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Gobet A, Moissonnier L, Chaptal V. CryoEM Data Analysis of Membrane Proteins. Practical Considerations on Amphipathic Belts, Ligands, and Variability Analysis. Methods Mol Biol 2024; 2715:471-483. [PMID: 37930545 DOI: 10.1007/978-1-0716-3445-5_28] [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] [Indexed: 11/07/2023]
Abstract
Membrane proteins data analysis by cryoEM shows some specificities, as can be found in other typical investigations such as biochemistry, biophysics, or X-ray crystallography. Membrane proteins are typically surrounded by an amphipathic belt that will have some degree of influence on the 3D reconstruction and analysis. In this chapter, we review our experience with the ABC transporter BmrA, as well as our statistical analysis of amphipathic belts around membrane proteins, to bring awareness on some particular features of membrane protein investigations by cryoEM.
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Affiliation(s)
- Alexia Gobet
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University Lyon 1, Lyon, France
| | - Loïck Moissonnier
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University Lyon 1, Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University Lyon 1, Lyon, France.
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Gobet A, Zampieri V, Magnard S, Pebay-Peyroula E, Falson P, Chaptal V. The non-Newtonian behavior of detergents during concentration is increased by macromolecules, in trans, and results in their over-concentration. Biochimie 2023; 205:53-60. [PMID: 36087644 DOI: 10.1016/j.biochi.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022]
Abstract
Concentration of pure membrane proteins in detergent solution results in detergent concentration, albeit in unknown amounts. This phenomenon is observed in every lab working on membrane proteins, but has seldom been investigated. In this study, we explored the behavior of detergents mixed with membrane proteins during the step of sample concentration using centrifugal devices. We show that detergent over-concentrate with the presence of polymers, typically membrane or soluble proteins but also polysaccharides. The over-concentration of detergents depends on centrifugal force applied to the device. With the use of a specific dye, we observed the formation of a mesh on the concentrator device. Importantly, reducing the centrifugal speed allows to reduce the concentration of detergents when mixed to macromolecules, as tested with 3 different membrane proteins. All together, these results highlight the non-Newtonian behavior of detergents and provides a solid framework to investigators to improve drastically biochemical and structural studies of membrane proteins.
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Affiliation(s)
- Alexia Gobet
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France
| | - Veronica Zampieri
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Sandrine Magnard
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France
| | | | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France.
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France.
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3
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Biou V. Lipid-membrane protein interaction visualised by cryo-EM: A review. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184068. [PMID: 36216098 DOI: 10.1016/j.bbamem.2022.184068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Membrane proteins reside at interfaces between aqueous and lipid media and solving their molecular structure relies most of the time on removing them from the membrane using detergent. Luckily, this solubilization process does not strip them from all the associated lipids and single-particle cryo-transmission electron microscopy (SP-TEM) has proved a very good tool to visualise both protein high-resolution structure and, often, many of its associated lipids. In this review, we observe membrane protein structures from the Protein DataBank and their associated maps in the Electron Microscopy DataBase and determine how the SP-TEM maps allow lipid visualization, the type of binding sites, the influence of symmetry, resolution and other factors. We illustrate lipid visualization around and inside the protein core, show that some lipid bilayers in the core can be shifted with respect to the membrane and how some proteins can actively bend the lipid bilayer that binds to them. We conclude that resolution improvement in SP-TEM will likely enable many more discoveries regarding the role of lipids bound to proteins.
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Affiliation(s)
- Valérie Biou
- Université de Paris, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique, F-75005 Paris, France.
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4
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Walker V, Vuister GW. Biochemistry and pathophysiology of the Transient Potential Receptor Vanilloid 6 (TRPV6) calcium channel. Adv Clin Chem 2023; 113:43-100. [PMID: 36858649 DOI: 10.1016/bs.acc.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
TRPV6 is a Transient Receptor Potential Vanilloid (TRPV) cation channel with high selectivity for Ca2+ ions. First identified in 1999 in a search for the gene which mediates intestinal Ca2+ absorption, its far more extensive repertoire as a guardian of intracellular Ca2+ has since become apparent. Studies on TRPV6-deficient mice demonstrated additional important roles in placental Ca2+ transport, fetal bone development and male fertility. The first reports of inherited deficiency in newborn babies appeared in 2018, revealing its physiological importance in humans. There is currently strong evidence that TRPV6 also contributes to the pathogenesis of some common cancers. The recently reported association of TRPV6 deficiency with non-alcoholic chronic pancreatitis suggests a role in normal pancreatic function. Over time and with greater awareness of TRPV6, other disease-associations are likely to emerge. Powerful analytical tools have provided invaluable insights into the structure and operation of TRPV6. Its roles in Ca2+ signaling and carcinogenesis, and the use of channel inhibitors in cancer treatment are being intensively investigated. This review first briefly describes the biochemistry and physiology of the channel, and analytical methods used to investigate these. The focus subsequently shifts to the clinical disorders associated with abnormal expression and the underlying pathophysiology. The aims of this review are to increase awareness of this channel, and to draw together findings from a wide range of sources which may help to formulate new ideas for further studies.
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Affiliation(s)
- Valerie Walker
- Department of Clinical Biochemistry, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, United Kingdom.
| | - Geerten W Vuister
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J Piper
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M Johnson
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022; 13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.
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Affiliation(s)
- Zhengdan Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Institute of Big Data Research, Beijing, China
| | - Zhenfeng Deng
- DP Technology, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Duo Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- DP Technology, Beijing, China
| | - Ruihan Xu
- DP Technology, Beijing, China
- National Engineering Research Center of Visual Technology, Peking University, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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Zampieri V, Hilpert C, Garnier M, Gestin Y, Delolme S, Martin J, Falson P, Launay G, Chaptal V. The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins. MEMBRANES 2021; 11:459. [PMID: 34206634 PMCID: PMC8307592 DOI: 10.3390/membranes11070459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 11/23/2022]
Abstract
Detergents wrap around membrane proteins to form a belt covering the hydrophobic part of the protein serving for membrane insertion and interaction with lipids. The number of detergent monomers forming this belt is usually unknown to investigators, unless dedicated detergent quantification is undertaken, which for many projects is difficult to setup. Yet, having an approximate knowledge of the amount of detergent forming the belt is extremely useful, to better grasp the protein of interest in interaction with its direct environment rather than picturing the membrane protein "naked". We created the Det.Belt server to dress up membrane proteins and represent in 3D the bulk made by detergent molecules wrapping in a belt. Many detergents are included in a database, allowing investigators to screen in silico the effect of different detergents around their membrane protein. The input number of detergents is changeable with fast recomputation of the belt for interactive usage. Metrics representing the belt are readily available together with scripts to render quality 3D images for publication. The Det.Belt server is a tool for biochemists to better grasp their sample.
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Affiliation(s)
- Veronica Zampieri
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, CEDEX 9, 38042 Grenoble, France;
| | - Cécile Hilpert
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Mélanie Garnier
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Yannick Gestin
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Sébastien Delolme
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Guillaume Launay
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), University of Lyon, IBCP, 7 Passage du Vercors, 69367 Lyon, France; (C.H.); (M.G.); (Y.G.); (S.D.); (J.M.); (P.F.)
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