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Nagasaka M, Tsuru S, Yamada Y. Metal-ligand delocalization of iron and cobalt porphyrin complexes in aqueous solutions probed by soft X-ray absorption spectroscopy. Phys Chem Chem Phys 2024; 26:23636-23645. [PMID: 39224033 DOI: 10.1039/d4cp02140a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Metal-ligand delocalization of metal porphyrin complexes in aqueous solutions was investigated by analyzing the electronic structure of both the metal and ligand sides using soft X-ray absorption spectroscopy (XAS) at the metal L2,3-edges and nitrogen K-edge, respectively. In the N K-edge XAS spectra of the ligands, the energies of the CN π* peaks of cobalt protoporphyrin IX (CoPPIX) are higher than iron protoporphyrin IX (FePPIX). The energy difference between the two lowest peaks in the XAS spectrum of CoPPIX is also larger than that of FePPIX. Nitrogen K-edge inner-shell calculations of metalloporphyrins with different central metals indicate that the energy differences between these peaks reflect the electronic configurations and spin multiplicities of metalloporphyrins. We also investigated the hydration structure of CoPPIX in aqueous solution by analyzing the electronic structure of the ligand and revealed that CoPPIX maintains its five-coordination geometry in aqueous solution. The present study shows high performance of N K-edge XAS of ligands for studying the coordination structures of metalloporphyrins in solutions rather than the metal L2,3-edges of central metals.
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Affiliation(s)
- Masanari Nagasaka
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki 444-8585, Japan
| | - Shota Tsuru
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
- RIKEN Center for Computational Science, RIKEN, Kobe 650-0047, Japan
| | - Yasuyuki Yamada
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Nagoya 464-8602, Japan
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2
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Schiell C, Rivard C, Portanguen S, Scislowski V, Mirade PS, Astruc T. Iron distribution and speciation in a 3D-printed hybrid food using synchrotron X-ray fluorescence and X-ray absorption spectroscopies. Food Chem 2024; 463:141058. [PMID: 39243607 DOI: 10.1016/j.foodchem.2024.141058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/04/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
The bioavailability of iron from a food depends on its concentration and chemical form but also on dietary factors and nutrient interactions, which are affected by storage conditions and time. Here we investigated the time-course profile of iron in a hybrid 3D-printed food composed of alternating layers of liver and lentils after 0, 5, 7, 14 and 21 days of storage at 4 °C under oxygen or nitrogen packaging. Synchrotron X-ray fluorescence highlighted major variations in iron distribution in both the animal and plant parts of the food as a function of storage conditions. FeP and FeS positive spatial correlations pointed to iron-associated compounds. X-ray absorption near-edge structure spectroscopy showed spectral signatures specific to the animal and plant mixtures, and then highlighted interactions between animal and plant parts during food storage, with a change in iron forms in the plant part.
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Affiliation(s)
- Coline Schiell
- ADIV (Association pour le Développement de l'Institut de la Viande), 10 rue Jacqueline Auriol, 63039 Clermont-Ferrand, France; Université Clermont Auvergne, INRAE, UR370 Qualité des Produits Animaux (QuaPA), 63122 Saint-Genès-Champanelle, France.
| | - Camille Rivard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette, France; INRAE, UAR1008 TRANSFORM, 44316 Nantes, France.
| | - Stéphane Portanguen
- Université Clermont Auvergne, INRAE, UR370 Qualité des Produits Animaux (QuaPA), 63122 Saint-Genès-Champanelle, France.
| | - Valérie Scislowski
- ADIV (Association pour le Développement de l'Institut de la Viande), 10 rue Jacqueline Auriol, 63039 Clermont-Ferrand, France.
| | - Pierre-Sylvain Mirade
- Université Clermont Auvergne, INRAE, UR370 Qualité des Produits Animaux (QuaPA), 63122 Saint-Genès-Champanelle, France.
| | - Thierry Astruc
- Université Clermont Auvergne, INRAE, UR370 Qualité des Produits Animaux (QuaPA), 63122 Saint-Genès-Champanelle, France.
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3
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Gardner AM, Gardner PR. Dioxygen and glucose force motion of the electron-transfer switch in the iron(III) flavohemoglobin-type nitric oxide dioxygenase. J Inorg Biochem 2023; 245:112257. [PMID: 37229820 DOI: 10.1016/j.jinorgbio.2023.112257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
Kinetic and structural investigations of the flavohemoglobin-type NO dioxygenase have suggested critical roles for transient Fe(III)O2 complex formation and O2-forced movements affecting hydride transfer to the FAD cofactor and electron-transfer to the Fe(III)O2 complex. Stark-effect theory together with structural models and dipole and internal electrostatic field determinations provided a semi-quantitative spectroscopic method for investigating the proposed Fe(III)O2 complex and O2-forced movements. Deoxygenation of the enzyme causes Stark effects on the ferric heme Soret and charge-transfer bands revealing the Fe(III)O2 complex. Deoxygenation also elicits Stark effects on the FAD that expose forces and motions that create a more restricted NADH access to FAD for hydride transfer and switch electron-transfer off. Glucose also forces the enzyme toward an off state. Amino acid substitutions at the B10, E7, E11, G8, D5, and F7 positions influence the Stark effects of O2 on resting heme spin states and FAD consistent with the proposed roles of the side chains in the enzyme mechanism. Deoxygenation of ferric myoglobin and hemoglobin A also induces Stark effects on the hemes suggesting a common 'oxy-met' state. The ferric myoglobin and hemoglobin heme spectra are also glucose-responsive. A conserved glucose or glucose-6-phosphate binding site is found bridging the BC-corner and G-helix in flavohemoglobin and myoglobin suggesting novel allosteric effector roles for glucose or glucose-6-phosphate in the NO dioxygenase and O2 storage functions. The results support the proposed roles of a ferric O2 intermediate and protein motions in regulating electron-transfer during NO dioxygenase turnover.
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Affiliation(s)
- Anne M Gardner
- Research and Development Division, Miami Valley Biotech, Suite 2445, 1001 E. 2(nd) Street, Dayton, OH 45402, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, R033, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
| | - Paul R Gardner
- Research and Development Division, Miami Valley Biotech, Suite 2445, 1001 E. 2(nd) Street, Dayton, OH 45402, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, R033, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Chemistry and Biochemistry Department, University of Dayton, 300 College Park, Dayton, OH 45469, USA.
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4
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Hasegawa N, Takahashi Y, Itai T. Tissue-variation of iron stable isotopes in marine fish coupled with speciation analysis using X-ray absorption fine structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163449. [PMID: 37061065 DOI: 10.1016/j.scitotenv.2023.163449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/23/2023] [Accepted: 04/07/2023] [Indexed: 06/01/2023]
Abstract
The Fe stable isotope ratio (δ56Fe) in tissues is a potential parameter for examining the Fe metabolism in marine fish. Although the effect of ferritin storage has been proposed as a possible cause of heavy isotope (56Fe) enrichment in the liver, no speciation and stable isotope ratio coupling data are available. Here, we report the δ56Fe values measured by multicollector ICP-MS and the result of Fe K-edge X-ray absorption near-edge structure (XANES) analysis of multiple tissues obtained from a skipjack tuna (Katsuwonus pelamis) and a chub mackerel (Scomber japonicus). Apparent isotopic fractionation between the liver and the muscle samples (Δ56FeL-M = δ56Feliver - δ56Femuscle) from these species was observed (0.85 ‰ and 0.57 ‰, respectively). The dominant Fe species in the muscle was heme Fe (the sum of methemoglobin, oxyhemoglobin, and deoxyhemoglobin), while ferritin was not detected according to the linear combination fitting of the XANES spectra. In the liver, ferritin contribution was ca. 28 %-54 % of the total Fe content. The apparent difference in δ56Fe between heme Fe and ferritin was estimated to range from 1.41 ‰ to 1.52 ‰ based on the tissue-specific δ56Fe values and the XANES results. These results indicate that the Fe storage as ferritin does not induce the lowering of δ56Fe in the muscle, considering the low contribution of the liver Fe to the total Fe content in the body.
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Affiliation(s)
- Nanako Hasegawa
- Department of Earth and Planetary Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshio Takahashi
- Department of Earth and Planetary Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takaaki Itai
- Department of Earth and Planetary Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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5
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Can M, Abernathy MJ, Wiley S, Griffith C, James CD, Xiong J, Guo Y, Hoffman BM, Ragsdale SW, Sarangi R. Characterization of Methyl- and Acetyl-Ni Intermediates in Acetyl CoA Synthase Formed during Anaerobic CO 2 and CO Fixation. J Am Chem Soc 2023; 145:13696-13708. [PMID: 37306669 PMCID: PMC10311460 DOI: 10.1021/jacs.3c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Indexed: 06/13/2023]
Abstract
The Wood-Ljungdahl Pathway is a unique biological mechanism of carbon dioxide and carbon monoxide fixation proposed to operate through nickel-based organometallic intermediates. The most unusual steps in this metabolic cycle involve a complex of two distinct nickel-iron-sulfur proteins: CO dehydrogenase and acetyl-CoA synthase (CODH/ACS). Here, we describe the nickel-methyl and nickel-acetyl intermediates in ACS completing the characterization of all its proposed organometallic intermediates. A single nickel site (Nip) within the A cluster of ACS undergoes major geometric and redox changes as it transits the planar Nip, tetrahedral Nip-CO and planar Nip-Me and Nip-Ac intermediates. We propose that the Nip intermediates equilibrate among different redox states, driven by an electrochemical-chemical (EC) coupling process, and that geometric changes in the A-cluster linked to large protein conformational changes control entry of CO and the methyl group.
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Affiliation(s)
- Mehmet Can
- Department
of Biochemistry, Faculty of Pharmacy, Ankara
Medipol University, Ankara 06050, Turkey
| | - Macon J. Abernathy
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Seth Wiley
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Claire Griffith
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Christopher D. James
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jin Xiong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Stephen W. Ragsdale
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ritimukta Sarangi
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
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6
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Cheng L, Chen H, Ren Y, Cheng Z, Fan M, Liu Y, Shen Z, Yuan T. Study on enhancement of hemoglobin antitoxic ability modified with chromium and ruthenium. Int J Biol Macromol 2023; 242:124756. [PMID: 37178891 DOI: 10.1016/j.ijbiomac.2023.124756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/17/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Hemoglobin is essential for carrying oxygen (O2) in the blood. However, its ability to bind excessively to carbon monoxide (CO) makes it susceptible to CO poisoning. To reduce the risk of CO poisoning, Cr-based heme and Ru-based heme were selected from among many transition metal-based hemes based on their characteristics of adsorption conformation, binding intensity, spin multiplicity, and electronic properties. The results showed that hemoglobin modified by Cr-based heme and Ru-based heme had strong anti-CO poisoning abilities. The Cr-based heme and Ru-based heme exhibited much stronger affinity for O2 (-190.67 kJ/mol and -143.18 kJ/mol, respectively) than Fe-based heme (-44.60 kJ/mol). Moreover, Cr-based heme and Ru-based heme exhibited much weaker affinity for CO (-121.50 kJ/mol and -120.88 kJ/mol, respectively) than their affinity for O2, suggesting that they were less likely to cause CO poisoning. The electronic structure analysis also supported this conclusion. Additionally, molecular dynamics analysis showed that hemoglobin modified by Cr-based heme and Ru-based heme was stable. Our findings offer a novel and effective strategy for enhancing the reconstructed hemoglobin's ability to bind O2 and reduce its potential for CO poisoning.
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Affiliation(s)
- Luwei Cheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hongjiang Chen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yuanyang Ren
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhiwen Cheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai Academy of Environment Sciences, Shanghai 200233, PR China
| | - Maohong Fan
- College of Engineering & Applied Science, University of Wyoming, Laramie 82070, WY, USA
| | - Yawei Liu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhemin Shen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai 200233, PR China; Shanghai Engineering Research Center of Solid Waste Treatment and Resource Recovery, Shanghai 200240, China.
| | - Tao Yuan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai 200233, PR China; Shanghai Engineering Research Center of Solid Waste Treatment and Resource Recovery, Shanghai 200240, China
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7
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Giraudon--Colas G, Devineau S, Marichal L, Barruet E, Zitolo A, Renault JP, Pin S. How Nanoparticles Modify Adsorbed Proteins: Impact of Silica Nanoparticles on the Hemoglobin Active Site. Int J Mol Sci 2023; 24:3659. [PMID: 36835069 PMCID: PMC9967434 DOI: 10.3390/ijms24043659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The adsorption of proteins on surfaces has been studied for a long time, but the relationship between the structural and functional properties of the adsorbed protein and the adsorption mechanism remains unclear. Using hemoglobin adsorbed on silica nanoparticles, we have previously shown that hemoglobin's affinity towards oxygen increases with adsorption. Nevertheless, it was also shown that there were no significant changes in the quaternary and secondary structures. In order to understand the change in activity, we decided in this work to focus on the active sites of hemoglobin, the heme and its iron. After measuring adsorption isotherms of porcine hemoglobin on Ludox silica nanoparticles, we analyzed the structural modifications of adsorbed hemoglobin by X-ray absorption spectroscopy and circular dichroism spectra in the Soret region. It was found that upon adsorption, there were modifications in the heme pocket environment due to changes in the angles of the heme vinyl functions. These alterations can explain the greater affinity observed.
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Affiliation(s)
| | - Stéphanie Devineau
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Elodie Barruet
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Andrea Zitolo
- Synchrotron SOLEIL, L’Orme des Merisiers, BP 48 Saint Aubin, 91192 Gif-sur-Yvette, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
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8
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Ren W, Schulz CE, Shroyer MH, Xu W, Xi S, An P, Guo W, Li J. Electronic Configurations and the Effect of Peripheral Substituents of (Nitrosyl)iron Corroles. Inorg Chem 2022; 61:20385-20396. [DOI: 10.1021/acs.inorgchem.2c03026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wanjie Ren
- College of Materials Science and Optoelectronic Technology and Chinese Academy of Sciences Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing101408, P. R. China
| | - Charles E. Schulz
- Department of Physics and Astronomy, Knox College, Galesburg, Illinois61401, United States
| | - Mark H. Shroyer
- Department of Physics and Astronomy, Knox College, Galesburg, Illinois61401, United States
| | - Wei Xu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing100049, P. R. China
- RICMASS, Rome International Center for Materials Science Superstripes, Via dei Sabelli 119A, Rome00185, Italy
| | - Shibo Xi
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Jurong Island, Singapore627833, Singapore
| | - Pengfei An
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing100049, P. R. China
| | - Wenping Guo
- National Energy Center for Coal to Clean Fuels, Synfuels China Co., Ltd., Huairou District, Beijing101400, P. R. China
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology and Chinese Academy of Sciences Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing101408, P. R. China
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9
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Lu X, Wang S, Qin JH. Isolating Fe-O 2 Intermediates in Dioxygen Activation by Iron Porphyrin Complexes. Molecules 2022; 27:4690. [PMID: 35897870 PMCID: PMC9332324 DOI: 10.3390/molecules27154690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
Dioxygen (O2) is an environmentally benign and abundant oxidant whose utilization is of great interest in the design of bioinspired synthetic catalytic oxidation systems to reduce energy consumption. However, it is unfortunate that utilization of O2 is a significant challenge because of the thermodynamic stability of O2 in its triplet ground state. Nevertheless, nature is able to overcome the spin state barrier using enzymes, which contain transition metals with unpaired d-electrons facilitating the activation of O2 by metal coordination. This inspires bioinorganic chemists to synthesize biomimetic small-molecule iron porphyrin complexes to carry out the O2 activation, wherein Fe-O2 species have been implicated as the key reactive intermediates. In recent years, a number of Fe-O2 intermediates have been synthesized by activating O2 at iron centers supported on porphyrin ligands. In this review, we focus on a few examples of these advances with emphasis in each case on the particular design of iron porphyrin complexes and particular reaction environments to stabilize and isolate metal-O2 intermediates in dioxygen activation, which will provide clues to elucidate structures of reactive intermediates and mechanistic insights in biological processes.
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Affiliation(s)
- Xiaoyan Lu
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China; (S.W.); (J.-H.Q.)
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10
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Singha A, Mittra K, Dey A. Synthetic heme dioxygen adducts: electronic structure and reactivity. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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Samajdar RN, Bhattacharyya AJ. Structure-Redox Response Correlation in a Few Select Heme Systems Using X-ray Absorption Spectroelectrochemistry. J Phys Chem B 2021; 125:5258-5264. [PMID: 33983739 DOI: 10.1021/acs.jpcb.1c02180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme based biomolecules control some of the most crucial life processes, such as oxygen and electron transport during respiration and energy metabolism, respectively. The active site of the heme, viz., the metal center, plays a key role and attributes functionality to these biomolecules. During the oxygen binding and debinding processes, it is important to note that the oxidation state of iron in hemoglobin (+II in the native form) does not undergo any change. However, the spin states of the metal center change. We present here a comprehensive study of the redox response of such molecules, based on the electronic structure of the active site. The local electronic structure of heme in a few selective molecular systems is studied in operando via synchrotron X-ray absorption spectroscopy (Fe K-edge) and cyclic voltammetry. Our objective is to identify the electronic structural parameters that can effectively be correlated with the redox reversibility. Evolution in these parameters can be followed to trace the overall changes in redox state of the system. Our data indicate that axial coordination and spin state of the iron center are two such parameters that are intimately connected with the redox response.
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Affiliation(s)
- Rudra N Samajdar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aninda J Bhattacharyya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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12
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Shelby ML, Wildman A, Hayes D, Mara MW, Lestrange PJ, Cammarata M, Balducci L, Artamonov M, Lemke HT, Zhu D, Seideman T, Hoffman BM, Li X, Chen LX. Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations. Proc Natl Acad Sci U S A 2021; 118:e2018966118. [PMID: 33782122 PMCID: PMC8040624 DOI: 10.1073/pnas.2018966118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ultrafast structural dynamics with different spatial and temporal scales were investigated during photodissociation of carbon monoxide (CO) from iron(II)-heme in bovine myoglobin during the first 3 ps following laser excitation. We used simultaneous X-ray transient absorption (XTA) spectroscopy and X-ray transient solution scattering (XSS) at an X-ray free electron laser source with a time resolution of 80 fs. Kinetic traces at different characteristic X-ray energies were collected to give a global picture of the multistep pathway in the photodissociation of CO from heme. In order to extract the reaction coordinates along different directions of the CO departure, XTA data were collected with parallel and perpendicular relative polarizations of the laser pump and X-ray probe pulse to isolate the contributions of electronic spin state transition, bond breaking, and heme macrocycle nuclear relaxation. The time evolution of the iron K-edge X-ray absorption near edge structure (XANES) features along the two major photochemical reaction coordinates, i.e., the iron(II)-CO bond elongation and the heme macrocycle doming relaxation were modeled by time-dependent density functional theory calculations. Combined results from the experiments and computations reveal insight into interplays between the nuclear and electronic structural dynamics along the CO photodissociation trajectory. Time-resolved small-angle X-ray scattering data during the same process are also simultaneously collected, which show that the local CO dissociation causes a protein quake propagating on different spatial and temporal scales. These studies are important for understanding gas transport and protein deligation processes and shed light on the interplay of active site conformational changes and large-scale protein reorganization.
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Affiliation(s)
- Megan L Shelby
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Dugan Hayes
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
| | - Michael W Mara
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | | | - Marco Cammarata
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Lodovico Balducci
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Maxim Artamonov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Tamar Seideman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195;
| | - Lin X Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
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13
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Alsharabasy AM, Pandit A, Farràs P. Recent Advances in the Design and Sensing Applications of Hemin/Coordination Polymer-Based Nanocomposites. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2003883. [PMID: 33217074 DOI: 10.1002/adma.202003883] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/10/2020] [Indexed: 06/11/2023]
Abstract
The fabrication of biomimetic catalysts as substituents for enzymes is of critical interest in the field due to the problems associated with the extraction, purification, and storage of enzymes in sensing applications. Of these mimetics, hemin/coordination polymer-based nanocomposites, mainly hemin/metal-organic frameworks (MOF), have been developed for various biosensing applications because of the unique properties of each component, while trying to mimic the normal biological functions of heme within the protein milieu of enzymes. This critical review first discusses the different catalytic functions of heme in the body in the form of enzyme/protein structures. The properties of hemin dimerization are then elucidated with the supposed models of hemin oxidation. After that, the progress in the fabrication of hemin/MOF nanocomposites for the sensing of diverse biological molecules is discussed. Finally, the challenges in developing this type of composites are examined as well as possible proposals for future directions to enhance the sensing performance in this field further.
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Affiliation(s)
- Amir M Alsharabasy
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, H91W2TY, Ireland
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, H91W2TY, Ireland
| | - Pau Farràs
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, H91W2TY, Ireland
- School of Chemistry, Ryan Institute, National University of Ireland Galway, Galway, H91CF50, Ireland
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14
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Weak O 2 binding and strong H 2O 2 binding at the non-heme diiron center of trypanosome alternative oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148356. [PMID: 33385341 DOI: 10.1016/j.bbabio.2020.148356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/20/2022]
Abstract
Alternative oxidase (AOX) catalyzes the four-electron reduction of dioxygen to water as an additional terminal oxidase, and the catalytic reaction is critical for the parasite to survive in its bloodstream form. Recently, the X-ray crystal structure of trypanosome alternative oxidase (TAO) complexed with ferulenol was reported and the molecular structure of the non-heme diiron center was determined. The binding of O2 was a unique side-on type compared to other iron proteins. In order to characterize the O2 binding state of TAO, the O2 binding states were searched at a quantum mechanics/molecular mechanics (QM/MM) theoretical level in the present study. We found that the most stable O2 binding state is the end-on type, and the binding states of the side-on type are higher in energy. Based on the binding energies and electronic structure analyses, O2 binds very weakly to the TAO iron center (ΔE =6.7 kcal mol-1) in the electronic state of Fe(II)…OO, not in the suggested charge transferred state such as the superoxide state (Fe(III)OO· -) as seen in hemerythrin. Coordination of other ligands such as water, Cl-, CN-, CO, N3- and H2O2 was also examined, and H2O2 was found to bind most strongly to the Fe(II) site by ΔE = 14.0 kcal mol-1. This was confirmed experimentally through the measurement of ubiquinol oxidase activity of TAO and Cryptosporidium parvum AOX which was found to be inhibited by H2O2 in a dose-dependent and reversible manner.
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15
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Hollings AL, Lam V, Takechi R, Mamo JCL, Reinhardt J, de Jonge MD, Kappen P, Hackett MJ. Revealing differences in the chemical form of zinc in brain tissue using K-edge X-ray absorption near-edge structure spectroscopy. Metallomics 2020; 12:2134-2144. [PMID: 33300524 DOI: 10.1039/d0mt00198h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc is a prominent trace metal required for normal memory function. Memory loss and cognitive decline during natural ageing and neurodegenerative disease have been associated with altered brain-Zn homeostasis. Yet, the exact chemical pathways through which Zn influences memory function during health, natural ageing, or neurodegenerative disease remain unknown. The gap in the literature may in part be due to the difficulty to simultaneously image, and therefore, study the different chemical forms of Zn within the brain (or biological samples in general). To this extent, we have begun developing and optimising protocols that incorporate X-ray absorption near-edge structure (XANES) spectroscopic analysis of tissue at the Zn K-edge as an analytical tool to study Zn speciation in the brain. XANES is ideally suited for this task as all chemical forms of Zn are detected, the technique requires minimal sample preparation that may otherwise redistribute or alter the chemical form of Zn, and the Zn K-edge has known sensitivity to coordination geometry and ligand type. Herein, we report our initial results where we fit K-edge spectra collected from micro-dissected flash-frozen brain tissue, to a spectral library prepared from standard solutions, to demonstrate differences in the chemical form of Zn that exist between two brain regions, the hippocampus and cerebellum. Lastly, we have used an X-ray microprobe to demonstrate differences in Zn speciation within sub-regions of thin air-dried sections of the murine hippocampus; but, the corresponding results highlight that the chemical form of Zn is easily perturbed by sample preparation such as tissue sectioning or air-drying, which must be a critical consideration for future work.
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Affiliation(s)
- Ashley L Hollings
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
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16
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Geng J, Weitz AC, Dornevil K, Hendrich MP, Liu A. Kinetic and Spectroscopic Characterization of the Catalytic Ternary Complex of Tryptophan 2,3-Dioxygenase. Biochemistry 2020; 59:2813-2822. [PMID: 32659080 DOI: 10.1021/acs.biochem.0c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first step of the kynurenine pathway for l-tryptophan (l-Trp) degradation is catalyzed by heme-dependent dioxygenases, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase. In this work, we employed stopped-flow optical absorption spectroscopy to study the kinetic behavior of the Michaelis complex of Cupriavidus metallidurans TDO (cmTDO) to improve our understanding of oxygen activation and initial oxidation of l-Trp. On the basis of the stopped-flow results, rapid freeze-quench (RFQ) experiments were performed to capture and characterize this intermediate by Mössbauer spectroscopy. By incorporating the chlorite dismutase-chlorite system to produce high concentrations of solubilized O2, we were able to capture the Michaelis complex of cmTDO in a nearly quantitative yield. The RFQ-Mössbauer results confirmed the identity of the Michaelis complex as an O2-bound ferrous species. They revealed remarkable similarities between the electronic properties of the Michaelis complex and those of the O2 adduct of myoglobin. We also found that the decay of this reactive intermediate is the rate-limiting step of the catalytic reaction. An inverse α-secondary substrate kinetic isotope effect was observed with a kH/kD of 0.87 ± 0.03 when (indole-d5)-l-Trp was employed as the substrate. This work provides an important piece of spectroscopic evidence of the chemical identity of the Michaelis complex of bacterial TDO.
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Affiliation(s)
- Jiafeng Geng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kednerlin Dornevil
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Aimin Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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17
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Chen WT, Hsu CW, Lee JF, Pao CW, Hsu IJ. Theoretical Analysis of Fe K-Edge XANES on Iron Pentacarbonyl. ACS OMEGA 2020; 5:4991-5000. [PMID: 32201785 PMCID: PMC7081404 DOI: 10.1021/acsomega.9b03887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/21/2020] [Indexed: 05/21/2023]
Abstract
Iron pentacarbonyl (Fe(CO)5) is a versatile material that is utilized as an inhibitor of flame, shows soot suppressibility, and is used as a precursor for focused electron-beam-induced deposition (FEBID). X-ray absorption near-edge structure (XANES) of the K edge, which is a powerful technique for monitoring the oxidation states and coordination environment of metal sites, can be used to gain insight into Fe(CO)5-related reaction mechanisms in in situ experiments. We use a finite difference method (FDM) and molecular-orbital-based time-dependent density functional theory (TDDFT) calculations to clarify the Fe K-edge XANES features of Fe(CO)5. The two pre-edge peaks P1 and P2 are mainly the Fe(1s) → Fe-C(σ*) and Fe(1s) → Fe-C(π*) transitions, respectively. When the geometry transformed from D 3h to C 4v symmetry, a ∼30% decrease of the pre-edge P2 intensity was observed in the simulated spectra. This implies that the π bonding of Fe and CO is sensitive to changes in geometry. The following rising edge and white line regions are assigned to the Fe(1s) → Fe(4p)(mixing C(2p)) transitions. Our results may provide useful information to interpret XANES spectra variations of in situ reactions of metal-CO or similar compounds with π acceptor ligandlike metal-CN complexes.
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Affiliation(s)
- Wei-Ting Chen
- Department
of Molecular Science and Engineering, National
Taipei University of Technology, Taipei 10608, Taiwan
| | - Che-Wei Hsu
- Department
of Molecular Science and Engineering, National
Taipei University of Technology, Taipei 10608, Taiwan
| | - Jyh-Fu Lee
- National
Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Chih-Wen Pao
- National
Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - I-Jui Hsu
- Department
of Molecular Science and Engineering, National
Taipei University of Technology, Taipei 10608, Taiwan
- Research
and Development Center for Smart Textile Technology, National Taipei University of Technology, Taipei 10608, Taiwan
- E-mail: .
Tel: +886-2-27712171#2420
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18
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Affiliation(s)
- Charles W. Machan
- University of Virginia, McCormick Road,
PO Box 400319, Charlottesville, Virginia 22904-4319, United States
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19
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Hait D, Head-Gordon M. Highly Accurate Prediction of Core Spectra of Molecules at Density Functional Theory Cost: Attaining Sub-electronvolt Error from a Restricted Open-Shell Kohn-Sham Approach. J Phys Chem Lett 2020; 11:775-786. [PMID: 31917579 DOI: 10.1021/acs.jpclett.9b03661] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We present the use of the recently developed square gradient minimization (SGM) algorithm for excited-state orbital optimization to obtain spin-pure restricted open-shell Kohn-Sham (ROKS) energies for core excited states of molecules. The SGM algorithm is robust against variational collapse and offers a reliable route to converging orbitals for target excited states at only 2-3 times the cost of ground-state orbital optimization (per iteration). ROKS/SGM with the modern SCAN/ωB97X-V functionals is found to predict the K-edge of C, N, O, and F to a root mean squared error of ∼0.3 eV. ROKS/SGM is equally effective at predicting L-edge spectra of third period elements, provided a perturbative spin-orbit correction is employed. This high accuracy can be contrasted with traditional time-dependent density functional theory (TDDFT), which typically has greater than 10 eV error and requires translation of computed spectra to align with experiment. ROKS is computationally affordable (having the same scaling as ground-state DFT and a slightly larger prefactor) and can be applied to geometry optimizations/ab initio molecular dynamics of core excited states, as well as condensed phase simulations. ROKS can also model doubly excited/ionized states with one broken electron pair, which are beyond the ability of linear response based methods.
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Affiliation(s)
- Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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20
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Novikova NN, Yakunin SN, Koval’chuk MV, Yur’eva EA, Stepina ND, Rogachev AV, Kremennaya MA, Yalovega GE, Kosmachevskaya OV, Topunov AF. Possibilities of X-Ray Absorption Spectroscopy in the Total External Reflection Geometry for Studying Protein Films on Liquids. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774519060130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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21
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Ehudin MA, Gee LB, Sabuncu S, Braun A, Moenne-Loccoz P, Hedman B, Hodgson KO, Solomon EI, Karlin KD. Tuning the Geometric and Electronic Structure of Synthetic High-Valent Heme Iron(IV)-Oxo Models in the Presence of a Lewis Acid and Various Axial Ligands. J Am Chem Soc 2019; 141:5942-5960. [PMID: 30860832 PMCID: PMC6611672 DOI: 10.1021/jacs.9b00795] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
High-valent ferryl species (e.g., (Por)FeIV═O, Cmpd-II) are observed or proposed key oxidizing intermediates in the catalytic cycles of heme-containing enzymes (P-450s, peroxidases, catalases, and cytochrome c oxidase) involved in biological respiration and oxidative metabolism. Herein, various axially ligated iron(IV)-oxo complexes were prepared to examine the influence of the identity of the base. These were generated by addition of various axial ligands (1,5-dicyclohexylimidazole (DCHIm), a tethered-imidazole system, and sodium derivatives of 3,5-dimethoxyphenolate and imidazolate). Characterization was carried out via UV-vis, electron paramagnetic resonance (EPR), 57Fe Mössbauer, Fe X-ray absorption (XAS), and 54/57Fe resonance Raman (rR) spectroscopies to confirm their formation and compare the axial ligand perturbation on the electronic and geometric structures of these heme iron(IV)-oxo species. Mössbauer studies confirmed that the axially ligated derivatives were iron(IV) and six-coordinate complexes. XAS and 54/57Fe rR data correlated with slight elongation of the iron-oxo bond with increasing donation from the axial ligands. The first reported synthetic H-bonded iron(IV)-oxo heme systems were made in the presence of the protic Lewis acid, 2,6-lutidinium triflate (LutH+), with (or without) DCHIm. Mössbauer, rR, and XAS spectroscopic data indicated the formation of molecular Lewis acid ferryl adducts (rather than full protonation). The reduction potentials of these novel Lewis acid adducts were bracketed through addition of outer-sphere reductants. The oxidizing capabilities of the ferryl species with or without Lewis acid vary drastically; addition of LutH+ to F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate) increased its reduction potential by more than 890 mV, experimentally confirming that H-bonding interactions can increase the reactivity of ferryl species.
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Affiliation(s)
- Melanie A. Ehudin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Leland B. Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sinan Sabuncu
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Pierre Moenne-Loccoz
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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22
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Schaefer AW, Ehudin MA, Quist DA, Tang JA, Karlin KD, Solomon EI. Spin Interconversion of Heme-Peroxo-Copper Complexes Facilitated by Intramolecular Hydrogen-Bonding Interactions. J Am Chem Soc 2019; 141:4936-4951. [PMID: 30836005 PMCID: PMC6457345 DOI: 10.1021/jacs.9b00118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Synthetic peroxo-bridged high-spin (HS) heme-(μ-η2:η1-O22-)-Cu(L) complexes incorporating (as part of the copper ligand) intramolecular hydrogen-bond (H-bond) capabilities and/or steric effects are herein demonstrated to affect the complex's electronic and geometric structure, notably impacting the spin state. An H-bonding interaction with the peroxo core favors a low-spin (LS) heme-(μ-η1:η1-O22-)-Cu(L) structure, resulting in a reversible temperature-dependent interconversion of spin state (5 coordinate HS to 6 coordinate LS). The LS state dominates at low temperatures, even in the absence of a strong trans-axial heme ligand. Lewis base addition inhibits the H-bond facilitated spin interconversion by competition for the H-bond donor, illustrating the precise H-bonding interaction required to induce spin-crossover (SCO). Resonance Raman spectroscopy (rR) shows that the H-bonding pendant interacts with the bridging peroxide ligand to stabilize the LS but not the HS state. The H-bond (to the Cu-bound O atom) acts to weaken the O-O bond and strengthen the Fe-O bond, exhibiting ν(M-O) and ν(O-O) values comparable to analogous known LS complexes with a strong donating trans-axial ligand, 1,5-dicyclohexylimidazole, (DCHIm)heme-(μ-η1:η1-O22-)-Cu(L). Variable-temperature (-90 to -130 °C) UV-vis and 2H NMR spectroscopies confirm the SCO process and implicate the involvement of solvent binding. Examining a case of solvent binding without SCO, thermodynamic parameters were obtained from a van't Hoff analysis, accounting for its contribution in SCO. Taken together, these data provide evidence for the H-bond group facilitating a core geometry change and allowing solvent to bind, stabilizing a LS state. The rR data, complemented by DFT analysis, reveal a stronger H-bonding interaction with the peroxo core in the LS compared to the HS complexes, which enthalpically favors the LS state. These insights enhance our fundamental understanding of secondary coordination sphere influences in metalloenzymes.
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Affiliation(s)
- Andrew W. Schaefer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Melanie A. Ehudin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joel A. Tang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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23
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Resonant inelastic X-ray scattering determination of the electronic structure of oxyhemoglobin and its model complex. Proc Natl Acad Sci U S A 2019; 116:2854-2859. [PMID: 30718404 DOI: 10.1073/pnas.1815981116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hemoglobin and myoglobin are oxygen-binding proteins with S = 0 heme {FeO2}8 active sites. The electronic structure of these sites has been the subject of much debate. This study utilizes Fe K-edge X-ray absorption spectroscopy (XAS) and 1s2p resonant inelastic X-ray scattering (RIXS) to study oxyhemoglobin and a related heme {FeO2}8 model compound, [(pfp)Fe(1-MeIm)(O2)] (pfp = meso-tetra(α,α,α,α-o-pivalamido-phenyl)porphyrin, or TpivPP, 1-MeIm = 1-methylimidazole) (pfpO2), which was previously analyzed using L-edge XAS. The K-edge XAS and RIXS data of pfpO2 and oxyhemoglobin are compared with the data for low-spin FeII and FeIII [Fe(tpp)(Im)2]0/+ (tpp = tetra-phenyl porphyrin) compounds, which serve as heme references. The X-ray data show that pfpO2 is similar to FeII, while oxyhemoglobin is qualitatively similar to FeIII, but with significant quantitative differences. Density-functional theory (DFT) calculations show that the difference between pfpO2 and oxyhemoglobin is due to a distal histidine H bond to O2 and the less hydrophobic environment in the protein, which lead to more backbonding into the O2 A valence bond configuration interaction multiplet model is used to analyze the RIXS data and show that pfpO2 is dominantly FeII with 6-8% FeIII character, while oxyhemoglobin has a very mixed wave function that has 50-77% FeIII character and a partially polarized Fe-O2 π-bond.
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24
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Wang H, Schulz CE, Wei X, Li J. New Insights into the Ligand Nature of Carbene: Synthesis and Characterizations of Six-Coordinate Iron(II) Carbene Porphyrin Complexes. Inorg Chem 2018; 58:143-151. [PMID: 30565937 DOI: 10.1021/acs.inorgchem.8b02043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Charles E. Schulz
- Department of Physics, Knox College, Galesburg, Illinois 61401, United States
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25
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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26
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Peng Q, Sage JT, Liu Y, Wang Z, Hu MY, Zhao J, Alp EE, Scheidt WR, Li J. How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN -) Analogues in the Axial Bond? Inorg Chem 2018; 57:8788-8795. [PMID: 30010336 DOI: 10.1021/acs.inorgchem.8b00574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Compared to well studied diatomic ligands (NO, CN-, CO), the axial bonds of carbene hemes is much less known although its significance in biological chemistry. The unusually large quadrupole splitting (Δ EQ = +2.2 mm·s-1) and asymmetric parameter (η = 0.9) of the five-coordinate heme carbene [Fe(TTP)(CCl2)], which is the largest among all known low spin ferrohemes, has driven investigations by means of Mössbauer effect Nuclear Resonance Vibrational Spectroscopy (NRVS). Three distinct measurements on one single crystal (two in-plane and one out-of-plane) have demonstrated comprehensive vibrational structures including stretch (429) and bending modes (472 cm-1) of the axial Fe-CCl2, and revealed iron vibrational anisotropy in three orthogonal directions for the first time. Frontier orbital analysis especially comparisons with diatomic analogues (NO, CN-, CO) suggest that CCl2, similar to NO, has led to strong but anisotropic π bonding in a ligand-based "4C"-coordinate which induced the vibrational anisotropies and very large Mössbauer parameters. This is contrasted to CN- and CO complexes which possess a porphyrin-based "4N"-coordinate electronic and vibrational structures due to inherent on-axis linear ligation.
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Affiliation(s)
- Qian Peng
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Yulong Liu
- College of Materials Science and Optoelectronic Technology , University of Chinese Academy of Sciences , Yanqi Lake, Huairou, Beijing 101408 , China
| | - Zijian Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Michael Y Hu
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - E Ercan Alp
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - W Robert Scheidt
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology , University of Chinese Academy of Sciences , Yanqi Lake, Huairou, Beijing 101408 , China
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27
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Lewis RD, Garcia-Borràs M, Chalkley MJ, Buller AR, Houk KN, Kan SBJ, Arnold FH. Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase. Proc Natl Acad Sci U S A 2018; 115:7308-7313. [PMID: 29946033 PMCID: PMC6048479 DOI: 10.1073/pnas.1807027115] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, heme proteins have been discovered and engineered by directed evolution to catalyze chemical transformations that are biochemically unprecedented. Many of these nonnatural enzyme-catalyzed reactions are assumed to proceed through a catalytic iron porphyrin carbene (IPC) intermediate, although this intermediate has never been observed in a protein. Using crystallographic, spectroscopic, and computational methods, we have captured and studied a catalytic IPC intermediate in the active site of an enzyme derived from thermostable Rhodothermus marinus (Rma) cytochrome c High-resolution crystal structures and computational methods reveal how directed evolution created an active site for carbene transfer in an electron transfer protein and how the laboratory-evolved enzyme achieves perfect carbene transfer stereoselectivity by holding the catalytic IPC in a single orientation. We also discovered that the IPC in Rma cytochrome c has a singlet ground electronic state and that the protein environment uses geometrical constraints and noncovalent interactions to influence different IPC electronic states. This information helps us to understand the impressive reactivity and selectivity of carbene transfer enzymes and offers insights that will guide and inspire future engineering efforts.
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Affiliation(s)
- Russell D Lewis
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Matthew J Chalkley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Andrew R Buller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
| | - S B Jennifer Kan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Frances H Arnold
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125;
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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28
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Sarangi R. A biological perspective towards a standard for information exchange and reporting in XAS. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:944-952. [PMID: 29979154 PMCID: PMC6038602 DOI: 10.1107/s1600577518008779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
The complex structural landscape of biological samples and their sensitivity to X-ray exposure leads to specific challenges in biological X-ray absorption spectroscopy (bio-XAS) research, which in turn has necessitated standardization of various aspects of bio-XAS data measurement, analysis and interpretation. The bio-XAS community is therefore well suited for the development of a data-reporting standard with the specific aim of creating a feedback loop for improving/standardizing data analysis protocols and optionally to make published data available to collaborators/researchers in a meaningful and quantitative format. The XIF (XAFS information file) reporting format presented here contains key experimental and analysis parameters, useful in developing a consistent platform for bio-XAS research worldwide. Such a reporting standard, enforced by the user community and publishing groups alike, can be an important step towards the standardization of data measurement and analysis techniques in bio-XAS.
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Affiliation(s)
- Ritimukta Sarangi
- Structural Molecular Biology, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94306, USA
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29
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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30
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Kucheryavy P, Lahanas N, Lockard JV. Spectroscopic Evidence of Pore Geometry Effect on Axial Coordination of Guest Molecules in Metalloporphyrin-Based Metal Organic Frameworks. Inorg Chem 2018; 57:3339-3347. [PMID: 29493232 DOI: 10.1021/acs.inorgchem.8b00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A systematic comparison of host-guest interactions in two iron porphyrin-based metal-organic frameworks (MOFs), FeCl-PCN222 and FeCl-PCN224, with drastically different pore sizes and geometries is reported in this fundamental spectroscopy study. Guest molecules (acetone, imidazole, and piperidine) of different sizes, axial binding strengths, and reactivity with the iron porphyrin centers are employed to demonstrate the range of possible interactions that occur at the porphyrin sites inside the pores of the MOF. Binding patterns of these guest species under the constraints of the pore geometries in the two frameworks are established using multiple spectroscopy methods, including UV-vis diffuse reflectance, Raman, X-ray absorption, and X-ray emission spectroscopy. Line shape analysis applied to the latter method provides quantitative information on axial ligation through its spin state sensitivity. The observed coordination behaviors derived from the spectroscopic analyses of the two MOF systems are compared to those predicted using space-filling models and relevant iron porphyrin molecular analogues. While the space-filling models show the ideal axial coordination behavior associated with these systems, the spectroscopic results provide powerful insight into the actual binding interactions that occur in practice. Evidence for potential side reactions occurring within the pores that may be responsible for the observed deviation from model coordination behavior in one of the MOF/guest molecule combinations is presented and discussed in the context of literature precedent.
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Affiliation(s)
- Pavel Kucheryavy
- Department of Chemistry , Rutgers University - Newark , Newark , New Jersey 07102 , United States
| | - Nicole Lahanas
- Department of Chemistry , Rutgers University - Newark , Newark , New Jersey 07102 , United States
| | - Jenny V Lockard
- Department of Chemistry , Rutgers University - Newark , Newark , New Jersey 07102 , United States
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31
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Terrell JR, Gumpper RH, Luo M. Hemoglobin crystals immersed in liquid oxygen reveal diffusion channels. Biochem Biophys Res Commun 2018; 495:1858-1863. [DOI: 10.1016/j.bbrc.2017.12.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 11/24/2022]
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32
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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33
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Phung QM, Pierloot K. The dioxygen adducts of iron and manganese porphyrins: electronic structure and binding energy. Phys Chem Chem Phys 2018; 20:17009-17019. [DOI: 10.1039/c8cp03078b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The electronic structures of adducts of O2 and metal porphyrins were thoroughly investigated by highly accurate DMRG-CASPT2.
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34
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Sharma SK, Schaefer AW, Lim H, Matsumura H, Moënne-Loccoz P, Hedman B, Hodgson KO, Solomon EI, Karlin KD. A Six-Coordinate Peroxynitrite Low-Spin Iron(III) Porphyrinate Complex-The Product of the Reaction of Nitrogen Monoxide (·NO (g)) with a Ferric-Superoxide Species. J Am Chem Soc 2017; 139:17421-17430. [PMID: 29091732 PMCID: PMC5783694 DOI: 10.1021/jacs.7b08468] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxynitrite (-OON═O, PN) is a reactive nitrogen species (RNS) which can effect deleterious nitrative or oxidative (bio)chemistry. It may derive from reaction of superoxide anion (O2•-) with nitric oxide (·NO) and has been suggested to form an as-yet unobserved bound heme-iron-PN intermediate in the catalytic cycle of nitric oxide dioxygenase (NOD) enzymes, which facilitate a ·NO homeostatic process, i.e., its oxidation to the nitrate anion. Here, a discrete six-coordinate low-spin porphyrinate-FeIII complex [(PIm)FeIII(-OON═O)] (3) (PIm; a porphyrin moiety with a covalently tethered imidazole axial "base" donor ligand) has been identified and characterized by various spectroscopies (UV-vis, NMR, EPR, XAS, resonance Raman) and DFT calculations, following its formation at -80 °C by addition of ·NO(g) to the heme-superoxo species, [(PIm)FeIII(O2•-)] (2). DFT calculations confirm that 3 is a six-coordinate low-spin species with the PN ligand coordinated to iron via its terminal peroxidic anionic O atom with the overall geometry being in a cis-configuration. Complex 3 thermally transforms to its isomeric low-spin nitrato form [(PIm)FeIII(NO3-)] (4a). While previous (bio)chemical studies show that phenolic substrates undergo nitration in the presence of PN or PN-metal complexes, in the present system, addition of 2,4-di-tert-butylphenol (2,4DTBP) to complex 3 does not lead to nitrated phenol; the nitrate complex 4a still forms. DFT calculations reveal that the phenolic H atom approaches the terminal PN O atom (farthest from the metal center and ring core), effecting O-O cleavage, giving nitrogen dioxide (·NO2) plus a ferryl compound [(PIm)FeIV═O] (7); this rebounds to give [(PIm)FeIII(NO3-)] (4a).The generation and characterization of the long sought after ferriheme peroxynitrite complex has been accomplished.
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Affiliation(s)
- Savita K. Sharma
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Andrew W. Schaefer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Hirotoshi Matsumura
- Division of Environmental & Biomolecular Systems, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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35
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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36
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Schuth N, Mebs S, Huwald D, Wrzolek P, Schwalbe M, Hemschemeier A, Haumann M. Effective intermediate-spin iron in O 2-transporting heme proteins. Proc Natl Acad Sci U S A 2017; 114:8556-8561. [PMID: 28739893 PMCID: PMC5559043 DOI: 10.1073/pnas.1706527114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Proteins carrying an iron-porphyrin (heme) cofactor are essential for biological O2 management. The nature of Fe-O2 bonding in hemoproteins is debated for decades. We used energy-sampling and rapid-scan X-ray Kβ emission and K-edge absorption spectroscopy as well as quantum chemistry to determine molecular and electronic structures of unligated (deoxy), CO-inhibited (carboxy), and O2-bound (oxy) hemes in myoglobin (MB) and hemoglobin (HB) solutions and in porphyrin compounds at 20-260 K. Similar metrical and spectral features revealed analogous heme sites in MB and HB and the absence of low-spin (LS) to high-spin (HS) conversion. Amplitudes of Kβ main-line emission spectra were directly related to the formal unpaired Fe(d) spin count, indicating HS Fe(II) in deoxy and LS Fe(II) in carboxy. For oxy, two unpaired Fe(d) spins and, thus by definition, an intermediate-spin iron center, were revealed by our static and kinetic X-ray data, as supported by (time-dependent) density functional theory and complete-active-space self-consistent-field calculations. The emerging Fe-O2 bonding situation includes in essence a ferrous iron center, minor superoxide character of the noninnocent ligand, significant double-bond properties of the interaction, and three-center electron delocalization as in ozone. It resolves the apparently contradictory classical models of Pauling, Weiss, and McClure/Goddard into a unifying view of O2 bonding, tuned toward reversible oxygen transport.
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Affiliation(s)
- Nils Schuth
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Dennis Huwald
- Department of Plant Biochemistry, Section of Photobiotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Pierre Wrzolek
- Department of Chemistry, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Matthias Schwalbe
- Department of Chemistry, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Anja Hemschemeier
- Department of Plant Biochemistry, Section of Photobiotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany;
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37
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Spectral insights into the transformation and distribution of CdSe quantum dots in microorganisms during food-chain transport. Sci Rep 2017; 7:4370. [PMID: 28663551 PMCID: PMC5491517 DOI: 10.1038/s41598-017-04694-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/18/2017] [Indexed: 11/17/2022] Open
Abstract
The discharge of engineered nanomaterials (ENMs) into environment is raising widespread concern not only due to their direction bio-toxicity but also their bio-concentration and bio-magnification through food web. However, the transformation and distribution of ENMs during food-chain transport are poorly understood, due to lack of accurate, reliable analytical methods. In this study, by using a suite of advanced spectrum techniques, we successfully tracked the distribution and biotransformation dynamics of CdSe quantum dots (QDs) during their transport from Shewanella onedensis to Caenorchabditis elegans in predation. Fluorescence microscopy and Raman mapping showed that the ingested QDs by C. elegans were located at the gut lumen and subcutaneous tissue, and were partially excreted from the nematode body over time. Micro-X-ray fluorescence (μ-XRF) spectroscopy and Se K-edge X-ray absorption fine structure (XAFS) results further revealed the changed distribution of Se element over time, and a shift in the major Se species from CdSe to Se0 and Na2SeO3IV. This work demonstrates the utility of advanced spectral techniques for characterizing QDs in vivo, and may facilitate a better understanding on the environmental transformation and fates of ENMs.
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38
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Liu Y, Xu W, Zhang J, Fuller W, Schulz CE, Li J. Electronic Configuration and Ligand Nature of Five-Coordinate Iron Porphyrin Carbene Complexes: An Experimental Study. J Am Chem Soc 2017; 139:5023-5026. [PMID: 28339195 DOI: 10.1021/jacs.7b01722] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The five-coordinate iron porphyrin carbene complexes [Fe(TPP) (CCl2)] (TPP = tetraphenylporphyrin), [Fe(TTP) (CCl2)] (TTP = tetratolylporphyrin) and [Fe(TFPP) (CPh2)] (TFPP = tetra(pentafluorophenyl)porphyrin), utilizing two types of carbene ligands (CCl2 and CPh2), have been investigated by single crystal X-ray, XANES (X-ray absorption near edge spectroscopy), Mössbauer, NMR and UV-vis spectroscopies. The XANES suggested the iron(II) oxidation state of the complexes. The multitemperature and high magnetic field Mössbauer experiments, which show very large quadrupole splittings (QS, ΔEQ), determined the S = 0 electronic configuration. More importantly, combined structural and Mössbauer studies, especially the comparison with the low spin iron(II) porphyrin complexes with strong diatomic ligands (CS, CO and CN-) revealed the covalent bond nature of the carbene ligands. A correlation between the iron isomer shifts (IS, δ) and the axial bond distances is established for the first time for these donor carbon ligands (:C-R).
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Affiliation(s)
- Yulong Liu
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences , Yanqi Lake, Huairou District, Beijing 101408, China
| | - Wei Xu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Jing Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - William Fuller
- Department of Physics, Knox College , Galesburg, Illinois 61401, United States
| | - Charles E Schulz
- Department of Physics, Knox College , Galesburg, Illinois 61401, United States
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences , Yanqi Lake, Huairou District, Beijing 101408, China
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39
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Bostelaar T, Vitvitsky V, Kumutima J, Lewis BE, Yadav PK, Brunold TC, Filipovic M, Lehnert N, Stemmler TL, Banerjee R. Hydrogen Sulfide Oxidation by Myoglobin. J Am Chem Soc 2016; 138:8476-88. [PMID: 27310035 PMCID: PMC5464954 DOI: 10.1021/jacs.6b03456] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enzymes in the sulfur network generate the signaling molecule, hydrogen sulfide (H2S), from the amino acids cysteine and homocysteine. Since it is toxic at elevated concentrations, cells are equipped to clear H2S. A canonical sulfide oxidation pathway operates in mitochondria, converting H2S to thiosulfate and sulfate. We have recently discovered the ability of ferric hemoglobin to oxidize sulfide to thiosulfate and iron-bound hydropolysulfides. In this study, we report that myoglobin exhibits a similar capacity for sulfide oxidation. We have trapped and characterized iron-bound sulfur intermediates using cryo-mass spectrometry and X-ray absorption spectroscopy. Further support for the postulated intermediates in the chemically challenging conversion of H2S to thiosulfate and iron-bound catenated sulfur products is provided by EPR and resonance Raman spectroscopy in addition to density functional theory computational results. We speculate that the unusual sensitivity of skeletal muscle cytochrome c oxidase to sulfide poisoning in ethylmalonic encephalopathy, resulting from the deficiency in a mitochondrial sulfide oxidation enzyme, might be due to the concentration of H2S by myoglobin in this tissue.
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Affiliation(s)
- Trever Bostelaar
- Department of Biological Chemistry, University of Michigan,
Ann Arbor, Michigan 48109, United States
| | - Victor Vitvitsky
- Department of Biological Chemistry, University of Michigan,
Ann Arbor, Michigan 48109, United States
| | - Jacques Kumutima
- Department of Chemistry and Department of Biophysics,
University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brianne E. Lewis
- Department of Pharmaceutical Science, Wayne State
University, Detroit, Michigan 48201-2417, United States
| | - Pramod K. Yadav
- Department of Biological Chemistry, University of Michigan,
Ann Arbor, Michigan 48109, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin, Madison,
Wisconsin 53706, United States
| | - Milos Filipovic
- University of Bordeaux, IBGC, and CNRS, IBGC, UMR 5095,
F-33077 Bordeaux, France
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics,
University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Timothy L. Stemmler
- Department of Pharmaceutical Science, Wayne State
University, Detroit, Michigan 48201-2417, United States
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan,
Ann Arbor, Michigan 48109, United States
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40
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Kucheryavy P, Lahanas N, Velasco E, Sun CJ, Lockard JV. Probing Framework-Restricted Metal Axial Ligation and Spin State Patterns in a Post-Synthetically Reduced Iron-Porphyrin-Based Metal-Organic Framework. J Phys Chem Lett 2016; 7:1109-1115. [PMID: 26950260 DOI: 10.1021/acs.jpclett.6b00302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An iron-porphyrin-based metal organic framework PCN-222(Fe) is investigated upon postsynthetic reduction with piperidine. Fe K-edge X-ray absorption and Kβ mainline emission spectroscopy measurements reveal the local coordination geometry, oxidation, and spin state changes experienced by the Fe sites upon reaction with this axially coordinating reducing agent. Analysis and fitting of these data confirm the binding pattern predicted by a space-filling model of the structurally constrained pore environments. These results are further supported by UV-vis diffuse reflectance, IR, and resonance Raman spectroscopy data.
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Affiliation(s)
- Pavel Kucheryavy
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
| | - Nicole Lahanas
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
| | - Ever Velasco
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
| | - Cheng-Jun Sun
- X-ray Science Division, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jenny V Lockard
- Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States
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41
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Discovery of the magnetic behavior of hemoglobin: A beginning of bioinorganic chemistry. Proc Natl Acad Sci U S A 2016; 112:13123-7. [PMID: 26508205 DOI: 10.1073/pnas.1515704112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two articles published by Pauling and Coryell in PNAS nearly 80 years ago described in detail the magnetic properties of oxy- and deoxyhemoglobin, as well as those of closely related compounds containing hemes. Their measurements revealed a large difference in magnetism between oxygenated and deoxygenated forms of the protein and, along with consideration of the observed diamagnetism of the carbonmonoxy derivative, led to an electronic structural formulation of oxyhemoglobin. The key role of hemoglobin as the main oxygen carrier in mammalian blood had been established earlier, and its allosteric behavior had been described in the 1920s. The Pauling-Coryell articles on hemoglobin represent truly seminal contributions to the field of bioinorganic chemistry because they are the first to make connections between active site electronic structure and the function of a metalloprotein.
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42
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Mebs S, Braun B, Kositzki R, Limberg C, Haumann M. Abrupt versus Gradual Spin-Crossover in Fe(II)(phen)2(NCS)2 and Fe(III)(dedtc)3 Compared by X-ray Absorption and Emission Spectroscopy and Quantum-Chemical Calculations. Inorg Chem 2015; 54:11606-24. [PMID: 26624918 DOI: 10.1021/acs.inorgchem.5b01822] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular spin-crossover (SCO) compounds are attractive for information storage and photovoltaic technologies. We compared two prototypic SCO compounds with Fe(II)N6 (1, [Fe(phen)2(NCS)2], with phen = 1,10-phenanthroline) or Fe(III)S6 (2, [Fe(dedtc)3], with dedtc = N,N'-diethyldithiocarbamate) centers, which show abrupt (1) or gradual (2) thermally induced SCO, using K-edge X-ray absorption and Kβ emission spectroscopy (XAS/XES) in a 8-315 K temperature range, single-crystal X-ray diffraction (XRD), and density functional theory (DFT). Core-to-valence and valence-to-core electronic transitions in the XAS/XES spectra and bond lengths change from XRD provided benchmark data, verifying the adequacy of the TPSSh/TZVP DFT approach for the description of low-spin (LS) and high-spin (HS) species. Determination of the spin densities, charge distributions, bonding descriptors, and valence-level configurations, as well as similar experimental and calculated enthalpy changes (ΔH), suggested that the varying metal-ligand bonding properties and deviating electronic structures converge to similar enthalpic contributions to the free-energy change (ΔG) and thus presumably are not decisive for the differing SCO behavior of 1 and 2. Rather, SCO seems to be governed by vibrational contributions to the entropy changes (ΔS) in both complexes. Intra- and intermolecular interactions in crystals of 1 and 2 were identified by atoms-in-molecules analysis. Thermal excitation of individual dedtc ligand vibrations accompanies the gradual SCO in 2. In contrast, extensive inter- and intramolecular phen/NCS vibrational mode coupling may be an important factor in the cooperative SCO behavior of 1.
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Affiliation(s)
- Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Beatrice Braun
- Institut für Chemie, Humboldt-Universität zu Berlin , 12489 Berlin, Germany
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin , 12489 Berlin, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
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Sowole MA, Vuong S, Konermann L. Interactions of hemoglobin and myoglobin with their ligands CN(-), CO, and O2 monitored by electrospray ionization-mass spectrometry. Anal Chem 2015; 87:9538-45. [PMID: 26327529 DOI: 10.1021/acs.analchem.5b02506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electrospray ionization (ESI)-mass spectrometry (MS) can provide information on protein-ligand interactions via detection of the corresponding complexes as gaseous ions. Unfortunately, some systems are prone to dissociation upon transfer into the gas phase. The reversible oxygen binding to hemoglobin (Hb) has been extensively studied in solution using a wide range of biophysical techniques. In addition to O2, ferrous (Fe(II)) Hb can bind CO. High affinity interactions with CN(-) are limited to the ferric (Fe(III)) state. In analogous fashion, CN(-), CO, and O2 bind to myoglobin (Mb). It remains unclear whether any of these ligand-bound forms can be observed by ESI-MS. In this work we demonstrate the successful detection of MbCN, while MbCO and MbO2 do not survive under ESI-MS conditions. Control experiments suggest that an older report of "MbO2" detection by ESI-MS may involve the misassignment of oxidation artifacts formed under corona discharge conditions. The situation is more favorable for ESI-MS studies on Hb. The most intense signal in the HbCN mass distribution corresponds to the expected complex with four cyanide moieties bound. Ligand loss during ESI-MS is around 20%. HbCO is detectable as well, albeit with a more noticeable level of ligand dissociation (∼50%) which produces the 2CO-bound state as the highest intensity ion in the spectrum. In addition, our data suggest that low levels of HbO2 can survive the transition into the gas phase, evident from +64 Da and +128 Da signals that can be assigned to Hb carrying two and four oxygen molecules, respectively. The application of collisional activation induces neutral ligand loss for all three Hb derivatives. It appears that this is the first report on the detection of MbCN, HbCO, and HbO2 in the gas phase. We hope that this work will pave the way towards future spectroscopic investigations of desolvated Mb and Hb, complementing the extensive literature on CN(-), CO, and O2 bound globins in the condensed phase.
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Affiliation(s)
- Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Stephanie Vuong
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
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Huwald D, Schrapers P, Kositzki R, Haumann M, Hemschemeier A. Characterization of unusual truncated hemoglobins of Chlamydomonas reinhardtii suggests specialized functions. PLANTA 2015; 242:167-85. [PMID: 25893868 DOI: 10.1007/s00425-015-2294-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/27/2015] [Indexed: 05/04/2023]
Abstract
Annotated hemoglobin genes in Chlamydomonas reinhardtii form functional globins, despite unusual architectures. Spectral characteristics show subtle biochemical differences. Multiple globins might help the alga to cope with its versatile environment. The unicellular green alga C. reinhardtii is a photosynthetic, often soil-dwelling organism, subjected to a changeable environment in nature. The alga contains 12 genes encoding so-called truncated hemoglobins that feature a two-on-two helical fold instead of the three-on-three helix arrangement of the long-studied vertebrate globins or plant symbiotic and non-symbiotic hemoglobins. In plants, non-symbiotic hemoglobins often play a role in acclimation to stress, and we could show recently that one of the C. reinhardtii globin genes is vital for anoxic growth. Here, three further globin encoding transcripts (Cre16.g661000.t1.1, Cre16.g661300.t2.1 and Cre16.g662750.t1.2) were heterologously expressed along with the recently studied THB1. UV-Vis and X-ray absorption spectroscopy analyses show that the sequences indeed encode functional hemoglobins, despite their uncommon primary sequences, which include long C-termini without any predictable function, or a split heme-binding domain. The proteins show some variations regarding the coordination of the heme iron or the interaction with diatomic ligands, indicating different functionalities. The respective transcripts are not responsive to the nitrogen source, in contrast to results reported for THB1, but they accumulate in darkness. This work advances experimental data on the very large globin family in general, and, more specifically, on hemoglobins in photosynthetic organisms.
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Affiliation(s)
- Dennis Huwald
- Work Group Photobiotechnology, Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, ND2/134, 44801, Bochum, Germany
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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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Davydov R, Laryukhin M, Ledbetter-Rogers A, Sono M, Dawson JH, Hoffman BM. Electron paramagnetic resonance and electron-nuclear double resonance studies of the reactions of cryogenerated hydroperoxoferric-hemoprotein intermediates. Biochemistry 2014; 53:4894-903. [PMID: 25046203 PMCID: PMC4144713 DOI: 10.1021/bi500296d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The fleeting ferric peroxo and hydroperoxo
intermediates of dioxygen
activation by hemoproteins can be readily trapped and characterized
during cryoradiolytic reduction of ferrous hemoprotein–O2 complexes at 77 K. Previous cryoannealing studies suggested
that the relaxation of cryogenerated hydroperoxoferric intermediates
of myoglobin (Mb), hemoglobin, and horseradish peroxidase (HRP), either
trapped directly at 77 K or generated by cryoannealing of a trapped
peroxo-ferric state, proceeds through dissociation of bound H2O2 and formation of the ferric heme without formation
of the ferryl porphyrin π-cation radical intermediate, compound
I (Cpd I). Herein we have reinvestigated the mechanism of decays of
the cryogenerated hydroperoxyferric intermediates of α- and
β-chains of human hemoglobin, HRP, and chloroperoxidase (CPO).
The latter two proteins are well-known to form spectroscopically detectable
quasistable Cpds I. Peroxoferric intermediates are trapped during
77 K cryoreduction of oxy Mb, α-chains, and β-chains of
human hemoglobin and CPO. They convert into hydroperoxoferric intermediates
during annealing at temperatures above 160 K. The hydroperoxoferric
intermediate of HRP is trapped directly at 77 K. All studied hydroperoxoferric
intermediates decay with measurable rates at temperatures above 170
K with appreciable solvent kinetic isotope effects. The hydroperoxoferric
intermediate of β-chains converts to the S =
3/2 Cpd I, which in turn decays to an electron paramagnetic resonance
(EPR)-silent product at temperature above 220 K. For all the other
hemoproteins studied, cryoannealing of the hydroperoxo intermediate
directly yields an EPR-silent majority product. In each case, a second
follow-up 77 K γ-irradiation of the annealed samples yields
low-spin EPR signals characteristic of cryoreduced ferrylheme (compound
II, Cpd II). This indicates that in general the hydroperoxoferric
intermediates relax to Cpd I during cryoanealing at low temperatures,
but when this state is not captured by reaction with a bound substrate,
it is reduced to Cpd II by redox-active products of radiolysis.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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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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48
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Xu W, Dziedzic-Kocurek K, Yu M, Wu Z, Marcelli A. Spectroscopic study and electronic structure of prototypical iron porphyrins and their μ-oxo-dimer derivatives with different functional configurations. RSC Adv 2014. [DOI: 10.1039/c4ra04685d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The electronic structures and the charge dynamics of prototypical porphyrins and their μ-oxo-dimer derivatives have been investigated to provide insight into their molecular biophysical mechanisms.
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Affiliation(s)
- Wei Xu
- Beijing Synchrotron Radiation Facility
- Institute of High Energy Physics
- Beijing, China
| | | | - Meijuan Yu
- Beijing Synchrotron Radiation Facility
- Institute of High Energy Physics
- Beijing, China
| | - Ziyu Wu
- Beijing Synchrotron Radiation Facility
- Institute of High Energy Physics
- Beijing, China
- NSRL
- University of Science and Technology of China
| | - Augusto Marcelli
- NSRL
- University of Science and Technology of China
- Hefei 230026, China
- INFN - Laboratori Nazionali di Frascati
- Frascati, Italy
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