1
|
Ascorbate Peroxidase Neofunctionalization at the Origin of APX-R and APX-L: Evidence from Basal Archaeplastida. Antioxidants (Basel) 2021; 10:antiox10040597. [PMID: 33924520 PMCID: PMC8069737 DOI: 10.3390/antiox10040597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 11/17/2022] Open
Abstract
Ascorbate peroxidases (APX) are class I members of the Peroxidase-Catalase superfamily, a large group of evolutionarily related but rather divergent enzymes. Through mining in public databases, unusual subsets of APX homologs were identified, disclosing the existence of two yet uncharacterized families of peroxidases named ascorbate peroxidase-related (APX-R) and ascorbate peroxidase-like (APX-L). As APX, APX-R harbor all catalytic residues required for peroxidatic activity. Nevertheless, proteins of this family do not contain residues known to be critical for ascorbate binding and therefore cannot use it as an electron donor. On the other hand, APX-L proteins not only lack ascorbate-binding residues, but also every other residue known to be essential for peroxidase activity. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, the present study discloses the existence of hybrid proteins, which combine features of these three families. The results here presented show that the prevalence of hybrid proteins varies among distinct groups of organisms, accounting for up to 33% of total APX homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APX-R and APX-L and suggests the occurrence of a process characterized by the progressive deterioration of ascorbate-binding and catalytic sites towards neofunctionalization.
Collapse
|
2
|
Samavarchi-Tehrani P, Samson R, Gingras AC. Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches. Mol Cell Proteomics 2020; 19:757-773. [PMID: 32127388 PMCID: PMC7196579 DOI: 10.1074/mcp.r120.001941] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
Collapse
Affiliation(s)
| | - Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| |
Collapse
|
3
|
Cheng HM, Yuan H, Wang XJ, Xu JK, Gao SQ, Wen GB, Tan X, Lin YW. Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen. J Inorg Biochem 2018; 182:141-149. [PMID: 29477977 DOI: 10.1016/j.jinorgbio.2018.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022]
Abstract
The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O2, as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16 Da, likely due to hydroxylation of the α‑carbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H2O2. This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.
Collapse
Affiliation(s)
- Hui-Min Cheng
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jia-Kun Xu
- Yellow Sea Fisheries Research Institute, Qingdao 266071, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Lab of Protein Structure and Function, University of South China, Hengyang 421001, China.
| |
Collapse
|
4
|
Kathiresan M, English AM. LC-MS/MS suggests that hole hopping in cytochrome c peroxidase protects its heme from oxidative modification by excess H 2O 2. Chem Sci 2017; 8:1152-1162. [PMID: 28451256 PMCID: PMC5369544 DOI: 10.1039/c6sc03125k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/06/2016] [Indexed: 12/20/2022] Open
Abstract
We recently reported that cytochrome c peroxidase (Ccp1) functions as a H2O2 sensor protein when H2O2 levels rise in respiring yeast. The availability of its reducing substrate, ferrocytochrome c (CycII), determines whether Ccp1 acts as a H2O2 sensor or peroxidase. For H2O2 to serve as a signal it must modify its receptor so we employed high-performance LC-MS/MS to investigate in detail the oxidation of Ccp1 by 1, 5 and 10 M eq. of H2O2 in the absence of CycII to prevent peroxidase activity. We observe strictly heme-mediated oxidation, implicating sequential cycles of binding and reduction of H2O2 at Ccp1's heme. This results in the incorporation of ∼20 oxygen atoms predominantly at methionine and tryptophan residues. Extensive intramolecular dityrosine crosslinking involving neighboring residues was uncovered by LC-MS/MS sequencing of the crosslinked peptides. The proximal heme ligand, H175, is converted to oxo-histidine, which labilizes the heme but irreversible heme oxidation is avoided by hole hopping to the polypeptide until oxidation of the catalytic distal H52 in Ccp1 treated with 10 M eq. of H2O2 shuts down heterolytic cleavage of H2O2 at the heme. Mapping of the 24 oxidized residues in Ccp1 reveals that hole hopping from the heme is directed to three polypeptide zones rich in redox-active residues. This unprecedented analysis unveils the remarkable capacity of a polypeptide to direct hole hopping away from its active site, consistent with heme labilization being a key outcome of Ccp1-mediated H2O2 signaling. LC-MS/MS identification of the oxidized residues also exposes the bias of electron paramagnetic resonance (EPR) detection toward transient radicals with low O2 reactivity.
Collapse
Affiliation(s)
- Meena Kathiresan
- Concordia University Faculty of Arts and Science, and PROTEOhttp://www.proteo.ca/index.html , Chemistry and Biochemistry , Montreal , Canada .
| | - Ann M English
- Concordia University Faculty of Arts and Science, and PROTEOhttp://www.proteo.ca/index.html , Chemistry and Biochemistry , Montreal , Canada .
| |
Collapse
|
5
|
Lin YW. The broad diversity of heme-protein cross-links: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:844-59. [DOI: 10.1016/j.bbapap.2015.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/26/2015] [Accepted: 04/17/2015] [Indexed: 12/30/2022]
|
6
|
Molitor B, Stassen M, Modi A, El-Mashtoly SF, Laurich C, Lubitz W, Dawson JH, Rother M, Frankenberg-Dinkel N. A heme-based redox sensor in the methanogenic archaeon Methanosarcina acetivorans. J Biol Chem 2013; 288:18458-72. [PMID: 23661702 PMCID: PMC3689988 DOI: 10.1074/jbc.m113.476267] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/08/2013] [Indexed: 11/06/2022] Open
Abstract
Based on a bioinformatics study, the protein MA4561 from the methanogenic archaeon Methanosarcina acetivorans was originally predicted to be a multidomain phytochrome-like photosensory kinase possibly binding open-chain tetrapyrroles. Although we were able to show that recombinantly produced and purified protein does not bind any known phytochrome chromophores, UV-visible spectroscopy revealed the presence of a heme tetrapyrrole cofactor. In contrast to many other known cytoplasmic heme-containing proteins, the heme was covalently attached via one vinyl side chain to cysteine 656 in the second GAF domain. This GAF domain by itself is sufficient for covalent attachment. Resonance Raman and magnetic circular dichroism data support a model of a six-coordinate heme species with additional features of a five-coordination structure. The heme cofactor is redox-active and able to coordinate various ligands like imidazole, dimethyl sulfide, and carbon monoxide depending on the redox state. Interestingly, the redox state of the heme cofactor has a substantial influence on autophosphorylation activity. Although reduced protein does not autophosphorylate, oxidized protein gives a strong autophosphorylation signal independent from bound external ligands. Based on its genomic localization, MA4561 is most likely a sensor kinase of a two-component system effecting regulation of the Mts system, a set of three homologous corrinoid/methyltransferase fusion protein isoforms involved in methyl sulfide metabolism. Consistent with this prediction, an M. acetivorans mutant devoid of MA4561 constitutively synthesized MtsF. On the basis of our results, we postulate a heme-based redox/dimethyl sulfide sensory function of MA4561 and propose to designate it MsmS (methyl sulfide methyltransferase-associated sensor).
Collapse
Affiliation(s)
| | - Marc Stassen
- Institute of Molecular Biosciences, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
| | - Anuja Modi
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Samir F. El-Mashtoly
- Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany
| | - Christoph Laurich
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Michael Rother
- Institute of Molecular Biosciences, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
- Institute of Microbiology, Technical University Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | | |
Collapse
|
7
|
Aicart-Ramos C, Valhondo Falcón M, Ortiz de Montellano PR, Rodriguez-Crespo I. Covalent attachment of heme to the protein moiety in an insect E75 nitric oxide sensor. Biochemistry 2012; 51:7403-16. [PMID: 22946928 DOI: 10.1021/bi300848x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have recombinantly expressed and purified the ligand binding domains (LBDs) of four insect nuclear receptors of the E75 family. The Drosophila melanogaster and Bombyx mori nuclear receptors were purified as ferric hemoproteins with Soret maxima at 424 nm, whereas their ferrous forms had a Soret maximum at 425 nm that responds to (•)NO and CO binding. In contrast, the purified LBD of Oncopeltus fasciatus displayed a Soret maximum at 415 nm for the ferric protein that shifted to 425 nm in its ferrous state. Binding of (•)NO to the heme moiety of the D. melanogaster and B. mori E75 LBD resulted in the appearance of a peak at 385 nm, whereas this peak appeared at 416 nm in the case of the O. fasciatus hemoprotein, resembling the behavior displayed by its human homologue, Rev-erbβ. High-performance liquid chromatography analysis revealed that, unlike the D. melanogaster and B. mori counterparts, the heme group of O. fasciatus is covalently attached to the protein through the side chains of two amino acids. The high degree of sequence homology with O. fasciatus E75 led us to clone and express the LBD of Blattella germanica, which established that its spectral properties closely resemble those of O. fasciatus and that it also has the heme group covalently bound to the protein. Hence, (•)NO/CO regulation of the transcriptional activity of these nuclear receptors might be differently controlled among various insect species. In addition, covalent heme binding provides strong evidence that at least some of these nuclear receptors function as diatomic gas sensors rather than heme sensors. Finally, our findings expand the classes of hemoproteins in which the heme group is normally covalently attached to the polypeptide chain.
Collapse
Affiliation(s)
- Clara Aicart-Ramos
- Departamento de Bioquímica y Biología Molecular I, Universidad Complutense, 28040 Madrid, Spain
| | | | | | | |
Collapse
|
8
|
Geoghegan KF, Varghese AH, Feng X, Bessire AJ, Conboy JJ, Ruggeri RB, Ahn K, Spath SN, Filippov SV, Conrad SJ, Carpino PA, Guimarães CRW, Vajdos FF. Deconstruction of Activity-Dependent Covalent Modification of Heme in Human Neutrophil Myeloperoxidase by Multistage Mass Spectrometry (MS4). Biochemistry 2012; 51:2065-77. [DOI: 10.1021/bi201872j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Xidong Feng
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | | | - James J. Conboy
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | - Roger B. Ruggeri
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | - Kay Ahn
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | | | | | - Steven J. Conrad
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| | | | | | - Felix F. Vajdos
- Pfizer Worldwide Research, Groton, Connecticut
06340, United States
| |
Collapse
|
9
|
Guallar V, Wallrapp FH. QM/MM methods: looking inside heme proteins biochemistry. Biophys Chem 2010; 149:1-11. [PMID: 20400222 DOI: 10.1016/j.bpc.2010.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 11/29/2022]
Abstract
Mixed quantum mechanics/molecular mechanics methods offer a valuable computational tool for understanding biochemical events. When combined with conformational sampling techniques, they allow for an exhaustive exploration of the enzymatic mechanism. Heme proteins are ubiquitous and essential for every organism. In this review we summarize our efforts towards the understanding of heme biochemistry. We present: 1) results on ligand migration on globins coupled to the ligand binding event, 2) results on the localization of the spin density in compound I of cytochromes and peroxidases, 3) novel methodologies for mapping the electron transfer pathways and 4) novel data on Tryptophan 2,3-dioxygenase. For this enzyme our results strongly indicate that the distal oxygen will end up on the C3 indole carbon, whereas the proximal oxygen will end up in the C2 position. Interestingly, the process involves the formation of an epoxide and a heme ferryl intermediate. The overall energy profile indicates an energy barrier of approximately 18 kcal/mol and an exothermic driving force of almost 80 kcal/mol.
Collapse
Affiliation(s)
- Victor Guallar
- Life Science Department, Barcelona Supercomputing Center, Jordi Girona, 29, 08034 Barcelona, Spain.
| | | |
Collapse
|
10
|
Pipirou Z, Guallar V, Basran J, Metcalfe CL, Murphy EJ, Bottrill AR, Mistry SC, Raven EL. Peroxide-Dependent Formation of a Covalent Link between Trp51 and the Heme in Cytochrome c Peroxidase. Biochemistry 2009; 48:3593-9. [DOI: 10.1021/bi802210g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zoi Pipirou
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Victor Guallar
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Jaswir Basran
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Clive L. Metcalfe
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Emma J. Murphy
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Andrew R. Bottrill
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Sharad C. Mistry
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Emma Lloyd Raven
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| |
Collapse
|
11
|
Guallar V, Wallrapp F. Mapping protein electron transfer pathways with QM/MM methods. J R Soc Interface 2009; 5 Suppl 3:S233-9. [PMID: 18445553 DOI: 10.1098/rsif.2008.0061.focus] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mixed quantum mechanics/molecular mechanics (QM/MM) methods offer a valuable computational tool for understanding the electron transfer pathway in protein-substrate interactions and protein-protein complexes. These hybrid methods are capable of solving the Schrödinger equation on a small subset of the protein, the quantum region, describing its electronic structure under the polarization effects of the remainder of the protein. By selectively turning on and off different residues in the quantum region, we are able to obtain the electron pathway for short- and large-range interactions. Here, we summarize recent studies involving the protein-substrate interaction in cytochrome P450 camphor, ascorbate peroxidase and cytochrome c peroxidase, and propose a novel approach for the long-range protein-protein electron transfer. The results on ascorbate peroxidase and cytochrome c peroxidase reveal the importance of the propionate groups in the electron transfer pathway. The long-range protein-protein electron transfer has been studied on the cytochrome c peroxidase-cytochrome c complex. The results indicate the importance of Phe82 and Cys81 on cytochrome c, and of Asn196, Ala194, Ala176 and His175 on cytochrome c peroxidase.
Collapse
Affiliation(s)
- Victor Guallar
- Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona, Spain.
| | | |
Collapse
|
12
|
Kitajima S. Hydrogen Peroxide-mediated Inactivation of Two Chloroplastic Peroxidases, Ascorbate Peroxidase and 2-Cys Peroxiredoxin†. Photochem Photobiol 2008; 84:1404-9. [DOI: 10.1111/j.1751-1097.2008.00452.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
13
|
Guallar V. Heme Electron Transfer in Peroxidases: The Propionate e-Pathway. J Phys Chem B 2008; 112:13460-4. [DOI: 10.1021/jp806435d] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Victor Guallar
- ICREA Research Professor, Life Science Department, Barcelona Supercomputing Center, Jordi Girona, 29, 08034 Barcelona (Spain)
| |
Collapse
|
14
|
Sicking W, Korth HG, de Groot H, Sustmann R. On the functional role of a water molecule in clade 3 catalases: a proposal for the mechanism by which NADPH prevents the formation of compound II. J Am Chem Soc 2008; 130:7345-56. [PMID: 18479132 DOI: 10.1021/ja077787e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
X-ray structures of the 13 different monofunctional heme catalases published to date were scrutinized in order to gain insight in the mechanism by which NADPH in Clade 3 catalases may protect the reactive ferryloxo intermediate Compound I (Cpd I; por (*+)Fe (IV)O) against deactivation to the catalytically inactive intermediate Compound II (Cpd II; porFe (IV)O). Striking similarities in the molecular network of the protein subunits encompassing the heme center and the surface-bound NADPH were found for all of the Clade 3 catalases. Unique features in this region are the presence of a water molecule (W1) adjacent to the 4-vinyl group of heme and a serine residue or a second water molecule hydrogen-bonded to both W1 and the carbonyl group of a threonine-proline linkage, with the proline in van der Waals contact with the dihydronicotinamide group of NADPH. A mechanism is proposed in which a hydroxyl anion released from W1 undergoes reversible nucleophilic addition to the terminal carbon of the 4-vinyl group of Cpd I, thereby producing a neutral porphyrin pi-radical ferryloxo (HO-por (*)Fe (IV)O) species of reduced reactivity. This structure is suggested to be the elusive Cpd II' intermediate proposed in previous studies. An accompanying proton-shifting process along the hydrogen-bonded network is believed to facilitate the NADPH-mediated reduction of Cpd I to ferricatalase and to serve as a funnel for electron transfer from NADPH to the heme center to restore the catalase Fe (III) resting state. The proposed reaction paths were fully supported as chemically reasonable and energetically feasible by means of density functional theory calculations at the (U)B3LYP/6-31G* level. A particularly attractive feature of the present mechanism is that the previously discussed formation of protein-derived radicals is avoided.
Collapse
Affiliation(s)
- Willi Sicking
- Institut für Organische Chemie, Universität Duisburg-Essen, 45117 Essen, Germany
| | | | | | | |
Collapse
|
15
|
Kitajima S, Kurioka M, Yoshimoto T, Shindo M, Kanaori K, Tajima K, Oda K. A cysteine residue near the propionate side chain of heme is the radical site in ascorbate peroxidase. FEBS J 2008; 275:470-80. [PMID: 18167143 DOI: 10.1111/j.1742-4658.2007.06214.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The radical scavenger 2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO(*)) and the spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) were used in conjunction with mass spectrometry to identify the protein-based radical sites of the H(2)O(2)-tolerant ascorbate peroxidase (APX) of the red alga Galdieria partita and the H(2)O(2)-sensitive stromal APX of tobacco. A cysteine residue in the vicinity of the propionate side chain of heme in both enzymes was labeled with TEMPO(*) and DMPO in an H(2)O(2)-dependent manner, indicating that these cysteine residues form thiyl radicals through interaction of APX with H(2)O(2). TEMPO(*) bound to the cysteine thiyl radicals, and sulfinylated and sulfonylated them. Other oxidized cysteine residues were found in both APXs. Experiments with a cysteine-to-serine point mutation showed that formation of TEMPO adducts and subsequent oxidation of the cysteine residue located near the propionate group of heme leads to loss of enzyme activity, in particular in the Galdieria APX. When treated with glutathione and H(2)O(2), both cysteine residues in both enzymes were glutathionylated. These results suggest that, under oxidative stress in vivo, cysteine oxidation is involved in the inactivation of APXs in addition to the proposed H(2)O(2)-mediated crosslinking of heme to the distal tryptophan residue [Kitajima S, Shimaoka T, Kurioka M & Yokota A (2007) FEBS J274, 3013-3020], and that glutathione protects APX from irreversible oxidation of the cysteine thiol and loss of enzyme activity by binding to the cysteine thiol group.
Collapse
Affiliation(s)
- Sakihito Kitajima
- Graduate School of Science and Technology, Kyoto Institute of Technology, Japan.
| | | | | | | | | | | | | |
Collapse
|
16
|
Kitajima S, Shimaoka T, Kurioka M, Yokota A. Irreversible cross-linking of heme to the distal tryptophan of stromal ascorbate peroxidase in response to rapid inactivation by H2O2. FEBS J 2007; 274:3013-20. [PMID: 17509080 DOI: 10.1111/j.1742-4658.2007.05829.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ascorbate peroxidase (APX) isoforms localized in the stroma and thylakoid membrane of chloroplasts play a central role in scavenging reactive oxygen species generated by photosystems. These enzymes are inactivated within minutes by H2O2 when the reducing substrate, ascorbate, is depleted. We found that, when the enzyme is inactivated by H2O2, a heme at the catalytic site of a stromal APX isoform is irreversibly cross-linked to a tryptophan residue facing the distal cavity. Mutation of this tryptophan to phenylalanine abolished the cross-linking and increased the half-time for inactivation from <10 to 62 s. In contrast with H2O2-tolerant peroxidases, rapid formation of the cross-link in APXs suggests that a radical in the reaction intermediate tends to be located in the distal tryptophan so that heme is easily cross-linked to it. This is the first report of a mutation that improves the tolerance of chloroplast APXs to H2O2.
Collapse
Affiliation(s)
- Sakihito Kitajima
- Graduate School of Science and Technology, Kyoto Institute of Technology, Japan.
| | | | | | | |
Collapse
|