1
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Trouvé J, Youssef K, Kasemthaveechok S, Gramage-Doria R. Catalyst Complexity in a Highly Active and Selective Wacker-Type Markovnikov Oxidation of Olefins with a Bioinspired Iron Complex. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Affiliation(s)
| | - Khalil Youssef
- Univ Rennes, CNRS, ISCR-UMR6226, FR-35000 Rennes, France
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2
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Kanai Y, Harada A, Shibata T, Nishimura R, Namiki K, Watanabe M, Nakamura S, Yumoto F, Senda T, Suzuki A, Neya S, Yamamoto Y. Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor. Biochemistry 2017; 56:4500-4508. [DOI: 10.1021/acs.biochem.7b00457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Kanai
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ayaka Harada
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tomokazu Shibata
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kosuke Namiki
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Miho Watanabe
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shunpei Nakamura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Fumiaki Yumoto
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department
of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life
Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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3
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Piccioli M, Turano P. Transient iron coordination sites in proteins: Exploiting the dual nature of paramagnetic NMR. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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4
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Basova LV, Tiktopulo EI, Kutyshenko VP, Mauk AG, Bychkova VE. Phospholipid membranes affect tertiary structure of the soluble cytochrome b5 heme-binding domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1015-26. [PMID: 18275841 DOI: 10.1016/j.bbamem.2007.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 12/21/2007] [Accepted: 12/28/2007] [Indexed: 11/30/2022]
Abstract
The influence of charged phospholipid membranes on the conformational state of the water-soluble fragment of cytochrome b5 has been investigated by a variety of techniques at neutral pH. The results of this work provide the first evidence that aqueous solutions with high phospholipid/protein molar ratios (pH 7.2) induce the cytochrome to undergo a structural transition from the native conformation to an intermediate state with molten-globule like properties that occur in the presence of an artificial membrane surface and that leads to binding of the protein to the membrane. At other phospholipid/protein ratios, equilibrium was observed between cytochrome free in solution and cytochrome bound to the surface of vesicles. Inhibition of protein binding to the vesicles with increasing ionic strength indicated for the most part an electrostatic contribution to the stability of cytochrome b5-vesicle interactions at pH 7.2. The possible physiological role of membrane-induced conformational change in the structure of cytochrome b5 upon the interaction with its redox partners is discussed.
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Affiliation(s)
- Liana V Basova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
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6
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SHIM YOUNGKEY, PANDEY RAVINDRAK, SMITH KEVINM. Synthesis of the 6,7-bis[2-methoxycarbonyl(1,1- dideutero)-ethyl] derivative of protoporphyrin IX dimethyl ester. J PORPHYR PHTHALOCYA 2000. [DOI: 10.1002/(sici)1099-1409(200003)4:2<185::aid-jpp179>3.0.co;2-i] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A new total synthesis of a protoporphyrin IX derivative in which the α-methylene protons of the 13,17-(2-methoxycarbonylethyl) substituents are regioselectively deuterated is described. The deuterated porphyrin was obtained using the oxidative cyclization of an a,c-biladiene dihydrobromide.
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Affiliation(s)
- YOUNG KEY SHIM
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - RAVINDRA K. PANDEY
- Department of Chemistry, University of California, Davis, CA 95616, USA
- Chemistry Section, Photodynamic Therapy Center, Department of Radiation Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - KEVIN M. SMITH
- Department of Chemistry, University of California, Davis, CA 95616, USA
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7
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Wei X, Ming LJ, Cannons AC, Solomonson LP. 1H and 13C NMR studies of a truncated heme domain from Chlorella vulgaris nitrate reductase: signal assignment of the heme moiety. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1382:129-36. [PMID: 9507089 DOI: 10.1016/s0167-4838(97)00160-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A water soluble truncated heme domain (a tetramer of MW = 45 kDa) of the tetrameric nitrate reductase complex from the green alga Chlorella vulgaris has been overexpressed and purified. This truncated heme domain with four identical subunits has a high redox potential (midpoint potential E1/2 = +16 mV) as compared with other heme-containing flavoproteins. We have undertaken a determination of the detailed configuration of the heme moiety in order to understand the unique electrochemical property of the heme moiety of this enzyme. We report here the study of the heme prosthetic group of the truncated heme domain by the use of 2D 1H and 13C NMR techniques. A complete signal assignment of the heme has been achieved. Our observations suggest that the heme configuration is similar to that of the crystal structure of the membrane-bound bovine liver cytochrome b5.
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Affiliation(s)
- X Wei
- Department of Chemistry, University of South Florida, Tampa 33620-5250, USA
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8
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Lee KB, Kweon J, Park H. Assignment of hyperfine-shifted heme carbon resonances in ferricytochrome b5. FEBS Lett 1995; 367:77-80. [PMID: 7601289 DOI: 10.1016/0014-5793(95)00500-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The reverse detection heteronuclear multiple quantum coherence, HMQC, study of native bovine ferricytochrome b5 has provided the complete assignment of hyperfine shifted resonances of heme carbons attached proton(s). The dominant delocalized pi-spin density to vinyl groups gives rise to contact shifts which have opposite direction for a carbon and its attached proton(s). The most hyperfine shifted 13C heme signals are mainly generated from 3rd heme pyrrole ring substituents which identifies that the molecular orbital for facile electron transfer is oriented to exposed heme edge. Magnetic/electronic asymmetry of heme induced by two axial His makes spread the hyperfine shifted heme carbon resonances over the range of 280 ppm at 25 degrees C, which would be the more sensitive probe than those of proton resonances in characterizing the nature of heme electronic structure of ferricytochrome b5.
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Affiliation(s)
- K B Lee
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul
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9
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Gettins PG. 1H- and 19F-NMR approaches to the study of the structure of proteins larger than 25 kDa. Int J Biol Macromol 1994; 16:227-35. [PMID: 7893627 DOI: 10.1016/0141-8130(94)90027-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The three-dimensional solution structures of proteins larger than about 25 kDa cannot at present be determined by multi-dimensional nuclear magnetic resonance (NMR) methods. However, for proteins that are larger than 25 kDa, for which X-ray structural information is not available, there are a variety of mostly one-dimensional NMR methods that still represent some of the most informative approaches to obtaining structural answers to questions of biochemical interest. This paper provides recent illustrative examples of 1H- and 19F-NMR experiments that describe ways to focus on proteins by region, by amino acid type, or by individual amino acid. Methods to focus on a particular region of a protein include exploiting domain mobility, using transferred nuclear Overhauser enhancements, the use of difference spectroscopy, the use of paramagnetic species, and domain fragmentation. Particular types of amino acid can be identified using selective deuteration, by incorporation of fluorinated amino acid analogues, by using photochemically induced dynamic nuclear polarization, and from the pH dependence of histidine residues. Individual amino acids can be identified by mutagenesis and, in special circumstances, by chemical shift. Many of the examples given are of plasma proteinases and their protein inhibitors, but other classes of protein are also discussed, including antibodies and DNA-binding proteins.
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Affiliation(s)
- P G Gettins
- Department of Biochemistry, University of Illinois, Chicago 60612
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10
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Abstract
The family of b5-like cytochromes encompasses, besides cytochrome b5 itself, hemoprotein domains covalently associated with other redox proteins, in flavocytochrome b2 (L-lactate dehydrogenase), sulfite oxidase and assimilatory nitrate reductase. A comparison of about 40 amino acid sequences deposited in data banks shows that eight residues are invariant and about 15 positions carry strongly conservative substitutions. Examination of the location of these invariant and conserved positions in the light of the three-dimensional structures of beef cytochrome b5 and S cerevisiae flavocytochrome b2 suggests a strongly conserved protein structure for the b5-like heme-binding domain throughout evolution. Numerous NMR studies have demonstrated the existence of a positional isomerism for the heme, which involves both a 180 degree-rotation around the heme alpha,gamma-meso carbon atoms and a rotation through an axis normal to the heme plane at the iron. NMR studies did not detect significant differences in protein structure between reduced and oxidized states, or between species. The role of a number of side chains was probed by site-directed mutagenesis. Studies of complex formation and of electron transfer rates between cytochrome b5 and redox partners have led to the idea that complexation is driven by electrostatic forces, that it is generally the exposed heme edge which makes contact with electron donors and acceptors, but that there are multiple overlapping sites within this general area. For the bi- and trifunctional members of the family, extrapolation of available data would suggest a mobile heme-binding domain within a complex structure. In these cases the existence of a single interaction area for both electron donor and acceptor, or of two different ones, remains open to discussion.
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Affiliation(s)
- F Lederer
- CNRS-URA 1461, Hôpital Necker, Paris, France
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11
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Fernandez M, Frydman RB, Hurst J, Buldain G. Structure/activity relationships in porphobilinogen oxygenase and horseradish peroxidase. An analysis using synthetic hemins. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 218:251-9. [PMID: 8243471 DOI: 10.1111/j.1432-1033.1993.tb18372.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The apo-enzymes of porphobilinogen oxygenase and horseradish peroxidase were reconstituted with hemin IX, deuterohemin IX, 2,4-diacetyldeuterohemin IX, 2-vinyl-4-deuterohemin IX and hemin I. The apoproteins did not reconstitute with the dimethyl or diethyl esters of hemin IX. The native enzymes and the synthetic hemoproteins showed similar oxygenase activities toward porphobilinogen in the presence of dithionite and oxygen. They also showed peroxidase activity in the presence of H2O2, which was affected by the side-chain substitution pattern of the hemes. Oxygenase activities, however, were not affected by the heme structure. Iron chelators completely inhibited the oxygenase, but not the peroxidase activities. The EPR spectra of the native and synthetic porphobilinogen oxygenase showed that dithionite reduction produced a rapid disappearance of the high-spin heme-iron signal at g = 6.0. It reappeared 1 min later but the enzyme retained its catalytic activity. The changes in the EPR spectra could be correlated with the biphasic kinetics of the oxygenase reaction which was very fast during the first minute and then decreased to a half-value rate. The oxygenase reaction was inhibited by addition of superoxide dismutase during the fast rate phase, but not during the slower phase. These results could be explained by the formation of a superoxide anion during the first minute of the oxygenase reaction, after which a protein-stabilized radical (g = 2.0) is generated (very likely a tyrosyl radical). The latter then oxidizes the substrate porphobilinogen and facilitates its reaction with O2 to give oxopyrrolenines.
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Affiliation(s)
- M Fernandez
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
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12
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Lee KB, La Mar GN, Mansfield KE, Smith KM, Pochapsky TC, Sligar SG. Interpretation of hyperfine shift patterns in ferricytochromes b5 in terms of angular position of the heme: a sensitive probe for peripheral heme protein interactions. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1202:189-99. [PMID: 8399380 DOI: 10.1016/0167-4838(93)90004-b] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The 1H-NMR hyperfine shift pattern of the heme in a variety of low-spin ferricytochromes b5 has been analyzed in terms of the angular position of the prosthetic group within a structurally and magnetically-conserved protein matrix. A simple model is presented in which the changes in the spread of the predominantly contact shifted methyl and predominantly dipolar shifted meso-H signals of the heme, as well as shift trends for individual signals, provide sensitive indicators of the orientation of the heme relative to the orbital hole (singly-occupied d orbital), which in turn is related to the rhombic magnetic axes. The invariance of the axial His and non-coordinated residue hyperfine shifts show that it is the heme within a relatively rigid protein matrix, rather than the magnetic coordinate system, which is displaced angularly about the heme normal in order to accommodate variations in the polypeptide, orientation of the heme about the alpha,gamma-meso axis, and the length of heme carboxylate chains. Native heme shows increased counterclockwise rotation about the heme normal in the order rat-->beef-->chicken ferricytochrome b5, which is attributed largely to increased bulk of a variable sequence hydrophobic cluster consisting of residues 23, 25 and 32. The two alternate heme orientations about the alpha,gamma-meso axis are shown to also differ by rotation about the heme normal. A semiquantitative estimate of the degree of angular accommodation based on the spread of the meso-H rhombic dipolar shifts indicate rotations of 2-10 degrees. Possible functional consequences of such angular accommodation in relation to the role of these proteins in electron transfer are discussed.
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Affiliation(s)
- K B Lee
- Department of Chemistry, University of California, Davis 95616
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13
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Yamamoto Y, Suzuki T. NMR study of the molecular and electronic structure of the heme cavity in Dolabella met-cyano myoglobin. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1163:287-96. [PMID: 8507668 DOI: 10.1016/0167-4838(93)90164-m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The molecular and electronic structure of the active site of the cyanide-ligated ferric complex of the myoglobin from the mollusc Dolabella auricularia has been investigated using NMR. Analysis of nuclear Overhauser effects has revealed that the correlation times for the internal motion of the heme propionate alpha-CH2 and beta-CH2 groups at ambient temperature are about 5 and 4 ns, respectively. These correlation times indicate that the terminal carboxylate groups of both the heme propionates are not bound to the protein via salt bridges. Although the absence of the propionate-protein interaction does not influence the equilibrium population of the two heme orientational isomers involving rotation about the alpha,gamma-meso axis, it allows the heme to rotate about the iron-His bond in the active site of the myoglobin. Such rotational motion of the heme resulted in an anomalous temperature-dependence of the heme methyl-proton hyperfine shift. Thus the present myoglobin studies provide the first example demonstrating the rotation of the heme about the iron-His bond in native myoglobin.
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Affiliation(s)
- Y Yamamoto
- Department of Biomolecular Engineering, Tokyo Institute of Technology, Japan
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