet associated with Fe1. Density functional theory (DFT) calculations verify the consistency of the experimentally observed perturbation with that expected for deprotonation of the Fe1-coordinated water ligand. The results thus provide the first evidence that the diiron cluster of this prototypical class Ia RNR functions not only in its well-known role as generator of the enzyme's essential Y122(•), but also directly in catalysis.
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Affiliation(s)
- Bigna Wörsdörfer
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Denise A. Conner
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kenichi Yokoyama
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jovan Livada
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Wei Jiang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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