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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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2
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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3
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Jin WT, Wang H, Wang SY, Dapper CH, Li X, Newton WE, Zhou ZH, Cramer SP. Preliminary Assignment of Protonated and Deprotonated Homocitrates in Extracted FeMo-Cofactors by Comparisons with Molybdenum(IV) Lactates and Oxidovanadium Glycolates. Inorg Chem 2019; 58:2523-2532. [PMID: 30726074 DOI: 10.1021/acs.inorgchem.8b03108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A similar pair of protonated and deprotonated mononuclear oxidovanadium glycolates [VO(Hglyc)(phen)(H2O)]Cl·2H2O (1) and [VO(glyc)(bpy)(H2O)] (2) and a mixed-(de)protonated oxidovanadium triglycolate (NH4)2[VO(Hglyc)2(glyc)]·H2O (3) were isolated and examined. The ≡C-O(H) (≡C-OH or ≡C-O) groups coordinated to vanadium were spectroscopically and structurally identified. The glycolate in 1 features a bidentate chelation through protonated α-hydroxy and α-carboxy groups, whereas the glycolate in 2 coordinates through deprotonated α-alkoxy and α-carboxy groups. The glycolates in 3 coordinate to vanadium through α-alkoxy or α-hydroxy and α-carboxy groups and thus have both protonated ≡C-OH and deprotonated ≡C-O bonds simultaneously. Structural investigations revealed that the longer protonated V-Oα-hydroxy bonds [2.234(2) Å and 2.244(2) Å] in 1 and 3 are close to those of FeV-cofactor (FeV-co) 2.17 Å1 (FeMo-co 2.17 Å2), while deprotonated V-Oα-alkoxy bonds [2, 1.930(2); 3, 1.927(2) Å] were obviously shorter. This shows a similar elongated trend as the Mo-O distances in the previously reported deprotonated vs protonated molybdenum lactates (Wang, S. Y. et al. Dalton Trans. 2018, 47, 7412-7421) and these vanadium and molybdenum complexes have the same local V/Mo-homocitrate structures as those of FeV/Mo-cos of nitrogenases. The IR spectra of these oxidovanadium and the previously synthesized molybdenum complexes including different substituted ≡C-O(H) model compounds show red-shifts for ≡C-OH vs ≡C-O alternation, which further assign the two IR bands of extracted FeMo-co at 1084 and 1031 cm-1 to ≡C-O and ≡C-OH vibrations, respectively. Although the structural data or IR spectra for some of the previously synthesized Mo/V complexes and extracted FeMo-co were measured earlier, this is the first time that the ≡C-O(H) coordinated peaks are assigned. The overall structural and IR results well suggest the coexistence of homocitrates coordinated with α-alkoxy (deprotonated) and α-hydroxy (protonated) groups in the extracted FeMo-co.
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Affiliation(s)
- Wan-Ting Jin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Si-Yuan Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Christie H Dapper
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Xing Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - William E Newton
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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4
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Mao Z, Carroll EC, Kim PW, Cramer SP, Larsen DS. Ultrafast Charge-Transfer Dynamics in the Iron-Sulfur Complex of Rhodobacter capsulatus Ferredoxin VI. J Phys Chem Lett 2017; 8:4498-4503. [PMID: 28872878 PMCID: PMC7187928 DOI: 10.1021/acs.jpclett.7b02026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Iron-sulfur proteins play essential roles in various biological processes. Their electronic structure and vibrational dynamics are key to their rich chemistry but nontrivial to unravel. Here, the first ultrafast transient absorption and impulsive coherent vibrational spectroscopic (ICVS) studies on 2Fe-2S clusters in Rhodobacter capsulatus ferreodoxin VI are characterized. Photoexcitation initiated populations on multiple excited electronic states that evolve into each other in a long-lived charge-transfer state. This suggests a potential light-induced electron-transfer pathway as well as the possibility of using iron-sulfur proteins as photosensitizers for light-dependent enzymes. A tyrosine chain near the active site suggests potential hole-transfer pathways and affirms this electron-transfer pathway. The ICVS data revealed vibrational bands at 417 and 484 cm-1, with the latter attributed to an excited-state mode. The temperature dependence of the ICVS modes suggests that the temperature effect on protein structure or conformational heterogeneities needs to be considered during cryogenic temperature studies.
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Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elizabeth C. Carroll
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Stephen P. Cramer
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Corresponding Authors: &
| | - Delmar S. Larsen
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Corresponding Authors: &
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5
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Maiuri M, Delfino I, Cerullo G, Manzoni C, Pelmenschikov V, Guo Y, Wang H, Gee LB, Dapper CH, Newton WE, Cramer SP. Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration. J Inorg Biochem 2015; 153:128-135. [PMID: 26343576 DOI: 10.1016/j.jinorgbio.2015.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/18/2015] [Accepted: 07/09/2015] [Indexed: 11/28/2022]
Abstract
We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.
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Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Leland B Gee
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Christie H Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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6
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Delfino I, Viola D, Cerullo G, Lepore M. Ultrafast excited-state charge-transfer dynamics in laccase type I copper site. Biophys Chem 2015; 200-201:41-7. [PMID: 25819432 DOI: 10.1016/j.bpc.2015.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 11/27/2022]
Abstract
Femtosecond pump-probe spectroscopy was used to investigate the excited state dynamics of the T1 copper site of laccase from Pleurotus ostreatus, by exciting its 600 nm charge transfer band with a 15-fs pulse and probing over a broad range in the visible region. The decay of the pump-induced ground-state bleaching occurs in a single step and is modulated by clearly visible oscillations. Global analysis of the two-dimensional differential transmission map shows that the excited state exponentially decays with a time constant of 375 fs, thus featuring a decay rate slower than those occurring in quite all the investigated T1 copper site proteins. The ultrashort pump pulse induces a vibrational coherence in the protein, which is mainly assigned to ground state activity, as expected in a system with fast excited state decay. Vibrational features are discussed also in comparison with the traditional resonance Raman spectrum of the enzyme. The results indicate that both excited state dynamics and vibrational modes associated with the T1 Cu laccase charge transfer have main characteristics similar to those of all the T1 copper site-containing proteins. On the other hand, the differences observed for laccase from P. ostreatus further confirm the peculiar hypothesized trigonal T1 Cu site geometry.
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Affiliation(s)
- Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università snc, I-01100 Viterbo, Italy.
| | - Daniele Viola
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Maria Lepore
- Dipartimento di Medicina Sperimentale, Seconda Università di Napoli, Via Costantinopoli 16, I-80100 Napoli, Italy
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Horch M, Hildebrandt P, Zebger I. Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes. Phys Chem Chem Phys 2015; 17:18222-37. [DOI: 10.1039/c5cp02447a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Challenges and chances in bio-molecular spectroscopy are exemplified by vibrational case studies on metalloenzymes.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
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8
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Scott A, Pelmenschikov V, Guo Y, Yan L, Wang H, George SJ, Dapper CH, Newton WE, Yoda Y, Tanaka Y, Cramer SP. Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom. J Am Chem Soc 2014; 136:15942-54. [PMID: 25275608 PMCID: PMC4235365 DOI: 10.1021/ja505720m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 01/21/2023]
Abstract
The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.
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Affiliation(s)
- Aubrey
D. Scott
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | | | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lifen Yan
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Hongxin Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Simon J. George
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Christie H. Dapper
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - William E. Newton
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - Yoshitaka Yoda
- Research
and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- SR
Materials Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Stephen P. Cramer
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
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