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Chertkova RV, Oleynikov IP, Pakhomov AA, Sudakov RV, Orlov VN, Semenova MA, Arutyunyan AM, Ptushenko VV, Kirpichnikov MP, Dolgikh DA, Vygodina TV. Mutant Cytochrome C as a Potential Detector of Superoxide Generation: Effect of Mutations on the Function and Properties. Cells 2023; 12:2316. [PMID: 37759538 PMCID: PMC10528150 DOI: 10.3390/cells12182316] [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: 08/03/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Cytochrome c (CytC) is a single-electron carrier between complex bc1 and cytochrome c-oxidase (CcO) in the electron transport chain (ETC). It is also known as a good radical scavenger but its participation in electron flow through the ETC makes it impossible to use CytC as a radical sensor. To solve this problem, a series of mutants were constructed with substitutions of Lys residues in the universal binding site (UBS) which interact electrostatically with negatively charged Asp and Glu residues at the binding sites of CytC partners, bc1 complex and CcO. The aim of this study was to select a mutant that had lost its function as an electron carrier in the ETC, retaining the structure and ability to quench radicals. It was shown that a mutant CytC with substitutions of five (8Mut) and four (5Mut) Lys residues in the UBS was almost inactive toward CcO. However, all mutant proteins kept their antioxidant activity sufficiently with respect to the superoxide radical. Mutations shifted the dipole moment of the CytC molecule due to seriously changed electrostatics on the surface of the protein. In addition, a decrease in the redox potential of the protein as revealed by the redox titrations of 8Mut was detected. Nevertheless, the CD spectrum and dynamic light scattering suggested no significant changes in the secondary structure or aggregation of the molecules of CytC 8Mut. Thus, a variant 8Mut with multiple mutations in the UBS which lost its ability to electron transfer and saved most of its physico-chemical properties can be effectively used as a detector of superoxide generation both in mitochondria and in other systems.
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Affiliation(s)
- Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Ilya P. Oleynikov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Alexey A. Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Roman V. Sudakov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Victor N. Orlov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Marina A. Semenova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Alexander M. Arutyunyan
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
| | - Vasily V. Ptushenko
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, 119334 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, M.V. Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.P.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, M.V. Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Tatiana V. Vygodina
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gory 1, Bld. 40, 119992 Moscow, Russia; (I.P.O.); (R.V.S.); (V.N.O.); (A.M.A.); (T.V.V.)
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2
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Samsri S, Pornsuwan S. Influence of cysteine-directed mutations at the Ω-loops on peroxidase activity of human cytochrome c. Arch Biochem Biophys 2021; 709:108980. [PMID: 34224685 DOI: 10.1016/j.abb.2021.108980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/19/2022]
Abstract
Cytochrome c (Cytc) is a multifunctional protein associated with electron shuttling in the inner membrane of mitochondria and also involving in the apoptotic pathway. It has been identified that mutations located in the flexible central 40-57 Ω-loop including the naturally occurring G41S, Y48H, and A51V mutants, which are found in patients with thrombocytopenia 4, a platelet disorder, alter the structural properties of human Cytc (hCytc) that associated to enhanced peroxidase activity. In this work we compared the cysteine-directed mutants of hCytc located in three different parts of Ω-loops, i.e., T28C and G34C (proximal Ω-loop), and A50C (central Ω-loop), with respect to the wild-type (WT) hCytc. The mutants and WT hCytc were structurally characterized by circular dichroism, heating and chemical denaturations, and fluorescence spectroscopy. The flexibility at the cysteine mutated sites was directly determined by site-directed spin-labeling Electron Spin Resonance. Alkaline transitions were determined by pH titration and the alkaline conformers were related to peroxidase activity of all hCytc proteins. Structural and dynamic characterizations were rationally correlated to the modulation of peroxidase activity in these mutants in comparison to the WT hCytc. We found that the cysteine mutations at residues T28 and G34, both located in the same region of Ω-loop, developed different conformations and dynamical properties that lead to different effects on the rates of peroxidase activity (G34C was ~2.6 folds higher), whereas the rate of G34C was closer to that of A50C mutant. The results implied that the flexibility and local structures of the proximal Ω-loop could also play an important role in modulating the peroxidase activity which can be associated to apoptosis.
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Affiliation(s)
- Sasiprapa Samsri
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Soraya Pornsuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
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3
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Dulchavsky M, Clark CT, Bardwell JCA, Stull F. A cytochrome c is the natural electron acceptor for nicotine oxidoreductase. Nat Chem Biol 2021; 17:344-350. [PMID: 33432238 PMCID: PMC7904663 DOI: 10.1038/s41589-020-00712-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 01/28/2023]
Abstract
Nicotine oxidoreductase (NicA2), a member of the flavin-containing amine oxidase family, is of medical relevance as it shows potential as a therapeutic to aid cessation of smoking due to its ability to oxidize nicotine into a non-psychoactive metabolite. However, the use of NicA2 in this capacity is stymied by its dismal O2-dependent activity. Unlike other enzymes in the amine oxidase family, NicA2 reacts very slowly with O2, severely limiting its nicotine-degrading activity. Instead of using O2 as an oxidant, we discovered that NicA2 donates electrons to a cytochrome c, which means that NicA2 is actually a dehydrogenase. This is surprising, as enzymes of the flavin-containing amine oxidase family were invariably thought to use O2 as an electron acceptor. Our findings establish new perspectives for engineering this potentially useful therapeutic and prompt a reconsideration of the term 'oxidase' in referring to members of the flavin-containing amine 'oxidase' family.
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Affiliation(s)
- Mark Dulchavsky
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | | | - James C. A. Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA., or
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA., or
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4
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Osmotic pressure effects identify dehydration upon cytochrome c-cytochrome c oxidase complex formation contributing to a specific electron pathway formation. Biochem J 2020; 477:1565-1578. [PMID: 32250438 DOI: 10.1042/bcj20200023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 01/18/2023]
Abstract
In the electron transfer (ET) reaction from cytochrome c (Cyt c) to cytochrome c oxidase (CcO), we determined the number and sites of the hydration water released from the protein surface upon the formation of the ET complex by evaluating the osmotic pressure dependence of kinetics for the ET from Cyt c to CcO. We identified that ∼20 water molecules were dehydrated in complex formation under turnover conditions, and systematic Cyt c mutations in the interaction site for CcO revealed that nearly half of the released hydration water during the complexation were located around Ile81, one of the hydrophobic amino acid residues near the exposed heme periphery of Cyt c. Such a dehydration dominantly compensates for the entropy decrease due to the association of Cyt c with CcO, resulting in the entropy-driven ET reaction. The energetic analysis of the interprotein interactions in the ET complex predicted by the docking simulation suggested the formation of hydrophobic interaction sites surrounding the exposed heme periphery of Cyt c in the Cyt c-CcO interface (a 'molecular breakwater'). Such sites would contribute to the formation of the hydrophobic ET pathway from Cyt c to CcO by blocking water access from the bulk water phase.
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5
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Guerra-Castellano A, Márquez I, Pérez-Mejías G, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-Translational Modifications of Cytochrome c in Cell Life and Disease. Int J Mol Sci 2020; 21:E8483. [PMID: 33187249 PMCID: PMC7697256 DOI: 10.3390/ijms21228483] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are the powerhouses of the cell, whilst their malfunction is related to several human pathologies, including neurodegenerative diseases, cardiovascular diseases, and various types of cancer. In mitochondrial metabolism, cytochrome c is a small soluble heme protein that acts as an essential redox carrier in the respiratory electron transport chain. However, cytochrome c is likewise an essential protein in the cytoplasm acting as an activator of programmed cell death. Such a dual role of cytochrome c in cell life and death is indeed fine-regulated by a wide variety of protein post-translational modifications. In this work, we show how these modifications can alter cytochrome c structure and functionality, thus emerging as a control mechanism of cell metabolism but also as a key element in development and prevention of pathologies.
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Affiliation(s)
| | | | | | | | | | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain; (A.G.-C.); (I.M.); (G.P.-M.); (A.D.-Q.); (M.A.D.l.R.)
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6
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Müller F, Graziadei A, Rappsilber J. Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes. Anal Chem 2019; 91:9041-9048. [PMID: 31274288 PMCID: PMC6639777 DOI: 10.1021/acs.analchem.9b01339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Protein structures respond to changes in their chemical and physical environment. However, studying such conformational changes is notoriously difficult, as many structural biology techniques are also affected by these parameters. Here, the use of photo-crosslinking, coupled with quantitative crosslinking mass spectrometry (QCLMS), offers an opportunity, since the reactivity of photo-crosslinkers is unaffected by changes in environmental parameters. In this study, we introduce a workflow combining photo-crosslinking using sulfosuccinimidyl 4,4'-azipentanoate (sulfo-SDA) with our recently developed data-independent acquisition (DIA)-QCLMS. This novel photo-DIA-QCLMS approach is then used to quantify pH-dependent conformational changes in human serum albumin (HSA) and cytochrome C by monitoring crosslink abundances as a function of pH. Both proteins show pH-dependent conformational changes resulting in acidic and alkaline transitions. 93% and 95% of unique residue pairs (URP) were quantifiable across triplicates for HSA and cytochrome C, respectively. Abundance changes of URPs and hence conformational changes of both proteins were visualized using hierarchical clustering. For HSA we distinguished the N-F and the N-B form from the native conformation. In addition, we observed for cytochrome C acidic and basic conformations. In conclusion, our photo-DIA-QCLMS approach distinguished pH-dependent conformers of both proteins.
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Affiliation(s)
- Fränze Müller
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
| | - Andrea Graziadei
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
- Wellcome
Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
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7
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5,7,3′,4′-Hydroxy substituted flavonoids reduce the heme of cytochrome c with a range of rate constants. Biochimie 2019; 162:167-175. [DOI: 10.1016/j.biochi.2019.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/25/2019] [Indexed: 12/20/2022]
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8
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Fortes-Dias CL, Fernandes CAH, Ortolani PL, Campos PC, Melo LA, Felicori LF, Fontes MRM. Identification, description and structural analysis of beta phospholipase A 2 inhibitors (sbβPLIs) from Latin American pit vipers indicate a binding site region for basic snake venom phospholipases A 2. Toxicon X 2019; 2:100009. [PMID: 32550566 PMCID: PMC7286088 DOI: 10.1016/j.toxcx.2019.100009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/04/2019] [Accepted: 02/13/2019] [Indexed: 11/17/2022] Open
Abstract
Several snake species possess, in their circulating blood, endogenous PLA2 inhibitors (sbPLIs) with the primary function of natural protection against toxic enzymes from homologous and heterologous venoms. Among the three structural classes of sbPLIs – named α, β, and γ − the β class (sbβPLIs) is the least known with only four identified sequences, so far. The last class of inhibitors encompass molecules with leucine rich repeats (LRRs) motifs containing repeating amino acid segments. In the present study, we identified and characterized putative sbβPLIs from the liver and venom glands of six Latin American pit vipers belonging to Bothrops and Crotalus genera. The inhibitor from Crotalus durissus terrificus snakes (CdtsbβPLI) was chosen as a reference for the construction of the first in silico structural model for this class of inhibitors, using molecular modeling and molecular dynamics simulations. Detailed analyses of the electrostatic surface of the CdtsbβPLI model and protein-protein docking with crotoxin B from homologous venoms predict the interacting surface between these proteins. Transcripts of phospholipases A2 inhibitors from the β-class (sbβPLIs) were identified in Latin American pit vipers. Structural features of sbβPLIs were compared and discussed, including their characteristic leucine-rich repeats (LRRs). One sbβPLI (CdtsbβPLI) was chosen for the in silico construction of the first structural model of a sbβPLI. A possible mechanism of interaction between sbβPLIs and basic snake venom PLA2s was suggested. Docking predictions between CdtsbβPLI and crotoxin B highlighted the amino acids residues at the interaction surfaces.
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Affiliation(s)
- Consuelo Latorre Fortes-Dias
- Serviço de Enzimologia, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias (FUNED), Belo Horizonte, MG, Brazil
| | - Carlos Alexandre H Fernandes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Paula Ladeira Ortolani
- Serviço de Enzimologia, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias (FUNED), Belo Horizonte, MG, Brazil
| | - Patrícia Cota Campos
- Serviço de Enzimologia, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias (FUNED), Belo Horizonte, MG, Brazil
| | - L A Melo
- Serviço de Enzimologia, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias (FUNED), Belo Horizonte, MG, Brazil
| | - Liza Figueiredo Felicori
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Marcos Roberto M Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
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9
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A neutral evolution test derived from a theoretical amino acid substitution model. J Theor Biol 2019; 467:31-38. [PMID: 30711455 DOI: 10.1016/j.jtbi.2019.01.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/14/2019] [Accepted: 01/28/2019] [Indexed: 12/27/2022]
Abstract
A neutral evolution model that explicitly considers codons, amino acids, and the degeneracy of the genetic code is developed. The model is built from nucleotides up to amino acids, and it represents a refinement of the neutral theory of molecular evolution. The model is based on a stochastic process that leads to a stationary probability distribution of amino acids. The latter is used as a neutral test of evolution. We provide some examples for assessing the neutrality test for a small set of protein sequences. The Jukes-Cantor model is generalized to deal with amino acids and it is compared with our neutral model, along with the empirical BLOSUM62 substitution model. The neutral test provides a baseline to which the evolution of any protein can be analyzed, and it clearly helps in discerning putative amino acids with unexpected frequencies that might be under positive or negative selection. Our model and neutral test are as universal as the standard genetic code.
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10
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Deng Y, Zhong F, Alden SL, Hoke KR, Pletneva EV. The K79G Mutation Reshapes the Heme Crevice and Alters Redox Properties of Cytochrome c. Biochemistry 2018; 57:5827-5840. [PMID: 30142276 DOI: 10.1021/acs.biochem.8b00650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The two roles of cytochrome c (cyt c), in oxidative phosphorylation and apoptosis, critically depend on redox properties of its heme iron center. The K79G mutant has served as a parent protein for a series of mutants of yeast iso-1 cyt c. The mutation preserves the Met80 coordination to the heme iron, as found in WT* (K72A/C102S), and many spectroscopic properties of K79G and WT* are indistinguishable. The K79G mutation does not alter the global stability, fold, rate of Met80 dissociation, or thermodynamics of the alkaline transition (p Ka) of the protein. However, the reduction potential of the heme iron decreases; further, the p KH of the trigger group and the rate of the Met-to-Lys ligand exchange associated with the alkaline transition decrease, suggesting changes in the environment of the heme. The rates of electron self-exchange and bimolecular electron transfer (ET) with positively charged inorganic complexes increase, as does the intrinsic peroxidase activity. Analysis of the reaction rates suggests that there is increased accessibility of the heme edge in K79G and supports the importance of the Lys79 site for bimolecular ET reactions of cyt c, including those with some of its native redox partners. Structural modeling rationalizes the observed effects to arise from changes in the volume of the heme pocket and solvent accessibility of the heme group. Kinetic and structural analyses of WT* characterize the properties of the heme crevice of this commonly employed reference variant. This study highlights the important role of Lys79 for defining functional redox properties of cyt c.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Fangfang Zhong
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Stephanie L Alden
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Kevin R Hoke
- Department of Chemistry and Biochemistry , Berry College , Mount Berry , Georgia 30149 , United States
| | - Ekaterina V Pletneva
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
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11
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Abstract
Cytochrome c (Cyt c) was rapidly oxidized by molecular oxygen in the presence, but not absence of PEG. The redox potential of heme c was determined by the potentiometric titration to be +236 ± 3 mV in the absence of PEG, which was negatively shifted to +200 ± 4 mV in the presence of PEG. The underlying the rapid oxidation was explored by examining the structural changes in Cyt c in the presence of PEG using UV-visible absorption, circular dichroism, resonance Raman, and fluorescence spectroscopies. These spectroscopic analyses suggested that heme oxidation was induced by a modest tertiary structural change accompanied by a slight shift in the heme position (<1.0 Å) rather than by partial denaturation, as is observed in the presence of cardiolipin. The near-infrared spectra showed that PEG induced dehydration from Cyt c, which triggered heme displacement. The primary dehydration site was estimated to be around surface-exposed hydrophobic residues near the heme center: Ile81 and Val83. These findings and our previous studies, which showed that hydrated water molecules around Ile81 and Val83 are expelled when Cyt c forms a complex with CcO, proposed that dehydration of these residues is functionally significant to electron transfer from Cyt c to CcO.
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12
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Uzelac JJ, Stanić M, Krstić D, Čolović M, Djurić D. Effects of homocysteine and its related compounds on oxygen consumption of the rat heart tissue homogenate: the role of different gasotransmitters. Mol Cell Biochem 2017; 444:143-148. [DOI: 10.1007/s11010-017-3238-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/24/2017] [Indexed: 10/18/2022]
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13
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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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14
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Alleyne T, Ignacio DN, Sampson VB, Ashe D, Wilson M. Simulating the slow to fast switch in cytochrome c oxidase catalysis by introducing a loop flip near the enzyme's cytochrome c (substrate) binding site. Biotechnol Appl Biochem 2017; 64:677-685. [PMID: 27489224 DOI: 10.1002/bab.1526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/30/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Trevor Alleyne
- Biochemistry Unit, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - Diane N Ignacio
- Biochemistry Unit, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - Valerie B Sampson
- Nemours Center for Cancer and Blood Disorders, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Damian Ashe
- Biochemistry Unit, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - Michael Wilson
- School of Biological Sciences, University of Essex, Colchester, Essex, UK
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15
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Chertkova RV, Brazhe NA, Bryantseva TV, Nekrasov AN, Dolgikh DA, Yusipovich AI, Sosnovtseva O, Maksimov GV, Rubin AB, Kirpichnikov MP. New insight into the mechanism of mitochondrial cytochrome c function. PLoS One 2017; 12:e0178280. [PMID: 28562658 PMCID: PMC5451065 DOI: 10.1371/journal.pone.0178280] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/10/2017] [Indexed: 11/22/2022] Open
Abstract
We investigate functional role of the P76GTKMIFA83 fragment of the primary structure of cytochrome c. Based on the data obtained by the analysis of informational structure (ANIS), we propose a model of functioning of cytochrome c. According to this model, conformational rearrangements of the P76GTKMIFA83 loop fragment have a significant effect on conformational mobility of the heme. It is suggested that the conformational mobility of cytochrome c heme is responsible for its optimal orientation with respect to electron donor and acceptor within ubiquinol–cytochrome c oxidoreductase (complex III) and cytochrome c oxidase (complex IV), respectively, thus, ensuring electron transfer from complex III to complex IV. To validate the model, we design several mutant variants of horse cytochrome c with multiple substitutions of amino acid residues in the P76GTKMIFA83 sequence that reduce its ability to undergo conformational rearrangements. With this, we study the succinate–cytochrome c reductase and cytochrome c oxidase activities of rat liver mitoplasts in the presence of mutant variants of cytochrome c. The electron transport activity of the mutant variants decreases to different extent. Resonance Raman spectroscopy (RRS) and surface-enhanced Raman spectroscopy (SERS) data demonstrate, that all mutant cytochromes possess heme with the higher degree of ruffling deformation, than that of the wild-type (WT) cytochrome c. The increase in the ruffled deformation of the heme of oxidized cytochromes correlated with the decrease in the electron transport rate of ubiquinol–cytochrome c reductase (complex III). Besides, all mutant cytochromes have lower mobility of the pyrrol rings and methine bridges, than WT cytochrome c. We show that a decrease in electron transport activity in the mutant variants correlates with conformational changes and reduced mobility of heme porphyrin. This points to a significant role of the P76GTKMIFA83 fragment in the electron transport function of cytochrome c.
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Affiliation(s)
- Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- * E-mail: (RVC); (NAB)
| | - Nadezda A. Brazhe
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (RVC); (NAB)
| | - Tatiana V. Bryantseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey N. Nekrasov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander I. Yusipovich
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Sosnovtseva
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Georgy V. Maksimov
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Andrei B. Rubin
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
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16
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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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17
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Feifel SC, Stieger KR, Kapp A, Weber D, Allegrozzi M, Piccioli M, Turano P, Lisdat F. Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix. ACS OMEGA 2016; 1:1058-1066. [PMID: 30023500 PMCID: PMC6044710 DOI: 10.1021/acsomega.6b00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/04/2016] [Indexed: 06/08/2023]
Abstract
The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.
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Affiliation(s)
- Sven Christian Feifel
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Kai Ralf Stieger
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Andreas Kapp
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Dennis Weber
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Marco Allegrozzi
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Mario Piccioli
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Fred Lisdat
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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18
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Hannibal L, Tomasina F, Capdevila DA, Demicheli V, Tórtora V, Alvarez-Paggi D, Jemmerson R, Murgida DH, Radi R. Alternative Conformations of Cytochrome c: Structure, Function, and Detection. Biochemistry 2016; 55:407-28. [DOI: 10.1021/acs.biochem.5b01385] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Luciana Hannibal
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Center
for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Mathildenstrasse 1, Freiburg D-79106, Germany
| | - Florencia Tomasina
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Daiana A. Capdevila
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Verónica Demicheli
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Verónica Tórtora
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ronald Jemmerson
- Department
of Microbiology and Immunology, University of Minnesota, MMC 196,
420 Delaware Street, Southeast, Minneapolis, Minnesota 55455, United States
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Rafael Radi
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
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19
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Li J, Sun R, Hao C, He G, Zhang L, Wang J. The behavior of the adsorption of cytochrome C on lipid monolayers: A study by the Langmuir–Blodgett technique and theoretical analysis. Biophys Chem 2015; 205:33-40. [DOI: 10.1016/j.bpc.2015.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
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20
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McClelland LJ, Seagraves SM, Khan MKA, Cherney MM, Bandi S, Culbertson JE, Bowler BE. The response of Ω-loop D dynamics to truncation of trimethyllysine 72 of yeast iso-1-cytochrome c depends on the nature of loop deformation. J Biol Inorg Chem 2015; 20:805-19. [PMID: 25948392 PMCID: PMC4485566 DOI: 10.1007/s00775-015-1267-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 04/27/2015] [Indexed: 11/24/2022]
Abstract
Trimethyllysine 72 (tmK72) has been suggested to play a role in sterically constraining the heme crevice dynamics of yeast iso-1-cytochrome c mediated by the Ω-loop D cooperative substructure (residues 70-85). A tmK72A mutation causes a gain in peroxidase activity, a function of cytochrome c that is important early in apoptosis. More than one higher energy state is accessible for the Ω-loop D substructure via tier 0 dynamics. Two of these are alkaline conformers mediated by Lys73 and Lys79. In the current work, the effect of the tmK72A mutation on the thermodynamic and kinetic properties of wild-type iso-1-cytochrome c (yWT versus WT*) and on variants carrying a K73H mutation (yWT/K73H versus WT*/K73H) is studied. Whereas the tmK72A mutation confers increased peroxidase activity in wild-type yeast iso-1-cytochrome c and increased dynamics for formation of a previously studied His79-heme alkaline conformer, the tmK72A mutation speeds return of the His73-heme alkaline conformer to the native state through destabilization of the His73-heme alkaline conformer relative to the native conformer. These opposing behaviors demonstrate that the response of the dynamics of a protein substructure to mutation depends on the nature of the perturbation to the substructure. For a protein substructure which mediates more than one function of a protein through multiple non-native structures, a mutation could change the partitioning between these functions. The current results suggest that the tier 0 dynamics of Ω-loop D that mediates peroxidase activity has similarities to the tier 0 dynamics required to form the His79-heme alkaline conformer.
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Affiliation(s)
- Levi J McClelland
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA
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21
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Amacher JF, Zhong F, Lisi GP, Zhu MQ, Alden SL, Hoke KR, Madden DR, Pletneva EV. A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch. J Am Chem Soc 2015; 137:8435-49. [PMID: 26038984 DOI: 10.1021/jacs.5b01493] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
It has been suggested that the alkaline form of cytochrome c (cyt c) regulates function of this protein as an electron carrier in oxidative phosphorylation and as a peroxidase that reacts with cardiolipin (CL) during apoptosis. In this form, Met80, the native ligand to the heme iron, is replaced by a Lys. While it has become clear that the structure of cyt c changes, the extent and sequence of conformational rearrangements associated with this ligand replacement remain a subject of debate. Herein we report a high-resolution crystal structure of a Lys73-ligated cyt c conformation that reveals intricate change in the heme environment upon this switch in the heme iron ligation. The structure is surprisingly compact, and the heme coordination loop refolds into a β-hairpin with a turn formed by the highly conserved residues Pro76 and Gly77. Repositioning of residue 78 modifies the intraprotein hydrogen-bonding network and, together with adjustments of residues 52 and 74, increases the volume of the heme pocket to allow for insertion of one of the CL acyl moieties next to Asn52. Derivatization of Cys78 with maleimide creates a solution mimic of the Lys-ligated cyt c that has enhanced peroxidase activity, adding support for a role of the Lys-ligated cyt c in the apoptotic mechanism. Experiments with the heme peptide microperoxidase-8 and engineered model proteins provide a thermodynamic rationale for the switch to Lys ligation upon perturbations in the protein scaffold.
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Affiliation(s)
- Jeanine F Amacher
- †Department of Biochemistry, Geisel School of Medicine, Hanover, New Hampshire 03755, United States
| | - Fangfang Zhong
- ‡Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - George P Lisi
- ‡Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Michael Q Zhu
- ‡Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Stephanie L Alden
- ‡Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Kevin R Hoke
- §Department of Chemistry, Berry College, Mount Berry, Georgia 30149, United States
| | - Dean R Madden
- †Department of Biochemistry, Geisel School of Medicine, Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- †Department of Biochemistry, Geisel School of Medicine, Hanover, New Hampshire 03755, United States.,‡Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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22
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Pandiscia LA, Schweitzer-Stenner R. Coexistence of Native-like and Non-Native Partially Unfolded Ferricytochrome c on the Surface of Cardiolipin-Containing Liposomes. J Phys Chem B 2015; 119:1334-49. [DOI: 10.1021/jp5104752] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Leah A. Pandiscia
- Department
of Chemistry, Drexel University, Philadelphia, PA 19104, United States
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23
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Cytochrome c: A Multifunctional Protein Combining Conformational Rigidity with Flexibility. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/484538] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytochrome has served as a model system for studying redox reactions, protein folding, and more recently peroxidase activity induced by partial unfolding on membranes. This review illuminates some important aspects of the research on this biomolecule. The first part summarizes the results of structural analyses of its active site. Owing to heme-protein interactions the heme group is subject to both in-plane and out-of-plane deformations. The unfolding of the protein as discussed in detail in the second part of this review can be induced by changes of pH and temperature and most prominently by the addition of denaturing agents. Both the kinetic and thermodynamic folding and unfolding involve intermediate states with regard to all unfolding conditions. If allowed to sit at alkaline pH (11.5) for a week, the protein does not return to its folding state when the solvent is switched back to neutral pH. It rather adopts a misfolded state that is prone to aggregation via domain swapping. On the surface of cardiolipin containing liposomes, the protein can adopt a variety of partially unfolded states. Apparently, ferricytochrome c can perform biological functions even if it is only partially folded.
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24
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De March M, Demitri N, De Zorzi R, Casini A, Gabbiani C, Guerri A, Messori L, Geremia S. Nitrate as a probe of cytochrome c surface: Crystallographic identification of crucial “hot spots” for protein–protein recognition. J Inorg Biochem 2014; 135:58-67. [DOI: 10.1016/j.jinorgbio.2014.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 02/23/2014] [Accepted: 02/27/2014] [Indexed: 11/30/2022]
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25
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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26
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Surface-enhanced resonance Raman scattering (SERRS) as a tool for the studies of electron transfer proteins attached to biomimetic surfaces: Case of cytochrome c. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.08.140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Cherney MM, Junior CC, Bergquist BB, Bowler BE. Dynamics of the His79-heme alkaline transition of yeast iso-1-cytochrome c probed by conformationally gated electron transfer with Co(II)bis(terpyridine). J Am Chem Soc 2013; 135:12772-82. [PMID: 23899348 PMCID: PMC3856690 DOI: 10.1021/ja405725f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Alkaline conformers of cytochrome c may be involved in both its electron transport and apoptotic functions. We use cobalt(II)bis(terpyridine), Co(terpy)2(2+), as a reagent for conformationally gated electron-transfer (gated ET) experiments to study the alkaline conformational transition of K79H variants of yeast iso-1-cytochrome c expressed in Escherichia coli , WT*K79H, with alanine at position 72 and Saccharomyces cerevisiae , yK79H, with trimethyllysine (Tml) at position 72. Co(terpy)2(2+) is well-suited to the 100 ms to 1 s time scale of the His79-mediated alkaline conformational transition of these variants. Reduction of the His79-heme alkaline conformer by Co(terpy)2(2+) occurs primarily by gated ET, which involves conversion to the native state followed by reduction, with a small fraction of the His79-heme alkaline conformer directly reduced by Co(terpy)2(2+). The gated ET experiments show that the mechanism of formation of the His79-heme alkaline conformer involves only two ionizable groups. In previous work, we showed that the mechanism of the His73-mediated alkaline conformational transition requires three ionizable groups. Thus, the mechanism of heme crevice opening depends upon the position of the ligand mediating the process. The microscopic rate constants provided by gated ET studies show that mutation of Tml72 (yK79H variant) in the heme crevice loop to Ala72 (WT*K79H variant) affects the dynamics of heme crevice opening through a small destabilization of both the native conformer and the transition state relative to the His79-heme alkaline conformer. Previous pH jump data had indicated that the Tml72→Ala mutation primarily stabilized the transition state for the His79-mediated alkaline conformational transition.
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Affiliation(s)
| | - Carolyn C. Junior
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Bryan B. Bergquist
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
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28
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Soffer JB, Fradkin E, Pandiscia LA, Schweitzer-Stenner R. The (Not Completely Irreversible) Population of a Misfolded State of Cytochrome c under Folding Conditions. Biochemistry 2013; 52:1397-408. [DOI: 10.1021/bi301586e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jonathan B. Soffer
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
| | - Emma Fradkin
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
| | - Leah A. Pandiscia
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
| | - Reinhard Schweitzer-Stenner
- Departments of Chemistry and
Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
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29
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Bandi S, Bowler BE. A cytochromeCelectron transfer switch modulated by heme ligation and isomerization of a peptidyl-prolyl bond. Biopolymers 2013; 100:114-24. [DOI: 10.1002/bip.22164] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/28/2012] [Accepted: 09/23/2012] [Indexed: 11/10/2022]
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30
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KOBAYASHI E, HIROSE Y, KAMACHI T, TABATA K, OKURA I, ASAKURA N. Investigation of the Key Heme in Cytchrome <i>c</i><sub>3</sub> to the Electron Pool Effect by Highly Sensitive EQCM Technique. ELECTROCHEMISTRY 2012. [DOI: 10.5796/electrochemistry.80.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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31
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Bandi S, Bowler BE. Probing the Dynamics of a His73–Heme Alkaline Transition in a Destabilized Variant of Yeast Iso-1-cytochrome c with Conformationally Gated Electron Transfer Methods. Biochemistry 2011; 50:10027-40. [DOI: 10.1021/bi201082h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Swati Bandi
- Department of Chemistry
and Biochemistry and Center
for Biomolecular Structure and Dynamics, The University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry
and Biochemistry and Center
for Biomolecular Structure and Dynamics, The University of Montana, Missoula, Montana 59812, United States
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32
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Wegerich F, Turano P, Allegrozzi M, Möhwald H, Lisdat F. Electroactive multilayer assemblies of bilirubin oxidase and human cytochrome C mutants: insight in formation and kinetic behavior. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:4202-11. [PMID: 21401056 DOI: 10.1021/la104964z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Here, we report on cytochrome c/bilirubin oxidase multilayer electrodes with different cytochrome c (cyt c) forms including mutant forms of human cyt c, which exhibit different reaction rates with bilirubin oxidase (BOD) in solution. The multilayer formation via the layer-by-layer technique and the kinetic behavior of the mono (only cyt c) and biprotein (cyt c and BOD) multilayer systems are studied by SPR and cyclic voltammetry. For the layer construction, sulfonated polyaniline is used. The only cyt c containing multilayer electrodes show that the quantity of deposited protein and the kinetic behavior depend on the cyt c form incorporated. In the case of the biprotein multilayer with BOD, it is demonstrated that the catalytic signal chain from the electrode via cyt c to BOD and oxygen can be established with all chosen cyt c forms. However, the magnitude of the catalytic current as well as the kinetic behavior differ significantly. We conclude that the different cytochrome c forms affect three parameters, identified here, to be important for the functionality of the multilayer system: the amount of molecules per layer, which can be immobilized on the electrodes, the cyt c self-exchange rate, and the rate constant for the reaction with BOD.
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Affiliation(s)
- Franziska Wegerich
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam-Golm, Germany
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33
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Weinkam P, Romesberg FE, Wolynes PG. Chemical frustration in the protein folding landscape: grand canonical ensemble simulations of cytochrome c. Biochemistry 2010; 48:2394-402. [PMID: 19199810 DOI: 10.1021/bi802293m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A grand canonical formalism is developed to combine discrete simulations for chemically distinct species in equilibrium. Each simulation is based on a perturbed funneled landscape. The formalism is illustrated using the alkaline-induced transitions of cytochrome c as observed by FTIR spectroscopy and with various other experimental approaches. The grand canonical simulation method accounts for the acid/base chemistry of deprotonation, the inorganic chemistry of heme ligation and misligation, and the minimally frustrated folding energy landscape, thus elucidating the physics of protein folding involved with an acid/base titration of a protein. The formalism combines simulations for each of the relevant chemical species, varying by protonation and ligation states. In contrast to models based on perfectly funneled energy landscapes that contain only contacts found in the native structure, this study introduces "chemical frustration" from deprotonation and misligation that gives rise to many intermediates at alkaline pH. While the nature of these intermediates cannot be easily inferred from available experimental data, this study provides specific structural details of these intermediates, thus extending our understanding of how cytochrome c changes with an increase in pH. The results demonstrate the importance of chemical frustration for understanding biomolecular energy landscapes.
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Affiliation(s)
- Patrick Weinkam
- Center for Theoretical Biological Physics and Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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34
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Zhao J, Zhu W, Liu T, Yang J, Li G. Electrochemical probing into cytochrome c modification with homocysteine-thiolactone. Anal Bioanal Chem 2010; 397:695-701. [DOI: 10.1007/s00216-010-3553-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 01/28/2010] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
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35
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Farivar F, Moosavi-Movahedi AA, Sefidbakht Y, Nazari K, Hong J, Sheibani N. Cytochrome c in sodium dodecyl sulfate reverse micelle nanocage: From a classic electron carrier protein to an artificial peroxidase enzyme. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2009.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Pepelina TY, Chertkova RV, Dolgikh DA, Kirpichnikov MP. The role of individual lysine residues of horse cytochrome c in the formation of reactive complexes with components of the respiratory chain. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:98-104. [DOI: 10.1134/s1068162010010097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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De Biase PM, Paggi DA, Doctorovich F, Hildebrandt P, Estrin DA, Murgida DH, Marti MA. Molecular basis for the electric field modulation of cytochrome C structure and function. J Am Chem Soc 2010; 131:16248-56. [PMID: 19886701 DOI: 10.1021/ja906726n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c (Cyt) is a small soluble heme protein with a hexacoordinated heme and functions as an electron shuttle in the mitochondria and in early events of apoptosis when released to the cytoplasm. Using molecular dynamics simulations, we show here that biologically relevant electric fields induce an increased mobility and structural distortion of key protein segments that leads to the detachment of the sixth axial ligand Met80 from the heme iron. This electric-field-induced conformational transition is energetically and entropically driven and leads to a pentacoordinated high spin heme that is characterized by a drastically lowered reduction potential as well as by an increased peroxidase activity. The simulations provide a detailed atomistic picture of the structural effects of the electric field on the structure of Cyt, which allows a sound interpretation of recent experimental results. The observed conformational change may modulate the electron transfer reactions of Cyt in the mitochondria and, furthermore, may constitute a switch from the redox function in the respiratory chain to the peroxidase function in the early events of apoptosis.
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Affiliation(s)
- Pablo M De Biase
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, Pab. 2, C1428EHA, Buenos Aires, Argentina
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38
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Schröper F, Baumann A, Offenhäusser A, Mayer D. Bidirectional immobilization of affinity-tagged cytochrome c on electrode surfaces. Chem Commun (Camb) 2010; 46:5295-7. [DOI: 10.1039/c0cc00850h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Pepelina TY, Chertkova RV, Ostroverkhova TV, Dolgikh DA, Kirpichnikov MP, Grivennikova VG, Vinogradov AD. Site-directed mutagenesis of cytochrome c: Reactions with respiratory chain components and superoxide radical. BIOCHEMISTRY (MOSCOW) 2009; 74:625-32. [DOI: 10.1134/s0006297909060066] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Patriarca A, Eliseo T, Sinibaldi F, Piro MC, Melis R, Paci M, Cicero DO, Polticelli F, Santucci R, Fiorucci L. ATP acts as a regulatory effector in modulating structural transitions of cytochrome c: implications for apoptotic activity. Biochemistry 2009; 48:3279-87. [PMID: 19231839 DOI: 10.1021/bi801837e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of lipids (free fatty acids as well as acidic phospholipids) to cytochrome c (cyt c) induces conformational changes and partial unfolding of the protein, strongly influencing cyt c oxidase/peroxidase activity. ATP is unique among the nucleotides in being able to turn non-native states of cyt c back to the native conformation. The peroxidase activity acquired by lipid-bound cyt c turns out to be very critical in the early stages of apoptosis. Nucleotide specificity is observed for apoptosome formation and caspase activation, the cleavage occurring only in the presence of dATP or ATP. In this study, we demonstrate the connection between peroxidase activity and oleic acid-induced conformational transitions of cyt c and show how ATP is capable of modulating such interplay. By NMR measurement, we have demonstrated that ATP interacts with a site (S1) formed by K88, R91, and E62 and such interaction was weakened by mutation of E62, suggesting the selective role in the interaction played by the base moiety. Interestingly, the interactions of ATP and GTP with cyt c are significantly different at low nucleotide concentrations, with GTP being less effective in perturbing the S1 site and in eliciting apoptotic activity. To gain insights into the structural features of cyt c required for its pro-apoptotic activity and to demonstrate a regulatory role for ATP (compared to the effect of GTP), we have performed experiments on cell lysates by using cyt c proteins mutated on amino acid residues that, as suggested by NMR measurements, belong to S1. Thus, we provide evidence that ATP acts as an allosteric effector, regulating structural transitions among different conformations and different oxidation states of cyt c, which are endowed with apoptotic activity or not. On this basis, we suggest a previously unrecognized role for ATP binding to cyt c at low millimolar concentrations in the cytosol, beyond the known regulatory role during the oxidative phosphorylation in mitochondria.
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Affiliation(s)
- Antonella Patriarca
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
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41
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Schweitzer-Stenner R, Hagarman A, Verbaro D, Soffer JB. Conformational Stability of Cytochrome c Probed by Optical Spectroscopy. Methods Enzymol 2009; 466:109-53. [DOI: 10.1016/s0076-6879(09)66006-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Hagarman A, Duitch L, Schweitzer-Stenner R. The conformational manifold of ferricytochrome c explored by visible and far-UV electronic circular dichroism spectroscopy. Biochemistry 2008; 47:9667-77. [PMID: 18702508 DOI: 10.1021/bi800729w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidized state of cytochrome c is a subject of continuous interest, owing to the multitude of conformations which the protein can adopt in solution and on surfaces of artificial and cell membranes. The structural diversity corresponds to a variety of functions in electron transfer, peroxidase and apoptosis processes. In spite of numerous studies, a comprehensive analysis and comparison of native and non-native states of ferricytochrome c has thus far not been achieved. This results in part from the fact that the influence of solvent conditions (i.e., ionic strength, anion concentration, temperature dependence of pH values) on structure, function and equilibrium thermodynamics has not yet been thoroughly assessed. The current study is a first step in this direction, in that it provides the necessary experimental data to compare different non-native states adopted at high temperature and alkaline pH. To this end, we employed visible electronic circular dichroism (ECD) and absorption spectroscopy to probe structural changes of the heme environment in bovine and horse heart ferricytochrome c as a function of temperature between 278 and 363 K at different neutral and alkaline pH values. A careful selection of buffers enabled us to monitor the partial unfolding of the native state at room temperature while avoiding a change to an alkaline state at high temperatures. We found compelling evidence for the existence of a thermodynamic intermediate of the thermal unfolding/folding process, termed III h, which is structurally different from the alkaline states, IV 1 and IV 2, contrary to current belief. At neutral or slightly acidic pH, III h is populated in a temperature region between 320 and 345 K. The unfolded state of the protein becomes populated at higher temperatures. The ECD spectra of the B-bands of bovine and horse heart cytochrome c (pH 7.0) exhibit a pronounced couplet that is maintained below 343 K, before protein unfolding replaces it by a rather strong positive Cotton band. A preliminary vibronic analysis of the B-band profile reveals that the couplet reflects a B-band splitting of 350 cm (-1), which is mostly of electronic origin, due to the internal electric field in the heme cavity. Our results suggest that the conformational transition from the native state, III, into a thermally activated intermediate state, III h, does not substantially affect the internal electric field and causes only moderate rearrangements of the heme pocket, which involves changes, rather than a rupture, of the Fe (3+)-M80 linkage. In the unfolded state, as well as in the alkaline states IV and V, the band splitting is practically eliminated, but the positive Cotton effect observed for the B-band suggests that the proximal environment, encompassing H18 and the two cysteine residues 14 and 17, is most likely still intact and covalently bound to the heme chromophore. Both alkaline states IV and V were found to melt via intermediate states. Unfolded states probed at neutral and alkaline pH can be discriminated, owing to the different intensities of the Cotton bands of the respective B-band transitions. Differences between the ECD intensities of the B-bands of the different unfolded states and alkaline states most likely reflect different degrees of openness of the corresponding heme crevice.
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Affiliation(s)
- Andrew Hagarman
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, USA
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43
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Laia CAT, Costa SMB. Interaction of Zinc Tetrasulfonated Phthalocyanine with Cytochromecin Water and Triton-X 100 Micelles. J Phys Chem B 2008; 112:4276-82. [DOI: 10.1021/jp076100+] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Murgida DH, Hildebrandt P. Disentangling interfacial redox processes of proteins by SERR spectroscopy. Chem Soc Rev 2008; 37:937-45. [DOI: 10.1039/b705976k] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Moghaddam AB, Ganjali MR, Dinarvand R, Saboury AA, Razavi T, Moosavi-Movahedi AA, Norouzi P. Fundamental studies of the cytochrome c immobilization by the potential cycling method on nanometer-scale nickel oxide surfaces. Biophys Chem 2007; 129:259-68. [PMID: 17628321 DOI: 10.1016/j.bpc.2007.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/13/2007] [Accepted: 06/14/2007] [Indexed: 11/28/2022]
Abstract
This work describes the performance of cytochrome c/nickel oxide nanoparticles/glassy carbon electrode, prepared by the electrochemical deposition of the nickel oxide nanoparticles (NiO NPs) on the glassy carbon (GC) electrode surface and the cytochrome c immobilization on the nickel oxide nanoparticle surfaces. An extensive sample examination with the help of the SEM and AFM presented the existence of different geometrical shapes of the nickel oxide particles. These geometrical structures could lead to the better immobilization of proteins on their surfaces. The resulting electrode displayed an excellent behavior for the redox of the cytochrome c. Also, the resulting heme protein exhibited a direct electrical contact with the electrode because of the structural alignment of the heme protein on the nanometer-scale nickel oxide surfaces. This method could be suitable for applications to nanofabricated devices. In the end, it was concluded that the cytochrome c could be tethered to the nanometer-scale nickel oxide surfaces.
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Affiliation(s)
- Abdolmajid Bayandori Moghaddam
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box: 14155-6455, Tehran, Iran
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46
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Bandi S, Baddam S, Bowler BE. Alkaline conformational transition and gated electron transfer with a Lys 79 --> his variant of iso-1-cytochrome c. Biochemistry 2007; 46:10643-54. [PMID: 17713929 DOI: 10.1021/bi700992y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To probe the mechanism of the alkaline conformational transition and its effect on the dynamics of gated electron transfer (ET) reactions, a Lys 79 --> His (K79H) variant of iso-1-cytochrome c has been prepared. Guanidine hydrochloride denaturation monitored by circular dichroism and absorbance at 695 nm indicates that this variant unfolds from a partially unfolded state. The conformation of the wild type (WT) and K79H proteins was monitored at 695 nm from pH 2 to 11. These data indicate that acid unfolding is multi-state for both K79H and WT proteins and that the His 79-heme alkaline conformer is more stable than a previously reported His 73-heme alkaline conformer. Fast and slow phases are observed in the kinetics of the alkaline transition of the K79H variant. The pH dependence of the fast phase kinetic data shows that ionizable groups with pKa values near 6.8 and 9 modulate the formation of the His 79-heme alkaline conformer. The slow phase kinetic data are consistent with a single ionizable group with a pKa near 9.5 promoting the Lys 73-heme alkaline transition. In the broader context of data on the alkaline transition, ionization of the ligand replacing Met 80 appears to play a primary role in promoting the formation of the alkaline conformer, with other ionizable groups acting as secondary modulators. Intermolecular ET with hexaammineruthenium(II) chloride shows conformational gating due to both His 79-heme and Lys 73-heme alkaline conformers. Both the position and the nature of the alkaline state ligand modulate the dynamics of ET gating.
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Affiliation(s)
- Swati Bandi
- Department of Chemistry and Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, Montana 59812, USA
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47
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Heering HA, Williams KA, de Vries S, Dekker C. Specific vectorial immobilization of oligonucleotide-modified yeast cytochrome C on carbon nanotubes. Chemphyschem 2007; 7:1705-9. [PMID: 16807958 DOI: 10.1002/cphc.200600108] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Iso-1-cytochrome c from the yeast Saccharomyces cerevisiae (YCC) contains a surface cysteine residue, Cys102, that is located opposite to the lysine-rich side containing the exposed heme edge, which is the docking site for enzymes. Site-specific vectorial immobilization of YCC via Cys102 on single-walled carbon nanotubes (SWNT) thus provides a selective interface between nanoscopic electronic devices and complex enzymes. We have achieved this by modification of Cys102 with an oligonucleotide (dT(18)). Atomic force microscopy, fluorescence imaging, and cyclic voltammetry show the specific adsorption of YCC, modified with dT(18), on the SWNT sidewall with retention of its native properties. Pretreatment of the SWNT with Triton-X405 blocks the nonspecific binding of untreated YCC but does not interfere with binding of the oligonucleotide-modified YCC.
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Affiliation(s)
- Hendrik A Heering
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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48
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Battistuzzi G, Bellei M, Dennison C, Di Rocco G, Sato K, Sola M, Yanagisawa S. Thermodynamics of the alkaline transition in phytocyanins. J Biol Inorg Chem 2007; 12:895-900. [PMID: 17569996 DOI: 10.1007/s00775-007-0245-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Accepted: 04/29/2007] [Indexed: 10/23/2022]
Abstract
The thermodynamics of the alkaline transition which influences the spectral and redox properties of the type 1 copper center in phytocyanins has been determined spectroscopically. The proteins investigated include Rhus vernicifera stellacyanin, cucumber basic protein and its Met89Gln variant, and umecyanin, the stellacyanin from horseradish roots, along with its Gln95Met variant. The changes in reaction enthalpy and entropy within the protein series show partial compensatory behavior. Thus, the reaction free energy change (hence the pK (a) value) is rather variable. This indicates that species-dependent differences in reaction thermodynamics, although containing an important contribution from changes in the hydrogen-bonding network of water molecules in the hydration sphere of the protein (which feature enthalpy-entropy compensation), are to a large extent protein-based. The data for axial ligand variants are consistent with the hypothesis of a copper-binding His as the deprotonating residue responsible for this transition.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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49
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Bernad S, Leygue N, Korri-Youssoufi H, Lecomte S. Kinetics of the electron transfer reaction of Cytochrome c 552 adsorbed on biomimetic electrode studied by time-resolved surface-enhanced resonance Raman spectroscopy and electrochemistry. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:1039-48. [PMID: 17549469 DOI: 10.1007/s00249-007-0173-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 04/23/2007] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
Cytochrome c (552) (Cyt-c (552)) and its redox partner ba ( 3 )-oxidase from Thermus thermophilus possess structural differences compared with Horse heart cytochrome c (cyt-c)/cytochrome c oxidase (CcO) system, where the recognition between partners and the electron transfer (ET) process is initiated via electrostatic interactions. We demonstrated in a previous study by surface-enhanced resonance Raman (SERR) spectroscopy that roughened silver electrodes coated with uncharged mixed self-assembled monolayers HS-(CH(2))( n )-CH(3)/HS-(CH(2))( n + 1)-OH 50/50, n = 5, 10 or 15, was a good model to mimic the Cyt-c (552) redox partner. All the adsorbed molecules are well oriented on such biomimetic electrodes and transfer one electron during the redox process. The present work focuses on the kinetic part of the heterogeneous ET process of Cyt-c (552) adsorbed onto electrodes coated with such mixed SAMs of different alkyl chain length. For that purpose, two complementary methods were combined. Firstly cyclic voltammetry shows that the ET between the adsorbed Cyt-c (552) and the biomimetic electrode is direct and reversible. Furthermore, it allows the estimation of both the density surface coverage of adsorbed Cyt-c (552) and the kinetic constants values. Secondly, time-resolved SERR (TR-SERR) spectroscopy showed that the ET process occurs without conformational change of the Cyt-c (552) heme group and allows the determination of kinetic constants. Results show that the kinetic constant values obtained by TR-SERR spectroscopy could be compared to those obtained from cyclic voltammetry. They are estimated at 200, 150 and 40 s(-1) for the ET of Cyt-c (552) adsorbed onto electrodes coated with mixed SAMs HS-(CH(2))( n )-CH(3)/HS-(CH(2))( n + 1)-OH 50/50, n = 5, 10 or 15, respectively.
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Affiliation(s)
- Sophie Bernad
- LADIR, CNRS/UPMC (UMR 7075), 2 rue Henri Dunant, 94320, Thiais, France
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50
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Perła-Kaján J, Marczak Ł, Kaján L, Skowronek P, Twardowski T, Jakubowski H. Modification by Homocysteine Thiolactone Affects Redox Status of Cytochrome c. Biochemistry 2007; 46:6225-31. [PMID: 17474717 DOI: 10.1021/bi602463m] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Homocysteine (Hcy)-thiolactone mediates a post-translational incorporation of Hcy into protein in humans. Protein N-homocysteinylation is detrimental to protein structure and function and is linked to pathophysiology of hyperhomocysteinemia observed in humans and experimental animals. The modification by Hcy-thiolactone can be detrimental directly by affecting the function of an essential lysine residue or indirectly by interfering with the function of other essential residues or cofactors. Previous work has shown that cytochrome c is very sensitive to Hcy-thiolactone, which causes formation of N-Hcy-cytochrome c multimers. However, it was unclear what sites in cytochrome c were prone to Hcy attachment and whether N-linked Hcy can affect the structure and redox function of cytochrome c. Here we show that 4 lysine residues (Lys8 or -13, Lys86 or -87, Lys99, and Lys100) of cytochrome c are susceptible to N-homocysteinylation. We also show that N-homocysteinylation of 1 mol of lysine/mol of protein affects the redox state of the heme ligand of cytochrome c by rendering it reduced. The modification causes subtle structural changes, manifested as increased resistance of the N-Hcy-cytochrome c to proteolysis by trypsin, chymotrypsin, and Pronase. However, no major secondary structure perturbations were observed as shown by circular dichroism spectroscopy. Our data illustrate how N-homocysteinylation can interfere with the function of heme-containing proteins.
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Affiliation(s)
- Joanna Perła-Kaján
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznań, Poland.
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