1
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Park JY, Han S, Kim D, Nguyen TVT, Nam Y, Kim SM, Chang R, Kim YH. Enhancing the thermostability of lignin peroxidase: Heme as a keystone cofactor driving stability changes in heme enzymes. Heliyon 2024; 10:e37235. [PMID: 39319129 PMCID: PMC11419925 DOI: 10.1016/j.heliyon.2024.e37235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/15/2024] [Accepted: 08/29/2024] [Indexed: 09/26/2024] Open
Abstract
Heme-containing enzymes, critical across life's domains and promising for industrial use, face stability challenges. Despite the demand for robust industrial biocatalysts, the mechanisms underlying the thermal stability of heme enzymes remain poorly understood. Addressing this, our research utilizes a 'keystone cofactor heme-interaction approach' to enhance ligand binding and improve the stability of lignin peroxidase (LiP). We engineered mutants of the white-rot fungus PcLiP (Phanerochaete chrysosporium) to increase thermal stability by 8.66 °C and extend half-life by 29 times without losing catalytic efficiency at 60 °C, where typically, wild-type enzymes degrade. Molecular dynamics simulations reveal that an interlocked cofactor moiety contributes to enhanced structural stability in LiP variants. Additionally, a stability index developed from these simulations accurately predicts stabilizing mutations in other PcLiP isozymes. Using milled wood lignin, these mutants achieved triple the conversion yields at 40 °C compared to the wild type, offering insights for more sustainable white biotechnology through improved enzyme stability.
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Affiliation(s)
- Joo Yeong Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Seunghyun Han
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Doa Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Trang Vu Thien Nguyen
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Youhyun Nam
- Department of Applied Chemistry, University of Seoul, 163, Seoulsiripdae-ro, Seoul, 02504, Republic of Korea
| | - Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Rakwoo Chang
- Department of Applied Chemistry, University of Seoul, 163, Seoulsiripdae-ro, Seoul, 02504, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan, 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan, 44919, Republic of Korea
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2
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Lukas J, Družeta I, Kühl T. Comparative studies of soluble and immobilized Fe(III) heme-peptide complexes as alternative heterogeneous biocatalysts. Biol Chem 2022; 403:1099-1105. [PMID: 36257922 DOI: 10.1515/hsz-2022-0199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Fe(III) heme is known to possess low catalytic activity when exposed to hydrogen peroxide and a reducing substrate. Efficient non-covalently linked Fe(III) heme-peptide complexes may represent suitable alternatives as a new group of green catalysts. Here, we evaluated a set of heme-peptide complexes by determination of their peroxidase-like activity and the kinetics of the catalytic conversion in both, the soluble and the immobilized state. We show the impact of peptide length on binding of the peptides to Fe(III) heme and the catalytic activity. Immobilization of the peptide onto a polymer support maintains the catalytic performance of the Fe(III) heme-peptide complex. This study thus opens up a new perspective with regard to the development of heterogeneous biocatalysts with a peroxidase-like activity.
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Affiliation(s)
- Joey Lukas
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Ivona Družeta
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
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3
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Samhan-Arias AK, Cordas CM, Carepo MS, Maia LB, Gutierrez-Merino C, Moura I, Moura JJG. Ligand accessibility to heme cytochrome b 5 coordinating sphere and enzymatic activity enhancement upon tyrosine ionization. J Biol Inorg Chem 2019; 24:317-330. [PMID: 29317202 DOI: 10.1007/s00775-019-01649-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/21/2019] [Indexed: 01/21/2023]
Abstract
Recently, we observed that at extreme alkaline pH, cytochrome b5 (Cb5) acquires a peroxidase-like activity upon formation of a low spin hemichrome associated with a non-native state. A functional characterization of Cb5, in a wide pH range, shows that oxygenase/peroxidase activities are stimulated in alkaline media, and a correlation between tyrosine ionization and the attained enzymatic activities was noticed, associated with an altered heme spin state, when compared to acidic pH values at which the heme group is released. In these conditions, a competitive assay between imidazole binding and Cb5 endogenous heme ligands revealed the appearance of a binding site for this exogenous ligand that promotes a heme group exposure to the solvent upon ligation. Our results shed light on the mechanism behind Cb5 oxygenase/peroxidase activity stimulation in alkaline media and reveal a role of tyrosinate anion enhancing Cb5 enzymatic activities on the distorted protein before maximum protein unfolding.
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Affiliation(s)
- Alejandro K Samhan-Arias
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal.
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - Marta S Carepo
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - Luisa B Maia
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - Carlos Gutierrez-Merino
- Department of Biochemistry and Molecular Biology, Faculty of Sciences and Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006, Badajoz, Spain
| | - Isabel Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - José J G Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal.
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4
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Zhang K, Zhou H, Hu P, Lu Q. The direct electrochemistry and bioelectrocatalysis of nitrate reductase at a gold nanoparticles/aminated graphene sheets modified glassy carbon electrode. RSC Adv 2019; 9:37207-37213. [PMID: 35542297 PMCID: PMC9075544 DOI: 10.1039/c9ra07082f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
The aminated graphene sheets could immobilize nitrate reductase stably and control its orientation through electrostatic attractions, achieving its direct electrochemistry.
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Affiliation(s)
- Ke Zhang
- Institute of Environmental Medicine
- State Key Laboratory of Environment Health (Incubation)
- Key Laboratory of Environment and Health
- Ministry of Education
- Key Laboratory of Environment and Health (Wuhan)
| | - Hao Zhou
- Institute of Environmental Medicine
- State Key Laboratory of Environment Health (Incubation)
- Key Laboratory of Environment and Health
- Ministry of Education
- Key Laboratory of Environment and Health (Wuhan)
| | - Ping Hu
- Institute of Environmental Medicine
- State Key Laboratory of Environment Health (Incubation)
- Key Laboratory of Environment and Health
- Ministry of Education
- Key Laboratory of Environment and Health (Wuhan)
| | - Qing Lu
- Institute of Environmental Medicine
- State Key Laboratory of Environment Health (Incubation)
- Key Laboratory of Environment and Health
- Ministry of Education
- Key Laboratory of Environment and Health (Wuhan)
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5
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Hu S, He B, Wang XJ, Gao SQ, Wen GB, Lin YW. Stabilization of cytochrome b 5 by a conserved tyrosine in the secondary sphere of heme active site: A spectroscopic and computational study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:118-123. [PMID: 27888781 DOI: 10.1016/j.saa.2016.11.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
Heme proteins perform a large array of biological functions, with the heme group bound non-covalently or covalently. To probe the stabilization role of conserved tyrosine residue in the secondary sphere of heme site in heme proteins, we herein used cytochrome b5 (Cyt b5) as a model protein, and mutated Tyr30 to Phe or His by removal of Tyr30 associated H-bond network and hydrophobic interaction. We performed thermal-induced unfolding studies for the two mutants, Y30F Cyt b5 and Y30H Cyt b5, as monitored by both UV-Vis and CD spectroscopy, as well as heme transfer studies from these proteins to apo-myoglobin, with wild-type Cyt b5 under the same conditions for comparison. The reduced stability of both mutants indicates that both the H-bonding and hydrophobic interactions associated with Tyr30 contribute to the protein stability. Moreover, we performed molecular modeling studies, which revealed that the hydrophobic interaction in the local region of Y30F Cyt b5 was well-remained, whereas Y30H Cyt b5 formed an H-bond network. These observations suggest that the conserved Tyr30 in Cyt b5 is not replaceable due to the presence of both the H-bond network and hydrophobic interaction in the secondary sphere of the heme active site. As demonstrated here for Cyt b5, it may be of practical importance for design of artificial heme proteins by engineering a Tyr in the secondary sphere with improved properties and functions.
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Affiliation(s)
- Shan Hu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
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6
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Ratautas D, Laurynėnas A, Dagys M, Marcinkevičienė L, Meškys R, Kulys J. High current, low redox potential mediatorless bioanode based on gold nanoparticles and glucose dehydrogenase from Ewingella americana. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.03.087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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7
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Ghosh C, Mukherjee S, Seal M, Dey SG. Peroxidase to Cytochrome b Type Transition in the Active Site of Heme-Bound Amyloid β Peptides Relevant to Alzheimer’s Disease. Inorg Chem 2016; 55:1748-57. [DOI: 10.1021/acs.inorgchem.5b02683] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Chandradeep Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Soumya Mukherjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Manas Seal
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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8
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Hirano Y, Kimura S, Tamada T. High-resolution crystal structures of the solubilized domain of porcine cytochrome b5. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1572-81. [PMID: 26143928 PMCID: PMC4498607 DOI: 10.1107/s1399004715009438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/18/2015] [Indexed: 11/11/2022]
Abstract
Mammalian microsomal cytochrome b5 has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochrome b5 from porcine liver were determined at sub-angstrom resolution (0.76-0.95 Å) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.
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Affiliation(s)
- Yu Hirano
- Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Shigenobu Kimura
- Department of Biomolecular Functional Engineering, Faculty of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Taro Tamada
- Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
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9
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Hlavica P. Mechanistic basis of electron transfer to cytochromes p450 by natural redox partners and artificial donor constructs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:247-97. [PMID: 26002739 DOI: 10.1007/978-3-319-16009-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochromes P450 (P450s) are hemoproteins catalyzing oxidative biotransformation of a vast array of natural and xenobiotic compounds. Reducing equivalents required for dioxygen cleavage and substrate hydroxylation originate from different redox partners including diflavin reductases, flavodoxins, ferredoxins and phthalate dioxygenase reductase (PDR)-type proteins. Accordingly, circumstantial analysis of structural and physicochemical features governing donor-acceptor recognition and electron transfer poses an intriguing challenge. Thus, conformational flexibility reflected by togging between closed and open states of solvent exposed patches on the redox components was shown to be instrumental to steered electron transmission. Here, the membrane-interactive tails of the P450 enzymes and donor proteins were recognized to be crucial to proper orientation toward each other of surface sites on the redox modules steering functional coupling. Also, mobile electron shuttling may come into play. While charge-pairing mechanisms are of primary importance in attraction and complexation of the redox partners, hydrophobic and van der Waals cohesion forces play a minor role in docking events. Due to catalytic plasticity of P450 enzymes, there is considerable promise in biotechnological applications. Here, deeper insight into the mechanistic basis of the redox machinery will permit optimization of redox processes via directed evolution and DNA shuffling. Thus, creation of hybrid systems by fusion of the modified heme domain of P450s with proteinaceous electron carriers helps obviate the tedious reconstitution procedure and induces novel activities. Also, P450-based amperometric biosensors may open new vistas in pharmaceutical and clinical implementation and environmental monitoring.
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Affiliation(s)
- Peter Hlavica
- Walther-Straub-Institut für Pharmakologie und Toxikologie der LMU, Goethestrasse 33, 80336, München, Germany,
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10
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Sun MH, Liu SQ, Du KJ, Nie CM, Lin YW. A spectroscopic study of uranyl-cytochrome b5/cytochrome c interactions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:130-137. [PMID: 24051281 DOI: 10.1016/j.saa.2013.08.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 08/28/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Uranium is harmful to human health due to its radiation damage and the ability of uranyl ion (UO2(2+)) to interact with various proteins and disturb their biological functions. Cytochrome b5 (cyt b5) is a highly negatively charged heme protein and plays a key role in mediating cytochrome c (cyt c) signaling in apoptosis by forming a dynamic cyt b5-cyt c complex. In previous molecular modeling study in combination with UV-Vis studies, we found that UO2(2+) is capable of binding to cyt b5 at surface residues, Glu37 and Glu43. In this study, we further investigated the structural consequences of cyt b5 and cyt c, as well as cyt b5-cyt c complex, upon uranyl binding, by fluorescence spectroscopic and circular dichroism techniques. Moreover, we proposed a uranyl binding site for cyt c at surface residues, Glu66 and Glu69, by performing a molecular modeling study. It was shown that uranyl binds to cyt b5 (KD=10 μM), cyt c (KD=87 μM), and cyt b5-cyt c complex (KD=30 μM) with a different affinity, which slightly alters the protein conformation and disturbs the interaction of cyt b5-cyt c complex. Additionally, we investigated the functional consequences of uranyl binding to the protein surface, which decreases the inherent peroxidase activity of cyt c. The information of uranyl-cyt b5/cyt c interactions gained in this study likely provides a clue for the mechanism of uranyl toxicity.
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Affiliation(s)
- Mei-Hui Sun
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
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11
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Sommer DJ, Vaughn MD, Ghirlanda G. Protein secondary-shell interactions enhance the photoinduced hydrogen production of cobalt protoporphyrin IX. Chem Commun (Camb) 2014; 50:15852-5. [DOI: 10.1039/c4cc06700b] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An efficient molecular catalyst for hydrogen production is generated by incorporating Co-protoporphyrin IX into myoglobin. The activity is modulated by engineered mutations.
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12
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Lin YW, Sawyer EB, Wang J. Rational heme protein design: all roads lead to Rome. Chem Asian J 2013; 8:2534-44. [PMID: 23704071 DOI: 10.1002/asia.201300291] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 01/03/2023]
Abstract
Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C-H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme-binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure-property-reactivity-function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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13
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Lin YW, You XX, Chen LS, Wu YM. Peroxidase-like Enzymes Designed from Cytochrome b5 Exhibit Enhanced Hydrolysis Activity. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China
| | - Xiao-Xing You
- Institute of Pathogenic Biology, University of South China
| | - Lie-Song Chen
- Institute of Pathogenic Biology, University of South China
| | - Yi-Mou Wu
- Institute of Pathogenic Biology, University of South China
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14
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Human mitochondrial holocytochrome c synthase's heme binding, maturation determinants, and complex formation with cytochrome c. Proc Natl Acad Sci U S A 2012; 110:E788-97. [PMID: 23150584 DOI: 10.1073/pnas.1213897109] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Proper functioning of the mitochondrion requires the orchestrated assembly of respiratory complexes with their cofactors. Cytochrome c, an essential electron carrier in mitochondria and a critical component of the apoptotic pathway, contains a heme cofactor covalently attached to the protein at a conserved CXXCH motif. Although it has been known for more than two decades that heme attachment requires the mitochondrial protein holocytochrome c synthase (HCCS), the mechanism remained unknown. We purified membrane-bound human HCCS with endogenous heme and in complex with its cognate human apocytochrome c. Spectroscopic analyses of HCCS alone and complexes of HCCS with site-directed variants of cytochrome c revealed the fundamental steps of heme attachment and maturation. A conserved histidine in HCCS (His154) provided the key ligand to the heme iron. Formation of the HCCS:heme complex served as the platform for interaction with apocytochrome c. Heme was the central molecule mediating contact between HCCS and apocytochrome c. A conserved histidine in apocytochrome c (His19 of CXXCH) supplied the second axial ligand to heme in the trapped HCCS:heme:cytochrome c complex. We also examined the substrate specificity of human HCCS and converted a bacterial cytochrome c into a robust substrate for the HCCS. The results allow us to describe the molecular mechanisms underlying the HCCS reaction.
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15
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Lin YW, Sun MH, Wan D, Liao LF. Observation of heme transfer from cytochrome b5 to DNA aptamer. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 96:365-369. [PMID: 22717695 DOI: 10.1016/j.saa.2012.05.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/12/2012] [Accepted: 05/25/2012] [Indexed: 06/01/2023]
Abstract
Heme transfer is commonly observed from one heme protein to the other such as from cytochrome b(5) (cyt b(5)) to apo-myoglobin. In this study, instead of to another heme protein, we observed the heme transfer from wild-type (WT) cyt b(5), H39C cyt b(5) with heme axial ligand His39 mutated to Cys39, and DME cyt b(5) with heme replaced by protoporphyrin IX dimethyl ester, to a heme DNA aptamer, PS2.M, respectively, with a different rate constant. The heme transfer was further confirmed by the enhancement of peroxidase activity of the cyt b(5)s-PS2.M system due to the formation of catalytic PS2.M-heme complex. This study provides valuable insights into both cyt b(5)-heme and PS2.M-heme interactions and shows that heme transfer from heme protein to heme-aptamer can be used to evaluate the relative stability of heme proteins. In addition, this study sheds light on the maturation of heme proteins in vivo by interacting with DNA/RNA enzymes.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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16
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Idkowiak J, Randell T, Dhir V, Patel P, Shackleton CHL, Taylor NF, Krone N, Arlt W. A missense mutation in the human cytochrome b5 gene causes 46,XY disorder of sex development due to true isolated 17,20 lyase deficiency. J Clin Endocrinol Metab 2012; 97:E465-75. [PMID: 22170710 PMCID: PMC3388247 DOI: 10.1210/jc.2011-2413] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 11/11/2011] [Indexed: 11/29/2022]
Abstract
CONTEXT Isolated 17,20 lyase deficiency is commonly defined by apparently normal 17α-hydroxylase activity but severely reduced 17,20 lyase activity of the bifunctional enzyme cytochrome P450 (CYP) enzyme 17A1 (CYP17A1), resulting in sex steroid deficiency but normal glucocorticoid and mineralocorticoid reserve. Cytochrome b5 (CYB5A) is thought to selectively enhance 17,20 lyase activity by facilitating the allosteric interaction of CYP17A1 with its electron donor P450 oxidoreductase (POR). OBJECTIVE We investigated a large consanguineous family including three siblings with 46,XY disorder of sex development (DSD) presenting with isolated 17,20 lyase deficiency. DESIGN We investigated the clinical and biochemical phenotype, conducted genetic analyses, and functionally characterized the identified CYB5A mutation in cell-based CYP17A1 coexpression assays. RESULTS All three siblings presented with 46,XY DSD, sex steroid deficiency, normal mineralocorticoids and glucocorticoids, and a urine steroid metabolome suggestive of isolated 17,20 lyase deficiency. CYP17A1 and POR sequences were normal, but we detected a homozygous CYB5A missense mutation (g.28,400A→T; p.H44L). Functional in vitro analysis revealed normal CYP17A1 17α-hydroxylase activity but severely impaired 17,20 lyase activity. In silico analysis suggested the disruption of CYB5A heme binding by p.H44L. CONCLUSION We have identified the first human CYB5A missense mutation as the cause of isolated 17,20 lyase deficiency in three individuals with 46,XY DSD. Detailed review of previously reported cases with apparently isolated 17,20 lyase deficiency due to mutant CYP17A1 and POR reveals impaired 17α-hydroxylase activity as assessed by steroid metabolome analysis and short cosyntropin testing. This suggests that truly isolated 17,20 lyase deficiency is observed only in individuals with inactivating CYB5A mutations.
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Affiliation(s)
- Jan Idkowiak
- Centre for Endocrinology, Diabetes, and Metabolism, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham B15 2TT, United Kingdom
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17
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San Francisco B, Bretsnyder EC, Rodgers KR, Kranz RG. Heme ligand identification and redox properties of the cytochrome c synthetase, CcmF. Biochemistry 2011; 50:10974-85. [PMID: 22066495 DOI: 10.1021/bi201508t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c maturation in many bacteria, archaea, and plant mitochondria involves the integral membrane protein CcmF, which is thought to function as a cytochrome c synthetase by facilitating the final covalent attachment of heme to the apocytochrome c. We previously reported that the E. coli CcmF protein contains a b-type heme that is stably and stoichiometrically associated with the protein and is not the heme attached to apocytochrome c. Here, we show that mutation of either of two conserved transmembrane histidines (His261 or His491) impairs stoichiometric b-heme binding in CcmF and results in spectral perturbations in the remaining heme. Exogeneous imidazole is able to correct cytochrome c maturation for His261 and His491 substitutions with small side chains (Ala or Gly), suggesting that a "cavity" is formed in these CcmF mutants in which imidazole binds and acts as a functional ligand to the b-heme. The results of resonance Raman spectroscopy on wild-type CcmF are consistent with a hexacoordinate low-spin b-heme with at least one endogeneous axial His ligand. Analysis of purified recombinant CcmF proteins from diverse prokaryotes reveals that the b-heme in CcmF is widely conserved. We have also determined the reduction potential of the CcmF b-heme (E(m,7) = -147 mV). We discuss these results in the context of CcmF structure and functions as a heme reductase and cytochrome c synthetase.
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Affiliation(s)
- Brian San Francisco
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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18
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Meitzler JL, Ortiz de Montellano PR. Structural stability and heme binding potential of the truncated human dual oxidase 2 (DUOX2) peroxidase domain. Arch Biochem Biophys 2011; 512:197-203. [PMID: 21704604 PMCID: PMC3139011 DOI: 10.1016/j.abb.2011.05.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/24/2011] [Accepted: 05/31/2011] [Indexed: 01/29/2023]
Abstract
The essential role of human dual oxidase 2 (hDUOX2) in thyroid hormone biosynthesis defines this member of the NOX/DUOX family, whose absence due to mutation has been directly related to disease, specifically hypothyroidism. Both human DUOX isoforms, hDUOX1 and hDUOX2, are expressed in thyroid tissue; however, hDUOX1 cannot compensate for inactivation of hDUOX2, suggesting that each enzyme is differentially regulated and/or functions in a unique manner. In efforts to uncover relevant structural and functional differences we have expressed and purified the peroxidase domain of hDUOX2(1-599) for direct comparison with the previously studied hDUOX1(1-593). As was shown for hDUOX1, the truncated hDUOX2 domain purifies without a bound heme co-factor and displays no peroxidase activity. However, hDUOX2(1-599) displays greater stability than hDUOX1(1-593). Surprisingly, upon titration with heme, both isoforms bind heme with a low micromolar affinity, demonstrating that they retain a heme binding site. A conformational difference in the full-length protein and/or a protein-protein interaction may be required to increase the heme binding affinity.
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Affiliation(s)
- Jennifer L. Meitzler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517
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19
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Wan D, Liao LF, Zhao MM, Wu ML, Wu YM, Lin YW. Interactions of uranyl ion with cytochrome b 5 and its His39Ser variant as revealed by molecular simulation in combination with experimental methods. J Mol Model 2011; 18:1009-13. [DOI: 10.1007/s00894-011-1097-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 03/22/2011] [Indexed: 11/24/2022]
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20
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Correia MA, Sinclair PR, De Matteis F. Cytochrome P450 regulation: the interplay between its heme and apoprotein moieties in synthesis, assembly, repair, and disposal. Drug Metab Rev 2010; 43:1-26. [PMID: 20860521 DOI: 10.3109/03602532.2010.515222] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Heme is vital to our aerobic universe. Heme cellular content is finely tuned through an exquisite control of synthesis and degradation. Heme deficiency is deleterious to cells, whereas excess heme is toxic. Most of the cellular heme serves as the prosthetic moiety of functionally diverse hemoproteins, including cytochromes P450 (P450s). In the liver, P450s are its major consumers, with >50% of hepatic heme committed to their synthesis. Prosthetic heme is the sine qua non of P450 catalytic biotransformation of both endo- and xenobiotics. This well-recognized functional role notwithstanding, heme also regulates P450 protein synthesis, assembly, repair, and disposal. These less well-appreciated aspects are reviewed herein.
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Affiliation(s)
- Maria Almira Correia
- Department of Cellular and Molecular Pharmacology, The Liver Center, University of California, San Francisco, 94158, USA.
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21
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Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b 5. J Mol Model 2010; 17:971-8. [DOI: 10.1007/s00894-010-0795-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 06/25/2010] [Indexed: 12/17/2022]
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22
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A conserved haem redox and trafficking pathway for cofactor attachment. EMBO J 2009; 28:2349-59. [PMID: 19629033 DOI: 10.1038/emboj.2009.189] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 06/15/2009] [Indexed: 01/25/2023] Open
Abstract
A pathway for cytochrome c maturation (Ccm) in bacteria, archaea and eukaryotes (mitochondria) requires the genes encoding eight membrane proteins (CcmABCDEFGH). The CcmABCDE proteins are proposed to traffic haem to the cytochrome c synthetase (CcmF/H) for covalent attachment to cytochrome c by unknown mechanisms. For the first time, we purify pathway complexes with trapped haem to elucidate the molecular mechanisms of haem binding, trafficking and redox control. We discovered an early step in trafficking that involves oxidation of haem (to Fe(3+)), yet the final attachment requires reduced haem (Fe(2+)). Surprisingly, CcmF is a cytochrome b with a haem never before realized, and in vitro, CcmF functions as a quinol:haem oxidoreductase. Thus, this ancient pathway has conserved and orchestrated mechanisms for trafficking, storing and reducing haem, which assure its use for cytochrome c synthesis even in limiting haem (iron) environments and reducing haem in oxidizing environments.
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CcsBA is a cytochrome c synthetase that also functions in heme transport. Proc Natl Acad Sci U S A 2009; 106:10201-6. [PMID: 19509336 DOI: 10.1073/pnas.0903132106] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Little is known about trafficking of heme from its sites of synthesis to sites of heme-protein assembly. We describe an integral membrane protein that allows trapping of endogenous heme to elucidate trafficking mechanisms. We show that CcsBA, a representative of a superfamily of integral membrane proteins involved in cytochrome c biosynthesis, exports and protects heme from oxidation. CcsBA has 10 transmembrane domains (TMDs) and reconstitutes cytochrome c synthesis in the Escherichia coli periplasm; thus, CcsBA is a cytochrome c synthetase. Purified CcsBA contains heme in an "external heme binding domain" for which two external histidines are shown to serve as axial ligands that protect the heme iron from oxidation. This is likely the active site of the synthetase. Furthermore, two conserved histidines in TMDs are required for heme to travel to the external heme binding domain. Remarkably, the function of CcsBA with mutations in these TMD histidines is corrected by exogenous imidazole, a result analogous to correction of heme binding by myoglobin when its proximal histidine is mutated. These data suggest that CcsBA has a heme binding site within the bilayer and that CcsBA is a heme channel.
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Lin YW, Ying TL, Liao LF. Dynamic consequences of mutating the typical HPGG motif of apocytochrome b5 revealed by computer simulation. CHINESE CHEM LETT 2009. [DOI: 10.1016/j.cclet.2009.01.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Lin YW, Ni FY, Ying TL. Early events in thermal unfolding of apocytochrome b562 and its double-cysteine mutant as revealed by molecular dynamics simulation. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Vetter SW, Terentis AC, Osborne RL, Dawson JH, Goodin DB. Replacement of the axial histidine heme ligand with cysteine in nitrophorin 1: spectroscopic and crystallographic characterization. J Biol Inorg Chem 2009; 14:179-91. [PMID: 18923851 PMCID: PMC2635096 DOI: 10.1007/s00775-008-0436-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022]
Abstract
To evaluate the potential of using heme-containing lipocalin nitrophorin 1 (NP1) as a template for protein engineering, we have replaced the native axial heme-coordinating histidine residue with glycine, alanine, and cysteine. We report here the characterization of the cysteine mutant H60C_NP1 by spectroscopic and crystallographic methods. The UV/vis, resonance Raman, and magnetic circular dichroism spectra suggest weak thiolate coordination of the ferric heme in the H60C_NP1 mutant. Reduction to the ferrous state resulted in loss of cysteine coordination, while addition of exogenous imidazole ligands gave coordination changes that varied with the ligand. Depending on the substitution of the imidazole, we could distinguish three heme coordination states: five-coordinate monoimidazole, six-coordinate bisimidazole, and six-coordinate imidazole/thiolate. Ligand binding affinities were measured and found to be generally 2-3 orders of magnitude lower for the H60C mutant relative to NP1. Two crystal structures of the H60C_NP1 in complex with imidazole and histamine were solved to 1.7- and 1.96-A resolution, respectively. Both structures show that the H60C mutation is well tolerated by the protein scaffold and suggest that heme-thiolate coordination in H60C_NP1 requires some movement of the heme within its binding cavity. This adjustment may be responsible for the ease with which the engineered heme-thiolate coordination can be displaced by exogenous ligands.
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Affiliation(s)
- Stefan W Vetter
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Hoy JA, Robinson H, Trent JT, Kakar S, Smagghe BJ, Hargrove MS. Plant hemoglobins: a molecular fossil record for the evolution of oxygen transport. J Mol Biol 2007; 371:168-79. [PMID: 17560601 DOI: 10.1016/j.jmb.2007.05.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 05/07/2007] [Accepted: 05/09/2007] [Indexed: 10/23/2022]
Abstract
The evolution of oxygen transport hemoglobins occurred on at least two independent occasions. The earliest event led to myoglobin and red blood cell hemoglobin in animals. In plants, oxygen transport "leghemoglobins" evolved much more recently. In both events, pentacoordinate heme sites capable of inert oxygen transfer evolved from hexacoordinate hemoglobins that have unrelated functions. High sequence homology between hexacoordinate and pentacoordinate hemoglobins in plants has poised them for potential structural analysis leading to a molecular understanding of this important evolutionary event. However, the lack of a plant hexacoordinate hemoglobin structure in the exogenously ligand-bound form has prevented such comparison. Here we report the crystal structure of the cyanide-bound hexacoordinate hemoglobin from barley. This presents the first opportunity to examine conformational changes in plant hexacoordinate hemoglobins upon exogenous ligand binding, and reveals structural mechanisms for stabilizing the high-energy pentacoordinate heme conformation critical to the evolution of reversible oxygen binding hemoglobins.
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Affiliation(s)
- Julie A Hoy
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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29
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Lin YW, Wang WH, Zhang Q, Lu HJ, Yang PY, Xie Y, Huang ZX, Wu HM. Converting Cytochrome b5 into cytochrome c-like protein. Chembiochem 2005; 6:1356-9. [PMID: 15977276 DOI: 10.1002/cbic.200500030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ying-Wu Lin
- Chemical Biology Lab, Department of Chemistry, Fudan University, Shanghai 200433, China
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Lin YW, Zhao DX, Wang ZH, Yu WH, Huang ZX. Expression of lipase-solubilized bovine liver microsomal cytochrome b5 in Escherichia coli as a glutathione S-transferase fusion protein (GST-cyt b5). Protein Expr Purif 2005; 45:352-8. [PMID: 16146697 DOI: 10.1016/j.pep.2005.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2005] [Revised: 06/04/2005] [Accepted: 06/06/2005] [Indexed: 11/21/2022]
Abstract
The gene coding for the lipase-solubilized bovine liver microsomal cytochrome b5 (cyt b5) was expressed in Escherichia coli BL21 cells as a glutathione S-transferase fusion protein (GST-cyt b5) using the constructed expression vector pGEX-cyt b). The GST-cyt b5 fusion protein can be matured in vivo as a holoprotein with heme incorporated into cyt b5 during the fermentation, and the purification procedures were simplified by using a one-step affinity column chromatography with glutathione-agarose gel. The fusion protein was characterized by its spectroscopic and electrochemical properties, the interaction between GST-cyt b5 and cyt c was also investigated. The results show that GST-cyt b5 fusion protein shares similar properties and functions to that of isolated cyt b5. Although cyt b5 and GST were fused together, the two partners have not made significant structural and functional alterations of their counterparts, the protein-protein interactions between them are apparently very weak. To our knowledge, the present study is the first report to express cyt b5 as a GST-cyt b5 fusion protein, which provides a good example for the in vivo maturation of a hemoprotein as a GST fusion protein and sheds new light on the protein-protein interactions within the GST fusion protein.
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Affiliation(s)
- Ying-Wu Lin
- Chemical Biology Lab, Department of Chemistry, Fudan University, Shanghai 200433, PR China
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31
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Campbell CL, Vandyke KA, Letchworth GJ, Drolet BS, Hanekamp T, Wilson WC. Midgut and salivary gland transcriptomes of the arbovirus vector Culicoides sonorensis (Diptera: Ceratopogonidae). INSECT MOLECULAR BIOLOGY 2005; 14:121-136. [PMID: 15796745 DOI: 10.1111/j.1365-2583.2004.00537.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Numerous Culicoides spp. are important vectors of livestock or human disease pathogens. Transcriptome information from midguts and salivary glands of adult female Culicoides sonorensis provides new insight into vector biology. Of 1719 expressed sequence tags (ESTs) from adult serum-fed female midguts harvested within 5 h of feeding, twenty-eight clusters of serine proteases were derived. Four clusters encode putative iron binding proteins (FER1, FERL, PXDL1, PXDL2), and two clusters encode metalloendopeptidases (MDP6C, MDP6D) that probably function in bloodmeal catabolism. In addition, a diverse variety of housekeeping cDNAs were identified. Selected midgut protease transcripts were analysed by quantitative real-time PCR (q-PCR): TRY1_115 and MDP6C mRNAs were induced in adult female midguts upon feeding, whereas TRY1_156 and CHYM1 were abundant in midguts both before and immediately after feeding. Of 708 salivary gland ESTs analysed, clusters representing two new classes of protein families were identified: a new class of D7 proteins and a new class of Kunitz-type protease inhibitors. Additional cDNAs representing putative immunomodulatory proteins were also identified: 5' nucleotidases, antigen 5-related proteins, a hyaluronidase, a platelet-activating factor acetylhydrolase, mucins and several immune response cDNAs. Analysis by q-PCR showed that all D7 and Kunitz domain transcripts tested were highly enriched in female heads compared with other tissues and were generally absent from males. The mRNAs of two additional protease inhibitors, TFPI1 and TFPI2, were detected in salivary glands of paraffin-embedded females by in situ hybridization.
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Affiliation(s)
- C L Campbell
- USDA, ARS, Arthropod-Borne Animal Diseases Research Laboratory, College of Agriculture, Department 3354, 1000 E. University, Laramie, WY 82071, USA.
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