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Iritani Y, Ishikawa H, Mizuno M, Mizutani Y. Heme Pocket Structure and Its Functional Implications in an Ancestral Globin Protein. Biochemistry 2023; 62:2727-2737. [PMID: 37647623 DOI: 10.1021/acs.biochem.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Proteins have undergone evolutionary processes to achieve optimal stability, increased functionality, and novel functions. Comparative analysis of existent and ancestral proteins provides insights into the factors that influence protein stability and function. Ancestral sequence reconstruction allows us to deduce the amino acid sequences of ancestral proteins. Here, we present the structural and functional characteristics of an ancestral protein, AncMH, reconstructed to be the last common ancestor of hemoglobins and myoglobins. Our findings reveal that AncMH harbors heme and that the heme binds oxygen. Furthermore, we demonstrate that the ferrous heme in AncMH is pentacoordinated, similar to that of human adult hemoglobin and horse myoglobin. A detailed comparison of the heme pocket structure indicates that the heme pocket in AncMH is more similar to that of hemoglobin than that of myoglobin. However, the autoxidation of AncMH is faster than that of both hemoglobin and myoglobin. Collectively, our results suggest that ancestral proteins of hemoglobins and myoglobins evolved in steps, including the hexa- to pentacoordination transition, followed by stabilization of the oxygen-bound form.
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Affiliation(s)
- Yu Iritani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Haruto Ishikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Antonio JJ, Kraka E. Noncovalent π Interactions in Mutated Aquomet-Myoglobin Proteins: A QM/MM and Local Vibrational Mode Study. Biochemistry 2023; 62:2325-2337. [PMID: 37458402 DOI: 10.1021/acs.biochem.3c00192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Protein dynamics and function is strongly connected to the energy flow taking place. Myoglobin (Mb) and its mutations are ideal systems to study the process of vibrational energy transfer (VET) at the molecular level. Anti-Stokes ultraviolet resonance Raman studies using a tryptophan (Trp) probe, introduced at different Mb positions by amino acid replacement, have suggested that the amount of VET depends on the position of the Trp probe relative to the heme group. Inspired by this experimental work, we explored the strength of noncovalent π interactions, as well as covalent interactions for both the axial and distal ligands bound to iron in aquomet-Mb with the local vibrational mode analysis (LMA), originally developed by Konkoli and Cremer. Two sets of noncovalent interactions were investigated: (1) the interaction between the water ligand and Trp rings and (2) the interaction between the Trp and the porphyrin rings of the heme group. We assessed the strength of these noncovalent interactions via a special local mode force constant. Various Trp-modified water-bound ferric Mb proteins in the ground state were studied (6 in total) using gas-phase and QM/MM calculations followed by LMA. Our results disclose that VET is indeed dependent on the position of the Trp probe relative to the heme group but also on the tautomeric nature of distal histidine. They provide new guidelines on how to assess noncovalent π interactions in proteins utilizing LMA and how to use these data to explore VET, and more generally protein dynamics and function.
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Affiliation(s)
- Juliana J Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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3
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Rout J, Swain BC, Subadini S, Mishra PP, Sahoo H, Tripathy U. Conformational dynamics of myoglobin in the presence of vitamin B12: A spectroscopic and in silico investigation. Int J Biol Macromol 2021; 192:564-573. [PMID: 34653439 DOI: 10.1016/j.ijbiomac.2021.10.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
Myoglobin is an essential transport protein of heart and muscle tissues that acts as a local oxygen reservoir and a marker in different diseased conditions. On the other hand, Vitamin B12 is a vital nutrient that helps synthesize red blood cells, DNA, and proteins. To understand the ability of vitamin B12 to bind to the excess of myoglobin produced in the body under certain conditions (muscle injuries, severe trauma, etc.), it is essential to dig into the interaction between them. Therefore, the present study reports the binding interaction of vitamin B12 and myoglobin employing different spectroscopic and computational methods. The myoglobin's intrinsic fluorescence is quenched by vitamin B12 via static nature as observed from steady-state as well as time-resolved fluorescence measurements. The microenvironment of myoglobin's tryptophan residue gets affected, but there is no change observed in its α-helical content by vitamin B12 as seen from synchronous fluorescence and circular dichroism measurements. The probable binding of vitamin B12 on myoglobin was elucidated through molecular docking, and the interaction stability was studied by molecular dynamics simulation. The determination of vitamin B12's affinity to myoglobin and its effect on the conformational transitions of myoglobin might afford valuable insight for clinical pharmacology.
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Affiliation(s)
- Janmejaya Rout
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad 826004, Jharkhand, India
| | - Bikash Chandra Swain
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad 826004, Jharkhand, India
| | - Suchismita Subadini
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Padmaja Prasad Mishra
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, West Bengal, India
| | - Harekrushna Sahoo
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Umakanta Tripathy
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad 826004, Jharkhand, India.
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4
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Soldatov M, Polozhentsev O, Zolotukhin P, Belanova A, Cotte M, Castillo-Michel H, Pradas del Real A, Kuchma E, Soldatov A. Micro-XANES analysis of superparamagnetic iron-oxide nanoparticles in biological tissues. Radiat Phys Chem Oxf Engl 1993 2021. [DOI: 10.1016/j.radphyschem.2020.109162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Kravtsova AN, Guda LV, Polozhentsev OE, Pankin IA, Soldatov AV. Xanes Specroscopic Diagnostics of the 3D Local Atomic Structure of Nanostructured Materials. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618070259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Kravtsova AN, Pankin IA, Soldatov MA, Butova VV, Bobrova IA, Soldatov AV. Analysis of the local atomic structure of quantum dots of the CdS family. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476616070179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Choi J, Tojo S, Fujitsuka M, Majima T. Dynamics in the heme geometry of myoglobin induced by the one-electron reduction. Int J Radiat Biol 2014; 90:459-67. [DOI: 10.3109/09553002.2013.876115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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8
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X-ray absorption spectroscopic investigation of the electronic structure differences in solution and crystalline oxyhemoglobin. Proc Natl Acad Sci U S A 2013; 110:16333-8. [PMID: 24062465 DOI: 10.1073/pnas.1315734110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hemoglobin (Hb) is the heme-containing O2 transport protein essential for life in all vertebrates. The resting high-spin (S = 2) ferrous form, deoxy-Hb, combines with triplet O2, forming diamagnetic (S = 0) oxy-Hb. Understanding this electronic structure is the key first step in understanding transition metal-O2 interaction. However, despite intense spectroscopic and theoretical studies, the electronic structure description of oxy-Hb remains elusive, with at least three different descriptions proposed by Pauling, Weiss, and McClure-Goddard, based on theory, spectroscopy, and crystallography. Here, a combination of X-ray absorption spectroscopy and extended X-ray absorption fine structure, supported by density functional theory calculations, help resolve this debate. X-ray absorption spectroscopy data on solution and crystalline oxy-Hb indicate both geometric and electronic structure differences suggesting that two of the previous descriptions are correct for the Fe-O2 center in oxy-Hb. These results support the multiconfigurational nature of the ground state developed by theoretical results. Additionally, it is shown here that small differences in hydrogen bonding and solvation effects can tune the ground state, tipping it into one of the two probable configurations. These data underscore the importance of solution spectroscopy and show that the electronic structure in the crystalline form may not always reflect the true ground-state description in solution.
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Hayes JR, Grosvenor AP. An investigation of the electronic structure of Cu2FeSn3−xTixS8 (0≤x≤3) thiospinel spin-crossover materials by X-ray absorption spectroscopy and electronic structure calculations. J SOLID STATE CHEM 2013. [DOI: 10.1016/j.jssc.2012.08.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Lange KM, Golnak R, Bonhommeau S, Aziz EF. Ligand discrimination of myoglobin in solution: an iron L-edge X-ray absorption study of the active centre. Chem Commun (Camb) 2013; 49:4163-5. [DOI: 10.1039/c3cc37973f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron L-edge X-ray absorption spectra of the active centre of myoglobin in the met-form, in the reduced form and upon ligation to O2, CO, NO and CN are presented.
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Affiliation(s)
| | - Ronny Golnak
- Joint Ultrafast Dynamics Lab in Solutions and at Interfaces (JULiq)
- Helmholtz-Zentrum Berlin für Materialien und Energie
- 12489 Berlin
- Germany
| | | | - Emad F. Aziz
- Joint Ultrafast Dynamics Lab in Solutions and at Interfaces (JULiq)
- Helmholtz-Zentrum Berlin für Materialien und Energie
- 12489 Berlin
- Germany
- Freie Universität Berlin
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11
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Sarangi R. X-ray absorption near-edge spectroscopy in bioinorganic chemistry: Application to M-O 2 systems. Coord Chem Rev 2012; 257:459-472. [PMID: 23525635 DOI: 10.1016/j.ccr.2012.06.024] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Metal K-edge X-ray absorption spectroscopy (XAS) has been extensively applied to bioinorganic chemistry to obtain geometric structure information on metalloprotein and biomimetic model complex active sites by analyzing the higher energy extended X-ray absorption fine structure (EXAFS) region of the spectrum. In recent years, focus has been on developing methodologies to interpret the lower energy K-pre-edge and rising-edge regions (XANES) and using it for electronic structure determination in complex bioinorganic systems. In this review, the evolution and progress of 3d-transition metal K-pre-edge and rising-edge methodology development is presented with particular focus on applications to bioinorganic systems. Applications to biomimetic transition metal-O2 intermediates (M = Fe, Co, Ni and Cu) are reviewed, which demonstrate the power of the method as an electronic structure determination technique and its impact in understanding the role of supporting ligands in tuning the electronic configuration of transition metal-O2 systems.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, Stanford National Accelerator Laboratory, MS 69, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
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12
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Probing the local electronic and geometric properties of the heme iron center in a H-NOX domain. J Inorg Biochem 2011; 105:784-92. [PMID: 21497576 DOI: 10.1016/j.jinorgbio.2011.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/03/2011] [Accepted: 03/04/2011] [Indexed: 11/23/2022]
Abstract
Heme-Nitric oxide and/or OXygen binding (H-NOX) proteins are a family of diatomic gas binding hemoproteins that have attracted intense research interest. Here we employ X-ray absorption near-edge structure (XANES) spectroscopy to study the nitric oxide (NO) binding site of H-NOX. This is the first time this technique has been utilized to examine the NO/H-NOX signaling pathway. XANES spectra of wildtype and a point mutant (proline 115 to alanine, P115A) of the H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) were obtained and analyzed for ferrous and ferric complexes of the protein. This work provides specific structural characterization of the solution state of several Tt H-NOX ferrous complexes (-unligated, -NO, and -CO) that were previously unavailable. Our iron K-edges indicate effective charge on the iron center in the various complexes and report on the electronic environment of heme iron. We analyzed the ligand field indicator ratio (LFIR), which is extracted from XANES spectra, for each complex, providing an understanding of ligand field strength, spin state of the central iron, movement of the iron atom upon ligation, and ligand binding properties. In particular, our LFIRs indicate that the heme iron is dramatically displaced towards the distal pocket during ligand binding. Based on these results, we propose that iron displacement towards the distal heme pocket is an essential step in signal initiation in H-NOX proteins. This provides a mechanistic link between ligand binding and the changes in heme and protein conformation that have been observed for H-NOX family members during signaling.
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13
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Lin X, Zhao W, Wang X. Characterization of conformational changes and noncovalent complexes of myoglobin by electrospray ionization mass spectrometry, circular dichroism and fluorescence spectroscopy. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:618-626. [PMID: 20527030 DOI: 10.1002/jms.1747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) was employed to monitor the heme release and the conformational changes of myoglobin (Mb) under different solvent conditions, and to observe ligand bindings of Mb. ESI-MS, complemented by circular dichroism and fluorescence spectroscopy, was used to study the mechanism of acid- and organic solvent-induced denaturation by probing the changes in the secondary and the tertiary structure of Mb. The results obtained show that complete disruption of the heme-protein interactions occurs when Mb is subjected to one of the following solution conditions: pH 3.2-3.6, or solution containing 20-30% acetonitrile or 40-50% methanol. Outside these ranges, Mb is present entirely in its native state (binding with a heme group) or as apomyoglobin (i.e. without the heme). Spectroscopic data demonstrate that the denaturation mechanism of Mb induced by acid may be significantly different from that by the organic solvent. Low pH reduces helices in Mb, whereas certain organic content level in solution results in the loss of the tertiary structure. ESI-MS conditions were established to observe the H(2)O- and CO-bound Mb complexes, respectively. H(2)O binding to metmyoglobin (17,585 Da), where the heme iron is in the ferric oxidation state, is observed in ESI-MS. CO binding to Mb (17,595 Da), on the other hand, can be only observed after the heme iron is reduced to the ferrous form. Therefore, ESI-MS combined with spectroscopic techniques provides a useful means for probing the formation of ligand-binding complexes and characterizing protein conformational changes.
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Affiliation(s)
- Xin Lin
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei 430074, China
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15
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Wang B, Feng WY, Wang M, Shi JW, Zhang F, Ouyang H, Zhao YL, Chai ZF, Huang YY, Xie YN, Wang HF, Wang J. Transport of intranasally instilled fine Fe2O3 particles into the brain: micro-distribution, chemical states, and histopathological observation. Biol Trace Elem Res 2007; 118:233-43. [PMID: 17916926 DOI: 10.1007/s12011-007-0028-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 01/17/2007] [Accepted: 02/24/2007] [Indexed: 11/27/2022]
Abstract
It has been demonstrated that inhaled fine (d < 2.5 microm) and ultrafine (d < 100 nm) particles produce more severe toxicity than coarse particles. Some recent data support the concept that the central nervous system (CNS) may be a target for the inhaled fine particulates. This work describes initial observation of the transport of intranasally instilled fine ferric oxide (Fe2O3) particles in animal brain. The iron micro-distribution and chemical state in the mice olfactory bulb and brain stem on day 14 after intranasal instillation of fine Fe2O3 particle (280 +/- 80 nm) suspension at a single dose of 40 mg/kg body weight were analyzed by synchrotron radiation x-ray fluorescence and x-ray absorption near-edge structure (XANES). The micro-distribution map of iron in the olfactory bulb and brain stem shows an obvious increase of Fe contents in the olfactory nerve and the trigeminus of brain stem, suggesting that Fe2O3 particles were possibly transported via uptake by sensory nerve endings of the olfactory nerve and trigeminus. The XANES results indicate that the ratios of Fe (III)/Fe (II) were increased in the olfactory bulb and brain stem. The further histopathological observation showed that the neuron fatty degeneration occurred in the CA3 area of hippocampus. Such results imply an adverse impact of inhalation of fine Fe2O3 particles on CNS.
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Affiliation(s)
- Bing Wang
- Laboratory for Bio-Environmental Effects of Nanomaterials and Nanosafety and Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
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16
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Metselaar GA, Schwartz E, de Gelder R, Feiters MC, Nikitenko S, Smolentsev G, Yalovega GE, Soldatov AV, Cornelissen JJLM, Rowan AE, Nolte RJM. X-Ray Spectroscopic and Diffraction Study of the Structure of the Active Species in the NiII-Catalyzed Polymerization of Isocyanides. Chemphyschem 2007; 8:1850-6. [PMID: 17647252 DOI: 10.1002/cphc.200700251] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structure of the active complex in the Ni-catalyzed polymerization of isocyanides to give polyisocyanides is investigated. It is shown by X-ray absorption spectroscopy (XAS), including EXAFS (extended X-ray absorption fine structure) and XANES (X-ray absorption near edge structure), and single-crystal X-ray diffraction, to contain a carbene-like ligand. This is the first structural characterization of a crucial intermediate in the so-called merry-go-round mechanism for Ni-catalyzed isocyanide polymerization.
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Affiliation(s)
- Gerald A Metselaar
- Institute for Molecules and Materials, University of Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands
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17
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Hsu IJ, Shiu YJ, Jeng US, Chen TH, Huang YS, Lai YH, Tsai LN, Jang LY, Lee JF, Lin LJ, Lin SH, Wang Y. A solution study on the local and global structure changes of cytochrome c: an unfolding process induced by urea. J Phys Chem A 2007; 111:9286-90. [PMID: 17696324 DOI: 10.1021/jp073031q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The local and global structural changes of cytochrome c induced by urea in aqueous solution have been studied using X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering (SAXS). According to the XAS result, both the native (folded) protein and the unfolded protein exhibit the same preedge features taken at Fe K-edge, indicating that the Fe(III) in the heme group of the protein maintains a six-coordinated local structure in both the folded and unfolded states. Furthermore, the discernible differences in the X-ray absorption near-edge structure (XANES) of these two states are attributed to a possible spin transition of the Fe(III) from a low-spin state to a high-spin state during the unfolding process. The perseverance of six-coordination and the spin transition of the iron are reconciled by a proposed ligand exchange, with urea and water molecules replacing the methionine-80 and histidine-18 axial ligands, respectively. The SAXS result reveals a significant morphology change of cytochrome c from a globular shape of a radius of gyration R(g) = 12.8 A of the native protein to an elongated ellipsoid shape of R(g) = 29.7 A for the unfolded protein in the presence of concentrated urea. The extended X-ray absorption fine structure (EXAFS) data unveil the coordination geometries of Fe(III) in both the folded and unfolded state of cytochrome c. An initial spin transition of Fe(III) followed by an axial ligand exchange, accompanied by the change in the global envelope, is proposed for what happened in the protein unfolding process of cytochrome c.
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Affiliation(s)
- I-Jui Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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18
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Stone KL, Behan RK, Green MT. Resonance Raman spectroscopy of chloroperoxidase compound II provides direct evidence for the existence of an iron(IV)-hydroxide. Proc Natl Acad Sci U S A 2006; 103:12307-10. [PMID: 16895990 PMCID: PMC1567876 DOI: 10.1073/pnas.0603159103] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report direct evidence for the existence of an iron(IV)-hydroxide. Resonance Raman measurements on chloroperoxidase compound II (CPO-II) reveal an isotope ((18)O and (2)H)-sensitive band at nu(Fe-O) = 565 cm(-1). Preparation of CPO-II in H(2)O using H(2)(18)O(2) results in a red-shift of 22 cm(-1), while preparation of CPO-II in (2)H(2)O using H(2)O(2) results in a red-shift of 13 cm(-1). These values are in good agreement with the isotopic shifts predicted (23 and 12 cm(-1), respectively) for an Fe-OH harmonic oscillator. The measured Fe-O stretching frequency is also in good agreement with the 1.82-A Fe-O bond reported for CPO-II. A Badger's rule analysis of this distance provides an Fe-O stretching frequency of nu(Badger) = 563 cm(-1). We also present X-band electron nuclear double resonance (ENDOR) data for cryoreduced CPO-II. Cryogenic reduction (77 K) of the EPR-silent Fe(IV)OH center in CPO-II results in an EPR-active Fe(III)OH species with a strongly coupled (13.4 MHz) exchangeable proton. Based on comparisons with alkaline myoglobin, we assign this resonance to the hydroxide proton of cryoreduced CPO-II.
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Affiliation(s)
- Kari L Stone
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
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19
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Feiters MC, Metselaar GA, Wentzel BB, Nolte RJM, Nikitenko S, Sherrington DC, Joly Y, Smolentsev GY, Kravtsova AN, Soldatov AV. X-ray Absorption Spectroscopic Studies on Nickel Catalysts for Epoxidation. Ind Eng Chem Res 2005. [DOI: 10.1021/ie050208z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin C. Feiters
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Gerald A. Metselaar
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Bastienne B. Wentzel
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Roeland J. M. Nolte
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Serge Nikitenko
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - David C. Sherrington
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Yves Joly
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Grigory Yu. Smolentsev
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Antonina N. Kravtsova
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
| | - Alexander V. Soldatov
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 1 Toernooiveld, 6525 ED Nijmegen, The Netherlands, DUBBLE CRG/ESRF (FWO), c/o ESRF BP 220, F-38043 Grenoble Cedex, France, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK, Laboratoire de Cristallographie, Centre National de la Recherche Scientifique, Associé à l'Université Joseph Fourier, Boîte Postale 166, F-30842 Grenoble Cedex 9, France, and
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D'Angelo P, Lucarelli D, della Longa S, Benfatto M, Hazemann JL, Feis A, Smulevich G, Ilari A, Bonamore A, Boffi A. Unusual heme iron-lipid acyl chain coordination in Escherichia coli flavohemoglobin. Biophys J 2004; 86:3882-92. [PMID: 15189885 PMCID: PMC1304290 DOI: 10.1529/biophysj.103.034876] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Accepted: 01/05/2004] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli flavohemoglobin is endowed with the notable property of binding specifically unsaturated and/or cyclopropanated fatty acids both as free acids or incorporated into a phospholipid molecule. Unsaturated or cyclopropanated fatty acid binding to the ferric heme results in a spectral change observed in the visible absorption, resonance Raman, extended x-ray absorption fine spectroscopy (EXAFS), and x-ray absorption near edge spectroscopy (XANES) spectra. Resonance Raman spectra, measured on the flavohemoglobin heme domain, demonstrate that the lipid (linoleic acid or total lipid extracts)-induced spectral signals correspond to a transition from a five-coordinated (typical of the ligand-free protein) to a hexacoordinated, high spin heme iron. EXAFS and XANES measurements have been carried out both on the lipid-free and on the lipid-bound protein to assign the nature of ligand in the sixth coordination position of the ferric heme iron. EXAFS data analysis is consistent with the presence of a couple of atoms in the sixth coordination position at 2.7 A in the lipid-bound derivative (bonding interaction), whereas a contribution at 3.54 A (nonbonding interaction) can be singled out in the lipid-free protein. This last contribution is assigned to the CD1 carbon atoms of the distal LeuE11, in full agreement with crystallographic data on the lipid-free protein at 1.6 A resolution obtained in the present work. Thus, the contributions at 2.7 A distance from the heme iron are assigned to a couple of carbon atoms of the lipid acyl chain, possibly corresponding to the unsaturated carbons of the linoleic acid.
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Affiliation(s)
- Paola D'Angelo
- Department of Chemistry University "La Sapienza", Rome, and Istituto Nazionale per la Fisica della Materia UdF, Camerino, Italy
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21
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Guidi A, Castigliego L, Preziuso S, Gaspari P, Gianfaldoni D, Del Bono G. Immunological and histochemical investigation of darkened turkey muscles. Vet Res Commun 2003; 27 Suppl 1:687-90. [PMID: 14535498 DOI: 10.1023/b:verc.0000014248.41842.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- A Guidi
- Department of Animal Pathology, Prophylaxis and Food Hygiene, University of Pisa, Viale delle Piagge 2, Pisa, Italy.
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22
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Della Longa S, Arcovito A, Benfatto M, Congiu-Castellano A, Girasole M, Hazemann JL, Lo Bosco A. Redox-induced structural dynamics of Fe-heme ligand in myoglobin by X-ray absorption spectroscopy. Biophys J 2003; 85:549-58. [PMID: 12829509 PMCID: PMC1303110 DOI: 10.1016/s0006-3495(03)74499-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The Fe(III) --> Fe(II) reduction of the heme iron in aquomet-myoglobin, induced by x-rays at cryogenics temperatures, produces a thermally trapped nonequilibrium state in which a water molecule is still bound to the iron. Water dissociates at T > 160 K, when the protein can relax toward its new equilibrium, deoxy form. Synchrotron radiation x-ray absorption spectroscopy provides information on both the redox state and the Fe-heme structure. Owing to the development of a novel method to analyze the low-energy region of x-ray absorption spectroscopy, we obtain structural pictures of this photo-inducible, irreversible process, with 0.02-0.06-A accuracy, on the protein in solution as well as in crystal. After photo-reduction, the iron-proximal histidine bond is shortened by 0.15 A, a reinforcement that should destabilize the iron in-plane position favoring water dissociation. Moreover, we are able to get the distance of the water molecule even after dissociation from the iron, with a 0.16-A statistical error.
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Affiliation(s)
- S Della Longa
- Department of Experimental Medicine, Università L'Aquila, L'Aquila, Italy.
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23
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Boffi F, Bonincontro A, Cinelli S, Congiu Castellano A, De Francesco A, Della Longa S, Girasole M, Onori G. pH-dependent local structure of ferricytochrome c studied by x-ray absorption spectroscopy. Biophys J 2001; 80:1473-9. [PMID: 11222307 PMCID: PMC1301338 DOI: 10.1016/s0006-3495(01)76119-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We have studied, using x-ray absorption spectroscopy by synchrotron radiation, the native state of the horse heart cytochrome c (N), the HCl denatured state (U(1) at pH 2), the NaOH denatured state (U(2) at pH 12), the intermediate HCl induced state (A(1) at pH 0.5), and the intermediate NaCl induced state (A(2) at pH 2). Although many results concerning the native and denatured states of this protein have been published, a site-specific structure analysis of the denatured and intermediate solvent induced states has never been attempted before. Model systems and myoglobin in different states of coordination are compared with cytochrome c spectra to have insight into the protein site structure in our experimental conditions. New features are evidenced by our results: 1) x-ray absorption near edge structure (XANES) of the HCl intermediate state (A(1)) presents typical structures of a pentacoordinate Fe(III) system, and 2) local site structures of the two intermediate states (A(1) and A(2)) are different.
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Affiliation(s)
- F Boffi
- Dipartimento di Fisica, Università "La Sapienza" Roma, INFM.
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