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Ferric heme as a CO/NO sensor in the nuclear receptor Rev-Erbß by coupling gas binding to electron transfer. Proc Natl Acad Sci U S A 2021; 118:2016717118. [PMID: 33436410 DOI: 10.1073/pnas.2016717118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rev-Erbβ is a nuclear receptor that couples circadian rhythm, metabolism, and inflammation. Heme binding to the protein modulates its function as a repressor, its stability, its ability to bind other proteins, and its activity in gas sensing. Rev-Erbβ binds Fe3+-heme more tightly than Fe2+-heme, suggesting its activities may be regulated by the heme redox state. Yet, this critical role of heme redox chemistry in defining the protein's resting state and function is unknown. We demonstrate by electrochemical and whole-cell electron paramagnetic resonance experiments that Rev-Erbβ exists in the Fe3+ form within the cell allowing the protein to be heme replete even at low concentrations of labile heme in the nucleus. However, being in the Fe3+ redox state contradicts Rev-Erb's known function as a gas sensor, which dogma asserts must be Fe2+ This paper explains why the resting Fe3+ state is congruent both with heme binding and cellular gas sensing. We show that the binding of CO/NO elicits a striking increase in the redox potential of the Fe3+/Fe2+ couple, characteristic of an EC mechanism in which the unfavorable Electrochemical reduction of heme is coupled to the highly favorable Chemical reaction of gas binding, making the reduction spontaneous. Thus, Fe3+-Rev-Erbβ remains heme-loaded, crucial for its repressor activity, and undergoes reduction when diatomic gases are present. This work has broad implications for proteins in which ligand-triggered redox changes cause conformational changes influencing its function or interprotein interactions (e.g., between NCoR1 and Rev-Erbβ). This study opens up the possibility of CO/NO-mediated regulation of the circadian rhythm through redox changes in Rev-Erbβ.
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Liu HX, Li L, Yang XZ, Wei CW, Cheng HM, Gao SQ, Wen GB, Lin YW. Enhancement of protein stability by an additional disulfide bond designed in human neuroglobin. RSC Adv 2019; 9:4172-4179. [PMID: 35520156 PMCID: PMC9062612 DOI: 10.1039/c8ra10390a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Human neuroglobin (Ngb) forms an intramolecular disulfide bond between Cys46 and Cys55, with a third Cys120 near the protein surface, which is a promising protein model for heme protein design. In order to protect the free Cys120 and to enhance the protein stability, we herein developed a strategy by designing an additional disulfide bond between Cys120 and Cys15 via A15C mutation. The design was supported by molecular modeling, and the formation of Cys15–Cys120 disulfide bond was confirmed experimentally by ESI-MS analysis. Molecular modeling, UV-Vis and CD spectroscopy showed that the additional disulfide bond caused minimal structural alterations of Ngb. Meanwhile, the disulfide bond of Cys15–Cys120 was found to enhance both Gdn·HCl-induced unfolding stability (increased by ∼0.64 M) and pH-induced unfolding stability (decreased by ∼0.69 pH unit), as compared to those of WT Ngb with a single native disulfide bond of Cys46–Cys55. Moreover, the half denaturation temperature (Tm) of A15C Ngb was determined to be higher than 100 °C. In addition, the disulfide bond of Cys15–Cys120 has slight effects on protein function, such as an increase in the rate of O2 release by ∼1.4-fold. This study not only suggests a crucial role of the artificial disulfide in protein stabilization, but also lays the groundwork for further investigation of the structure and function of Ngb, as well as for the design of other functional heme proteins, based on the scaffold of A15C Ngb with an enhanced stability. A disulfide bond of Cys120 and Cys15 was rationally designed in human neuroglobin (Ngb) by A15C mutation, which caused minimal structural alterations, whereas enhanced both chemical and pH stability, with a thermal stability higher than 100 °C.![]()
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Affiliation(s)
- Hai-Xiao Liu
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Xin-Zhi Yang
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Chuan-Wan Wei
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hui-Min Cheng
- 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
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Lin YW. Structure and function of heme proteins regulated by diverse post-translational modifications. Arch Biochem Biophys 2018; 641:1-30. [DOI: 10.1016/j.abb.2018.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 01/08/2023]
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Deshpande MS, Junedi S, Prakash H, Nagao S, Yamanaka M, Hirota S. DNA cleavage by oxymyoglobin and cysteine-introduced metmyoglobin. Chem Commun (Camb) 2014; 50:15034-6. [DOI: 10.1039/c4cc06617k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA was cleaved oxidatively by oxygenated myoglobin, whereas Lys96Cys metmyoglobin functioned as an artificial nuclease under air by formation of an oxygenated species.
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Affiliation(s)
| | - Sendy Junedi
- Graduate School of Materials Science
- Nara Institute of Science and Technology
- Ikoma, Japan
| | - Halan Prakash
- Graduate School of Materials Science
- Nara Institute of Science and Technology
- Ikoma, Japan
- Department of Chemistry
- Birla Institute of Technology and Science
| | - Satoshi Nagao
- Graduate School of Materials Science
- Nara Institute of Science and Technology
- Ikoma, Japan
| | - Masaru Yamanaka
- Graduate School of Materials Science
- Nara Institute of Science and Technology
- Ikoma, Japan
| | - Shun Hirota
- Graduate School of Materials Science
- Nara Institute of Science and Technology
- Ikoma, Japan
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Carbon monoxide promotes respiratory hemoproteins iron reduction using peroxides as electron donors. PLoS One 2012; 7:e33039. [PMID: 22427940 PMCID: PMC3299724 DOI: 10.1371/journal.pone.0033039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 02/09/2012] [Indexed: 01/27/2023] Open
Abstract
The physiological role of the respiratory hemoproteins (RH), hemoglobin and myoglobin, is to deliver O(2) via its binding to their ferrous (Fe(II)) heme-iron. Under variety of pathological conditions RH proteins leak to blood plasma and oxidized to ferric (Fe(III), met) forms becoming the source of oxidative vascular damage. However, recent studies have indicated that both metRH and peroxides induce Heme Oxygenase (HO) enzyme producing carbon monoxide (CO). The gas has an extremely high affinity for the ferrous heme-iron and is known to reduce ferric hemoproteins in the presence of suitable electron donors. We hypothesized that under in vivo plasma conditions, peroxides at low concentration can assist the reduction of metRH in presence of CO. The effect of CO on interaction of metRH with hydrophilic or hydrophobic peroxides was analyzed by following Soret and visible light absorption changes in reaction mixtures. It was found that under anaerobic conditions and low concentrations of RH and peroxides mimicking plasma conditions, peroxides served as electron donors and RH were reduced to their ferrous carboxy forms. The reaction rates were dependent on CO as well as peroxide concentrations. These results demonstrate that oxidative activity of acellular ferric RH and peroxides may be amended by CO turning on the reducing potential of peroxides and facilitating the formation of redox-inactive carboxyRH. Our data suggest the possible role of HO/CO in protection of vascular system from oxidative damage.
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Sher EA, Shaklai M, Shaklai N. Interaction of CORM-2 with hydrophobic sites: Beyond CO. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/abc.2012.22023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Dynamics comparison of two myoglobins with a distinct heme active site. J Mol Model 2011; 18:1591-6. [DOI: 10.1007/s00894-011-1192-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 07/18/2011] [Indexed: 10/17/2022]
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Nagao S, Asami O, Yasui H, Hirota S. Efficient reduction of Cys110 thiyl radical by glutathione in human myoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:480-6. [DOI: 10.1016/j.bbapap.2011.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 12/28/2010] [Accepted: 01/13/2011] [Indexed: 11/16/2022]
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Igamberdiev AU, Bykova NV, Hill RD. Structural and functional properties of class 1 plant hemoglobins. IUBMB Life 2011; 63:146-52. [DOI: 10.1002/iub.439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Ochiai Y, Ueki N, Watabe S. Effects of point mutations on the structural stability of tuna myoglobins. Comp Biochem Physiol B Biochem Mol Biol 2009; 153:223-8. [PMID: 19285151 DOI: 10.1016/j.cbpb.2009.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2009] [Revised: 03/04/2009] [Accepted: 03/04/2009] [Indexed: 11/27/2022]
Abstract
Structural stabilities of myoglobin (Mb) from several tuna fish species significantly differ from each other, although the amino acid sequence identities are very high (>95%), suggesting that limited number of substitutions greatly affect the stability of Mb. To address this hypothesis, attempts were made to elaborate recombinant tuna Mbs with point mutations on the different residues among fish Mbs. The expression plasmid constructs were based on bigeye tuna Mb cDNA sequence, and the recombinant proteins were expressed as GST-fusion proteins in Escherichia coli. After removal of the GST segment and affinity purification, the stability of five Mb mutants, namely, A49G, T91K, K92Q, V108A, and H112Q, together with the wild type (WT) were measured, taking temperature dependency of alpha-helical content and denaturant (urea and guanidine-HCl) concentration dependency of Soret band absorbance as parameters. As a result, the mutant H112Q showed much higher stability than WT, while the structures of K92Q, T91K and A49G mutants were destabilized. No essential change in helical content was observed for V108A, but the mutant was found to be destabilized easier by the denaturants. These findings suggested that the highly conserved residues among tuna species are responsible for their stability of Mbs, but a few non-conserved residues dramatically give rise to the differences in stability of Mbs among species.
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Affiliation(s)
- Yoshihiro Ochiai
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
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Feducia J, Dumarieh R, Gilvey LBG, Smirnova T, Franzen S, Ghiladi RA. Characterization of dehaloperoxidase compound ES and its reactivity with trihalophenols. Biochemistry 2009; 48:995-1005. [PMID: 19187035 DOI: 10.1021/bi801916j] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dehaloperoxidase (DHP), the oxygen transport hemoglobin from the terebellid polychaete Amphitrite ornata, is the first globin identified to possess a biologically relevant peroxidase activity. DHP has been shown to oxidize trihalophenols to dihaloquinones in a dehalogenation reaction that uses hydrogen peroxide as a substrate. Herein, we demonstrate that the first detectable intermediate following the addition of hydrogen peroxide to ferric DHP contains both a ferryl heme and a tyrosyl radical, analogous to Compound ES of cytochrome c peroxidase. Furthermore, we provide a detailed kinetic description for the reaction of preformed DHP Compound ES with the substrate 2,4,6-trichlorophenol and demonstrate the catalytic competency of this intermediate in generating the product 2,4-dichloroquinone. Using rapid-freeze-quench electron paramagnetic resonance spectroscopy, we detected a g approximately 2.0058 signal confirming the presence of a protein radical in DHP Compound ES. In the absence of substrate, DHP Compound ES evolves to a new species, Compound RH, which is functionally unique to dehaloperoxidase. We propose that this intermediate plays a protective role against heme bleaching. While unreactive toward further oxidation, Compound RH can be reduced and subsequently bind dioxygen, generating oxyferrous DHP, which may represent the catalytic link between peroxidase and oxygen transport activities in this bifunctional protein.
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Affiliation(s)
- Jeremiah Feducia
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Ueki N, Ochiai Y. Effect of amino acid replacements on the structural stability of fish myoglobin. J Biochem 2006; 140:649-56. [PMID: 16987944 DOI: 10.1093/jb/mvj192] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Structural stabilities of myoglobin (Mb) from several fish (scombridae) species differ significantly, although their amino acid sequence identity is very high (>95%), suggesting that only a few substitutions greatly affect the stability of Mb. Accordingly, recombinant Mbs with point mutation(s) derived from bigeye tuna Mb cDNA were expressed as GST-fusion proteins in the soluble fractions of Escherichia coli. After removal of the GST segment, the stability of five mutants, namely, P13A, I21M, V57I, A62G, and I21M/V57I, together with the wild type (WT) were investigated, taking temperature dependency of alpha-helical content and denaturant concentration dependency of Soret band absorbance as parameters. As a result, the stability of P13A against denaturants and its alpha-helical content at 10 degrees C was found to be the highest among the mutants, whereas those of A62G were the lowest. The stabilities of V57I and I21M/V57I were higher than that of WT, though that of I21M was nearly the same as WT. These findings suggest that the structural stability of fish Mb is tuned up only by the substitutions of a few amino acid residues located in the alpha-helical segments forming the hydrophobic heme pocket.
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Affiliation(s)
- Nobuhiko Ueki
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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Bykova NV, Igamberdiev AU, Ens W, Hill RD. Identification of an intermolecular disulfide bond in barley hemoglobin. Biochem Biophys Res Commun 2006; 347:301-9. [PMID: 16815306 DOI: 10.1016/j.bbrc.2006.06.091] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Accepted: 06/15/2006] [Indexed: 11/23/2022]
Abstract
Barley class-1 hemoglobin (Hb) and its mutated version (Cys(79) replaced by Ser) were overexpressed in Escherichia coli and purified to near homogeneity. Nano-electrospray ionization mass spectrometry (nano-ESI MS) showed that the mutated barley Hb was more readily dissociated to a monomer and was more susceptible to denaturation than the native form. The mutated Hb was oxidized to the ferric state approximately 10(3) times faster than the non-mutated form. The increased oxidation of the mutated Hb was a result of substitution of the cysteine with a serine and not a consequence of monomer formation, per se. Tandem mass spectrometry (MS/MS) analysis revealed that Cys(79) participated in intermolecular S-S bond formation. The rates of nitric oxide scavenging by non-mutated and mutated Hb were similar. We conclude that the cysteine residue is an important contributor to the quaternary and tertiary structure of barley hemoglobin. It however has no direct effect on nitric oxide-scavenging activity of barley Hb.
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Affiliation(s)
- Natalia V Bykova
- Department of Plant Science, University of Manitoba, Winnipeg, Man., Canada
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