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Schweitzer-Stenner R. Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy. J Inorg Biochem 2024; 259:112641. [PMID: 38901065 DOI: 10.1016/j.jinorgbio.2024.112641] [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: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.
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2
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Ripanti F, Di Venere A, Cestelli Guidi M, Romani M, Filabozzi A, Carbonaro M, Piro MC, Sinibaldi F, Nucara A, Mei G. The Puzzling Problem of Cardiolipin Membrane-Cytochrome c Interactions: A Combined Infrared and Fluorescence Study. Int J Mol Sci 2021; 22:ijms22031334. [PMID: 33572777 PMCID: PMC7866282 DOI: 10.3390/ijms22031334] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/30/2022] Open
Abstract
The interaction of cytochrome c (cyt c) with natural and synthetic membranes is known to be a complex phenomenon, involving both protein and lipid conformational changes. In this paper, we combined infrared and fluorescence spectroscopy to study the structural transformation occurring to the lipid network of cardiolipin-containing large unilamellar vesicles (LUVs). The data, collected at increasing protein/lipid ratio, demonstrate the existence of a multi-phase process, which is characterized by: (i) the interaction of cyt c with the lipid polar heads; (ii) the lipid anchorage of the protein on the membrane surface; and (iii) a long-distance order/disorder transition of the cardiolipin acyl chains. Such effects have been quantitatively interpreted introducing specific order parameters and discussed in the frame of the models on cyt c activity reported in literature.
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Affiliation(s)
- Francesca Ripanti
- Department of Physics, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy;
| | - Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (M.C.P.); (F.S.); (G.M.)
| | | | - Martina Romani
- INFN-Laboratori Nazionali di Frascati, Via Enrico Fermi 40, 00044 Frascati, Italy; (M.C.G.); (M.R.)
| | - Alessandra Filabozzi
- Department of Physics, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Marina Carbonaro
- Council for Agricultural Research and Economics (CREA), Research Centre for Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy;
| | - Maria Cristina Piro
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (M.C.P.); (F.S.); (G.M.)
| | - Federica Sinibaldi
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (M.C.P.); (F.S.); (G.M.)
| | - Alessandro Nucara
- Department of Physics, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy;
- Correspondence:
| | - Giampiero Mei
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (M.C.P.); (F.S.); (G.M.)
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3
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Parigoris E, Dunkelmann DL, Murphy A, Wili N, Kaech A, Dumrese C, Jimenez-Rojo N, Silvan U. Facile generation of giant unilamellar vesicles using polyacrylamide gels. Sci Rep 2020; 10:4824. [PMID: 32179778 PMCID: PMC7075891 DOI: 10.1038/s41598-020-61655-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/23/2019] [Indexed: 12/30/2022] Open
Abstract
Giant unilamellar vesicles (GUVs) are model cell-sized systems that have broad applications including drug delivery, analysis of membrane biophysics, and synthetic reconstitution of cellular machineries. Although numerous methods for the generation of free-floating GUVs have been established over the past few decades, only a fraction have successfully produced uniform vesicle populations both from charged lipids and in buffers of physiological ionic strength. In the method described here, we generate large numbers of free-floating GUVs through the rehydration of lipid films deposited on soft polyacrylamide (PAA) gels. We show that this technique produces high GUV concentrations for a range of lipid types, including charged ones, independently of the ionic strength of the buffer used. We demonstrate that the gentle hydration of PAA gels results in predominantly unilamellar vesicles, which is in contrast to comparable methods analyzed in this work. Unilamellarity is a defining feature of GUVs and the generation of uniform populations is key for many downstream applications. The PAA method is widely applicable and can be easily implemented with commonly utilized laboratory reagents, making it an appealing platform for the study of membrane biophysics.
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Affiliation(s)
- Eric Parigoris
- University Hospital Balgrist, University of Zurich, Zürich, Switzerland.,Institute for Biomechanics, ETH Zurich, Zürich, Switzerland.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, USA
| | | | - Allan Murphy
- University Hospital Balgrist, University of Zurich, Zürich, Switzerland.,Institute for Biomechanics, ETH Zurich, Zürich, Switzerland
| | - Nino Wili
- Laboratory of Physical Chemistry, ETH Zurich, Zürich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Claudia Dumrese
- Flow Cytometry Facility, University of Zurich, Zurich, Switzerland
| | - Noemi Jimenez-Rojo
- NCCR Chemical Biology, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Unai Silvan
- University Hospital Balgrist, University of Zurich, Zürich, Switzerland. .,Institute for Biomechanics, ETH Zurich, Zürich, Switzerland.
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4
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Li M, Mandal A, Tyurin VA, DeLucia M, Ahn J, Kagan VE, van der Wel PCA. Surface-Binding to Cardiolipin Nanodomains Triggers Cytochrome c Pro-apoptotic Peroxidase Activity via Localized Dynamics. Structure 2019; 27:806-815.e4. [PMID: 30879887 DOI: 10.1016/j.str.2019.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
The peroxidation of cardiolipins by reactive oxygen species, which is regulated and enhanced by cytochrome c (cyt c), is a critical signaling event in mitochondrial apoptosis. We probe the molecular underpinnings of this mitochondrial death signal through structural and functional studies of horse heart cyt c binding to mixed-lipid membranes containing cardiolipin with mono- and polyunsaturated acyl chains. Lipidomics reveal the selective oxidation of polyunsaturated fatty acid (PUFA) cardiolipin (CL), while multidimensional solid-state NMR probes the structure and dynamics of the membrane and the peripherally bound protein. The hydrophilic milieu at the membrane interface stabilizes a native-like fold, but also leads to localized flexibility at the membrane-interacting protein face. PUFA CL acts as both a preferred substrate and a dynamic regulator by affecting the dynamics of the cyt c N70-I85 Ω loop, which covers the heme cavity.
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Affiliation(s)
- Mingyue Li
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maria DeLucia
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow State Medical University, Moscow 119146, Russian Federation
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
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Milorey B, Schweitzer-Stenner R, Kurbaj R, Malyshka D. pH-Induced Switch between Different Modes of Cytochrome c Binding to Cardiolipin-Containing Liposomes. ACS OMEGA 2019; 4:1386-1400. [PMID: 31459406 PMCID: PMC6647999 DOI: 10.1021/acsomega.8b02574] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/02/2019] [Indexed: 05/28/2023]
Abstract
Fluorescence, visible circular dichroism (CD), absorption, and resonance Raman spectroscopy techniques were combined to explore structural changes of ferricytochrome c upon its binding to cardiolipin-containing liposomes (20% 1,1',1,2'-tetraoleyolcardiolipin and 1,2-deoleyol-sn-glycero-3-phosphocholine) at acidic pH (6.5). According to the earlier work of Kawai [J. Biol. Chem.2005, 280, 34709-347171],cytochrome c binding at this pH is governed by interactions between the phosphate head groups of cardiolipin and amino acid side chains of the so-called L-site, which contains the charged residues K22, K25, K27, and potentially H26 and H33. We found that L-site binding causes a conformational transition that involves a change of the protein's ligation and spin state. In this paper, we report spectroscopic responses to an increasing number of cardiolipin-containing liposomes at pH 6.5 in the absence and presence of NaCl. The latter was found to mostly inhibit protein binding already with 50 mM concentration. The inhibition effect can be quantitatively reproduced by applying the electrostatic theory of Heimburg [Biophys. J.1995, 68, 536-546]. A comparison with corresponding spectroscopic response data obtained at pH 7.4 reveals major differences in that the latter indicates hydrophobic binding, followed by an electrostatically driven conformational change. Visible CD data suggest that structural changes in the heme pocket of liposome-bound ferricytochrome c resemble to some extent those in the denatured protein in urea at neutral and acidic pH. The measured noncoincidence between absorption and CD Soret band of cytochrome c in the presence of a large access of cardiolipin is caused by the electric field at the membrane surface. The very fact that its contribution to the internal electric field in the heme pocket is detectable by spectroscopic means suggests some penetration of the protein into membrane surface.
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Schweitzer-Stenner R. Relating the multi-functionality of cytochrome c to membrane binding and structural conversion. Biophys Rev 2018; 10:1151-1185. [PMID: 29574621 PMCID: PMC6082307 DOI: 10.1007/s12551-018-0409-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022] Open
Abstract
Cytochrome c is known as an electron-carrying protein in the respiratory chain of mitochondria. Over the last 20 years, however, alternative functions of this very versatile protein have become the focus of research interests. Upon binding to anionic lipids such as cardiolipin, the protein acquires peroxidase activity. Multiple lines of evidence suggest that this requires a conformational change of the protein which involves partial unfolding of its tertiary structure. This review summarizes the current state of knowledge of how cytochrome c interacts with cardiolipin-containing surfaces and how this affects its structure and function. In this context, we delineate partially conflicting results regarding the affinity of cytochrome c binding to cardiolipin-containing liposomes of different size and its influence on the structure of the protein and the morphology of the membrane.
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Malyshka D, Schweitzer-Stenner R. Photoreduction of ferricytochrome c in the presence of potassium ferrocyanide. Photochem Photobiol Sci 2018; 17:1462-1468. [DOI: 10.1039/c8pp00286j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferricytochrome c has been previously shown to photoreduce in the presence of ferrocyanide anions, but the process has been poorly understood.
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Milorey B, Malyshka D, Schweitzer-Stenner R. pH Dependence of Ferricytochrome c Conformational Transitions during Binding to Cardiolipin Membranes: Evidence for Histidine as the Distal Ligand at Neutral pH. J Phys Chem Lett 2017; 8:1993-1998. [PMID: 28418677 DOI: 10.1021/acs.jpclett.7b00597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The conformational changes of ferricytochrome c upon binding to cardiolipin-containing small unilamellar vesicles were studied at slightly acidic pH using fluorescence, visible circular dichroism, UV-visible absorption, and resonance Raman spectroscopy. The obtained spectroscopic response data suggest a mode of interaction, which is clearly distinct from the binding process observed at neutral pH. Evidence of a reversible and electrostatic binding mechanism under these conditions is provided through binding inhibition in the presence of 150 mM NaCl. Moreover, UV-visible absorption and resonance Raman spectra reveal that the conformational ensemble of membrane bound cytochrome c is dominated by a mixture of conformers with pentacoordinated and hexacoordinated high-spin heme irons, which contrast with the dominance of low-spin species at neutral pH. While our results confirm the L-site binding proposed by Kawai et al., they point to the protonation of a histidine ligand (H33) as conformational trigger.
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Affiliation(s)
- Bridget Milorey
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Dmitry Malyshka
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
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9
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Hu S, He B, Du KJ, Wang XJ, Gao SQ, Lin YW. Peroxidase Activity of a c-Type Cytochrome b5 in the Non-Native State is Comparable to that of Native Peroxidases. ChemistryOpen 2017. [PMID: 28638761 PMCID: PMC5474653 DOI: 10.1002/open.201700055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The design of artificial metalloenzymes has achieved tremendous progress, although few designs can achieve catalytic performances comparable to that of native enzymes. Moreover, the structure and function of artificial metalloenzymes in non‐native states has rarely been explored. Herein, we found that a c‐type cytochrome b5 (Cyt b5), N57C/S71C Cyt b5, with heme covalently attached to the protein matrix through two Cys–heme linkages, adopts a non‐native state with an open heme site after guanidine hydrochloride (Gdn⋅HCl)‐induced unfolding, which facilitates H2O2 activation and substrate binding. Stopped‐flow kinetic studies further revealed that c‐type Cyt b5 in the non‐native state exhibited impressive peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase. This study presents an alternative approach to the design of functional artificial metalloenzymes by exploring enzymatic functions in non‐native states.
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Affiliation(s)
- Shan Hu
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Bo He
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function University of South China Hengyang 421001 P.R. China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China.,Laboratory of Protein Structure and Function University of South China Hengyang 421001 P.R. China
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