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Development of a Versatile Method to Construct Direct Electron Transfer-Type Enzyme Complexes Employing SpyCatcher/SpyTag System. Int J Mol Sci 2023; 24:ijms24031837. [PMID: 36768169 PMCID: PMC9915066 DOI: 10.3390/ijms24031837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
The electrochemical enzyme sensors based on direct electron transfer (DET)-type oxidoreductase-based enzymes are ideal for continuous and in vivo monitoring. However, the number and types of DET-type oxidoreductases are limited. The aim of this research is the development of a versatile method to create a DET-type oxidoreductase complex based on the SpyCatcher/SpyTag technique by preparing SpyCatcher-fused heme c and SpyTag-fused non-DET-type oxidoreductases, and by the in vitro formation of DET-type oxidoreductase complexes. A heme c containing an electron transfer protein derived from Rhizobium radiobacter (CYTc) was selected to prepare SpyCatcher-fused heme c. Three non-DET-type oxidoreductases were selected as candidates for the SpyTag-fused enzyme: fungi-derived flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase (GDH), an engineered FAD-dependent d-amino acid oxidase (DAAOx), and an engineered FMN-dependent l-lactate oxidase (LOx). CYTc-SpyCatcher (CYTc-SC) and SpyTag-Enzymes (ST-GDH, ST-DAAOx, ST-LOx) were prepared as soluble molecules while maintaining their redox properties and catalytic activities, respectively. CYTc-SC/ST-Enzyme complexes were formed by mixing CYTc-SpyCatcher and SpyTag-Enzymes, and the complexes retained their original enzymatic activity. Remarkably, the heme domain served as an electron acceptor from complexed enzymes by intramolecular electron transfer; consequently, all constructed CYTc-SC/ST-Enzyme complexes showed DET ability to the electrode, demonstrating the versatility of this method.
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2
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Influence of heme c attachment on heme conformation and potential. J Biol Inorg Chem 2018; 23:1073-1083. [PMID: 30143872 DOI: 10.1007/s00775-018-1603-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX3CH or CX4CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX3CH and CX4CH variants of Hydrogenobacter thermophilus cytochrome c552. In addition, a novel CXCH variant is studied. 1H and 13C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX4CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.
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Kubie L, Amori AR, Chakraborty S, Bren KL, Krauss TD. Photoinduced charge separation in single-walled carbon nanotube/protein integrated systems. NANOSCALE HORIZONS 2017; 2:163-166. [PMID: 32260660 DOI: 10.1039/c6nh00172f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Zinc-substituted cytochrome c (Zn-cyt c) is noncovalently bound to single-walled carbon nanotubes (SWNTs), causing the Zn-cyt c fluorescence to be quenched by up to 95%, primarily due to photoinduced charge transfer. Deposition of Zn-cyt c/SWNT films onto conductive oxides allows for harvesting of photoexcited electrons with an internal quantum efficiency of over 5%.
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Affiliation(s)
- Lenore Kubie
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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Kleingardner JG, Bren KL. Biological significance and applications of heme c proteins and peptides. Acc Chem Res 2015; 48:1845-52. [PMID: 26083801 DOI: 10.1021/acs.accounts.5b00106] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Hemes are ubiquitous in biology and carry out a wide range of functions. The heme group is largely invariant across proteins with different functions, although there are a few variations seen in nature. The most common variant is heme c, which is formed by a post-translational modification in which heme is covalently linked to two Cys residues on the polypeptide via thioether bonds. In this Account, the influence of this covalent attachment on heme c properties and function is discussed, and examples of how covalent attachment has been used in selected applications are presented. Proteins that bind heme c are among the most well-characterized proteins in biochemistry. Most of these proteins are cytochromes c (cyts c) that serve as electron carriers in photosynthesis and respiration. Despite the intense study of cyts c, the functional significance of heme covalent attachment has remained elusive. One observation is that heme c reaches a lower reduction potential in nature than its noncovalently linked counterpart, heme b, when comparing proteins with the same axial ligands. Furthermore, covalent attachment is known to enhance protein stability and allow the heme to be relatively solvent exposed. However, an inorganic chemistry perspective on the effects of covalent attachment has been lacking. Spectroscopic measurements and computations on cyts c and model systems reveal a number of effects of covalent attachment on heme electronic structure and reactivity. One is that the predominant nonplanar ruffling distortion seen in heme c lowers heme reduction potential. Another is that covalent attachment influences the interaction of the heme iron with the proximal His ligand. Heme ruffling also has been shown to influence electronic coupling to redox partners and, therefore, electron transfer rates by altering the distribution of the orbital hole on the porphyrin in oxidized cyt c. Another consequence of heme covalent attachment is the strong vibrational coupling seen between the iron and the protein surface as revealed by nuclear resonance vibrational spectroscopy studies. Finally, heme covalent attachment is proposed to be an important feature supporting multiple roles of cyt c in programmed cell death (apoptosis). Heme covalent attachment is not only vital for the biological functions of cyt c but also provides a useful handle in a number of applications. For one, the engineering of heme c onto an exposed portion of a protein of interest has been shown to provide a visible affinity purification tag. In addition, peptides with covalently attached heme, known as microperoxidases, have been studied as model compounds and oxidation catalysts and, more recently, in applications for energy conversion and storage. The wealth of insight gained about heme c through fundamental studies of cyts c forms a basis for future efforts toward engineering natural and artificial cytochromes for a variety of applications.
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Affiliation(s)
- Jesse G. Kleingardner
- Department
of Chemistry, Ithaca College, Ithaca, New York 14850, United States
- Department
of Chemistry, University of Rochester, Rochester, New York 14618, United States
| | - Kara L. Bren
- Department
of Chemistry, University of Rochester, Rochester, New York 14618, United States
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Abstract
Protein affinity purification techniques are widely used for isolating pure target proteins for biochemical and structural characterization. Herein, we describe the protocol for affinity-based purification of proteins expressed in Escherichia coli that uses the coordination of a peptide tag covalently modified with heme c, known as a heme-tag, to an L-histidine immobilized Sepharose resin. This approach provides an affinity purification tag visible to the eye, facilitating tracking of the protein. In addition, we describe methods for specifically detecting heme-tagged proteins in SDS-PAGE gels using a heme-staining procedure and for quantifying the proteins using a pyridine hemochrome assay.
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Zhang Y, Stevens JM, Ferguson SJ. Substrate recognition of holocytochrome c synthase: N-terminal region and CXXCH motif of mitochondrial cytochrome c. FEBS Lett 2014; 588:3367-74. [PMID: 25084480 PMCID: PMC4158909 DOI: 10.1016/j.febslet.2014.07.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 11/25/2022]
Abstract
Holocytochrome c synthase (HCCS) does not attach heme to cytochromes lacking the histidine in the CXXCH motif. HCCS can recognise C-terminally truncated cytochromes c. The aromatic nature of, or possibly shape complementarity to, F15 in cytochrome c is important for recognition by HCCS. The spacing of the phenylalanine relative to the CXXCH is a recognition feature.
Holocytochrome c synthase (HCCS) attaches heme covalently to mitochondrial respiratory cytochromes c. Little is known about the reaction of heme attachment to apocytochromes c by HCCS, although recently it has been established that the CXXCH motif and the N-terminus of the apocytochrome polypeptide are important protein–protein recognition motifs. Here, we explore further the important features of the N-terminal sequence and investigate what variations in the CXXCH residues are productively recognised by HCCS in its substrate.
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Affiliation(s)
- Yulin Zhang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Julie M Stevens
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Stuart J Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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Verissimo AF, Daldal F. Cytochrome c biogenesis System I: an intricate process catalyzed by a maturase supercomplex? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:989-98. [PMID: 24631867 DOI: 10.1016/j.bbabio.2014.03.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/16/2022]
Abstract
Cytochromes c are ubiquitous heme proteins that are found in most living organisms and are essential for various energy production pathways as well as other cellular processes. Their biosynthesis relies on a complex post-translational process, called cytochrome c biogenesis, responsible for the formation of stereo-specific thioether bonds between the vinyl groups of heme b (protoporphyrin IX-Fe) and the thiol groups of apocytochromes c heme-binding site (C1XXC2H) cysteine residues. In some organisms this process involves up to nine (CcmABCDEFGHI) membrane proteins working together to achieve heme ligation, designated the Cytochrome c maturation (Ccm)-System I. Here, we review recent findings related to the Ccm-System I found in bacteria, archaea and plant mitochondria, with an emphasis on protein interactions between the Ccm components and their substrates (apocytochrome c and heme). We discuss the possibility that the Ccm proteins may form a multi subunit supercomplex (dubbed "Ccm machine"), and based on the currently available data, we present an updated version of a mechanistic model for Ccm. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA.
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Anderson JLR, Armstrong CT, Kodali G, Lichtenstein BR, Watkins DW, Mancini JA, Boyle AL, Farid TA, Crump MP, Moser CC, Dutton PL. Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette. Chem Sci 2013; 5:507-514. [PMID: 24634717 DOI: 10.1039/c3sc52019f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The successful use of man-made proteins to advance synthetic biology requires both the fabrication of functional artificial proteins in a living environment, and the ability of these proteins to interact productively with other proteins and substrates in that environment. Proteins made by the maquette method integrate sophisticated oxidoreductase function into evolutionarily naive, non-computationally designed protein constructs with sequences that are entirely unrelated to any natural protein. Nevertheless, we show here that we can efficiently interface with the natural cellular machinery that covalently incorporates heme into natural cytochromes c to produce in vivo an artificial c-type cytochrome maquette. Furthermore, this c-type cytochrome maquette is designed with a displaceable histidine heme ligand that opens to allow functional oxygen binding, the primary event in more sophisticated functions ranging from oxygen storage and transport to catalytic hydroxylation. To exploit the range of functions that comes from the freedom to bind a variety of redox cofactors within a single maquette framework, this c-type cytochrome maquette is designed with a second, non-heme C, tetrapyrrole binding site, enabling the construction of an elementary electron transport chain, and when the heme C iron is replaced with zinc to create a Zn porphyrin, a light-activatable artificial redox protein. The work we describe here represents a major advance in de novo protein design, offering a robust platform for new c-type heme based oxidoreductase designs and an equally important proof-of-principle that cofactor-equipped man-made proteins can be expressed in living cells, paving the way for constructing functionally useful man-made proteins in vivo.
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Affiliation(s)
- J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.,The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Craig T Armstrong
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Goutham Kodali
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Bruce R Lichtenstein
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Joshua A Mancini
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Aimee L Boyle
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Tammer A Farid
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Christopher C Moser
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - P Leslie Dutton
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
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Mavridou DAI, Ferguson SJ, Stevens JM. Cytochrome c assembly. IUBMB Life 2013; 65:209-16. [PMID: 23341334 DOI: 10.1002/iub.1123] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 11/29/2012] [Indexed: 11/08/2022]
Abstract
Cytochromes c are central proteins in energy transduction processes by virtue of their functions in electron transfer in respiration and photosynthesis. They have heme covalently attached to a characteristic CXXCH motif via protein-catalyzed post-translational modification reactions. Several systems with diverse constituent proteins have been identified in different organisms and are required to perform the heme attachment and associated functions. The necessary steps are translocation of the apocytochrome polypeptide to the site of heme attachment, transport and provision of heme to the appropriate compartment, reduction and chaperoning of the apocytochrome, and finally, formation of the thioether bonds between heme and two cysteines in the cytochrome. Here we summarize the established classical models for these processes and present recent progress in our understanding of the individual steps within the different cytochrome c biogenesis systems.
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