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Article ; Online: Detergent modulates the conformational equilibrium of SARS-CoV-2 Spike during cryo-EM structural determination.

Egri, Shawn B / Wang, Xue / Díaz-Salinas, Marco A / Luban, Jeremy / Dudkina, Natalya V / Munro, James B / Shen, Kuang

2023 Volume 14, Issue 1, Page(s) 2527

Abstract: The Spike glycoprotein of SARS-CoV-2 mediates viral entry into the host cell via the interaction between its receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2). Spike RBD has been reported to adopt two primary conformations, a ...

Abstract	The Spike glycoprotein of SARS-CoV-2 mediates viral entry into the host cell via the interaction between its receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2). Spike RBD has been reported to adopt two primary conformations, a closed conformation in which the binding site is shielded and unable to interact with ACE2, and an open conformation that is capable of binding ACE2. Many structural studies have probed the conformational space of the homotrimeric Spike from SARS-CoV-2. However, how sample buffer conditions used during structural determination influence the Spike conformation is currently unclear. Here, we systematically explored the impact of commonly used detergents on the conformational space of Spike. We show that in the presence of detergent, the Spike glycoprotein predominantly occupies a closed conformational state during cryo-EM structural determination. However, in the absence of detergent, such conformational compaction was neither observed by cryo-EM, nor by single-molecule FRET designed to visualize the movement of RBD in solution in real-time. Our results highlight the highly sensitive nature of the Spike conformational space to buffer composition during cryo-EM structural determination, and emphasize the importance of orthogonal biophysical approaches to validate the structural models obtained.
MeSH term(s)	Humans ; SARS-CoV-2/metabolism ; Detergents/pharmacology ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19 ; Cryoelectron Microscopy ; Protein Binding ; Glycoproteins/metabolism ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Detergents ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Glycoproteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2023-05-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38251-9
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Article ; Online: Towards structural and functional characterization of photosynthetic and mitochondrial supercomplexes.

Dudkina, Natalya V / Folea, I Mihaela / Boekema, Egbert J

Micron (Oxford, England : 1993)

2015 Volume 72, Page(s) 39–51

Abstract: Bioenergetic reactions in chloroplasts and mitochondria are catalyzed by large multi-subunit membrane proteins. About two decades ago it became clear that several of these large membrane proteins further associate into supercomplexes and since then a ... ...

Abstract	Bioenergetic reactions in chloroplasts and mitochondria are catalyzed by large multi-subunit membrane proteins. About two decades ago it became clear that several of these large membrane proteins further associate into supercomplexes and since then a number of new ones have been described. In this review we focus on supercomplexes involved in light harvesting and electron transfer in the primary reactions of oxygenic photosynthesis and on the mitochondrial supercomplexes that catalyze electron transfer and ATP synthesis in oxidative phosphorylation. Functional and structural aspects are overviewed. In addition, several relevant technical aspects are discussed, including membrane solubilization with suitable detergents and methods of purification. Some open questions are addressed, such as the lack of high-resolution structures, the outstanding gaps in the knowledge about supercomplexes involved in cyclic electron transport in photosynthesis and the unusual mitochondrial protein complexes of protists and in particular of ciliates.
MeSH term(s)	Chloroplasts/metabolism ; Chloroplasts/ultrastructure ; Electron Transport ; Microscopy, Electron ; Mitochondria/chemistry ; Mitochondria/metabolism ; Mitochondria/ultrastructure ; Mitochondrial Membranes/metabolism ; Mitochondrial Membranes/ultrastructure ; Mitochondrial Proteins/chemistry ; Mitochondrial Proteins/isolation & purification ; Mitochondrial Proteins/metabolism ; Mitochondrial Proteins/ultrastructure ; Models, Biological ; Models, Molecular ; Multiprotein Complexes/chemistry ; Multiprotein Complexes/isolation & purification ; Multiprotein Complexes/metabolism ; Multiprotein Complexes/ultrastructure ; Oxidative Phosphorylation ; Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/chemistry ; Photosynthetic Reaction Center Complex Proteins/isolation & purification ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Photosynthetic Reaction Center Complex Proteins/ultrastructure
Chemical Substances	Mitochondrial Proteins ; Multiprotein Complexes ; Photosynthetic Reaction Center Complex Proteins
Language	English
Publishing date	2015-05
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	207808-9
ISSN	1878-4291 ; 0047-7206 ; 0968-4328
ISSN (online)	1878-4291
ISSN	0047-7206 ; 0968-4328
DOI	10.1016/j.micron.2015.03.002
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Article: Structures of mitochondrial oxidative phosphorylation supercomplexes and mechanisms for their stabilisation.

Chaban, Yuriy / Boekema, Egbert J / Dudkina, Natalya V

Biochimica et biophysica acta

2014 Volume 1837, Issue 4, Page(s) 418–426

Abstract: Oxidative phosphorylation (OXPHOS) is the main source of energy in eukaryotic cells. This process is performed by means of electron flow between four enzymes, of which three are proton pumps, in the inner mitochondrial membrane. The energy accumulated in ...

Abstract	Oxidative phosphorylation (OXPHOS) is the main source of energy in eukaryotic cells. This process is performed by means of electron flow between four enzymes, of which three are proton pumps, in the inner mitochondrial membrane. The energy accumulated in the proton gradient over the inner membrane is utilized for ATP synthesis by a fifth OXPHOS complex, ATP synthase. Four of the OXPHOS protein complexes associate into stable entities called respiratory supercomplexes. This review summarises the current view on the arrangement of the electron transport chain in mitochondrial cristae. The functional role of the supramolecular organisation of the OXPHOS system and the factors that stabilise such organisation are highlighted. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components.
MeSH term(s)	Animals ; Electron Transport ; Electron Transport Chain Complex Proteins/chemistry ; Electron Transport Chain Complex Proteins/metabolism ; Humans ; Mitochondrial Membranes/metabolism ; Models, Biological ; Models, Molecular ; Oxidative Phosphorylation ; Plant Proteins/chemistry ; Plant Proteins/metabolism ; Protein Conformation
Chemical Substances	Electron Transport Chain Complex Proteins ; Plant Proteins
Language	English
Publishing date	2014-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbabio.2013.10.004
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Article ; Online: Atomic force microscopy of membrane pore formation by cholesterol dependent cytolysins.

Hodel, Adrian W / Leung, Carl / Dudkina, Natalya V / Saibil, Helen R / Hoogenboom, Bart W

Current opinion in structural biology

2016 Volume 39, Page(s) 8–15

MeSH term(s)	Bacteria ; Cell Membrane/ultrastructure ; Cholesterol/chemistry ; Cytotoxins/chemistry ; Microscopy, Atomic Force
Chemical Substances	Cytotoxins ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2016-04-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2016.03.005
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Article: Towards structural and functional characterization of photosynthetic and mitochondrial supercomplexes

Dudkina, Natalya V / Egbert J. Boekema / I. Mihaela Folea

Micron. 2015 May, v. 72

2015

Abstract	Bioenergetic reactions in chloroplasts and mitochondria are catalyzed by large multi-subunit membrane proteins. About two decades ago it became clear that several of these large membrane proteins further associate into supercomplexes and since then a number of new ones have been described. In this review we focus on supercomplexes involved in light harvesting and electron transfer in the primary reactions of oxygenic photosynthesis and on the mitochondrial supercomplexes that catalyze electron transfer and ATP synthesis in oxidative phosphorylation. Functional and structural aspects are overviewed. In addition, several relevant technical aspects are discussed, including membrane solubilization with suitable detergents and methods of purification. Some open questions are addressed, such as the lack of high-resolution structures, the outstanding gaps in the knowledge about supercomplexes involved in cyclic electron transport in photosynthesis and the unusual mitochondrial protein complexes of protists and in particular of ciliates.
Keywords	adenosine triphosphate ; chloroplasts ; Ciliophora ; detergents ; electron transfer ; membrane proteins ; mitochondria ; oxidative phosphorylation ; photosynthesis ; protists ; purification methods ; solubilization
Language	English
Dates of publication	2015-05
Size	p. 39-51.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	207808-9
ISSN	1878-4291 ; 0047-7206 ; 0968-4328
ISSN (online)	1878-4291
ISSN	0047-7206 ; 0968-4328
DOI	10.1016/j.micron.2015.03.002
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Article: Structures of mitochondrial oxidative phosphorylation supercomplexes and mechanisms for their stabilisation

Chaban, Yuriy / Egbert J. Boekema / Natalya V. Dudkina

Elsevier B.V. Biochimica et biophysica acta. 2014 Apr., v. 1837, no. 4

2014

Abstract	Oxidative phosphorylation (OXPHOS) is the main source of energy in eukaryotic cells. This process is performed by means of electron flow between four enzymes, of which three are proton pumps, in the inner mitochondrial membrane. The energy accumulated in the proton gradient over the inner membrane is utilized for ATP synthesis by a fifth OXPHOS complex, ATP synthase. Four of the OXPHOS protein complexes associate into stable entities called respiratory supercomplexes. This review summarises the current view on the arrangement of the electron transport chain in mitochondrial cristae. The functional role of the supramolecular organisation of the OXPHOS system and the factors that stabilise such organisation are highlighted. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components.
Keywords	H+/K+-exchanging ATPase ; H-transporting ATP synthase ; adenosine triphosphate ; energy ; eukaryotic cells ; mitochondria ; mitochondrial membrane ; oxidative phosphorylation ; proton pump ; ultrastructure
Language	English
Dates of publication	2014-04
Size	p. 418-426.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282711-6
ISSN	0005-2728 ; 0304-4173
ISSN	0005-2728 ; 0304-4173
DOI	10.1016/j.bbabio.2013.10.004
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Article ; Online: Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography.

Dudkina, Natalya V / Kudryashev, Mikhail / Stahlberg, Henning / Boekema, Egbert J

Proceedings of the National Academy of Sciences of the United States of America

2011 Volume 108, Issue 37, Page(s) 15196–15200

Abstract: The respirasome is a multisubunit supercomplex of the respiratory chain in mitochondria. Here we report the 3D reconstruction of the bovine heart respirasome, composed of dimeric complex III and single copies of complex I and IV, at about 2.2-nm ... ...

Abstract	The respirasome is a multisubunit supercomplex of the respiratory chain in mitochondria. Here we report the 3D reconstruction of the bovine heart respirasome, composed of dimeric complex III and single copies of complex I and IV, at about 2.2-nm resolution, determined by cryoelectron tomography and subvolume averaging. Fitting of X-ray structures of single complexes I, III(2), and IV with high fidelity allows interpretation of the model at the level of secondary structures and shows how the individual complexes interact within the respirasome. Surprisingly, the distance between cytochrome c binding sites of complexes III(2) and IV is about 10 nm. Modeling indicates a loose interaction between the three complexes and provides evidence that lipids are gluing them at the interfaces.
MeSH term(s)	Animals ; Cattle ; Cryoelectron Microscopy ; Electron Transport ; Electron Transport Chain Complex Proteins/metabolism ; Electron Transport Chain Complex Proteins/ultrastructure ; Electron Transport Complex I/metabolism ; Electron Transport Complex I/ultrastructure ; Electron Transport Complex III/metabolism ; Electron Transport Complex III/ultrastructure ; Electron Transport Complex IV/metabolism ; Electron Transport Complex IV/ultrastructure ; Mitochondria/metabolism ; Mitochondria/ultrastructure ; Models, Molecular ; Protein Binding ; Tomography/methods
Chemical Substances	Electron Transport Chain Complex Proteins ; Electron Transport Complex IV (EC 1.9.3.1) ; Electron Transport Complex I (EC 7.1.1.2) ; Electron Transport Complex III (EC 7.1.1.8)
Language	English
Publishing date	2011-08-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1107819108
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Article ; Online: Imaging of organelles by electron microscopy reveals protein-protein interactions in mitochondria and chloroplasts.

Dudkina, Natalya V / Kouril, Roman / Bultema, Jelle B / Boekema, Egbert J

FEBS letters

2010 Volume 584, Issue 12, Page(s) 2510–2515

Abstract: Ongoing progress in electron microscopy (EM) offers now an opening to visualize cells at the nanoscale by cryo-electron tomography (ET). Large protein complexes can be resolved at near-atomic resolution by single particle averaging. Some examples from ... ...

Abstract	Ongoing progress in electron microscopy (EM) offers now an opening to visualize cells at the nanoscale by cryo-electron tomography (ET). Large protein complexes can be resolved at near-atomic resolution by single particle averaging. Some examples from mitochondria and chloroplasts illustrate the possibilities with an emphasis on the membrane organization. Cryo-ET performed on non-chemically fixed, unstained, ice-embedded material can visualize specific large membrane protein complexes. In combination with averaging methods, 3D structures were calculated of mitochondrial ATP synthase at 6 nm resolution and of chloroplast photosystem II at 3.5 nm.
MeSH term(s)	Chloroplasts/metabolism ; Chloroplasts/ultrastructure ; Cryoelectron Microscopy/methods ; Electron Microscope Tomography/methods ; Membrane Proteins/metabolism ; Membrane Proteins/ultrastructure ; Microscopy, Electron/methods ; Mitochondria/metabolism ; Mitochondria/ultrastructure ; Mitochondrial Proteins/metabolism ; Mitochondrial Proteins/ultrastructure ; Multiprotein Complexes/metabolism ; Multiprotein Complexes/ultrastructure ; Nanotechnology ; Organelles/metabolism ; Organelles/ultrastructure ; Photosystem II Protein Complex/metabolism ; Photosystem II Protein Complex/ultrastructure ; Protein Interaction Domains and Motifs
Chemical Substances	Membrane Proteins ; Mitochondrial Proteins ; Multiprotein Complexes ; Photosystem II Protein Complex
Language	English
Publishing date	2010-06-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2010.03.027
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Article ; Online: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.

Cell

2020 Volume 183, Issue 3, Page(s) 739–751.e8

Abstract: The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells ... ...

Abstract	The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Animals ; Antibodies, Monoclonal/immunology ; Antibodies, Viral/immunology ; Betacoronavirus/pathogenicity ; Betacoronavirus/physiology ; Betacoronavirus/ultrastructure ; COVID-19 ; Cells, Cultured ; Coronavirus Infections/virology ; Female ; Genetic Variation ; HEK293 Cells ; Humans ; Male ; Models, Molecular ; Pandemics ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/virology ; Protein Conformation ; Protein Processing, Post-Translational ; Receptors, Coronavirus ; Receptors, Virus/metabolism ; SARS-CoV-2 ; Species Specificity ; Spike Glycoprotein, Coronavirus/physiology ; Spike Glycoprotein, Coronavirus/ultrastructure
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Viral ; Receptors, Coronavirus ; Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2020.09.032
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Article ; Online: Correction: Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin.

Leung, Carl / Dudkina, Natalya V / Lukoyanova, Natalya / Hodel, Adrian W / Farabella, Irene / Pandurangan, Arun P / Jahan, Nasrin / Damaso, Mafalda Pires / Osmanovi / ć, Dino / Reboul, Cyril F / Dunstone, Michelle A / Andrew, Peter W / Lonnen, Rana / Topf, Maya / Saibil, Helen R / Hoogenboom, Bart W

eLife

2014 Volume 4

Language	English
Publishing date	2014
Publishing country	England
Document type	Journal Article
ISSN	2050-084X
ISSN (online)	2050-084X
DOI	10.7554/eLife.06740
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