1
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Ekanayake RSK, Streltsov VA, Best SP, Chantler CT. Using XAS to monitor radiation damage in real time and post-analysis, and investigation of systematic errors of fluorescence XAS for Cu-bound amyloid-β. J Appl Crystallogr 2024; 57:125-139. [PMID: 38322727 PMCID: PMC10840304 DOI: 10.1107/s1600576723010890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024] Open
Abstract
X-ray absorption spectroscopy (XAS) is a promising technique for determining structural information from sensitive biological samples, but high-accuracy X-ray absorption fine structure (XAFS) requires corrections of systematic errors in experimental data. Low-temperature XAS and room-temperature X-ray absorption spectro-electrochemical (XAS-EC) measurements of N-truncated amyloid-β samples were collected and corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumber (k). A new protocol was developed using extended X-ray absorption fine structure (EXAFS) data analysis for monitoring radiation damage in real time and post-analysis. The reliability of the structural determinations and consistency were validated using the XAS measurement experimental uncertainty. The correction of detector pixel efficiencies improved the fitting χ2 by 12%. An improvement of about 2.5% of the structural fitting was obtained after dead-time corrections. Normalization allowed the elimination of 90% of the monochromator glitches. The remaining glitches were manually removed. The dispersion of spectra due to self-absorption was corrected. Standard errors of experimental measurements were propagated from pointwise variance of the spectra after systematic corrections. Calculated uncertainties were used in structural refinements for obtaining precise and reliable values of structural parameters including atomic bond lengths and thermal parameters. This has permitted hypothesis testing.
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Affiliation(s)
| | - Victor A. Streltsov
- School of Physics, University of Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Australia
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2
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Bacellar C, Rouxel JR, Ingle RA, Mancini GF, Kinschel D, Cannelli O, Zhao Y, Cirelli C, Knopp G, Szlachetko J, Lima FA, Menzi S, Ozerov D, Pamfilidis G, Kubicek K, Khakhulin D, Gawelda W, Rodriguez-Fernandez A, Biednov M, Bressler C, Arrell CA, Johnson PJM, Milne CJ, Chergui M. Ultrafast Energy Transfer from Photoexcited Tryptophan to the Haem in Cytochrome c. J Phys Chem Lett 2023; 14:2425-2432. [PMID: 36862109 DOI: 10.1021/acs.jpclett.3c00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report femtosecond Fe K-edge absorption (XAS) and nonresonant X-ray emission (XES) spectra of ferric cytochrome C (Cyt c) upon excitation of the haem (>300 nm) or mixed excitation of the haem and tryptophan (<300 nm). The XAS and XES transients obtained in both excitation energy ranges show no evidence for electron transfer processes between photoexcited tryptophan (Trp) and the haem, but rather an ultrafast energy transfer, in agreement with previous ultrafast optical fluorescence and transient absorption studies. The reported (J. Phys. Chem. B 2011, 115 (46), 13723-13730) decay times of Trp fluorescence in ferrous (∼350 fs) and ferric (∼700 fs) Cyt c are among the shortest ever reported for Trp in a protein. The observed time scales cannot be rationalized in terms of Förster or Dexter energy transfer mechanisms and call for a more thorough theoretical investigation.
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Affiliation(s)
- Camila Bacellar
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jérémy R Rouxel
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- Univ Lyon, UJM-Saint-Etienne, CNRS, Graduate School Optics Institute, Laboratoire Hubert Curien, UMR 5516, Saint-Etienne F-42023, France
| | - Rebecca A Ingle
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Giulia F Mancini
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
- 2Laboratory for Ultrafast X-ray and Electron Microscopy, Department of Physics, University of Pavia, Via Agostino Bassi 6, 27100 Pavia PV, Italy
| | - Dominik Kinschel
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
| | - Oliviero Cannelli
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
| | - Yang Zhao
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
| | - Claudio Cirelli
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jakub Szlachetko
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | | | - Samuel Menzi
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | | | | | | | - Wojciech Gawelda
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan, Poland
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- IMDEA Nanociencia, Calle Faraday 9, 28049 Madrid, Spain
| | | | - Mykola Biednov
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany
| | | | | | | | - Christopher J Milne
- SwissFEL, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
- European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide (LSU), ISIC and Lausanne Centre for Ultrafast Science (LACUS), CH-1015 Lausanne, Switzerland
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3
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Ovalle S, Malardier-Jugroot C. Choice of Functional for Iron Porphirin Density Functional Theory Studies: Geometry, Spin-State, and Binding Energy Analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Gaffney KJ. Capturing photochemical and photophysical transformations in iron complexes with ultrafast X-ray spectroscopy and scattering. Chem Sci 2021; 12:8010-8025. [PMID: 34194691 PMCID: PMC8208315 DOI: 10.1039/d1sc01864g] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2021] [Indexed: 12/31/2022] Open
Abstract
Light-driven chemical transformations provide a compelling approach to understanding chemical reactivity with the potential to use this understanding to advance solar energy and catalysis applications. Capturing the non-equilibrium trajectories of electronic excited states with precision, particularly for transition metal complexes, would provide a foundation for advancing both of these objectives. Of particular importance for 3d metal compounds is characterizing the population dynamics of charge-transfer (CT) and metal-centered (MC) electronic excited states and understanding how the inner coordination sphere structural dynamics mediate the interaction between these states. Recent advances in ultrafast X-ray laser science has enabled the electronic excited state dynamics in 3d metal complexes to be followed with unprecedented detail. This review will focus on simultaneous X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS) studies of iron coordination and organometallic complexes. These simultaneous XES-XSS studies have provided detailed insight into the mechanism of light-induced spin crossover in iron coordination compounds, the interaction of CT and MC excited states in iron carbene photosensitizers, and the mechanism of Fe-S bond dissociation in cytochrome c.
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Affiliation(s)
- Kelly J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University Menlo Park California 94025 USA
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5
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Gideon DA, Nirusimhan V, E JC, Sudarsha K, Manoj KM. Mechanism of electron transfers mediated by cytochromes c and b5 in mitochondria and endoplasmic reticulum: classical and murburn perspectives. J Biomol Struct Dyn 2021; 40:9235-9252. [PMID: 33998974 DOI: 10.1080/07391102.2021.1925154] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We explore the mechanism of electron transfers mediated by cytochrome c, a soluble protein involved in mitochondrial oxidative phosphorylation and cytochrome b5, a microsomal membrane protein acting as a redox aide in xenobiotic metabolism. We found minimal conservation in the sequence and surface amino acid residues of cytochrome c/b5 proteins among divergent species. Therefore, we question the evolutionary logic for electron transfer (ET) occurring through affinity binding via recognition of specific surface residues/topography. Also, analysis of putative protein-protein interactions in the crystal structures of these proteins and their redox partners did not point to any specific interaction logic. A comparison of the kinetic and thermodynamic constants of wildtype vs. mutants did not provide strong evidence to support the binding-based ET paradigm, but indicated support for diffusible reactive species (DRS)-mediated process. Topographically divergent cytochromes from one species have been substituted for reaction with proteins from other species, implying the involvement of non-specific interactions. We provide a viable alternative (murburn concept) to classical protein-protein binding-based long range ET mechanism. To account for the promiscuity of interactions and solvent-accessible hemes, we propose that the two proteins act as non- specific redox capacitors, mediating one-electron redox equilibriums involving DRS and unbound ions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India.,Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Vijay Nirusimhan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Jesu Castin E
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Karthik Sudarsha
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India
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6
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Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c. Nat Commun 2021; 12:1086. [PMID: 33597529 PMCID: PMC7889893 DOI: 10.1038/s41467-021-21423-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c. This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1s3p (Kβ) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.
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7
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Bacellar C, Kinschel D, Mancini GF, Ingle RA, Rouxel J, Cannelli O, Cirelli C, Knopp G, Szlachetko J, Lima FA, Menzi S, Pamfilidis G, Kubicek K, Khakhulin D, Gawelda W, Rodriguez-Fernandez A, Biednov M, Bressler C, Arrell CA, Johnson PJM, Milne CJ, Chergui M. Spin cascade and doming in ferric hemes: Femtosecond X-ray absorption and X-ray emission studies. Proc Natl Acad Sci U S A 2020; 117:21914-21920. [PMID: 32848065 PMCID: PMC7486745 DOI: 10.1073/pnas.2009490117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The structure-function relationship is at the heart of biology, and major protein deformations are correlated to specific functions. For ferrous heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobins. Cytochrome c (Cyt c) has evolved to become an important electron-transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe Kα and Kβ X-ray emission spectroscopy (XES) with Fe K-edge X-ray absorption near-edge structure (XANES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the iron ion, causing the ferric heme to undergo doming, which we identify. We also argue that this pattern is common to a wide diversity of ferric heme proteins, raising the question of the biological relevance of doming in such proteins.
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Affiliation(s)
- Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Dominik Kinschel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giulia F Mancini
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Rebecca A Ingle
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jérémy Rouxel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Oliviero Cannelli
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Claudio Cirelli
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Kraków, Poland
| | | | - Samuel Menzi
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Georgios Pamfilidis
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | | | | | - Wojciech Gawelda
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznan, Poland
| | | | - Mykola Biednov
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
| | | | - Christopher A Arrell
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Christopher J Milne
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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8
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Hsu DJ, Leshchev D, Rimmerman D, Hong J, Kelley MS, Kosheleva I, Zhang X, Chen LX. X-ray snapshots reveal conformational influence on active site ligation during metalloprotein folding. Chem Sci 2019; 10:9788-9800. [PMID: 32055348 PMCID: PMC6993610 DOI: 10.1039/c9sc02630d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/01/2019] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c (cyt c) has long been utilized as a model system to study metalloprotein folding dynamics and the interplay between active site ligation and tertiary structure. However, recent reports regarding the weakness of the native Fe(ii)-S bond (Fe-Met80) call into question the role of the active site ligation in the protein folding process. In order to investigate the interplay between protein conformation and active site structures, we directly tracked the evolution of both during a photolysis-induced folding reaction using X-ray transient absorption spectroscopy and time-resolved X-ray solution scattering techniques. We observe an intermediate Fe-Met80 species appearing on ∼2 μs timescale, which should not be sustained without stabilization from the folded protein structure. We also observe the appearance of a new active site intermediate: a weakly interacting Fe-H2O state. As both intermediates require stabilization of weak metal-ligand interactions, we surmise the existence of a local structure within the unfolded protein that protects and limits the movement of the ligands, similar to the entatic state found in the native cyt c fold. Furthermore, we observe that in some of the unfolded ensemble, the local stabilizing structure is lost, leading to expansion of the unfolded protein structure and misligation to His26/His33 residues.
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Affiliation(s)
- Darren J Hsu
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Denis Leshchev
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Dolev Rimmerman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Jiyun Hong
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Matthew S Kelley
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Irina Kosheleva
- Center for Advanced Radiation Sources , The University of Chicago , Illinois 60637 , USA
| | - Xiaoyi Zhang
- X-ray Sciences Division of the Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , USA
| | - Lin X Chen
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
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9
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Kwon IS, Kwak IH, Kim JY, Abbas HG, Debela TT, Seo J, Cho MK, Ahn JP, Park J, Kang HS. Two-dimensional MoS 2/Fe-phthalocyanine hybrid nanostructures as excellent electrocatalysts for hydrogen evolution and oxygen reduction reactions. NANOSCALE 2019; 11:14266-14275. [PMID: 31317997 DOI: 10.1039/c9nr04156g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Two-dimensional (2D) MoS2 nanostructures have been extensively investigated in recent years because of their fascinating electrocatalytic properties. Herein, we report 2D hybrid nanostructures consisting of 1T' phase MoS2 and Fe-phthalocyanine (FePc) molecules that exhibit excellent catalytic activity toward both the hydrogen evolution reaction (HER) and oxygen reduction reaction (ORR). X-ray absorption spectra revealed an increased Fe-N distance (2.04 Å) in the hybrid complex relative to the isolated FePc. Spin-polarized density functional theory calculations predicted that the Fe center moves toward the MoS2 layer and induces a non-planar structure with an increased Fe-N distance of 2.05 Å, which supports the experimental results. The experiments and calculations consistently show a significant charge transfer from FePc to stabilize the hybrid complex. The excellent HER catalytic performance of FePc-MoS2 is characterized by a low Tafel slope of 32 mV dec-1 at a current density of 10 mA cm-2 and an overpotential of 0.123 V. The ORR catalytic activity is superior to that of the commercial Pt/C catalyst in pH 13 electrolyte, with a more positive half-wave potential (0.89 vs. 0.84 V), a smaller Tafel slope (35 vs. 87 mV·dec-1), and a much better durability (9.3% vs. 40% degradation after 20 h). Such remarkable catalytic activity is ascribed to the HER-active 1T' phase MoS2 and the ORR-active nonplanar Fe-N4 site of FePc.
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Affiliation(s)
- Ik Seon Kwon
- Department of Chemistry, Korea University, Sejong 339-700, Republic of Korea.
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10
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Mara MW, Hadt RG, Reinhard ME, Kroll T, Lim H, Hartsock RW, Alonso-Mori R, Chollet M, Glownia JM, Nelson S, Sokaras D, Kunnus K, Hodgson KO, Hedman B, Bergmann U, Gaffney KJ, Solomon EI. Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy. Science 2018. [PMID: 28642436 DOI: 10.1126/science.aam6203] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe-S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe-S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.
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Affiliation(s)
- Michael W Mara
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ryan G Hadt
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Marco Eli Reinhard
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert W Hartsock
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Kristjan Kunnus
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Bergmann
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Kelly J Gaffney
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.,PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. .,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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11
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Abstract
This review focuses on the unique spectroscopic features of the blue copper active sites. These reflect a novel electronic structure that activates the site for rapid long-range electron transfer in its biological function. The role of the protein in determining the geometric and electronic structure of this site is defined, as is its contribution to function. This has been referred to as the entatic/rack-induced state. These concepts are then extended to cytochrome c, which is also determined to be in an entatic state.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ryan G Hadt
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Benjamin E R Snyder
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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12
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Best SP, Levina A, Glover C, Johannessen B, Kappen P, Lay PA. XAS spectroelectrochemistry: reliable measurement of X-ray absorption spectra from redox manipulated solutions at room temperature. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:743-750. [PMID: 27140154 DOI: 10.1107/s1600577516005464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/01/2016] [Indexed: 06/05/2023]
Abstract
The design and operation of a low-volume spectroelectrochemical cell for X-ray absorption spectroscopy (XAS) of solutions at room temperature is described. Fluorescence XAS measurements are obtained from samples contained in the void space of a 50 µL reticulated vitreous carbon (sponge) working electrode. Both rapid electrosynthesis and control of the effects of photoreduction are achieved by control over the flow properties of the solution through the working electrode, where a good balance between the rate of consumption of sample and the minimization of decomposition was obtained by pulsing the flow of the solution by 1-2 µL with duty cycle of ∼3 s while maintaining a small net flow rate (26-100 µL h(-1)). The performance of the cell in terms of control of the redox state of the sample and minimization of the effects of photoreduction was demonstrated by XAS measurements of aqueous solutions of the photosensitive Fe(III) species, [Fe(C2O4)3](3-), together with that of the electrogenerated [Fe(C2O4)3](4-) product. The current response from the cell during the collection of XAS spectra provides an independent measure of the stability of the sample of the measurement. The suitability of the approach for the study of small volumes of mM concentrations of protein samples was demonstrated by the measurement of the oxidized and electrochemically reduced forms of cytochrome c.
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Affiliation(s)
- Stephen P Best
- School of Chemistry, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
| | - Aviva Levina
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chris Glover
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Bernt Johannessen
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Peter Kappen
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Peter A Lay
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
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13
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Kroll T, Hadt RG, Wilson SA, Lundberg M, Yan JJ, Weng TC, Sokaras D, Alonso-Mori R, Casa D, Upton MH, Hedman B, Hodgson KO, Solomon EI. Resonant inelastic X-ray scattering on ferrous and ferric bis-imidazole porphyrin and cytochrome c: nature and role of the axial methionine-Fe bond. J Am Chem Soc 2014; 136:18087-99. [PMID: 25475739 PMCID: PMC4291809 DOI: 10.1021/ja5100367] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Axial Cu-S(Met) bonds in electron transfer (ET) active sites are generally found to lower their reduction potentials. An axial S(Met) bond is also present in cytochrome c (cyt c) and is generally thought to increase the reduction potential. The highly covalent nature of the porphyrin environment in heme proteins precludes using many spectroscopic approaches to directly study the Fe site to experimentally quantify this bond. Alternatively, L-edge X-ray absorption spectroscopy (XAS) enables one to directly focus on the 3d-orbitals in a highly covalent environment and has previously been successfully applied to porphyrin model complexes. However, this technique cannot be extended to metalloproteins in solution. Here, we use metal K-edge XAS to obtain L-edge like data through 1s2p resonance inelastic X-ray scattering (RIXS). It has been applied here to a bis-imidazole porphyrin model complex and cyt c. The RIXS data on the model complex are directly correlated to L-edge XAS data to develop the complementary nature of these two spectroscopic methods. Comparison between the bis-imidazole model complex and cyt c in ferrous and ferric oxidation states show quantitative differences that reflect differences in axial ligand covalency. The data reveal an increased covalency for the S(Met) relative to N(His) axial ligand and a higher degree of covalency for the ferric states relative to the ferrous states. These results are reproduced by DFT calculations, which are used to evaluate the thermodynamics of the Fe-S(Met) bond and its dependence on redox state. These results provide insight into a number of previous chemical and physical results on cyt c.
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Affiliation(s)
- Thomas Kroll
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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14
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Lima FA, Penfold TJ, van der Veen RM, Reinhard M, Abela R, Tavernelli I, Rothlisberger U, Benfatto M, Milne CJ, Chergui M. Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy. Phys Chem Chem Phys 2014; 16:1617-31. [PMID: 24317683 DOI: 10.1039/c3cp53683a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.
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Affiliation(s)
- Frederico A Lima
- École Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, CH, Switzerland.
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15
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The Fe-heme structure of met-indoleamine 2,3-dioxygenase-2 determined by X-ray absorption fine structure. Biochem Biophys Res Commun 2014; 450:25-9. [DOI: 10.1016/j.bbrc.2014.05.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 05/14/2014] [Indexed: 01/20/2023]
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16
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Cook PL, Liu X, Yang W, Himpsel FJ. X-ray absorption spectroscopy of biomimetic dye molecules for solar cells. J Chem Phys 2010; 131:194701. [PMID: 19929065 DOI: 10.1063/1.3257621] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Dye-sensitized solar cells are potentially inexpensive alternatives to traditional semiconductor solar cells. In order to optimize dyes for solar cells we systematically investigate the electronic structure of a variety of porphyrins and phthalocyanines. As a biological model system we use the heme group in cytochrome c which plays a role in biological charge transfer processes. X-ray absorption spectroscopy of the N 1s and C 1s edges reveals the unoccupied molecular orbitals and the orientation of the molecules in thin films. The transition metal 2p edges reflect the oxidation state of the central metal atom, its spin state, and the ligand field of the surrounding N atoms. The latter allows tuning of the energy position of the lowest unoccupied orbital by several tenths of an eV by tailoring the molecules and their deposition. Fe and Mn containing phthalocyanines oxidize easily from +2 to +3 in air and require vacuum deposition for obtaining a reproducible oxidation state. Chlorinated porphyrins, on the other hand, are reduced from +3 to +2 during vacuum deposition at elevated temperatures. These findings stress the importance of controlled thin film deposition for obtaining photovoltaic devices with an optimum match between the energy levels of the dye and those of the donor and acceptor electrodes, together with a molecular orientation for optimal overlap between the pi orbitals in the direction of the carrier transport.
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Affiliation(s)
- Peter L Cook
- Department of Physics, University of Wisconsin Madison, 1150 University Ave., Madison, Wisconsin 53706, USA
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17
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Leu BM, Ching TH, Zhao J, Sturhahn W, Alp EE, Sage JT. Vibrational dynamics of iron in cytochrome C. J Phys Chem B 2009; 113:2193-200. [PMID: 19173569 DOI: 10.1021/jp806574t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) and Raman spectroscopy on (54)Fe- and (57)Fe-enriched cytochrome c (cyt c) identify multiple bands involving vibrations of the heme Fe. Comparison with predictions from Fe isotope shifts reveals that 70% of the NRVS signal in the 300-450 cm(-1) frequency range corresponds to vibrations resolved in Soret-enhanced Raman spectra. This frequency range dominates the "stiffness", an effective force constant determined by the Fe vibrational density of states (VDOS), which measures the strength of nearest-neighbor interactions with Fe. The stiffness of the low-spin Fe environment in both oxidation states of cyt c significantly exceeds that for the high-spin Fe in deoxymyoglobin, where the 200-300 cm(-1) frequency range dominates the VDOS. This situation is reflected in the shorter Fe-ligand bond lengths in the former with respect to the latter. The longer Fe-S(Met80) in oxidized cyt c with respect to reduced cyt c leads to a decrease in the stiffness of the iron environment upon oxidation. Comparison with NRVS measurements allows us to assess assignments for vibrational modes resolved in this region of the heme Raman spectrum. We consider the possibility that the 372 cm(-1) band in reduced cyt c involves the Fe-S(Met80) bond.
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Affiliation(s)
- Bogdan M Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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18
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Leu BM, Zhang Y, Bu L, Straub JE, Zhao J, Sturhahn W, Alp EE, Sage JT. Resilience of the iron environment in heme proteins. Biophys J 2008; 95:5874-89. [PMID: 18835904 PMCID: PMC2599821 DOI: 10.1529/biophysj.108.138198] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 07/22/2008] [Indexed: 11/18/2022] Open
Abstract
Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.
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Affiliation(s)
- Bogdan M Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts, USA
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19
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Giachini L, Francia F, Cordone L, Boscherini F, Venturoli G. Cytochrome C in a dry trehalose matrix: structural and dynamical effects probed by x-ray absorption spectroscopy. Biophys J 2007; 92:1350-60. [PMID: 17142287 PMCID: PMC1783899 DOI: 10.1529/biophysj.106.092338] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 11/01/2006] [Indexed: 11/18/2022] Open
Abstract
We report on the structure and dynamics of the Fe ligand cluster of reduced horse heart cytochrome c in solution, in a dried polyvinyl alcohol (PVA) film, and in two trehalose matrices characterized by different contents of residual water. The effect of the solvent/matrix environment was studied at room temperature using Fe K-edge x-ray absorption fine structure (XAFS) spectroscopy. XAFS data were analyzed by combining ab initio simulations and multi-parameter fitting in an attempt to disentangle structural from disorder parameters. Essentially the same structural and disorder parameters account adequately for the XAFS spectra measured in solution, both in the absence and in the presence of glycerol, and in the PVA film, showing that this polymer interacts weakly with the embedded protein. Instead, incorporation in trehalose leads to severe structural changes, more prominent in the more dried matrix, consisting of 1), an increase up to 0.2 A of the distance between Fe and the imidazole N atom of the coordinating histidine residue and 2), an elongation up to 0.16 A of the distance between Fe and the fourth-shell C atoms of the heme pyrrolic units. These structural distortions are accompanied by a substantial decrease of the relative mean-square displacements of the first ligands. In the extensively dried trehalose matrix, extremely low values of the Debye Waller factors are obtained for the pyrrolic and for the imidazole N atoms. This finding is interpreted as reflecting a drastic hindering in the relative motions of the Fe ligand cluster atoms and an impressive decrease in the static disorder of the local Fe structure. It appears, therefore, that the dried trehalose matrix dramatically perturbs the energy landscape of cytochrome c, giving rise, at the level of local structure, to well-resolved structural distortions and restricting the ensemble of accessible conformational substates.
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Affiliation(s)
- Lisa Giachini
- Dipartimento di Fisica, Università di Bologna, 40126 Bologna, Italy
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20
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Díaz-Moreno I, Díaz-Moreno S, Subías G, De la Rosa MA, Díaz-Quintana A. The atypical iron-coordination geometry of cytochrome f remains unchanged upon binding to plastocyanin, as inferred by XAS. PHOTOSYNTHESIS RESEARCH 2006; 90:23-8. [PMID: 17111237 PMCID: PMC1769345 DOI: 10.1007/s11120-006-9102-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2006] [Accepted: 08/25/2006] [Indexed: 05/12/2023]
Abstract
The transient complex between cytochrome f and plastocyanin from the cyanobacterium Nostoc sp. PCC 7119 has been analysed by X-ray Absorption Spectroscopy in solution, using both proteins in their oxidized and reduced states. Fe K-edge data mainly shows that the atypical metal coordination geometry of cytochrome f, in which the N-terminal amino acid acts as an axial ligand of the heme group, remains unaltered upon binding to its redox partner, plastocyanin. This fact suggests that cytochrome f provides a stable binding site for plastocyanin and minimizes the reorganization energy required in the transient complex formation, which could facilitate the electron transfer between the two redox partners.
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Affiliation(s)
- Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y Consejo Superior de Investigaciones Científicas, Américo Vespucio 49, 41092, Sevilla, Spain.
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21
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Díaz-Moreno I, Díaz-Quintana A, Subías G, Mairs T, De la Rosa MA, Díaz-Moreno S. Detecting transient protein-protein interactions by X-ray absorption spectroscopy: The cytochromec6-photosystem I complex. FEBS Lett 2006; 580:3023-8. [PMID: 16678819 DOI: 10.1016/j.febslet.2006.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Revised: 04/18/2006] [Accepted: 04/18/2006] [Indexed: 11/18/2022]
Abstract
Reliable analysis of the functionality of metalloproteins demands a highly accurate description of both the redox state and geometry of the metal centre, not only in the isolated metalloprotein but also in the transient complex with its target. Here, we demonstrate that the transient interaction between soluble cytochrome c(6) and membrane-embedded photosystem I involves subtle changes in the heme iron, as inferred by X-ray absorption spectroscopy (XAS). A slight shift to lower energies of the absorption edge of Fe2+ in cytochrome c6 is observed upon interaction with photosystem I. This work constitutes a novel application of XAS to the analysis of weak complexes in solution.
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Affiliation(s)
- Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y Consejo Superior de Investigaciones Científicas, Américo Vespucio 49, 41092 Sevilla, Spain
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22
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Simonneaux G, Bondon A. Mechanism of Electron Transfer in Heme Proteins and Models: The NMR Approach. Chem Rev 2005; 105:2627-46. [PMID: 15941224 DOI: 10.1021/cr030731s] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gérard Simonneaux
- Laboratoire de Chimie Organométallique et Biologique, UMR CNRS 6509, Institut de Chimie, Université de Rennes 1, France.
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23
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Levina A, Armstrong RS, Lay PA. Three-dimensional structure determination using multiple-scattering analysis of XAFS: applications to metalloproteins and coordination chemistry. Coord Chem Rev 2005. [DOI: 10.1016/j.ccr.2004.10.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Guo M, Harvey I, Yang W, Coghill L, Campopiano DJ, Parkinson JA, MacGillivray RTA, Harris WR, Sadler PJ. Synergistic anion and metal binding to the ferric ion-binding protein from Neisseria gonorrhoeae. J Biol Chem 2003; 278:2490-502. [PMID: 12372824 DOI: 10.1074/jbc.m208776200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 34-kDa periplasmic iron-transport protein (FBP) from Neisseria gonorrhoeae (nFBP) contains Fe(III) and (hydrogen)phosphate (synergistic anion). It has a characteristic ligand-to-metal charge-transfer absorption band at 481 nm. Phosphate can be displaced by (bi)carbonate to give Fe.CO(3).nFBP (lambda(max) 459 nm). The local structures of native Fe-PO(4)-nFBP and Fe.CO(3).nFBP were determined by EXAFS at the FeK edge using full multiple scattering analysis. The EXAFS analysis reveals that both phosphate and carbonate ligands bind to FBP in monodentate mode in contrast to transferrins, which bind carbonate in bidentate mode. The EXAFS analysis also suggests an alternative to the crystallographically determined position of the Glu ligand, and this in turn suggests that an H-bonding network may help to stabilize monodentate binding of the synergistic anion. The anions oxalate, pyrophosphate, and nitrilotriacetate also appear to serve as synergistic anions but not sulfate or perchlorate. The oxidation of Fe(II) in the presence of nFBP led to a weak Fe(III).nFBP complex (lambda(max) 471 nm). Iron and phosphate can be removed from FBP at low pH (pH 4.5) in the presence of a large excess of citrate. Apo-FBP is less soluble and less stable than Fe.nFBP and binds relatively weakly to Ga(III) and Bi(III) but not to Co(III) ions, all of which bind strongly to apo-human serum transferrin.
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Affiliation(s)
- Maolin Guo
- School of Chemistry, University of Edinburgh, United Kingdom
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25
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Nakajima H, Honma Y, Tawara T, Kato T, Park SY, Miyatake H, Shiro Y, Aono S. Redox properties and coordination structure of the heme in the co-sensing transcriptional activator CooA. J Biol Chem 2001; 276:7055-61. [PMID: 11096066 DOI: 10.1074/jbc.m003972200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The CO-sensing transcriptional activator CooA contains a six-coordinate protoheme as a CO sensor. Cys(75) and His(77) are assigned to the fifth ligand of the ferric and ferrous hemes, respectively. In this study, we carried out alanine-scanning mutagenesis and EXAFS analyses to determine the coordination structure of the heme in CooA. Pro(2) is thought to be the sixth ligand of the ferric and ferrous hemes in CooA, which is consistent with the crystal structure of ferrous CooA (Lanzilotta, W. N., Schuller, D. J., Thorsteinsson, M. V., Kerby, R. L., Roberts, G. P., and Poulos, T. L. (2000) Nat. Struct. Biol. 7, 876-880). CooA exhibited anomalous redox chemistry, i.e. hysteresis was observed in electrochemical redox titrations in which the observed reduction and oxidation midpoint potentials were -320 mV and -260 mV, respectively. The redox-controlled ligand exchange of the heme between Cys(75) and His(77) is thought to cause the difference between the reduction and oxidation midpoint potentials.
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Affiliation(s)
- H Nakajima
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Nomi-gun, Ishikawa 923-1292, Japan
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