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Lučić M, Wilson MT, Pullin J, Hough MA, Svistunenko DA, Worrall JAR. New insights into controlling radical migration pathways in heme enzymes gained from the study of a dye-decolorising peroxidase. Chem Sci 2023; 14:12518-12534. [PMID: 38020392 PMCID: PMC10646903 DOI: 10.1039/d3sc04453j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
In heme enzymes, such as members of the dye-decolorising peroxidase (DyP) family, the formation of the highly oxidising catalytic Fe(iv)-oxo intermediates following reaction with hydrogen peroxide can lead to free radical migration (hole hopping) from the heme to form cationic tyrosine and/or tryptophan radicals. These species are highly oxidising (∼1 V vs. NHE) and under certain circumstances can catalyse the oxidation of organic substrates. Factors that govern which specific tyrosine or tryptophan the free radical migrates to in heme enzymes are not well understood, although in the case of tyrosyl radical formation the nearby proximity of a proton acceptor is a recognised facilitating factor. By using an A-type member of the DyP family (DtpAa) as an exemplar, we combine protein engineering, X-ray crystallography, hole-hopping calculations, EPR spectroscopy and kinetic modelling to provide compelling new insights into the control of radical migration pathways following reaction of the heme with hydrogen peroxide. We demonstrate that the presence of a tryptophan/tyrosine dyad motif displaying a T-shaped orientation of aromatic rings on the proximal side of the heme dominates the radical migration landscape in wild-type DtpAa and continues to do so following the rational engineering into DtpAa of a previously identified radical migration pathway in an A-type homolog on the distal side of the heme. Only on disrupting the proximal dyad, through removal of an oxygen atom, does the radical migration pathway then switch to the engineered distal pathway to form the desired tyrosyl radical. Implications for protein design and biocatalysis are discussed.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Jacob Pullin
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Michael A Hough
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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2
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Liu W, Berge-Lefranc D, Chaspoul F, Slaveykova VI. Cytochrome c - silver nanoparticle interactions: Spectroscopy, thermodynamic and enzymatic activity studies. Chem Biol Interact 2023; 382:110647. [PMID: 37499996 DOI: 10.1016/j.cbi.2023.110647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Cytochrome c, an iron containing metalloprotein in the mitochondria of the cells with an oxide/redox property, plays key role in the cell apoptotic pathway. In this study, the interaction of silver nanoparticles (AgNPs) with cytochrome c (Cyt c) was investigated by using a combination of spectroscopic, imaging and thermodynamic techniques, including dynamic light scattering (DLS), ultraviolet-visible (UV-vis) spectroscopy, transmission electron microscopy (TEM), fluorescence spectroscopy, near and far circular dichroism (CD) spectroscopy, and isothermal titration calorimetry (ITC). DLS and UV-vis analysis evidenced the formation of surface complexes of Cyt c on AgNPs. The saturation of surface coverage of AgNPs was observed at 4.36 Cyt c molecules per nm2 of AgNPs. The surface complexation resulted in a promotion of the Ag dissolution overtime. The negative sign of enthalpic (ΔH) contribution suggested that electrostatic forces are indicative forces in the interaction between protein and AgNPs. Moreover, the fluorescence spectra revealed that the conformation of protein was altered around tryptophan (Trp) and tyrosine (Tyr) residues indicating the alteration of the tertiary structure of Cyt c. CD analysis evidenced that the secondary structure of Cyt c was modified under AgNPs-Cyt c interactions and the binding of Cyt c onto AgNPs resulted in remarkable structural perturbation around the active site heme, which in turn alter the protein enzymatic activity. The results of the present study contributed to a deeper insight on the mechanisms of interaction between NPs and biomacromolecules and could help establish the in vivo fate of AgNPs on cellular redox homeostasis.
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Affiliation(s)
- Wei Liu
- University of Geneva, Faculty of Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Switzerland.
| | - David Berge-Lefranc
- ICR UMR Aix Marseille Université - CNRS 7273, IMBE UMR Aix Marseille Université - CNRS - IRD - AUPV 7263, France
| | - Florence Chaspoul
- ICR UMR Aix Marseille Université - CNRS 7273, IMBE UMR Aix Marseille Université - CNRS - IRD - AUPV 7263, France
| | - Vera I Slaveykova
- University of Geneva, Faculty of Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Switzerland
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3
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Li J, Ran X, Zhou M, Wang K, Wang H, Wang Y. Oxidative stress and antioxidant mechanisms of obligate anaerobes involved in biological waste treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156454. [PMID: 35667421 DOI: 10.1016/j.scitotenv.2022.156454] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
In-depth understanding of the molecular mechanisms and physiological consequences of oxidative stress is still limited for anaerobes. Anaerobic biotechnology has become widely accepted by the wastewater/sludge industry as a better alternative to more conventional but costly aerobic processes. However, the functional anaerobic microorganisms used in anaerobic biotechnology are frequently hampered by reactive oxygen/nitrogen species (ROS/RNS)-mediated oxidative stress caused by exposure to stressful factors (e.g., oxygen and heavy metals), which negatively impact treatment performance. Thus, identifying stressful factors and understanding antioxidative defense mechanisms of functional obligate anaerobes are crucial for the optimization of anaerobic bioprocesses. Herein, we present a comprehensive overview of oxidative stress and antioxidant mechanisms of obligate anaerobes involved in anaerobic bioprocesses; as examples, we focus on anaerobic ammonium oxidation bacteria and methanogenic archaea. We summarize the primary stress factors in anaerobic bioprocesses and the cellular antioxidant defense systems of functional anaerobes, a consortia of enzymatic and nonenzymatic mechanisms. The dual role of ROS/RNS in cellular processes is elaborated; at low concentrations, they have vital cell signaling functions, but at high concentrations, they cause oxidative damage. Finally, we highlight gaps in knowledge and future work to uncover antioxidant and damage repair mechanisms in obligate anaerobes. This review provides in-depth insights and guidance for future research on oxidative stress of obligate anaerobes to boost the accurate regulation of anaerobic bioprocesses in challenging and changing operating conditions.
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Affiliation(s)
- Jia Li
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Xiaochuan Ran
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Mingda Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Kaichong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
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4
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Yang Q, Yang J, Wang Y, Du J, Zhang J, Luisi BF, Liang W. Broad-spectrum chemicals block ROS detoxification to prevent plant fungal invasion. Curr Biol 2022; 32:3886-3897.e6. [PMID: 35932761 PMCID: PMC7613639 DOI: 10.1016/j.cub.2022.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/16/2022] [Accepted: 07/12/2022] [Indexed: 12/02/2022]
Abstract
Plant diseases cause a huge impact on food security and are of global concern. While application of agrochemicals is a common approach in the control of plant diseases currently, growing drug resistance and the impact of off-target effects of these compounds pose major challenges. The identification of pathogenicity-related virulence mechanisms and development of new chemicals that target these processes are urgently needed. One such virulence mechanism is the detoxification of reactive oxygen species (ROS) generated by host plants upon attack by pathogens. The machinery of ROS detoxification might therefore serve as a drug target for preventing plant diseases, but few anti-ROS-scavenging drugs have been developed. Here, we show that in the model system Botrytis cinerea secretion of the cytochrome c-peroxidase, BcCcp1 removes plant-produced H2O2 and promotes pathogen invasion. The peroxidase secretion is modulated by a Tom1-like protein, BcTol1, through physical interaction. We show that BcTol1 is regulated at different levels to enhance the secretion of BcCcp1 during the early infection stage. Inactivation of either BcTol1 or BcCcp1 leads to dramatically reduced virulence of B. cinerea. We identify two BcTol1-targeting small molecules that not only prevent B. cinerea invasion but also have effective activity against a wide range of plant fungal pathogens without detectable effect on the hosts. These findings reveal a conserved mechanism of ROS detoxification in fungi and provide a class of potential fungicides to control diverse plant diseases. The approach described here has wide implications for further drug discovery in related fields.
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Affiliation(s)
- Qianqian Yang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
| | - Jinguang Yang
- Tobacco Research Institute of CAAS, Qingdao 266100, China
| | - Yameng Wang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
| | - Juan Du
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jianan Zhang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Wenxing Liang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China.
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5
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Bin Mohd Yusof MS, Debnath T, Loh ZH. Observation of intra- and intermolecular vibrational coherences of the aqueous tryptophan radical induced by photodetachment. J Chem Phys 2021; 155:134306. [PMID: 34624987 DOI: 10.1063/5.0067335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The study of the photodetachment of amino acids in aqueous solution is pertinent to the understanding of elementary processes that follow the interaction of ionizing radiation with biological matter. In the case of tryptophan, the tryptophan radical that is produced by electron ejection also plays an important role in numerous redox reactions in biology, although studies of its ultrafast molecular dynamics are limited. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the ultrafast structural rearrangement dynamics that accompany the photodetachment of the aqueous tryptophan anion by intense, ∼5-fs laser pulses. The observed vibrational wave packet dynamics, in conjunction with density functional theory calculations, identify the vibrational modes of the tryptophan radical, which participate in structural rearrangement upon photodetachment. Aside from intramolecular vibrational modes, our results also point to the involvement of intermolecular modes that drive solvent reorganization about the N-H moiety of the indole sidechain. Our study offers new insight into the ultrafast molecular dynamics of ionized biomolecules and suggests that the present experimental approach can be extended to investigate the photoionization- or photodetachment-induced structural dynamics of larger biomolecules.
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Affiliation(s)
- Muhammad Shafiq Bin Mohd Yusof
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Tushar Debnath
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Zhi-Heng Loh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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6
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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7
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Gideon DA, Nirusimhan V, E JC, Sudarsha K, Manoj KM. Mechanism of electron transfers mediated by cytochromes c and b5 in mitochondria and endoplasmic reticulum: classical and murburn perspectives. J Biomol Struct Dyn 2021; 40:9235-9252. [PMID: 33998974 DOI: 10.1080/07391102.2021.1925154] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We explore the mechanism of electron transfers mediated by cytochrome c, a soluble protein involved in mitochondrial oxidative phosphorylation and cytochrome b5, a microsomal membrane protein acting as a redox aide in xenobiotic metabolism. We found minimal conservation in the sequence and surface amino acid residues of cytochrome c/b5 proteins among divergent species. Therefore, we question the evolutionary logic for electron transfer (ET) occurring through affinity binding via recognition of specific surface residues/topography. Also, analysis of putative protein-protein interactions in the crystal structures of these proteins and their redox partners did not point to any specific interaction logic. A comparison of the kinetic and thermodynamic constants of wildtype vs. mutants did not provide strong evidence to support the binding-based ET paradigm, but indicated support for diffusible reactive species (DRS)-mediated process. Topographically divergent cytochromes from one species have been substituted for reaction with proteins from other species, implying the involvement of non-specific interactions. We provide a viable alternative (murburn concept) to classical protein-protein binding-based long range ET mechanism. To account for the promiscuity of interactions and solvent-accessible hemes, we propose that the two proteins act as non- specific redox capacitors, mediating one-electron redox equilibriums involving DRS and unbound ions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India.,Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Vijay Nirusimhan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Jesu Castin E
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Karthik Sudarsha
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India
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8
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Gusev ID, Firsov AM, Chertkova RV, Kotova EA, Dolgikh DA, Kirpichnikov MP, Antonenko YN. Study of Interaction of Fluorescent Cytochrome C with Liposomes, Mitochondria, and Mitoplasts by Fluorescence Correlation Spectroscopy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020060084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Yin V, Holzscherer D, Konermann L. Delineating Heme-Mediated versus Direct Protein Oxidation in Peroxidase-Activated Cytochrome c by Top-Down Mass Spectrometry. Biochemistry 2020; 59:4108-4117. [PMID: 32991149 DOI: 10.1021/acs.biochem.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Oxidation of key residues in cytochrome c (cyt c) by chloramine T (CT) converts the protein from an electron transporter to a peroxidase. This peroxidase-activated state represents an important model system for exploring the early steps of apoptosis. CT-induced transformations include oxidation of the distal heme ligand Met80 (MetO, +16 Da) and carbonylation (LysCHO, -1 Da) in the range of Lys53/55/72/73. Remarkably, the 15 remaining Lys residues in cyt c are not susceptible to carbonylation. The cause of this unusual selectivity is unknown. Here we applied top-down mass spectrometry (MS) to examine whether CT-induced oxidation is catalyzed by heme. To this end, we compared the behavior of cyt c with (holo-cyt c) and without heme (apoSS-cyt c). CT caused MetO formation at Met80 for both holo- and apoSS-cyt c, implying that this transformation can proceed independently of heme. The aldehyde-specific label Girard's reagent T (GRT) reacted with oxidized holo-cyt c, consistent with the presence of several LysCHO. In contrast, oxidized apo-cyt c did not react with GRT, revealing that LysCHO forms only in the presence of heme. The heme dependence of LysCHO formation was further confirmed using microperoxidase-11 (MP11). CT exposure of apoSS-cyt c in the presence of MP11 caused extensive nonselective LysCHO formation. Our results imply that the selectivity of LysCHO formation at Lys53/55/72/73 in holo-cyt c is caused by the spatial proximity of these sites to the reactive (distal) heme face. Overall, this work highlights the utility of top-down MS for unravelling complex oxidative modifications.
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Affiliation(s)
- Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Derek Holzscherer
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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10
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Abstract
A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on the mean residence times of the transferring charge along these hopping pathways. The residence times are estimated by combining a kinetic model with well-known rate expressions for the charge-transfer steps in the pathways. We identify the most rapid hole hopping escape routes in cytochrome P450 monooxygenase, cytochrome c peroxidase, and benzylsuccinate synthase (BSS). This theoretical analysis supports the existence of hole hopping chains as a mechanism capable of providing hole escape from protein catalytic sites on biologically relevant timescales. Furthermore, we find that pathways involving the [4Fe4S] cluster as the terminal hole acceptor in BSS are accessible on the millisecond timescale, suggesting a potential protective role of redox-active cofactors for preventing protein oxidative damage.
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11
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Tarpani L, Bellezza F, Sassi P, Gambucci M, Cipiciani A, Latterini L. New Insights into the Effects of Surface Functionalization on the Peroxidase Activity of Cytochrome c Adsorbed on Silica Nanoparticles. J Phys Chem B 2019; 123:2567-2575. [DOI: 10.1021/acs.jpcb.8b11762] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Luigi Tarpani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Francesca Bellezza
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Marta Gambucci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Antonio Cipiciani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
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12
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Foerster J, Poehner I, Ullmann GM. MCMap-A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions. ACS OMEGA 2018; 3:6465-6475. [PMID: 31458826 PMCID: PMC6644659 DOI: 10.1021/acsomega.8b00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/22/2018] [Indexed: 06/10/2023]
Abstract
MCMap is a tool particularly well-suited for analyzing energy landscapes of transient macromolecular complexes. The program applies a Monte Carlo strategy, where the ligand moves randomly in the electrostatic field of the receptor. By applying importance sampling, the major interaction sites are mapped, resulting in a global distribution of ligand-receptor complexes. This approach displays the dynamic character of transiently interacting protein complexes where not a single complex but an ensemble of complexes better describes the protein interactions. The software provides a broad range of analysis options which allow for relating the simulations to experimental data and for interpreting them on a structural level. The application of MCMap is exemplified by the electron-transfer complex of cytochrome c peroxidase and cytochrome c from baker's yeast. The functionality of MCMap and the visualization of simulation data are in particular demonstrated by studying the dependence of the association on ionic strength and on the oxidation state of the binding partner. Furthermore, microscopically, a repulsion of a second ligand can be seen in the ternary complex upon the change of the oxidation state of the bound cytochrome c. The software is made available as open source software together with the example and can be downloaded free of charge from http://www.bisb.uni-bayreuth.de/index.php?page=downloads.
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13
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Yin V, Shaw GS, Konermann L. Cytochrome c as a Peroxidase: Activation of the Precatalytic Native State by H2O2-Induced Covalent Modifications. J Am Chem Soc 2017; 139:15701-15709. [DOI: 10.1021/jacs.7b07106] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Victor Yin
- Department of Chemistry and Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Gary S. Shaw
- Department of Chemistry and Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry and Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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14
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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15
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Hollingsworth SA, Nguyen BD, Chreifi G, Arce AP, Poulos TL. Insights into the Dynamics and Dissociation Mechanism of a Protein Redox Complex Using Molecular Dynamics. J Chem Inf Model 2017; 57:2344-2350. [PMID: 28841378 DOI: 10.1021/acs.jcim.7b00421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Leishmania major peroxidase (LmP) is structurally and functionally similar to the well-studied yeast Cytochrome c peroxidase (CCP). A recent Brownian dynamics study showed that L. major Cytochrome c (LmCytc) associates with LmP by forming an initial complex with the N-terminal helix A of LmP, followed by a movement toward the electron transfer (ET) site observed in the LmP-LmCytc crystal structure. Critical to forming the active electron transfer complex is an intermolecular Arg-Asp ion pair at the center of the interface. If the dissociation reaction is effectively the reverse of the association reaction, then rupture of the Asp-Arg ion pair should be followed by movement of LmCytc back toward LmP helix A. To test this possibility, we have performed multiple molecular dynamics (MD) simulations of the LmP-LmCytc complex. In five separate simulations, LmCytc is observed to indeed move toward helix A, and in two of the simulations, the Asp-Arg ion pair breaks, which frees LmCytc to fully associate with the LmP helix A secondary binding site. These results support the "bind and crawl" or "velcro" mechanism of association, wherein LmCytc forms a nonspecific electrostatic complex with LmP helix A, followed by a "crawl" toward the ET-active site, where the Asp-Arg ion pair holds the LmCytc in position for rapid ET. These simulations also point to Tyr134LmP as being important in the association/dissociation reactions. Experimentally mutating Tyr134 to Phe was found to decrease Km by 3.6-fold, which is consistent with its predicted role in complex formation by MD simulations.
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Affiliation(s)
- Scott A Hollingsworth
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
| | - Brian D Nguyen
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
| | - Georges Chreifi
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
| | - Anton P Arce
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
| | - Thomas L Poulos
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
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16
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Fukushima T, Gupta S, Rad B, Cornejo JA, Petzold CJ, Chan LJG, Mizrahi RA, Ralston CY, Ajo-Franklin CM. The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface. J Am Chem Soc 2017; 139:12647-12654. [DOI: 10.1021/jacs.7b06560] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Tatsuya Fukushima
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sayan Gupta
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Behzad Rad
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jose A. Cornejo
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leanne Jade G. Chan
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rena A. Mizrahi
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Corie Y. Ralston
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Caroline M. Ajo-Franklin
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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17
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Gu J, Shin DW, Pletneva EV. Remote Perturbations in Tertiary Contacts Trigger Ligation of Lysine to the Heme Iron in Cytochrome c. Biochemistry 2017; 56:2950-2966. [PMID: 28474881 DOI: 10.1021/acs.biochem.6b01187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Perturbations in protein structure define the mechanism of allosteric regulation and biological information transfer. In cytochrome c (cyt c), ligation of Met80 to the heme iron is critical for the protein's electron-transfer (ET) function in oxidative phosphorylation and for suppressing its peroxidase activity in apoptosis. The hard base Lys is a better match for the hard ferric iron than the soft base Met is, suggesting the key role of the protein scaffold in favoring Met ligation. To probe the role of the protein structure in the maintenance of Met ligation, mutations T49V and Y67R/M80A were designed to disrupt hydrogen bonding and packing of the heme coordination loop, respectively. Electronic absorption, nuclear magnetic resonance, and electron paramagnetic resonance spectra reveal that ferric forms of both variants are Lys-ligated at neutral pH. A minor change in the tertiary contacts in T49V, away from the heme coordination loop, appears to be sufficient to execute a change in ligation, suggesting a cross-talk between the different regions of the protein structure and a possibility of built-in conformational switches in cyt c. Analyses of thermodynamic stability, kinetics of Lys binding and dissociation, and the pH-dependent changes in ligation provide a detailed characterization of the Lys coordination in these variants and relate these properties to the extent of structural perturbations. The findings emphasize the importance of the hydrogen-bonding network in controlling ligation of the native Met80 to the heme iron.
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Affiliation(s)
- Jie Gu
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
| | - Dong-Woo Shin
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
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18
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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.
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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 .
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19
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Karsisiotis AI, Deacon OM, Wilson MT, Macdonald C, Blumenschein TMA, Moore GR, Worrall JAR. Increased dynamics in the 40-57 Ω-loop of the G41S variant of human cytochrome c promote its pro-apoptotic conformation. Sci Rep 2016; 6:30447. [PMID: 27461282 PMCID: PMC4962053 DOI: 10.1038/srep30447] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/05/2016] [Indexed: 12/26/2022] Open
Abstract
Thrombocytopenia 4 is an inherited autosomal dominant thrombocytopenia, which occurs due to mutations in the human gene for cytochrome c that results in enhanced mitochondrial apoptotic activity. The Gly41Ser mutation was the first to be reported. Here we report stopped-flow kinetic studies of azide binding to human ferricytochrome c and its Gly41Ser variant, together with backbone amide H/D exchange and 15N-relaxation dynamics using NMR spectroscopy, to show that alternative conformations are kinetically and thermodynamically more readily accessible for the Gly41Ser variant than for the wild-type protein. Our work reveals a direct conformational link between the 40–57 Ω-loop in which residue 41 resides and the dynamical properties of the axial ligand to the heme iron, Met80, such that the replacement of glycine by serine promotes the dissociation of the Met80 ligand, thereby increasing the population of a peroxidase active state, which is a key non-native conformational state in apoptosis.
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Affiliation(s)
| | - Oliver M Deacon
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Colin Macdonald
- School of Chemistry, University of East Anglia, Norwich Research Park, NR4 7TJ, UK
| | | | - Geoffrey R Moore
- School of Chemistry, University of East Anglia, Norwich Research Park, NR4 7TJ, UK
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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20
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Gunawan CA, Nam EV, Marquis CP, Gooding JJ, Thordarson P, Zhao C. Scanning Electrochemical Microscopy of Cytochrome
c
Peroxidase through the Orientation‐Controlled Immobilisation of Cytochrome
c. ChemElectroChem 2016. [DOI: 10.1002/celc.201600195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Ekaterina V. Nam
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Christopher P. Marquis
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney 2052 Australia
| | - J. Justin Gooding
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Pall Thordarson
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Chuan Zhao
- School of Chemistry The University of New South Wales Sydney 2052 Australia
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21
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Schilder J, Ubbink M. Weak self-association of cytochrome c peroxidase molecules observed by paramagnetic NMR. JOURNAL OF BIOMOLECULAR NMR 2016; 65:29-40. [PMID: 27236778 PMCID: PMC4908164 DOI: 10.1007/s10858-016-0035-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/03/2016] [Indexed: 06/05/2023]
Abstract
There is growing experimental evidence that many proteins exhibit a tendency for (ultra)weak homo- or hetero- oligomerization interactions. With the development of paramagnetic relaxation enhancement NMR spectroscopy it has become possible to characterize weak complexes experimentally and even detect complexes with affinities in the 1-25 mM range. We present evidence for a weak complex between cytochrome c peroxidase (CcP) molecules. In a previous study, we attached nitroxide based spin labels at three positions on CcP with the intent of observing intramolecular PRE effects. However, several intermolecular PRE effects were also observed suggesting a weak self-association between CcP molecules. The CcP-CcP complex was characterized using paramagnetic NMR and protein docking. The interaction occurs between the surface that is also part of the stereo-specific binding site for its physiological partner, cytochrome c (Cc), and several small, positively charged patches on the "back" of CcP. The CcP-CcP complex is not a stereo-specific complex. It is a dynamic ensemble of orientations, characteristic of an encounter state. The contact areas resemble those observed for CcP molecules in crystals. The CcP-CcP complex formation competes with that of the CcP-Cc complex. However, the affinity for Cc is much larger and thus it is expected that, under physiological conditions, auto-inhibition will be limited. A weak self-association between cytochrome c peroxidase molecules was characterized using paramagnetic NMR.
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Affiliation(s)
- Jesika Schilder
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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22
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Kathiresan M, English AM. Targeted proteomics identify metabolism-dependent interactors of yeast cytochrome c peroxidase: implications in stress response and heme trafficking. Metallomics 2016; 8:434-43. [PMID: 26980054 DOI: 10.1039/c5mt00330j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently we discovered that cytochrome c peroxidase (Ccp1) functions primarily as a mitochondrial H2O2 sensor and heme donor in yeast cells. When cells switch their metabolism from fermentation to respiration mitochondrial H2O2 levels spike, and overoxidation of its polypeptide labilizes Ccp1's heme. A large pool of heme-free Ccp1 exits the mitochondria and enters the nucleus and vacuole. To gain greater insight into the mechanisms of Ccp1's H2O2-sensing and heme-donor functions during the cell's different metabolic states, here we use glutathione-S-transferase (GST) pulldown assays, combined with 1D gel electrophoresis and mass spectrometry to probe for interactors of apo- and holoCcp1 in extracts from 1 d fermenting and 7 d stationary-phase respiring yeast. We identified Ccp1's peroxidase cosubstrate Cyc1 and 28 novel interactors of GST-apoCcp1 and GST-holoCcp1 including mitochondrial superoxide dismutase 2 (Sod2) and cytosolic Sod1, the mitochondrial transporter Pet9, the three yeast isoforms of glyceraldehyde-3-phosphate dehydrogenase (Tdh3/2/1), heat shock proteins including Hsp90 and Hsp70, and the main peroxiredoxin in yeast (Tsa1) as well as its cosubstrate, thioreoxin (Trx1). These new interactors expand the scope of Ccp1's possible roles in stress response and in heme trafficking and suggest several new lines of investigation. Furthermore, our targeted proteomics analysis underscores the limitations of large-scale interactome studies that found only 4 of the 30 Ccp1 interactors isolated here.
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Affiliation(s)
- M Kathiresan
- PROTEO and the Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St West, Montreal, Quebec, Canada H4B 1R6.
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23
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Prata JV, Barata PD. Fostering protein–calixarene interactions: from molecular recognition to sensing. RSC Adv 2016. [DOI: 10.1039/c5ra19887a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An highly selective direct sensing of cytochrome c by a bis-calix[4]arene-carbazole conjugate (CCC-1) in aqueous-based medium at nanomolar levels is disclosed. An electron transfer (ET) between complexed partners mediates the sensory event.
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Affiliation(s)
- José V. Prata
- Laboratório de Química Orgânica
- Departamento de Engenharia Química and Centro de Investigação de Engenharia Química e Biotecnologia
- Instituto Superior de Engenharia de Lisboa
- Instituto Politécnico de Lisboa
- Lisboa
| | - Patrícia D. Barata
- Laboratório de Química Orgânica
- Departamento de Engenharia Química and Centro de Investigação de Engenharia Química e Biotecnologia
- Instituto Superior de Engenharia de Lisboa
- Instituto Politécnico de Lisboa
- Lisboa
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24
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Abstract
Many biomolecular interactions proceed via lowly populated, transient intermediates. Believed to facilitate formation of a productive complex, these short-lived species are inaccessible to conventional biophysical and structural techniques and, until recently, could only be studied by theoretical simulations. Recent development of experimental approaches sensitive to the presence of minor species--in particular paramagnetic relaxation enhancement (PRE) NMR spectroscopy--has enabled direct visualization and detailed characterization of such lowly populated states. Collectively referred to as an encounter complex, the binding intermediates are particularly important in transient protein interactions, such as those orchestrating signaling cascades or energy-generating electron transfer (ET) chains. Here I discuss encounter complexes of redox proteins mediating biological ET reactions, which are essential for many vital cellular activities including oxidative phosphorylation and photosynthesis. In particular, this Account focuses on the complex of cytochrome c (Cc) and cytochrome c peroxidase (CcP), which is a paradigm of biomolecular ET and an attractive system for studying protein binding and enzymatic catalysis. The Cc-CcP complex formation proceeds via an encounter state, consisting of multiple protein-protein orientations sampled in the search of the dominant, functionally active bound form and exhibiting a broad spatial distribution, in striking agreement with earlier theoretical simulations. At low ionic strength, CcP binds another Cc molecule to form a weak ternary complex, initially inferred from kinetics experiments and postulated to account for the measured ET activity. Despite strenuous efforts, the ternary complex could not be observed directly and remained eagerly sought for the past two decades. Very recently, we have solved its structure in solution and shown that it consists of two binding forms: the dominant, ET-inactive geometry and an ensemble of lowly populated species with short separations between Cc and CcP cofactors, which summarily account for the measured ET rate. Unlike most protein complexes, which require accurate alignment of the binding surfaces in a single, well-defined orientation to carry out their function, redox proteins can form multiple productive complexes. As fast ET will occur any time the redox centers of the binding partners are close enough to ensure efficient electron tunneling across the interface, many protein-protein orientations are expected to be ET active. The present analysis confirms that the low-occupancy states can support the functional ET activity and contribute to the stability of redox protein complexes. As illustrated here, boundaries between the dominant and the encounter forms become blurred for many dynamic ET systems, which are more aptly described by ensembles of functionally and structurally heterogeneous bound forms.
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Affiliation(s)
- Alexander N. Volkov
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, and Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
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25
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Fields JB, Hollingsworth SA, Chreifi G, Heyden M, Arce AP, Magaña-Garcia HI, Poulos TL, Tobias DJ. "Bind and Crawl" Association Mechanism of Leishmania major Peroxidase and Cytochrome c Revealed by Brownian and Molecular Dynamics Simulations. Biochemistry 2015; 54:7272-82. [PMID: 26598276 DOI: 10.1021/acs.biochem.5b00569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Leishmania major, the parasitic causative agent of leishmaniasis, produces a heme peroxidase (LmP), which catalyzes the peroxidation of mitochondrial cytochrome c (LmCytc) for protection from reactive oxygen species produced by the host. The association of LmP and LmCytc, which is known from kinetics measurements to be very fast (∼10(8) M(-1) s(-1)), does not involve major conformational changes and has been suggested to be dominated by electrostatic interactions. We used Brownian dynamics simulations to investigate the mechanism of formation of the LmP-LmCytc complex. Our simulations confirm the importance of electrostatic interactions involving the negatively charged D211 residue at the LmP active site, and reveal a previously unrecognized role in complex formation for negatively charged residues in helix A of LmP. The crystal structure of the D211N mutant of LmP reported herein is essentially identical to that of wild-type LmP, reinforcing the notion that it is the loss of charge at the active site, and not a change in structure, that reduces the association rate of the D211N variant of LmP. The Brownian dynamics simulations further show that complex formation occurs via a "bind and crawl" mechanism, in which LmCytc first docks to a location on helix A that is far from the active site, forming an initial encounter complex, and then moves along helix A to the active site. An atomistic molecular dynamics simulation confirms the helix A binding site, and steady state activity assays and stopped-flow kinetics measurements confirm the role of helix A charges in the association mechanism.
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Affiliation(s)
- James B Fields
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Scott A Hollingsworth
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Georges Chreifi
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Matthias Heyden
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Anton P Arce
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Hugo I Magaña-Garcia
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Thomas L Poulos
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Douglas J Tobias
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
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26
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De March M, Brancatelli G, Demitri N, De Zorzi R, Hickey N, Geremia S. A general exit strategy of monoheme cytochromes c and c2 in electron transfer complexes? IUBMB Life 2015; 67:694-700. [PMID: 26311433 DOI: 10.1002/iub.1410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/28/2015] [Indexed: 11/06/2022]
Abstract
Using our previously reported maps of the electrostatic surface of horse heart ferri- and ferro-cyt c, comparisons were made between the complementary electrostatic surfaces of three cyt c peroxidase-cyt c complexes and the photosynthetic reaction center-cyt c complex, considering both iron oxidation states. The results obtained were consistent with a sliding mechanism for the electron shuttle on the surface of the protein complexes, promoted by the change in iron oxidation state. This mechanism was found to be in agreement with theoretical and NMR studies reported in the literature. Importantly, the analysis also provided a rationale for recognition of nonproductive associations. As we have previously reported the same conclusion on examination of redox partners of cyt c in the mitochondrial respiratory pathway, our hypothesis is that the proposed mechanism could represent a general exit strategy of monoheme cyts c and c2 in electron transfer complexes.
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Affiliation(s)
- Matteo De March
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Giovanna Brancatelli
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Nicola Demitri
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Neal Hickey
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
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27
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Fischer M, Shoichet BK, Fraser JS. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem 2015; 16:1560-4. [PMID: 26032594 PMCID: PMC4539595 DOI: 10.1002/cbic.201500196] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/08/2022]
Abstract
Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiation damage. However, it might also perturb protein conformations that can be accessed at room temperature. Using data from crystals measured consecutively at room temperature and at cryogenic temperature, we found that transient binding sites could be abolished at the cryogenic temperatures employed by standard approaches. Changing the temperature at which the crystallographic data was collected could provide a deliberate perturbation to the equilibrium of protein conformations and help to visualize hidden sites with great potential to allosterically modulate protein function.
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Affiliation(s)
- Marcus Fischer
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., Byers Hall, BH-501, Box 2550, San Francisco, CA 94158 (USA)
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., Byers Hall, BH-501, Box 2550, San Francisco, CA 94158 (USA)
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 600 16th St., Genentech Hall, S472E, Box 2240, San Francisco, CA 94158 (USA).
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28
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Chreifi G, Hollingsworth SA, Li H, Tripathi S, Arce AP, Magaña-Garcia HI, Poulos TL. Enzymatic Mechanism of Leishmania major Peroxidase and the Critical Role of Specific Ionic Interactions. Biochemistry 2015; 54:3328-36. [PMID: 25941976 DOI: 10.1021/acs.biochem.5b00338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leishmania major peroxidase (LmP) is very similar to the well-known yeast cytochrome c peroxidase (CcP). Both enzymes catalyze the peroxidation of cytochrome c. Like CcP, LmP reacts with H2O2 to form Compound I, which consists of a ferryl heme and a Trp radical, Fe(IV)═O;Trp(•+). Cytochrome c (Cytc) reduces the Trp radical to give Compound II, Fe(IV)═O;Trp, which is followed by an intramolecular electron transfer to give Fe(III)-OH;Trp(•+), and in the last step, Cytc reduces the Trp radical. In this study, we have used steady-state and single-turnover kinetics to improve our understanding of the overall mechanism of LmP catalysis. While the activity of CcP greatly increases with ionic strength, the kcat for LmP remains relatively constant at all ionic strengths tested. Therefore, unlike CcP, where dissociation of oxidized Cytc is limiting at low ionic strengths, association/dissociation reactions are not limiting at any ionic strength in LmP. We conclude that in LmP, the intramolecular electron transfer reaction, Fe(IV)═O;Trp to Fe(III)-OH;Trp(•+), is limiting at all ionic strengths. Unlike CcP, LmP depends on key intermolecular ion pairs to form the electron transfer competent complex. Mutating these sites causes the initial rate of association to decrease by 2 orders of magnitude and a substantial decrease in kcat. The drop in kcat is due to a switch in the rate-limiting step of the mutants from intramolecular electron transfer to the rate of association in forming the LmP-LmCytc complex. These studies show that while LmP and CcP form very similar complexes and exhibit similar activities, they substantially differ in how their activity changes as a function of ionic strength. This difference is primarily due to the heavy reliance of LmP on highly specific intermolecular ion pairs, while CcP relies mainly on nonpolar interactions.
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Affiliation(s)
- Georges Chreifi
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Scott A Hollingsworth
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Huiying Li
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Sarvind Tripathi
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Anton P Arce
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Hugo I Magaña-Garcia
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
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29
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The low-affinity complex of cytochrome c and its peroxidase. Nat Commun 2015; 6:7073. [PMID: 25944250 PMCID: PMC4432590 DOI: 10.1038/ncomms8073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/30/2015] [Indexed: 01/07/2023] Open
Abstract
The complex of yeast cytochrome c peroxidase and cytochrome c is a paradigm of the biological electron transfer (ET). Building on seven decades of research, two different models have been proposed to explain its functional redox activity. One postulates that the intermolecular ET occurs only in the dominant, high-affinity protein–protein orientation, while the other posits formation of an additional, low-affinity complex, which is much more active than the dominant one. Unlike the high-affinity interaction—extensively studied by X-ray crystallography and NMR spectroscopy—until now the binding of cytochrome c to the low-affinity site has not been observed directly, but inferred mainly from kinetics experiments. Here we report the structure of this elusive, weak protein complex and show that it consists of a dominant, inactive bound species and an ensemble of minor, ET-competent protein–protein orientations, which summarily account for the experimentally determined value of the ET rate constant. The redox activity of cytochrome c in complex with its peroxidase has been rationalized by two possible models; a readily observable high-affinity complex and a more elusive but potentially more active low-affinity complex. Here, the authors provide an NMR-based structural mapping of this low-affinity complex.
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30
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Winter DL, Abeygunawardena D, Hart-Smith G, Erce MA, Wilkins MR. Lysine methylation modulates the protein-protein interactions of yeast cytochrome C Cyc1p. Proteomics 2015; 15:2166-76. [PMID: 25755154 DOI: 10.1002/pmic.201400521] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/02/2015] [Accepted: 03/02/2015] [Indexed: 12/21/2022]
Abstract
In recent years, protein methylation has been established as a major intracellular PTM. It has also been proposed to modulate protein-protein interactions (PPIs) in the interactome. To investigate the effect of PTMs on PPIs, we recently developed the conditional two-hybrid (C2H) system. With this, we demonstrated that arginine methylation can modulate PPIs in the yeast interactome. Here, we used the C2H system to investigate the effect of lysine methylation. Specifically, we asked whether Ctm1p-mediated trimethylation of yeast cytochrome c Cyc1p, on lysine 78, modulates its interactions with Erv1p, Ccp1p, Cyc2p and Cyc3p. We show that the interactions between Cyc1p and Erv1p, and between Cyc1p and Cyc3p, are significantly increased upon trimethylation of lysine 78. This increase of interaction helps explain the reported facilitation of Cyc1p import into the mitochondrial intermembrane space upon methylation. This first application of the C2H system to the study of methyllysine-modulated interactions further confirms its robustness and flexibility.
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Affiliation(s)
- Daniel L Winter
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dhanushi Abeygunawardena
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Gene Hart-Smith
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Melissa A Erce
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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31
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Page TR, Hoffman BM. Control of cyclic photoinitiated electron transfer between cytochrome c peroxidase (W191F) and cytochrome c by formation of dynamic binary and ternary complexes. Biochemistry 2015; 54:1188-97. [PMID: 25629200 DOI: 10.1021/bi500888y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Extensive studies of the physiological protein-protein electron-transfer (ET) complex between yeast cytochrome c peroxidase (CcP) and cytochrome c (Cc) have left unresolved questions about how formation and dissociation of binary and ternary complexes influence ET. We probe this issue through a study of the photocycle of ET between Zn-protoporphyrin IX-substituted CcP(W191F) (ZnPCcP) and Cc. Photoexcitation of ZnPCcP in complex with Fe(3+)Cc initiates the photocycle: charge-separation ET, [(3)ZnPCcP, Fe(3+)Cc] → [ZnP(+)CcP, Fe(2+)Cc], followed by charge recombination, [ZnP(+)CcP, Fe(2+)Cc] → [ZnPCcP, Fe(3+)Cc]. The W191F mutation eliminates fast hole hopping through W191, enhancing accumulation of the charge-separated intermediate and extending the time scale for binding and dissociation of the charge-separated complex. Both triplet quenching and the charge-separated intermediate were monitored during titrations of ZnPCcP with Fe(3+)Cc, Fe(2+)Cc, and redox-inert CuCc. The results require a photocycle that includes dissociation and/or recombination of the charge-separated binary complex and a charge-separated ternary complex, [ZnP(+)CcP, Fe(2+)Cc, Fe(3+)Cc]. The expanded kinetic scheme formalizes earlier proposals of "substrate-assisted product dissociation" within the photocycle. The measurements yield the thermodynamic affinity constants for binding the first and second Cc: KI = 10(-7) M(-1), and KII = 10(-4) M(-1). However, two-site analysis of the thermodynamics of formation of the ternary complex reveals that Cc binds at the weaker-binding site with much greater affinity than previously recognized and places upper bounds on the contributions of repulsion between the two Cc's of the ternary complex. In conjunction with recent nuclear magnetic resonance studies, the analysis further suggests a dynamic view of the ternary complex, wherein neither Cc necessarily faithfully adopts the crystal-structure configuration because of Cc-Cc repulsion.
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Affiliation(s)
- Taylor R Page
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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32
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Respiration triggers heme transfer from cytochrome c peroxidase to catalase in yeast mitochondria. Proc Natl Acad Sci U S A 2014; 111:17468-73. [PMID: 25422453 DOI: 10.1073/pnas.1409692111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In exponentially growing yeast, the heme enzyme, cytochrome c peroxidase (Ccp1) is targeted to the mitochondrial intermembrane space. When the fermentable source (glucose) is depleted, cells switch to respiration and mitochondrial H2O2 levels rise. It has long been assumed that CCP activity detoxifies mitochondrial H2O2 because of the efficiency of this activity in vitro. However, we find that a large pool of Ccp1 exits the mitochondria of respiring cells. We detect no extramitochondrial CCP activity because Ccp1 crosses the outer mitochondrial membrane as the heme-free protein. In parallel with apoCcp1 export, cells exhibit increased activity of catalase A (Cta1), the mitochondrial and peroxisomal catalase isoform in yeast. This identifies Cta1 as a likely recipient of Ccp1 heme, which is supported by low Cta1 activity in ccp1Δ cells and the accumulation of holoCcp1 in cta1Δ mitochondria. We hypothesized that Ccp1's heme is labilized by hyperoxidation of the protein during the burst in H2O2 production as cells begin to respire. To test this hypothesis, recombinant Ccp1 was hyperoxidized with excess H2O2 in vitro, which accelerated heme transfer to apomyoglobin added as a surrogate heme acceptor. Furthermore, the proximal heme Fe ligand, His175, was found to be ∼ 85% oxidized to oxo-histidine in extramitochondrial Ccp1 isolated from 7-d cells, indicating that heme labilization results from oxidation of this ligand. We conclude that Ccp1 responds to respiration-derived H2O2 via a previously unidentified mechanism involving H2O2-activated heme transfer to apoCta1. Subsequently, the catalase activity of Cta1, not CCP activity, contributes to mitochondrial H2O2 detoxification.
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Sterckx YGJ, Volkov AN. Cofactor-Dependent Structural and Binding Properties of Yeast Cytochrome c Peroxidase. Biochemistry 2014; 53:4526-36. [DOI: 10.1021/bi500603w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yann G. J. Sterckx
- Research
Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Jean
Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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34
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Miner KD, Pfister TD, Hosseinzadeh P, Karaduman N, Donald LJ, Loewen PC, Lu Y, Ivancich A. Identifying the elusive sites of tyrosyl radicals in cytochrome c peroxidase: implications for oxidation of substrates bound at a site remote from the heme. Biochemistry 2014; 53:3781-9. [PMID: 24901481 PMCID: PMC4063442 DOI: 10.1021/bi500353p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The location of the Trp radical and the catalytic function of the [Fe(IV)═O Trp₁₉₁(•+)] intermediate in cytochrome c peroxidase (CcP) are well-established; however, the unambiguous identification of the site(s) for the formation of tyrosyl radical(s) and their possible biological roles remain elusive. We have now performed a systematic investigation of the location and reactivity of the Tyr radical(s) using multifrequency Electron Paramagnetic Resonance (EPR) spectroscopy combined with multiple-site Trp/Tyr mutations in CcP. Two tyrosines, Tyr71 and Tyr236, were identified as those contributing primarily to the EPR spectrum of the tyrosyl radical, recorded at 9 and 285 GHz. The EPR characterization also showed that the heme distal-side Trp51 is involved in the intramolecular electron transfer between Tyr71 and the heme and that formation of Tyr₇₁(•) and Tyr₂₃₆(•) is independent of the [Fe(IV)═O Trp₁₉₁(•+)] intermediate. Tyr71 is located in an optimal position to mediate the oxidation of substrates binding at a site, more than 20 Å from the heme, which has been reported recently in the crystal structures of CcP with bound guaicol and phenol [Murphy, E. J., et al. (2012) FEBS J. 279, 1632-1639]. The possibility of discriminating the radical intermediates by their EPR spectra allowed us to identify Tyr₇₁(•) as the reactive species with the guaiacol substrate. Our assignment of the surface-exposed Tyr236 as the other radical site agrees well with previous studies based on MNP labeling and protein cross-linking [Tsaprailis, G., and English, A. M. (2003) JBIC, J. Biol. Inorg. Chem. 8, 248-255] and on its covalent modification upon reaction of W191G CcP with 2-aminotriazole [Musah, R. A., and Goodin, D. B. (1997) Biochemistry 36, 11665-11674]. Accordingly, while Tyr71 acts as a true reactive intermediate for the oxidation of certain small substrates that bind at a site remote from the heme, the surface-exposed Tyr236 would be more likely related to oxidative stress signaling, as previously proposed. Our findings reinforce the view that CcP is the monofunctional peroxidase that most closely resembles its ancestor enzymes, the catalase-peroxidases, in terms of the higher complexity of the peroxidase reaction [Colin, J., et al. (2009) J. Am. Chem. Soc. 131, 8557-8563]. The strategy used to identify the elusive Tyr radical sites in CcP may be applied to other heme enzymes containing a large number of Tyr and Trp residues and for which Tyr (or Trp) radicals have been proposed to be involved in their peroxidase or peroxidase-like reaction.
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Affiliation(s)
- Kyle D Miner
- CNRS, Unité de Recherche Mixte CNRS/CEA/Université Paris-Sud (UMR 8221), Laboratoire de Bioénergétique, Métalloprotéines et Stress. Centre d'Etudes de Saclay, iBiTec-S, 91191 Gif-sur-Yvette, France
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35
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Schilder J, Löhr F, Schwalbe H, Ubbink M. The cytochrome c peroxidase and cytochrome c encounter complex: the other side of the story. FEBS Lett 2014; 588:1873-8. [PMID: 24726731 DOI: 10.1016/j.febslet.2014.03.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/18/2014] [Accepted: 03/26/2014] [Indexed: 11/18/2022]
Abstract
Formation of an encounter complex is important for efficient protein complex formation. The encounter state consists of an ensemble of orientations of two proteins in the complex. Experimental description of such ensembles inherently suffers from insufficient data availability. We have measured paramagnetic relaxation enhancements (PRE) on cytochrome c peroxidase (CcP) caused by its partner cytochrome c (Cc) carrying a spin label. The data complement earlier PRE data of spin labelled CcP, identifying several new interactions. This work demonstrates the need of obtaining as many independent data sets as possible to achieve the most accurate description of an encounter complex.
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Affiliation(s)
- Jesika Schilder
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Frank Löhr
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Centre for Biomolecular Magnetic Resonance, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular Magnetic Resonance, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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36
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Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California Irvine, Irvine, California 92697-3900
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37
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The transcription factor BcLTF1 regulates virulence and light responses in the necrotrophic plant pathogen Botrytis cinerea. PLoS Genet 2014; 10:e1004040. [PMID: 24415947 PMCID: PMC3886904 DOI: 10.1371/journal.pgen.1004040] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/01/2013] [Indexed: 01/16/2023] Open
Abstract
Botrytis cinerea is the causal agent of gray mold diseases in a range of dicotyledonous plant species. The fungus can reproduce asexually by forming macroconidia for dispersal and sclerotia for survival; the latter also participate in sexual reproduction by bearing the apothecia after fertilization by microconidia. Light induces the differentiation of conidia and apothecia, while sclerotia are exclusively formed in the absence of light. The relevance of light for virulence of the fungus is not obvious, but infections are observed under natural illumination as well as in constant darkness. By a random mutagenesis approach, we identified a novel virulence-related gene encoding a GATA transcription factor (BcLTF1 for light-responsive TF1) with characterized homologues in Aspergillus nidulans (NsdD) and Neurospora crassa (SUB-1). By deletion and over-expression of bcltf1, we confirmed the predicted role of the transcription factor in virulence, and discovered furthermore its functions in regulation of light-dependent differentiation, the equilibrium between production and scavenging of reactive oxygen species (ROS), and secondary metabolism. Microarray analyses revealed 293 light-responsive genes, and that the expression levels of the majority of these genes (66%) are modulated by BcLTF1. In addition, the deletion of bcltf1 affects the expression of 1,539 genes irrespective of the light conditions, including the overexpression of known and so far uncharacterized secondary metabolism-related genes. Increased expression of genes encoding alternative respiration enzymes, such as the alternative oxidase (AOX), suggest a mitochondrial dysfunction in the absence of bcltf1. The hypersensitivity of Δbctlf1 mutants to exogenously applied oxidative stress - even in the absence of light - and the restoration of virulence and growth rates in continuous light by antioxidants, indicate that BcLTF1 is required to cope with oxidative stress that is caused either by exposure to light or arising during host infection. Both fungal pathogens and their host plants respond to light, which represents an important environmental cue. Unlike plants using light for energy generation, filamentous fungi use light, or its absence, as a general signal for orientation (night/day, underground/on the surface). Therefore, dependent on the ecological niche of the fungus, light may control the development of reproductive structures (photomorphogenesis), the dispersal of propagules (phototropism of reproductive structures) and the circadian rhythm. As in other organisms, fungi have to protect themselves against the detrimental effects of light, i.e. the damage to macromolecules by emerging singlet oxygen. Adaptive responses are the accumulation of pigments, especially in the reproductive and survival structures such as spores, sclerotia and fruiting bodies. Light is sensed by fungal photoreceptors leading to quick responses on the transcriptional level, and is furthermore considered to result in the accumulation of reactive oxygen species (ROS). In this study, we provide evidence that an unbalanced ROS homoeostasis (generation outweighs detoxification) caused by the deletion of the light-responsive transcription factor BcLTF1 impairs the ability of the necrotrophic pathogen Botrytis cinerea to grow in the presence of additional oxidative stress arising during illumination or during infection of the host.
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38
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Van de Water K, van Nuland NAJ, Volkov AN. Transient protein encounters characterized by paramagnetic NMR. Chem Sci 2014. [DOI: 10.1039/c4sc01232a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multiple encounters, sampled by interacting proteins in search of the dominant, functionally active orientation, are visualized by paramagnetic NMR.
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Affiliation(s)
- K. Van de Water
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
| | - N. A. J. van Nuland
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
| | - A. N. Volkov
- Jean Jeener NMR Centre
- Structural Biology Brussels
- Vrije Universiteit Brussel
- 1050 Brussels, Belgium
- Molecular Recognition Unit
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39
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Höhner R, Barth J, Magneschi L, Jaeger D, Niehues A, Bald T, Grossman A, Fufezan C, Hippler M. The metabolic status drives acclimation of iron deficiency responses in Chlamydomonas reinhardtii as revealed by proteomics based hierarchical clustering and reverse genetics. Mol Cell Proteomics 2013; 12:2774-90. [PMID: 23820728 PMCID: PMC3790290 DOI: 10.1074/mcp.m113.029991] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/04/2013] [Indexed: 11/06/2022] Open
Abstract
Iron is a crucial cofactor in numerous redox-active proteins operating in bioenergetic pathways including respiration and photosynthesis. Cellular iron management is essential to sustain sufficient energy production and minimize oxidative stress. To produce energy for cell growth, the green alga Chlamydomonas reinhardtii possesses the metabolic flexibility to use light and/or carbon sources such as acetate. To investigate the interplay between the iron-deficiency response and growth requirements under distinct trophic conditions, we took a quantitative proteomics approach coupled to innovative hierarchical clustering using different "distance-linkage combinations" and random noise injection. Protein co-expression analyses of the combined data sets revealed insights into cellular responses governing acclimation to iron deprivation and regulation associated with photosynthesis dependent growth. Photoautotrophic growth requirements as well as the iron deficiency induced specific metabolic enzymes and stress related proteins, and yet differences in the set of induced enzymes, proteases, and redox-related polypeptides were evident, implying the establishment of distinct response networks under the different conditions. Moreover, our data clearly support the notion that the iron deficiency response includes a hierarchy for iron allocation within organelles in C. reinhardtii. Importantly, deletion of a bifunctional alcohol and acetaldehyde dehydrogenase (ADH1), which is induced under low iron based on the proteomic data, attenuates the remodeling of the photosynthetic machinery in response to iron deficiency, and at the same time stimulates expression of stress-related proteins such as NDA2, LHCSR3, and PGRL1. This finding provides evidence that the coordinated regulation of bioenergetics pathways and iron deficiency response is sensitive to the cellular and chloroplast metabolic and/or redox status, consistent with systems approach data.
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Affiliation(s)
- Ricarda Höhner
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
| | - Johannes Barth
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
| | - Leonardo Magneschi
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
| | - Daniel Jaeger
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
| | - Anna Niehues
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
| | - Till Bald
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
| | - Arthur Grossman
- §Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Christian Fufezan
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
| | - Michael Hippler
- From the ‡Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany
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40
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Capdevila DA, Marmisollé WA, Williams FJ, Murgida DH. Phosphate mediated adsorption and electron transfer of cytochrome c. A time-resolved SERR spectroelectrochemical study. Phys Chem Chem Phys 2013; 15:5386-94. [PMID: 23000972 DOI: 10.1039/c2cp42044a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of proteins immobilized on biomimetic or biocompatible electrodes represents an active field of research as it pursues both fundamental and technological interests. In this context, adsorption and redox properties of cytochrome c (Cyt) on different electrode surfaces have been extensively reported, although in some cases with contradictory results. Here we report a SERR spectroelectrochemical study of the adsorption and electron transfer behaviour of the basic protein Cyt on electrodes coated with amino-terminated monolayers. The obtained results show that inorganic phosphate (Pi) and ATP anions are able to mediate high affinity binding of the protein with preservation of the native structure and rendering an average orientation that guarantees efficient pathways for direct electron transfer. These findings aid the design of Cyt-based bioelectronic devices and understanding the modulation by Pi and ATP of physiological functions of Cyt.
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Affiliation(s)
- Daiana A Capdevila
- Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
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41
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Jiang N, Kuznetsov A, Nocek JM, Hoffman BM, Crane BR, Hu X, Beratan DN. Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies. J Phys Chem B 2013; 117:9129-41. [PMID: 23895339 PMCID: PMC3809023 DOI: 10.1021/jp401551t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and in complexes with four mutants of the Cc protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:Cc interface for the F82Y(I) mutants compared to that the WT and F82S(W) complexes are predicted to change the reorganization energies for the CcP:Cc ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor-acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, Duke University, Durham, NC 27708
| | | | - Judith M. Nocek
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, NC 27708
- Department of Biochemistry, Duke University, Durham, NC 27708
- Department of Physics, Duke University, Durham, NC 27708
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Volkov AN, van Nuland NAJ. Solution NMR study of the yeast cytochrome c peroxidase: cytochrome c interaction. JOURNAL OF BIOMOLECULAR NMR 2013; 56:255-263. [PMID: 23708935 DOI: 10.1007/s10858-013-9744-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 06/02/2023]
Abstract
Here we present a solution NMR study of the complex between yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP), a paradigm for understanding the biological electron transfer. Performed for the first time, the CcP-observed heteronuclear NMR experiments were used to probe the Cc binding in solution. Combining the Cc- and CcP-detected experiments, the binding interface on both proteins was mapped out, confirming that the X-ray structure of the complex is maintained in solution. Using NMR titrations and chemical shift perturbation analysis, we show that the interaction is independent of the CcP spin-state and is only weakly affected by the Cc redox state. Based on these findings, we argue that the complex of the ferrous Cc and the cyanide-bound CcP is a good mimic of the catalytically-active Cc-CcP compound I species. Finally, no chemical shift perturbations due to the Cc binding at the low-affinity CcP site were observed at low ionic strength. We discuss possible reasons for the absence of the effects and outline future research directions.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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43
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Lian LY. NMR studies of weak protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:59-72. [PMID: 23611315 DOI: 10.1016/j.pnmrs.2012.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Accepted: 11/22/2012] [Indexed: 06/02/2023]
Affiliation(s)
- Lu-Yun Lian
- NMR Centre for Structural Biology, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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44
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Volkov AN, Wohlkonig A, Soror SH, van Nuland NAJ. Expression, Purification, Characterization, and Solution Nuclear Magnetic Resonance Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility. Biochemistry 2013; 52:2165-75. [DOI: 10.1021/bi400220w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander N. Volkov
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Molecular Recognition Unit,
Department of Structural Biology, VIB,
Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexandre Wohlkonig
- JAST lab, Department of Structural
Biology, VIB, Pleinlaan 2, 1050 Brussels,
Belgium
| | - Sameh H. Soror
- JAST lab, Department of Structural
Biology, VIB, Pleinlaan 2, 1050 Brussels,
Belgium
- Department of Biochemistry
and
Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Nico A. J. van Nuland
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Molecular Recognition Unit,
Department of Structural Biology, VIB,
Pleinlaan 2, 1050 Brussels, Belgium
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45
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Carvalho M, Martins I, Medeiros J, Tavares S, Planchon S, Renaut J, Núñez O, Gallart-Ayala H, Galceran M, Hursthouse A, Silva Pereira C. The response of Mucor plumbeus to pentachlorophenol: A toxicoproteomics study. J Proteomics 2013. [DOI: 10.1016/j.jprot.2012.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Volkov AN, van Nuland NAJ. Electron transfer interactome of cytochrome C. PLoS Comput Biol 2012; 8:e1002807. [PMID: 23236271 PMCID: PMC3516563 DOI: 10.1371/journal.pcbi.1002807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/12/2012] [Indexed: 01/31/2023] Open
Abstract
Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility. A number of vital cellular processes such as respiration, photosynthesis, and multifarious metabolic conversions rely on a long-range electron transfer (ET) among protein molecules. Full understanding of the biological ET requires accurate description of the redox protein complexes, which is hampered by their pronounced mobility and short lifetimes. Here we used a simple computational approach to predict the ET properties of the physiological protein complexes of cytochrome c (Cc) – a small electron carrier that coordinates the electron flow among different redox partners. By performing extensive conformational sampling of the possible binding geometries, we mapped out functional epitopes in the Cc complexes and assessed their ET properties. Our study suggests that protein dynamics within redox complexes is the rate-limiting step in the intermolecular ET and indicates that the functional epitope size correlates with the extent of dynamics in the Cc complexes. We believe that the latter finding can be used as a diagnostic tool for protein mobility and expect that this work will engender future studies of the intermolecular ET in biological networks.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Belgium.
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47
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Crystal structure of the Leishmania major peroxidase-cytochrome c complex. Proc Natl Acad Sci U S A 2012; 109:18390-4. [PMID: 23100535 DOI: 10.1073/pnas.1213295109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The causative agent of leishmaniasis is the protozoan parasite Leishmania major. Part of the host protective mechanism is the production of reactive oxygen species including hydrogen peroxide. In response, L. major produces a peroxidase, L. major peroxidase (LmP), that helps to protect the parasite from oxidative stress. LmP is a heme peroxidase that catalyzes the peroxidation of mitochondrial cytochrome c. We have determined the crystal structure of LmP in a complex with its substrate, L. major cytochrome c (LmCytc) to 1.84 Å, and compared the structure to its close homolog, the yeast cytochrome c peroxidase-cytochrome c complex. The binding interface between LmP and LmCytc has one strong and one weak ionic interaction that the yeast system lacks. The differences between the steady-state kinetics correlate well with the Lm redox pair being more dependent on ionic interactions, whereas the yeast redox pair depends more on nonpolar interactions. Mutagenesis studies confirm that the ion pairs at the intermolecular interface are important to both k(cat) and K(M). Despite these differences, the electron transfer path, with respect to the distance between hemes, along the polypeptide chain is exactly the same in both redox systems. A potentially important difference, however, is the side chains involved. LmP has more polar groups (Asp and His) along the pathway compared with the nonpolar groups (Leu and Ala) in the yeast system, and as a result, the electrostatic environment along the presumed electron transfer path is substantially different.
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48
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Jasion VS, Poulos TL. Leishmania major peroxidase is a cytochrome c peroxidase. Biochemistry 2012; 51:2453-60. [PMID: 22372542 DOI: 10.1021/bi300169x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Leishmania major peroxidase (LmP) exhibits both ascorbate and cytochrome c peroxidase activities. Our previous results illustrated that LmP has a much higher activity against horse heart cytochrome c than ascorbate, suggesting that cytochrome c may be the biologically important substrate. To elucidate the biological function of LmP, we have recombinantly expressed, purified, and determined the 2.08 Å crystal structure of L. major cytochrome c (LmCytc). Like other types of cytochrome c, LmCytc has an electropositive surface surrounding the exposed heme edge that serves as the site of docking with redox partners. Kinetic assays performed with LmCytc and LmP show that LmCytc is a much better substrate for LmP than horse heart cytochrome c. Furthermore, unlike the well-studied yeast system, the reaction follows classic Michaelis-Menten kinetics and is sensitive to an increasing ionic strength. Using the yeast cocrystal as a control, protein-protein docking was performed using Rosetta to develop a model for the binding of LmP and LmCytc. These results suggest that the biological function of LmP is to act as a cytochrome c peroxidase.
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Affiliation(s)
- Victoria S Jasion
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
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49
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Cytochrome c signalosome in mitochondria. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1301-15. [DOI: 10.1007/s00249-011-0774-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/12/2011] [Accepted: 10/21/2011] [Indexed: 10/15/2022]
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