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Xu G, Li W, Xie H, Zhu J, Song L, Tang J, Miao Y, Han XX. In Situ Monitoring of Membrane Protein Electron Transfer via Surface-Enhanced Resonance Raman Spectroscopy. Anal Chem 2024; 96:6-11. [PMID: 38132829 DOI: 10.1021/acs.analchem.3c04700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In situ analysis of membrane protein-ligand interactions under physiological conditions is of significance for both fundamental and applied science, but it is still a big challenge due to the limits in sensitivity and selectivity. Here, we demonstrate the potential of surface-enhanced resonance Raman spectroscopy (SERRS) for the investigation of membrane protein-protein interactions. Lipid biolayers are successfully coated on silver nanoparticles through electrostatic interactions, and a highly sensitive and biomimetic membrane platform is obtained in vitro. Self-assembly and immobilization of the reduced cytochrome b5 on the coated membrane are achieved and protein native biological functions are preserved. Owing to resonance effect, the Raman fingerprint of the immobilized cytochrome b5 redox center is selectively enhanced, allowing for in situ and real-time monitoring of the electron transfer process between cytochrome b5 and their partners, cytochrome c and myoglobin. This study provides a sensitive analytical approach for membrane proteins and paves the way for in situ exploration of their structural basis and functions.
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Affiliation(s)
- Guangyang Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Han Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Jinyu Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Li Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Jinping Tang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Yu Miao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Xiao Xia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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Guéguen Y, Frerejacques M. Review of Knowledge of Uranium-Induced Kidney Toxicity for the Development of an Adverse Outcome Pathway to Renal Impairment. Int J Mol Sci 2022; 23:ijms23084397. [PMID: 35457214 PMCID: PMC9030063 DOI: 10.3390/ijms23084397] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
An adverse outcome pathway (AOP) is a conceptual construct of causally and sequentially linked events, which occur during exposure to stressors, with an adverse outcome relevant to risk assessment. The development of an AOP is a means of identifying knowledge gaps in order to prioritize research assessing the health risks associated with exposure to physical or chemical stressors. In this paper, a review of knowledge was proposed, examining experimental and epidemiological data, in order to identify relevant key events and potential key event relationships in an AOP for renal impairment, relevant to stressors such as uranium (U). Other stressors may promote similar pathways, and this review is a necessary step to compare and combine knowledge reported for nephrotoxicants. U metal ions are filtered through the glomerular membrane of the kidneys, then concentrate in the cortical and juxtaglomerular areas, and bind to the brush border membrane of the proximal convoluted tubules. U uptake by epithelial cells occurs through endocytosis and the sodium-dependent phosphate co-transporter (NaPi-IIa). The identified key events start with the inhibition of the mitochondria electron transfer chain and the collapse of mitochondrial membrane potential, due to cytochrome b5/cytochrome c disruption. In the nucleus, U directly interacts with negatively charged DNA phosphate, thereby inducing an adduct formation, and possibly DNA strand breaks or cross-links. U also compromises DNA repair by inhibiting zing finger proteins. Thereafter, U triggers the Nrf2, NF-κB, or endoplasmic reticulum stress pathways. The resulting cellular key events include oxidative stress, DNA strand breaks and chromosomal aberrations, apoptosis, and pro-inflammatory effects. Finally, the main adverse outcome is tubular damage of the S2 and S3 segments of the kidneys, leading to tubular cell death, and then kidney failure. The attribution of renal carcinogenesis due to U is controversial, and specific experimental or epidemiological studies must be conducted. A tentative construction of an AOP for uranium-induced kidney toxicity and failure was proposed.
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Lin YW. Uranyl Binding to Proteins and Structural-Functional Impacts. Biomolecules 2020; 10:biom10030457. [PMID: 32187982 PMCID: PMC7175365 DOI: 10.3390/biom10030457] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/08/2020] [Accepted: 03/13/2020] [Indexed: 01/29/2023] Open
Abstract
The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO22+). Although uranyl–protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl–protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl–protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; ; Tel.: +86-734-8578079
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes, University of South China, Hengyang 421001, China
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Liu HX, Li L, He B, Gao SQ, Wen GB, Lin YW. Neuroglobin is capable of self-oxidation of methionine64 introduced at the heme axial position. Dalton Trans 2018; 47:10847-10852. [PMID: 30027178 DOI: 10.1039/c8dt02397b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Neuroglobin (Ngb), with its physiological role not fully understood, was found to be capable of self-oxidation of methionine64 introduced at the heme axial position (H64M Ngb), adopting a high-spin heme state and producing both methionine sulfoxide (SO-Met) and sulfone (SO2-Met), which represents the structure and function of cytochrome c in a non-native state.
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Affiliation(s)
- Hai-Xiao Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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5
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Gentry KA, Prade E, Barnaba C, Zhang M, Mahajan M, Im SC, Anantharamaiah GM, Nagao S, Waskell L, Ramamoorthy A. Kinetic and Structural Characterization of the Effects of Membrane on the Complex of Cytochrome b 5 and Cytochrome c. Sci Rep 2017; 7:7793. [PMID: 28798301 PMCID: PMC5552742 DOI: 10.1038/s41598-017-08130-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022] Open
Abstract
Cytochrome b5 (cytb5) is a membrane protein vital for the regulation of cytochrome P450 (cytP450) metabolism and is capable of electron transfer to many redox partners. Here, using cyt c as a surrogate for cytP450, we report the effect of membrane on the interaction between full-length cytb5 and cyt c for the first time. As shown through stopped-flow kinetic experiments, electron transfer capable cytb5 - cyt c complexes were formed in the presence of bicelles and nanodiscs. Experimentally measured NMR parameters were used to map the cytb5-cyt c binding interface. Our experimental results identify differences in the binding epitope of cytb5 in the presence and absence of membrane. Notably, in the presence of membrane, cytb5 only engaged cyt c at its lower and upper clefts while the membrane-free cytb5 also uses a distal region. Using restraints generated from both cytb5 and cyt c, a complex structure was generated and a potential electron transfer pathway was identified. These results demonstrate the importance of studying protein-protein complex formation in membrane mimetic systems. Our results also demonstrate the successful preparation of novel peptide-based lipid nanodiscs, which are detergent-free and possesses size flexibility, and their use for NMR structural studies of membrane proteins.
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Affiliation(s)
| | - Elke Prade
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlo Barnaba
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meng Zhang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mukesh Mahajan
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - G M Anantharamaiah
- Department of Medicine, UAB Medical Center, Birmingham, Alabama, 35294, USA
| | - Satoshi Nagao
- Graduate School of Material Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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Liu Q, Zhang X, Zeng W, Wang J, Zhou Z. Origin of d-π Interaction in Cobalt(II) Porphyrins under Synergistic Effects of Core Contraction and Axial Ligation: Implications for a Ligand Effect of Natural Distorted Tetrapyrrole. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201600226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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7
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Hirano Y, Kimura S, Tamada T. High-resolution crystal structures of the solubilized domain of porcine cytochrome b5. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1572-81. [PMID: 26143928 PMCID: PMC4498607 DOI: 10.1107/s1399004715009438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/18/2015] [Indexed: 11/11/2022]
Abstract
Mammalian microsomal cytochrome b5 has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochrome b5 from porcine liver were determined at sub-angstrom resolution (0.76-0.95 Å) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.
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Affiliation(s)
- Yu Hirano
- Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Shigenobu Kimura
- Department of Biomolecular Functional Engineering, Faculty of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Taro Tamada
- Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
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Sun MH, Liu SQ, Du KJ, Nie CM, Lin YW. A spectroscopic study of uranyl-cytochrome b5/cytochrome c interactions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:130-137. [PMID: 24051281 DOI: 10.1016/j.saa.2013.08.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 08/28/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Uranium is harmful to human health due to its radiation damage and the ability of uranyl ion (UO2(2+)) to interact with various proteins and disturb their biological functions. Cytochrome b5 (cyt b5) is a highly negatively charged heme protein and plays a key role in mediating cytochrome c (cyt c) signaling in apoptosis by forming a dynamic cyt b5-cyt c complex. In previous molecular modeling study in combination with UV-Vis studies, we found that UO2(2+) is capable of binding to cyt b5 at surface residues, Glu37 and Glu43. In this study, we further investigated the structural consequences of cyt b5 and cyt c, as well as cyt b5-cyt c complex, upon uranyl binding, by fluorescence spectroscopic and circular dichroism techniques. Moreover, we proposed a uranyl binding site for cyt c at surface residues, Glu66 and Glu69, by performing a molecular modeling study. It was shown that uranyl binds to cyt b5 (KD=10 μM), cyt c (KD=87 μM), and cyt b5-cyt c complex (KD=30 μM) with a different affinity, which slightly alters the protein conformation and disturbs the interaction of cyt b5-cyt c complex. Additionally, we investigated the functional consequences of uranyl binding to the protein surface, which decreases the inherent peroxidase activity of cyt c. The information of uranyl-cyt b5/cyt c interactions gained in this study likely provides a clue for the mechanism of uranyl toxicity.
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Affiliation(s)
- Mei-Hui Sun
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
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9
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Ranieri A, Bortolotti CA, Battistuzzi G, Borsari M, Paltrinieri L, Di Rocco G, Sola M. Effect of motional restriction on the unfolding properties of a cytochrome c featuring a His/Met–His/His ligation switch. Metallomics 2014; 6:874-84. [DOI: 10.1039/c3mt00311f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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10
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Shumyantseva VV, Bulko TV, Lisitsyna VB, Urlacher VB, Kuzikov AV, Suprun EV, Archakov AI. Electrochemical measurement of intraprotein and interprotein electron transfer. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913030172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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11
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Jiang N, Kuznetsov A, Nocek JM, Hoffman BM, Crane BR, Hu X, Beratan DN. Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies. J Phys Chem B 2013; 117:9129-41. [PMID: 23895339 PMCID: PMC3809023 DOI: 10.1021/jp401551t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and in complexes with four mutants of the Cc protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:Cc interface for the F82Y(I) mutants compared to that the WT and F82S(W) complexes are predicted to change the reorganization energies for the CcP:Cc ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor-acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, Duke University, Durham, NC 27708
| | | | - Judith M. Nocek
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, NC 27708
- Department of Biochemistry, Duke University, Durham, NC 27708
- Department of Physics, Duke University, Durham, NC 27708
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12
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Lin YW, Wang J. Structure and function of heme proteins in non-native states: a mini-review. J Inorg Biochem 2013; 129:162-71. [PMID: 23916118 DOI: 10.1016/j.jinorgbio.2013.07.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/12/2022]
Abstract
Heme proteins perform various biological functions ranging from electron transfer, oxygen binding and transport, catalysis, to signaling. Although adopting proper native states is very important for these functions, progresses in representative heme proteins, including cytochrome c (cyt c), cytochrome b5 (cyt b5), myoglobin (Mb), neuroglobin (Ngb), cytochrome P450 (CYP) and heme-based sensor proteins such as CO sensor CooA, showed that various native functions, or new functions evolved, are also closely associated with non-native states. The structure and function relationship of heme proteins in non-native states is thus as important as that in native states for elucidating the precise roles of heme proteins in biological systems.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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13
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Volkov AN, van Nuland NAJ. Electron transfer interactome of cytochrome C. PLoS Comput Biol 2012; 8:e1002807. [PMID: 23236271 PMCID: PMC3516563 DOI: 10.1371/journal.pcbi.1002807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/12/2012] [Indexed: 01/31/2023] Open
Abstract
Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility. A number of vital cellular processes such as respiration, photosynthesis, and multifarious metabolic conversions rely on a long-range electron transfer (ET) among protein molecules. Full understanding of the biological ET requires accurate description of the redox protein complexes, which is hampered by their pronounced mobility and short lifetimes. Here we used a simple computational approach to predict the ET properties of the physiological protein complexes of cytochrome c (Cc) – a small electron carrier that coordinates the electron flow among different redox partners. By performing extensive conformational sampling of the possible binding geometries, we mapped out functional epitopes in the Cc complexes and assessed their ET properties. Our study suggests that protein dynamics within redox complexes is the rate-limiting step in the intermolecular ET and indicates that the functional epitope size correlates with the extent of dynamics in the Cc complexes. We believe that the latter finding can be used as a diagnostic tool for protein mobility and expect that this work will engender future studies of the intermolecular ET in biological networks.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Belgium.
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14
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Shinoda S, Tsukube H. Molecular recognition of cytochrome c by designed receptors for generation of in vivo and in vitro functions. Chem Sci 2011. [DOI: 10.1039/c1sc00162k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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15
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Wan D, Liao LF, Zhao MM, Wu ML, Wu YM, Lin YW. Interactions of uranyl ion with cytochrome b 5 and its His39Ser variant as revealed by molecular simulation in combination with experimental methods. J Mol Model 2011; 18:1009-13. [DOI: 10.1007/s00894-011-1097-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 03/22/2011] [Indexed: 11/24/2022]
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16
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Lederer F. Another look at the interaction between mitochondrial cytochrome c and flavocytochrome b (2). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1283-99. [PMID: 21503671 DOI: 10.1007/s00249-011-0697-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/28/2011] [Accepted: 03/16/2011] [Indexed: 11/29/2022]
Abstract
Yeast flavocytochrome b (2) tranfers reducing equivalents from lactate to oxygen via cytochrome c and cytochrome c oxidase. The enzyme catalytic cycle includes FMN reduction by lactate and reoxidation by intramolecular electron transfer to heme b (2). Each subunit of the soluble tetrameric enzyme consists of an N terminal b (5)-like heme-binding domain and a C terminal flavodehydrogenase. In the crystal structure, FMN and heme are face to face, and appear to be in a suitable orientation and at a suitable distance for exchanging electrons. But in one subunit out of two, the heme domain is disordered and invisible. This raises a central question: is this mobility required for interaction with the physiological acceptor cytochrome c, which only receives electrons from the heme and not from the FMN? The present review summarizes the results of the variety of methods used over the years that shed light on the interactions between the flavin and heme domains and between the enzyme and cytochrome c. The conclusion is that one should consider the interaction between the flavin and heme domains as a transient one, and that the cytochrome c and the flavin domain docking areas on the heme b (2) domain must overlap at least in part. The heme domain mobility is an essential component of the flavocytochrome b (2) functioning. In this respect, the enzyme bears similarity to a variety of redox enzyme systems, in particular those in which a cytochrome b (5)-like domain is fused to proteins carrying other redox functions.
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Affiliation(s)
- Florence Lederer
- Laboratoire de Chimie Physique, Université Paris-Sud, Orsay Cedex, France.
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17
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Lê KHD, Boussac A, Frangioni B, Léger C, Lederer F. Interdomain contacts in flavocytochrome b(2), a mutational analysis. Biochemistry 2009; 48:10803-9. [PMID: 19821613 DOI: 10.1021/bi901301r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Each flavocytochrome b(2) (l-lactate cytochrome c oxidoreductase) subunit consists of an N-terminal cytochrome domain and a C-terminal flavodehydrogenase (FDH) domain. In the enzyme crystal structure, only two heme domains are visible per enzyme tetramer, because of the mobility of the other two heme domains relative to the FDH domains. Evidence was subsequently provided that this mobility also exists in solution. Numerous kinetic studies showed that, during the catalytic cycle, electrons are transferred one by one from the reduced flavin to heme b(2) in the same subunit. In previous work, we provided evidence that a monoclonal antibody that abolishes flavin to heme electron transfer uses part of the interdomain interface for binding to its antigen, the native heme domain. In this work, we use a number of heme domain side chain substitutions in and around the interface to probe their effect on flavin to heme electron transfer. Using steady-state and pre-steady-state kinetics, as well as redox potential determinations and EPR measurements, we define several hydrophobic interactions and van der Waals contacts that are important for a catalytically competent docking of the heme domain onto the FDH domain. In addition, with several extremely slow mutant enzymes, we propose an isosbestic wavelength between oxidized and reduced heme for specifically following the kinetics of flavosemiquinone formation from two-electron reduced flavin.
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Affiliation(s)
- K H Diêp Lê
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR9063, 91198 Gif-sur-Yvette Cedex, France
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Gursahani S, Schoephoerster RT, Prabhakaran M. Exploring Electron Transfer Between Heme Proteins of Cytochrome c Super Family in Biosensors: A Molecular Mechanics Study. J Biomol Struct Dyn 2008; 26:329-38. [DOI: 10.1080/07391102.2008.10507248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Patel AD, Nocek JM, Hoffman BM. Kinetic-dynamic model for conformational control of an electron transfer photocycle: mixed-metal hemoglobin hybrids. J Phys Chem B 2008; 112:11827-37. [PMID: 18717535 PMCID: PMC2672620 DOI: 10.1021/jp8054679] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
It is becoming increasingly clear that the transfer of an electron across a protein-protein interface is coupled to the dynamics of conformational conversion between and within ensembles of interface conformations. Electron transfer (ET) reactions in conformationally mobile systems provide a "clock" against which the rapidity of a dynamic process may be measured, and we here report a simple kinetic (master equation) model that self-consistently incorporates conformational dynamics into an ET photocycle comprised of a photoinitiated "forward" step and thermal return to ground. This kinetic/dynamic (KD) model assumes an ET complex exists as multiple interconverting conformations which partition into an ET-optimized (reactive; R) population and a less-reactive population ( S). We take the members of each population to be equivalent by constraining them to have the same conformational energy, the same average rate constant for conversion to members of the other population, and the same rate constants for forward and back ET. The result is a mapping of a complicated energy surface onto the simple "gating", two-well surface, but with rate constants that are defined microscopically. This model successfully describes the changes in the ET photocycle within the "predocked" mixed-metal hemoglobin (Hb) hybrid, [alpha(Zn), beta(Fe3+N 3 (-))], as conformational kinetics are modulated by variations in viscosity (eta = 1-15 cP; 20 degrees C). The description reveals how the conformational "routes" by which a hybrid progresses through a photocycle differ in different dynamic regimes. Even at eta = 1 cP, the populations are not in fast exchange, and ET involves a complex interplay between conformational and ET processes; at intermediate viscosities the hybrid exhibits "differential dynamics" in which the forward and back ET processes involve different initial ensembles of configurational substates; by eta = 15 cP, the slow-exchange limit is approached. Even at low viscosity, the ET-coupled motions are fairly slow, with rate constants of <10 (3) s (-1). Current ideas about Hb function lead to the testable hypothesis that ET in the hybrid may be coupled to allosteric fluctuations of the two [alpha 1, beta 2] dimers of Hb.
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Affiliation(s)
- Ami D Patel
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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20
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Blumberger J. Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment. Phys Chem Chem Phys 2008; 10:5651-67. [PMID: 18956100 DOI: 10.1039/b807444e] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computer simulations of biological electron transfer reactions are reviewed with a focus on the calculation of reaction free energy (driving force) and reorganization free energy. Then a mixed quantum mechanical/molecular mechanical (QM/MM) approach is described which is designed for computation of these quantities for pure electron transfer reactions with large donor-acceptor separation distances. The method is applied to intra-protein electron transfer in Ru(bpy)(2)(im)His33 cytochrome c and the results compared to experimental data. Several modeling aspects which are important for successful calculation of free energies with QM/MM are discussed in detail.
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21
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Léger C, Bertrand P. Direct Electrochemistry of Redox Enzymes as a Tool for Mechanistic Studies. Chem Rev 2008; 108:2379-438. [DOI: 10.1021/cr0680742] [Citation(s) in RCA: 594] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Deep S, Im SC, Zuiderweg ER, Waskell L. Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data. Biochemistry 2005; 44:10654-68. [PMID: 16060674 PMCID: PMC2547882 DOI: 10.1021/bi050482x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To identify the binding site for bovine cytochrome b(5) (cyt b(5)) on horse cytochrome c (cyt c), cross-saturation transfer NMR experiments were performed with (2)H- and (15)N-enriched cyt c and unlabeled cyt b(5). In addition, chemical shift changes of the cyt c backbone amide and side chain methyl resonances were monitored as a function of cyt b(5) concentration. The chemical shift changes indicate that the complex is in fast exchange, and are consistent with a 1:1 stoichiometry. A K(a) of (4 +/- 3) x 10(5) M(-)(1) was obtained with a lower limit of 855 s(-)(1) for the dissociation rate of the complex. Mapping of the chemical shift variations and intensity changes upon cross-saturation NMR experiments in the complex reveals a single, contiguous interaction interface on cyt c. Using NMR data as constraints, a protein docking program was used to calculate two low-energy model complex clusters. Independent calculations of the effect of the cyt b(5) heme ring current-induced magnetic dipole on cyt c were used to discriminate between the different models. The interaction surface of horse cyt c in the current experimentally constrained model of the cyt c-cyt b(5) complex is similar but not identical to the interface predicted in yeast cyt c by Brownian dynamics and docking calculations. The occurrence of different amino acids at the protein-protein interface and the dissimilar assumptions employed in the calculations can largely account for the nonidentical interfaces.
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Affiliation(s)
- Shashank Deep
- Department of Anesthesiology, University of Michigan, VA Medical Center, 2215 Fuller Rd., Ann Arbor, MI 48105
- Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109
| | - Sang Choul Im
- Department of Anesthesiology, University of Michigan, VA Medical Center, 2215 Fuller Rd., Ann Arbor, MI 48105
| | - Erik R.P. Zuiderweg
- Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109
- Correspondence to be addressed to: Lucy Waskell, Phone (734) 769-7100 ext. 5858, or
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, VA Medical Center, 2215 Fuller Rd., Ann Arbor, MI 48105
- Correspondence to be addressed to: Lucy Waskell, Phone (734) 769-7100 ext. 5858, or
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23
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Kang SA, Crane BR. Effects of interface mutations on association modes and electron-transfer rates between proteins. Proc Natl Acad Sci U S A 2005; 102:15465-70. [PMID: 16227441 PMCID: PMC1266099 DOI: 10.1073/pnas.0505176102] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Accepted: 09/08/2005] [Indexed: 11/18/2022] Open
Abstract
Although bonding networks determine electron-transfer (ET) rates within proteins, the mechanism by which structure and dynamics influence ET across protein interfaces is not well understood. Measurements of photochemically induced ET and subsequent charge recombination between Zn-porphyrin-substituted cytochrome c peroxidase and cytochrome c in single crystals correlate reactivity with defined structures for different association modes of the redox partners. Structures and ET rates in crystals are consistent with tryptophan oxidation mediating charge recombination reactions. Conservative mutations at the interface can drastically affect how the proteins orient and dispose redox centers. Whereas some configurations are ET inactive, the wild-type complex exhibits the fastest recombination rate. Other association modes generate ET rates that do not correlate with predictions based on cofactor separations or simple bonding pathways. Inhibition of photoinduced ET at <273 K indicates gating by small-amplitude dynamics, even within the crystal. Thus, different associations achieve states of similar reactivity, and within those states conformational fluctuations enable interprotein ET.
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Affiliation(s)
- Seong A Kang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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24
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Lin YW, Wang WH, Zhang Q, Lu HJ, Yang PY, Xie Y, Huang ZX, Wu HM. Converting Cytochrome b5 into cytochrome c-like protein. Chembiochem 2005; 6:1356-9. [PMID: 15977276 DOI: 10.1002/cbic.200500030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ying-Wu Lin
- Chemical Biology Lab, Department of Chemistry, Fudan University, Shanghai 200433, China
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Lin YW, Zhao DX, Wang ZH, Yu WH, Huang ZX. Expression of lipase-solubilized bovine liver microsomal cytochrome b5 in Escherichia coli as a glutathione S-transferase fusion protein (GST-cyt b5). Protein Expr Purif 2005; 45:352-8. [PMID: 16146697 DOI: 10.1016/j.pep.2005.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2005] [Revised: 06/04/2005] [Accepted: 06/06/2005] [Indexed: 11/21/2022]
Abstract
The gene coding for the lipase-solubilized bovine liver microsomal cytochrome b5 (cyt b5) was expressed in Escherichia coli BL21 cells as a glutathione S-transferase fusion protein (GST-cyt b5) using the constructed expression vector pGEX-cyt b). The GST-cyt b5 fusion protein can be matured in vivo as a holoprotein with heme incorporated into cyt b5 during the fermentation, and the purification procedures were simplified by using a one-step affinity column chromatography with glutathione-agarose gel. The fusion protein was characterized by its spectroscopic and electrochemical properties, the interaction between GST-cyt b5 and cyt c was also investigated. The results show that GST-cyt b5 fusion protein shares similar properties and functions to that of isolated cyt b5. Although cyt b5 and GST were fused together, the two partners have not made significant structural and functional alterations of their counterparts, the protein-protein interactions between them are apparently very weak. To our knowledge, the present study is the first report to express cyt b5 as a GST-cyt b5 fusion protein, which provides a good example for the in vivo maturation of a hemoprotein as a GST fusion protein and sheds new light on the protein-protein interactions within the GST fusion protein.
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Affiliation(s)
- Ying-Wu Lin
- Chemical Biology Lab, Department of Chemistry, Fudan University, Shanghai 200433, PR China
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26
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Renugopalakrishnan V, Ortiz-Lombardía M, Verma C. Electrostatics of Cytochrome-c assemblies. J Mol Model 2005; 11:265-70. [PMID: 15868153 DOI: 10.1007/s00894-005-0244-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2004] [Accepted: 01/04/2005] [Indexed: 10/25/2022]
Abstract
Electrostatic potentials along with computational mutagenesis are used to obtain atomic level insights into Cytochrome-c in order to design efficient bionanosensors. The electrostatic properties of wild type and mutant Cytochrome-c are examined in the context of their assembly, i.e. are examined in the absence and presence of neighboring molecules from the assembly. An intense increase in the positive potential ensues when the neighboring molecules are taken into account. This suggests that in the extrapolation of electric field effects upon the design of assemblies, considering the properties of only the central molecule may not be sufficient. Additionally, the influence of the uncharged residues becomes quite diminished when the molecule is considered in an assembly. This could pave the way for making mutants that might be more soluble in different media used in the construction of devices. [Figure: see text]. The electrostatic potential, calculated using the program DELPHI mapped on to the surface of Cytochrome-c when it is considered by itself (in the left column) and in the presence of the electrostatic field generated by the presence of the surrounding 4 molecules on the right. The potentials range from -10kT in red to +10kT in blue. The central figure shows the regions that have been mutated to positively charged residues by placing a unit positive charge at the terminal atom of the respective side chain. The figures range from the wild type in the first row, followed by the Gln12, Asn70, Asp50, Glu90 and Ala83 mutants.
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Affiliation(s)
- V Renugopalakrishnan
- Bionanotechnology Group, Department of Biomedical Engineering, College of Engineering, Florida International University, Miami, FL 33174, USA
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Volkov AN, Ferrari D, Worrall JAR, Bonvin AMJJ, Ubbink M. The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Protein Sci 2005; 14:799-811. [PMID: 15689516 PMCID: PMC2279274 DOI: 10.1110/ps.041150205] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Revised: 09/30/2004] [Accepted: 11/19/2004] [Indexed: 10/25/2022]
Abstract
The interaction of bovine microsomal ferricytochrome b5 with yeast iso-1-ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical-shift perturbations for 1H and 15N nuclei of both cytochromes, arising from the interactions with the unlabeled partner proteins, were used for mapping the interacting surfaces on both proteins. The similarity of the binding shifts observed for oxidized and reduced cytochrome c indicates that the complex formation is not influenced by the oxidation state of the cytochrome c. Protein-protein docking simulations have been performed for the binary cytochrome b5-cytochrome c and ternary (cytochrome b5)-(cytochrome c)2 complexes using a novel HADDOCK approach. The docking procedure, which makes use of the experimental data to drive the docking, identified a range of orientations assumed by the proteins in the complex. It is demonstrated that cytochrome c uses a confined surface patch for interaction with a much more extensive surface area of cytochrome b5. Taken together, the experimental data suggest the presence of a dynamic ensemble of conformations assumed by the proteins in the complex.
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Affiliation(s)
- Alexander N Volkov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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