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Krawinski P, Smithers L, van Dalsen L, Boland C, Ostrovitsa N, Pérez J, Caffrey M. 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins. CRYSTAL GROWTH & DESIGN 2024; 24:2985-3001. [PMID: 38585376 PMCID: PMC10995948 DOI: 10.1021/acs.cgd.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
A novel monoacylglycerol, 7.10 MAG, has been produced for use in the in meso (lipid cubic phase) crystallization of membrane proteins and complexes. 7.10 MAG differs from monoolein, the most extensively used lipid for in meso crystallization, in that it is shorter in chain length by one methylene and its cis olefinic bond is two carbons closer to the glycerol headgroup. These changes in structure alter the phase behavior of the hydrated lipid and the microstructure of the corresponding mesophases formed. Temperature-composition phase diagrams for 7.10 MAG have been constructed using small- and wide-angle X-ray scattering over a range of temperatures and hydration levels that span those used for crystallization. The phase diagrams include lamellar crystalline, fluid isotropic, lamellar liquid-crystalline, cubic-Ia3d, and cubic-Pn3m phases, as observed with monoolein. Conspicuous by its absence is the inverted hexagonal phase which is rationalized on the basis of 7.10 MAG's chemical constitution. The cubic phase prepared with the new lipid facilitates the growth of crystals that were used to generate high-resolution structures of intramembrane β-barrel and α-helical proteins. Compatibility of fully hydrated 7.10 MAG with cholesterol and phosphatidylcholine means that these two lipids can be used as additives to optimize crystallogenesis in screening trials with 7.10 MAG as the host lipid.
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Affiliation(s)
- Pawel Krawinski
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Luke Smithers
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Leendert van Dalsen
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Coilin Boland
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Nikita Ostrovitsa
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Javier Pérez
- SWING
Beamline, Synchrotron Soleil, Saint-Aubin 91190, France
| | - Martin Caffrey
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
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2
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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3
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Marin E, Kovalev K, Poelman T, Veenstra R, Borshchevskiy V, Guskov A. Custom Design of a Humidifier Chamber for InMeso Crystallization. CRYSTAL GROWTH & DESIGN 2024; 24:325-330. [PMID: 38188264 PMCID: PMC10767699 DOI: 10.1021/acs.cgd.3c01034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/09/2024]
Abstract
Membrane proteins are indispensable for every living organism, yet their structural organization remains underexplored. Despite the recent advancements in single-particle cryogenic electron microscopy and cryogenic electron tomography, which have significantly increased the structural coverage of membrane proteins across various kingdoms, certain scientific methods, such as time-resolved crystallography, still mostly rely on crystallization techniques, such as lipidic cubic phase (LCP) or in meso crystallization. In this study, we present an open-access blueprint for a humidity control chamber designed for LCP/in meso crystallization experiments using a Gryphon crystallization robot. Using this chamber, we have obtained crystals of a transmembrane aspartate transporter GltTk from Thermococcus kodakarensis in a lipidic environment using in meso crystallization. The data collected from these crystals allowed us to perform an analysis of lipids bound to the transporter. With this publication of our open-access design of a humidity chamber, we aim to improve the accessibility of in meso protein crystallization for the scientific community.
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Affiliation(s)
- Egor Marin
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Kirill Kovalev
- European
Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607 Hamburg, Germany
| | | | - Rick Veenstra
- University
of Groningen, 9747AG Groningen, The Netherlands
| | | | - Albert Guskov
- Groningen
Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
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4
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Darmanin C, Babayekhorasani F, Formosa A, Spicer P, Abbey B. Polarisation and rheology characterisation of monoolein/water liquid crystal dynamical behaviour during high-viscosity injector extrusion. J Colloid Interface Sci 2024; 653:1123-1136. [PMID: 37783012 DOI: 10.1016/j.jcis.2023.09.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
HYPOTHESIS The use of monoolein/water mixtures in serial crystallography experiments using high-viscosity injectors (HVI) results in significant departures from equilibrium behaviour. This is expected to include changes in phase, viscosity, and associated flow behaviour. It should be possible to detect these changes, in-situ, using a combination of polarisation and rheology characterisation techniques. EXPERIMENTS A systematic study was performed using monoolein, varying the water content to create a range of mixtures. Injection induced phase changes within the HVI flow were established using real-time cross-polarization measurements. Dynamic flow characteristics and viscosity was characterized by particle tracking and rheology. FINDINGS HVI injection induces deformation and phase changes within monoolein (MO)/water mixtures which can be detected through variations in the transmitted intensity during in-situ polarisation studies. The heterogeneity of the extruded sample results in a highly viscous cubic phase in the central region of the stream and a less viscous lamellar-rich phase at the edges adjacent to the walls. The extent of these variations depends on sample composition and injection conditions. Shear-thinning behaviour and increasing heterogeneity in the vicinity of the capillary walls under dynamic flow conditions. This is the first report observing injection induced dynamical behaviour in MO/water mixtures under realistic flow conditions.
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Affiliation(s)
- Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Firoozeh Babayekhorasani
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia; School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Andrew Formosa
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Patrick Spicer
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Brian Abbey
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
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5
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Brasnett C, Squires AM, Smith AJ, Seddon AM. Lipid doping of the sponge (L 3) mesophase. SOFT MATTER 2023; 19:6569-6577. [PMID: 37603381 DOI: 10.1039/d3sm00578j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
The polymorphism of lipid aggregates has long attracted detailed study due to the myriad factors that determine the final mesophase observed. This study is driven by the need to understand mesophase behaviour for a number of applications, such as drug delivery and membrane protein crystallography. In the case of the latter, the role of the so-called 'sponge' (L3) mesophase has been often noted, but not extensively studied by itself. The L3 mesophase can be formed in monoolein/water systems on the addition of butanediol to water, which partitions the headgroup region of the membrane, and decreases its elastic moduli. Like cubic mesophases, it is bicontinuous, but unlike them, has no long-range translational symmetry. In our present study, we show that the formation of the L3 phase can delicately depend on the addition of dopant lipids to the mesophase. While electrostatically neutral molecules similar in shape to monoolein (DOPE, cholesterol) have little effect on the general mesophase behaviour, others (DOPC, DDM) significantly reduce the composition at which it can form. Additionally, we show that by combining cholesterol with the anionic lipid DOPG, it is possible to form the largest stable L3 mesophases observed to date, with characteristic lengths over 220 Å.
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Affiliation(s)
| | - Adam M Squires
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
| | - Andrew J Smith
- Diamond House, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Fermi Ave., Didcot, OX11 0DE, UK
| | - Annela M Seddon
- School of Physics, University of Bristol, Tyndall Avenue, Bristol, BS8 1FD, UK.
- Bristol Centre for Functional Nanomaterials, School of Physics, University of Bristol, Tyndall Avenue, Bristol, BS8 1FD, UK
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6
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Flynn AJ, Antonyuk SV, Eady RR, Muench SP, Hasnain SS. A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun 2023; 14:3416. [PMID: 37296134 PMCID: PMC10256718 DOI: 10.1038/s41467-023-39140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
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Affiliation(s)
- Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Robert R Eady
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England.
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7
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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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8
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Zatloukalova M, Poltorak L, Bilewicz R, Vacek J. Lipid-based liquid crystalline materials in electrochemical sensing and nanocarrier technology. Mikrochim Acta 2023; 190:187. [PMID: 37071228 PMCID: PMC10113356 DOI: 10.1007/s00604-023-05727-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/02/2023] [Indexed: 04/19/2023]
Abstract
Some biologically active substances are unstable and poorly soluble in aqueous media, at the same time exhibiting low bioavailability. The incorporation of these biologically active compounds into the structure of a lipid-based lyotropic liquid crystalline phase or nanoparticles can increase or improve their stability and transport properties, subsequent bioavailability, and applicability in general. The aim of this short overview is (1) to clarify the principle of self-assembly of lipidic amphiphilic molecules in an aqueous environment and (2) to present lipidic bicontinuous cubic and hexagonal phases and their current biosensing (with a focus on electrochemical protocols) and biomedical applications.
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Affiliation(s)
- Martina Zatloukalova
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15, Olomouc, Czech Republic.
| | - Lukasz Poltorak
- Electrochemistry@Soft Interfaces Team, Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91-403, Lodz, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15, Olomouc, Czech Republic.
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9
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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10
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Martin J, Robert X, Gouet P, Falson P, Chaptal V. Specific Xray diffraction patterns of membrane proteins caused by secondary structure collinearity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184065. [PMID: 36206830 DOI: 10.1016/j.bbamem.2022.184065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
Diffraction anisotropy is a phenomenon that impacts more specifically membrane proteins, compared to soluble ones, but the reasons for this discrepancy remained unclear. Often, it is referred to a difference in resolution limits between highest and lowest diffraction limits as a signature for anisotropy. We show in this article that there is no single correlation between anisotropy and difference in resolution limits, with notably a substantial number of structures displaying various anisotropy with no difference in resolution limits. We further investigated diffraction intensity profiles, and observed a peak centred on 4.9 Å resolution more predominant in membrane proteins. Since this peak is in the region corresponding to secondary structures, we investigated the influence of secondary structure ratio. We showed that secondary structure content has little influence on this profile, while secondary structure collinearity in membrane proteins correlate with a stronger peak. Finally, we could further show that the presence of this peak is linked to higher diffraction anisotropy. These results bring to light a specific diffraction of membrane protein crystals, which calls for a specific handling by crystallographic software. It also brings an explanation for investigators struggling with their anisotropic data.
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Affiliation(s)
- Juliette Martin
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France.
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11
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Wang H, Mörman C, Sternke-Hoffmann R, Huang CY, Prota A, Ma P, Luo J. Cu 2+ ions modulate the interaction between α-synuclein and lipid membranes. J Inorg Biochem 2022; 236:111945. [PMID: 35952593 DOI: 10.1016/j.jinorgbio.2022.111945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022]
Abstract
α-synuclein protein aggregates are the major constituent of Lewy bodies, which is a main pathogenic hallmark of Parkinson's disease. Both lipid membranes and Cu2+ ions can bind to α-synuclein and modulate its aggregation propensity and toxicity. However, the synergistic effect of copper ions and lipid membranes on α-synuclein remains to be explored. Here, we investigate how Cu2+ and α-synuclein simultaneously influence the lipidic structure of lipidic cubic phase(LCP) matrix by using small-angle X-ray scattering. α-Syn proteins destabilize the cubic-Pn3m phase of LCP that can be further recovered after the addition of Cu2 ions even at a low stoichiometric ratio. By using circular dichroism and nuclear magnetic resonance, we also study how lipid membranes and Cu2+ ions impact the secondary structures of α-synuclein at an atomic level. Although the secondary structure of α-synuclein with lipid membranes is not significantly changed to a large extent in the presence of Cu2+ ions, lipid membranes promote the interaction between α-synuclein C-terminus and Cu2+ ions. The modulation of Cu2+ ions and lipid membranes on α-synuclein dynamics and structure may play an important role in the molecular pathogenesis of Parkinson's disease.
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Affiliation(s)
- Hongzhi Wang
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Cecilia Mörman
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
| | | | - Chia-Ying Huang
- Swiss Light Source at Paul Scherrer Institut, Forschungstrasse 111, Villigen-PSI, Villigen 5232, Switzerland
| | - Andrea Prota
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Pikyee Ma
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Jinghui Luo
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland.
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12
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Meikle TG, Keizer DW, Separovic F, Yao S. A solution NMR view of Lipidic Cubic Phases: Structure, dynamics, and beyond. BBA ADVANCES 2022; 2:100062. [PMID: 37082598 PMCID: PMC10074910 DOI: 10.1016/j.bbadva.2022.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is well-established nowadays for the elucidation of the 3D structures of proteins and protein complexes, the evaluation of biomolecular dynamics with atomistic resolution across a range of time scales, the screening of drug candidates with site specificity, and for the quantitation of molecular translational diffusion. Lyotropic lipidic cubic phases (LCPs) are lipid bilayer-based materials with a complex geometry, formed via the spontaneous self-assembly of certain lipids in an aqueous environment at specific temperature ranges. LCPs have been successfully applied to the in meso crystallization of membrane proteins for structural studies by X-ray crystallography, and have also shown promising potential for serving as matrices for drug and nutrient delivery/release in vivo. The characterization of the structural and dynamics properties of LCPs is of significant interest for the application of these materials. Here we present a systematic review detailing the characterization of LCPs by solution NMR. Using LCPs formed by monoolein (MO) as an example, various aspects of LCPs readily accessible by solution NMR are covered, including spectral perturbation in the presence of additives, quantification of hydration levels, 13C relaxation-based measurements for studying atom-specific dynamics along the MO hydrocarbon chain, PGSE NMR measurement of translational diffusion and its correlation with release profiles, and the encapsulation of soluble proteins in LCPs. A brief discussion of future perspectives for the characterization of LCPs by solution NMR is also presented.
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13
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Disalvo EA, Rosa AS, Cejas JP, Frias MDLA. Water as a Link between Membrane and Colloidal Theories for Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154994. [PMID: 35956945 PMCID: PMC9370763 DOI: 10.3390/molecules27154994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/01/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022]
Abstract
This review is an attempt to incorporate water as a structural and thermodynamic component of biomembranes. With this purpose, the consideration of the membrane interphase as a bidimensional hydrated polar head group solution, coupled to the hydrocarbon region allows for the reconciliation of two theories on cells in dispute today: one considering the membrane as an essential part in terms of compartmentalization, and another in which lipid membranes are not necessary and cells can be treated as a colloidal system. The criterium followed is to describe the membrane state as an open, non-autonomous and responsive system using the approach of Thermodynamic of Irreversible Processes. The concept of an open/non-autonomous membrane system allows for the visualization of the interrelationship between metabolic events and membrane polymorphic changes. Therefore, the Association Induction Hypothesis (AIH) and lipid properties interplay should consider hydration in terms of free energy modulated by water activity and surface (lateral) pressure. Water in restricted regions at the lipid interphase has thermodynamic properties that explain the role of H-bonding networks in the propagation of events between membrane and cytoplasm that appears to be relevant in the context of crowded systems.
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14
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Protein Fusion Strategies for Membrane Protein Stabilization and Crystal Structure Determination. CRYSTALS 2022. [DOI: 10.3390/cryst12081041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Crystal structures of membrane proteins are highly desired for their use in the mechanistic understanding of their functions and the designing of new drugs. However, obtaining the membrane protein structures is difficult. One way to overcome this challenge is with protein fusion methods, which have been successfully used to determine the structures of many membrane proteins, including receptors, enzymes and adhesion molecules. Existing fusion strategies can be categorized into the N or C terminal fusion, the insertion fusion and the termini restraining. The fusions facilitate protein expression, purification, crystallization and phase determination. Successful applications often require further optimization of protein fusion linkers and interactions, whose design can be facilitated by a shared helix strategy and by AlphaFold prediction in the future.
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15
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Chavda VP, Dawre S, Pandya A, Vora LK, Modh DH, Shah V, Dave DJ, Patravale V. Lyotropic liquid crystals for parenteral drug delivery. J Control Release 2022; 349:533-549. [PMID: 35792188 DOI: 10.1016/j.jconrel.2022.06.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
Abstract
The necessity for long-term treatments of chronic diseases has encouraged the development of novel long-acting parenteral formulations intending to improve drug pharmacokinetics and therapeutic efficacy. Lately, one of the novel approaches has been developed based on lipid-based liquid crystals. The lyotropic liquid crystal (LLC) systems consist of amphiphilic molecules and are formed in presence of solvents with the most common types being cubic, hexagonal and lamellar mesophases. LC injectables have been recently developed based on polar lipids that spontaneously form liquid crystal nanoparticles in aqueous tissue environments to create the in-situ long-acting sustained-release depot to provide treatment efficacy over extended periods. In this manuscript, we have consolidated and summarized the various type of liquid crystals, recent formulation advancements, analytical evaluation, and therapeutic application of lyotropic liquid crystals in the field of parenteral sustained release drug delivery.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380009, India; Department of Pharmaceutics & Pharm, Technology, K. B. Institute of Pharmaceutical Education and Research, Kadi Sarva Vishwavidyalaya, Gandhinagar 382023, Gujarat, India.
| | - Shilpa Dawre
- Department of Pharmaceutics, SVKM's Narsee Monjee Institute of Management Studies (NMIMS), Shirpur, India
| | - Anjali Pandya
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400 019, India
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, BT9 7BL, UK.
| | - Dharti H Modh
- Department of Medicinal Chemistry, Bharati Vidyapeeth's Poona College of Pharmacy, Pune, India
| | - Vidhi Shah
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380009, India
| | - Divyang J Dave
- Department of Pharmaceutics & Pharm, Technology, K. B. Institute of Pharmaceutical Education and Research, Kadi Sarva Vishwavidyalaya, Gandhinagar 382023, Gujarat, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400 019, India
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16
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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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17
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Selenourea for Experimental Phasing of Membrane Protein Crystals Grown in Lipid Cubic Phase. CRYSTALS 2022. [DOI: 10.3390/cryst12070976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heavy-atom soaking has been a major method for experimental phasing, but it has been difficult for membrane proteins, partly owing to the lack of available sites in the scarce soluble domain for non-invasive heavy-metal binding. The lipid cubic phase (LCP) has proven to be a successful method for membrane protein crystallization, but experimental phasing with LCP-grown crystals remains difficult, and so far, only 68 such structures were phased experimentally. Here, the selenourea was tested as a soaking reagent for the single-wavelength anomalous dispersion (SAD) phasing of crystals grown in LCP. Using a single crystal, the structure of the glycerol 3-phosphate acyltransferase (PlsY, ~21 kDa), a very hydrophobic enzyme with 80% membrane-embedded residues, was solved. Remarkably, a total of 15 Se sites were found in the two monomers of PlsY, translating to one selenourea-binding site per every six residues in the accessible extramembrane protein. Structure analysis reveals that surface-exposed selenourea sites are mostly contributed by mainchain amides and carbonyls. This low-specificity binding pattern may explain its high loading ratio. Importantly, both the crystal diffraction quality and the LCP integrity were unaffected by selenourea soaking. Taken together, selenourea presents a promising and generally useful reagent for heavy-atom soaking of membrane protein crystals grown in LCP.
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18
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Mechanisms of membrane protein crystallization in 'bicelles'. Sci Rep 2022; 12:11109. [PMID: 35773455 PMCID: PMC9246360 DOI: 10.1038/s41598-022-13945-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/31/2022] [Indexed: 12/14/2022] Open
Abstract
Despite remarkable progress, mainly due to the development of LCP and ‘bicelle’ crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the “bicelle” crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of “bicelle” MP crystallization and will support rational design of crystallization.
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19
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Gildea RJ, Beilsten-Edmands J, Axford D, Horrell S, Aller P, Sandy J, Sanchez-Weatherby J, Owen CD, Lukacik P, Strain-Damerell C, Owen RL, Walsh MA, Winter G. xia2. multiplex: a multi-crystal data-analysis pipeline. Acta Crystallogr D Struct Biol 2022; 78:752-769. [PMID: 35647922 PMCID: PMC9159281 DOI: 10.1107/s2059798322004399] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/25/2022] [Indexed: 11/11/2022] Open
Abstract
A new program, xia2.multiplex, has been developed to facilitate symmetry analysis, scaling and merging of multi-crystal data sets. In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.
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20
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Yang M, Luo W, Zhang W, Wang H, Xue D, Wu Y, Zhao S, Zhao F, Zheng X, Tao H. Ugi Reaction Mediated Detergent Assembly for Membrane Protein Studies. Chem Asian J 2022; 17:e202200372. [PMID: 35575910 DOI: 10.1002/asia.202200372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/16/2022] [Indexed: 11/11/2022]
Abstract
Despite the continuous efforts, the current repertoire of detergents is still far from sufficient for the biophysics studies of membrane proteins (MPs). Toward the rapid expansion of detergent diversity, we herein report a new strategy based on Ugi reaction mediated modular assembly. Structural varieties, including hydrophobic tails and hydrophilic heads, could be conveniently introduced from the multiple reaction components. New detergents then were comprehensively evaluated in the physical properties and preliminarily screened by the thermal stabilization for a transporter MsbA and a spectrum of G protein-coupled receptors (GPCRs). For the glucagon-like peptide-1 receptor (GLP-1R), a class B GPCR, detergent M-23-M finally stood out in a second evaluation for the maintenance of homogeneity and was further illustrated its application in the improvement of NMR study. Besides the promising utility in the MP study, the current results exhibit intriguing structural-physical relationship that would allow the guidance in the tuning of detergent properties in the future.
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Affiliation(s)
- Meifang Yang
- University of South China, Department of Pharmacy, CHINA
| | - Weiling Luo
- ShanghaiTech University, iHuman Institute, CHINA
| | - Wei Zhang
- ShanghaiTech University, iHuman Institute, CHINA
| | - Huixia Wang
- ShanghaiTech University, iHuman Institute, CHINA
| | | | - Yiran Wu
- ShanghaiTech University, iHuman Institute, CHINA
| | - Suwen Zhao
- ShanghaiTech University, iHuman Institute, CHINA
| | - Fei Zhao
- ShanghaiTech University, iHuman Institute, 230 Haike Road, 201210, Shanghai, CHINA
| | - Xing Zheng
- University of South China, Department of Pharmacy, CHINA
| | - Houchao Tao
- Shanghai University of Traditional Chinese Medicine, Shanghai Frontiers Science Center of TCM Chemical Biology, Room 2421, Building 2, 1200 Cailun Road, 230032, Shanghai, CHINA
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21
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Wright NJ, Lee SY. Recent advances on the inhibition of human solute carriers: Therapeutic implications and mechanistic insights. Curr Opin Struct Biol 2022; 74:102378. [PMID: 35487145 DOI: 10.1016/j.sbi.2022.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 11/03/2022]
Abstract
Solute carriers (SLCs) are membrane transport proteins tasked with mediating passage of hydrophilic molecules across lipid bilayers. Despite the extensive roles played in all aspects of human biology, SLCs remain vastly under-explored as therapeutic targets. In this brief review, we first discuss a few successful cases of drugs that exert their mechanisms of action through inhibition of human SLCs, and introduce select examples of human SLCs that have untapped therapeutic potential. We then highlight two recent structural studies which uncovered detailed structural mechanisms of inhibition exhibited against two different human major facilitator superfamily (MFS) transporters of clinical relevance.
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Affiliation(s)
- Nicholas J Wright
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA. https://twitter.com/@nick_rite
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.
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22
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Zhang L, Wang K, Ning S, Pedersen PA, Duelli AS, Gourdon PE. Isolation and Crystallization of the D156C form of Optogenetic ChR2. Cells 2022; 11:cells11050895. [PMID: 35269517 PMCID: PMC8909857 DOI: 10.3390/cells11050895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels that are receiving increasing attention as optogenetic tools. Despite extensive efforts to gain understanding of how these channels function, the molecular events linking light absorption of the retinal cofactor to channel opening remain elusive. While dark-state structures of ChR2 or chimeric proteins have demonstrated the architecture of non-conducting states, there is a need for open- and desensitized-state structures to uncover the mechanistic principles underlying channel activity. To facilitate comprehensive structural studies of ChR2 in non-closed states, we report a production and purification procedure of the D156C form of ChR2, which displays prolonged channel opening compared to the wild type. We demonstrate considerable yields (0.45 mg/g fermenter cell culture) of recombinantly produced protein using S. cerevisiae, which is purified to high homogeneity both as opsin (retinal-free) and as functional ChR2 with added retinal. We also develop conditions that enable the growth of ChR2 crystals that scatter X-rays to 6 Å, and identify a molecular replacement solution that suggests that the packing is different from published structures. Consequently, our cost-effective production and purification pipeline opens the way for downstream structural studies of different ChR2 states, which may provide a foundation for further adaptation of this protein for optogenetic applications.
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Affiliation(s)
- Liying Zhang
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
| | - Shuo Ning
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China;
| | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen, Denmark;
| | - Annette Susanne Duelli
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
| | - Pontus Emanuel Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Nørre Allé 14, DK-2200 Copenhagen, Denmark; (L.Z.); (K.W.); (A.S.D.)
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84 Lund, Sweden
- Correspondence: ; Tel.: +45-50339990
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23
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Studying membrane proteins with MicroED. Biochem Soc Trans 2022; 50:231-239. [PMID: 35191473 PMCID: PMC9022970 DOI: 10.1042/bst20210911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
The structural investigation of biological macromolecules is indispensable in understanding the molecular mechanisms underlying diseases. Several structural biology techniques have been introduced to unravel the structural facets of biomolecules. Among these, the electron cryomicroscopy (cryo-EM) method microcrystal electron diffraction (MicroED) has produced atomic resolution structures of important biological and small molecules. Since its inception in 2013, MicroED established a demonstrated ability for solving structures of difficult samples using vanishingly small crystals. However, membrane proteins remain the next big frontier for MicroED. The intrinsic properties of membrane proteins necessitate improved sample handling and imaging techniques to be developed and optimized for MicroED. Here, we summarize the milestones of electron crystallography of two-dimensional crystals leading to MicroED of three-dimensional crystals. Then, we focus on four different membrane protein families and discuss representatives from each family solved by MicroED.
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24
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Miszta P, Nazaruk E, Nieciecka D, Możajew M, Krysiński P, Bilewicz R, Filipek S. The EcCLC antiporter embedded in lipidic liquid crystalline films - molecular dynamics simulations and electrochemical methods. Phys Chem Chem Phys 2022; 24:3066-3077. [PMID: 35040466 DOI: 10.1039/d1cp03992j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipidic-liquid crystalline nanostructures (lipidic cubic phases), which are biomimetic and stable in an excess of water, were used as a convenient environment to investigate the transport properties of the membrane antiporter E. coli CLC-1 (EcCLC). The chloride ion transfer by EcCLC was studied by all-atom molecular dynamics simulations combined with electrochemical methods at pH 7 and pH 5. The cubic phase film was used as the membrane between the chloride donor and receiving compartments and it was placed on the glassy carbon electrode and immersed in the chloride solution. Structural characterization of lipidic mesoscopic systems with and without the incorporation of EcCLC was performed using small-angle X-ray scattering. The EcCLC transported chloride ions more efficiently at more acidic pH, and the resistance of the film decreased at lower pH. 4,4-Diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS) employed as an inhibitor of the protein was shown to decrease the transport efficiency upon hydrolysis to DADS at both pH 7 and pH 5. The molecular dynamics simulations, performed for the first time in lipidic cubic phases for EcCLC, allowed studying the collective movements of chloride ions which can help in elucidating the mechanism of transporting the ions by the EcCLC antiporter. The protein modified lipidic cubic phase film is a convenient and simple system for screening potential inhibitors of integral membrane proteins, as demonstrated by the example of the EcCLC antiporter. The use of lipidic cubic phases may also be important for the further development of new electrochemical sensors for membrane proteins and enzyme electrodes.
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Affiliation(s)
- Przemysław Miszta
- Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland. .,Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Ewa Nazaruk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Dorota Nieciecka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Mariusz Możajew
- Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland. .,Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. .,Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Paweł Krysiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Renata Bilewicz
- Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland. .,Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Sławomir Filipek
- Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland. .,Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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25
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Methods of Measuring Mitochondrial Potassium Channels: A Critical Assessment. Int J Mol Sci 2022; 23:ijms23031210. [PMID: 35163132 PMCID: PMC8835872 DOI: 10.3390/ijms23031210] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/22/2022] Open
Abstract
In this paper, the techniques used to study the function of mitochondrial potassium channels are critically reviewed. The majority of these techniques have been known for many years as a result of research on plasma membrane ion channels. Hence, in this review, we focus on the critical evaluation of techniques used in the studies of mitochondrial potassium channels, describing their advantages and limitations. Functional analysis of mitochondrial potassium channels in comparison to that of plasmalemmal channels presents additional experimental challenges. The reliability of functional studies of mitochondrial potassium channels is often affected by the need to isolate mitochondria and by functional properties of mitochondria such as respiration, metabolic activity, swelling capacity, or high electrical potential. Three types of techniques are critically evaluated: electrophysiological techniques, potassium flux measurements, and biochemical techniques related to potassium flux measurements. Finally, new possible approaches to the study of the function of mitochondrial potassium channels are presented. We hope that this review will assist researchers in selecting reliable methods for studying, e.g., the effects of drugs on mitochondrial potassium channel function. Additionally, this review should aid in the critical evaluation of the results reported in various articles on mitochondrial potassium channels.
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26
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Pan D, Oyama R, Sato T, Nakane T, Mizunuma R, Matsuoka K, Joti Y, Tono K, Nango E, Iwata S, Nakatsu T, Kato H. Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX. IUCRJ 2022; 9:134-145. [PMID: 35059217 PMCID: PMC8733880 DOI: 10.1107/s2052252521011611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open-close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono-acyl-glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy-droxy-propyl methyl-cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.
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Affiliation(s)
- Dongqing Pan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryo Oyama
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomomi Sato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Mizunuma
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Keita Matsuoka
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Toru Nakatsu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroaki Kato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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27
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Krawinski P, Caffrey M. Thromboxane A 2 G Protein-Coupled Receptor Production and Crystallization for Structure Studies. Methods Mol Biol 2022; 2507:241-271. [PMID: 35773586 DOI: 10.1007/978-1-0716-2368-8_13] [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: 06/15/2023]
Abstract
G protein-coupled receptors (GPCRs) play vital roles in human physiology and pathophysiology. This makes the elucidation of the high-resolution blueprints of these high value membrane proteins of crucial importance for the structure-based design of novel therapeutics. However, the production and crystallization of GPCRs for structure determination comes with many challenges.In this chapter, we provide a comprehensive protocol for expressing and purifying the thromboxane A2 receptor (TPR), an attractive therapeutic target, for use in structure studies. Guidelines for crystallizing the TPR are also included. Together, these procedures provide a template for generating crystal structures of the TPR and indeed other GPCRs in complex with pharmacologically interesting ligands.
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Affiliation(s)
- Pawel Krawinski
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
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28
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Yang B, Yao H, Li D, Liu Z. The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface. Curr Res Struct Biol 2021; 3:312-323. [PMID: 34901881 PMCID: PMC8640168 DOI: 10.1016/j.crstbi.2021.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Phosphatidylglycerol is a crucial phospholipid found ubiquitously in biological membranes of prokaryotic and eukaryotic cells. The phosphatidylglycerol phosphate (PGP) synthase (PgsA), a membrane-embedded enzyme, catalyzes the primary reaction of phosphatidylglycerol biosynthesis. Mutations in pgsA frequently correlate with daptomycin resistance in Staphylococcus aureus and other prevalent infectious pathogens. Here we report the crystal structures of S. aureus PgsA (SaPgsA) captured at two distinct states of the catalytic process, with lipid substrate (cytidine diphosphate-diacylglycerol, CDP-DAG) or product (PGP) bound to the active site within a trifurcated amphipathic cavity. The hydrophilic head groups of CDP-DAG and PGP occupy two different pockets in the cavity, inducing local conformational changes. An elongated membrane-exposed surface groove accommodates the fatty acyl chains of CDP-DAG/PGP and opens a lateral portal for lipid entry/release. Remarkably, the daptomycin resistance-related mutations mostly cluster around the active site, causing reduction of enzymatic activity. Our results provide detailed mechanistic insights into the dynamic catalytic process of PgsA and structural frameworks beneficial for development of antimicrobial agents targeting PgsA from pathogenic bacteria. PgsA uses a trifurcated amphipathic cavity for binding of substrates or products. Conversion of CDP-DAG to PGP induces local conformational changes in PgsA. Daptomycin-resistant mutations of PgsA mostly lead to reduced catalytic activity. A structure-based five-state model is proposed for the synthesis of PGP by PgsA.
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Affiliation(s)
- Bowei Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hebang Yao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 201210, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 201210, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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29
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Smithers L, Olatunji S, Caffrey M. Bacterial Lipoprotein Posttranslational Modifications. New Insights and Opportunities for Antibiotic and Vaccine Development. Front Microbiol 2021; 12:788445. [PMID: 34950121 PMCID: PMC8689077 DOI: 10.3389/fmicb.2021.788445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
Lipoproteins are some of the most abundant proteins in bacteria. With a lipid anchor to the cell membrane, they function as enzymes, inhibitors, transporters, structural proteins, and as virulence factors. Lipoproteins activate the innate immune system and have biotechnological applications. The first lipoprotein was described by Braun and Rehn in 1969. Up until recently, however, work on lipoproteins has been sluggish, in part due to the challenges of handling proteins that are anchored to membranes by covalently linked lipids or are membrane integral. Activity in the area has quickened of late. In the past 5 years, high-resolution structures of the membrane enzymes of the canonical lipoprotein synthesis pathway have been determined, new lipoprotein types have been discovered and the enzymes responsible for their synthesis have been characterized biochemically. This has led to a flurry of activity aimed at developing novel antibiotics targeting these enzymes. In addition, surface exposed bacterial lipoproteins have been utilized as candidate vaccine antigens, and their potential to act as self-adjuvanting antigens is increasingly recognized. A summary of the latest developments in lipoproteins and their synthesis, as well as how this information is being exploited for therapeutic purposes is presented here.
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Affiliation(s)
- Luke Smithers
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Samir Olatunji
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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30
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Trampari S, Neumann C, Hjorth-Jensen SJ, Shahsavar A, Quistgaard EM, Nissen P. Insights into the mechanism of high lipid–detergent crystallization of membrane proteins. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721010669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Obtaining well diffracting crystals of membrane proteins is often challenging, but chances can be improved by crystallizing them in lipidic conditions that mimic their natural membrane environments. One approach is the high lipid–detergent (HiLiDe) method, which works by mixing the target protein with high concentrations of lipid and detergent prior to crystallization. Although this approach is convenient and flexible, understanding the effects of systematically varying lipid/detergent ratios and a characterization of the lipid phases that form during crystallization would be useful. Here, a HiLiDe phase diagram is reported for the model membrane protein MhsT, which tracks the precipitation and crystallization zones as a function of lipid and detergent concentrations, and is augmented with data on crystal sizes and diffraction properties. Additionally, the crystallization of SERCA1a solubilized directly with native lipids is characterized as a function of detergent concentration. Finally, HiLiDe crystallization drops are analysed with transmission electron microscopy, which among other features reveals liposomes, stacked lamellae that may represent crystal precursors, and mature crystals with clearly discernible packing arrangements. The results emphasize the significance of optimizing lipid/detergent ratios over broad ranges and provide insights into the mechanism of HiLiDe crystallization.
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31
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Ridolfi A, Humphreys B, Caselli L, Montis C, Nylander T, Berti D, Brucale M, Valle F. Nanoscale structural and mechanical characterization of thin bicontinuous cubic phase lipid films. Colloids Surf B Biointerfaces 2021; 210:112231. [PMID: 34838417 DOI: 10.1016/j.colsurfb.2021.112231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
Abstract
The mechanical response of lipid membranes to nanoscale deformations is of fundamental importance for understanding how these interfaces behave in multiple biological processes; in particular, the nanoscale mechanics of non-lamellar membranes represents a largely unexplored research field. Among these mesophases, inverse bicontinuous cubic phase QII membranes have been found to spontaneously occur in stressed or virally infected cells and to play a role in fundamental processes, such as cell fusion and food digestion. We herein report on the fabrication of thin ( ̴150 nm) supported QII cubic phase lipid films (SQIIFs) and on their characterization via multiple techniques including Small Angle X-Ray Scattering (SAXS), Ellipsometry and Atomic Force Microscopy (AFM). Moreover, we present the first nanomechanical characterization of a cubic phase lipid membrane, through AFM-based Force Spectroscopy (AFM-FS). Our analysis reveals that the mechanical response of these architectures is strictly related to their topology and structure. The observed properties are strikingly similar to those of macroscopic 3D printed cubic structures when subjected to compression tests in material science; suggesting that this behaviour depends on the 3D organisation, rather than on the length-scale of the architecture. We also show for the first time that AFM-FS can be used for characterizing the structure of non-lamellar mesophases, obtaining lattice parameters in agreement with SAXS data. In contrast to classical rheological studies, which can only probe bulk cubic phase solutions, our AFM-FS analysis allows probing the response of cubic membranes to deformations occurring at length and force scales similar to those found in biological interactions.
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Affiliation(s)
- Andrea Ridolfi
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Firenze, Italy; Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati, 40129 Bologna, Italy; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Firenze, Italy
| | - Ben Humphreys
- Physical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden; Lund Institute of Advanced Neutron and X-ray Science - LINXS, SE- 223 70 Lund, Sweden; NanoLund, Lund University, SE-221 00 Lund, Sweden
| | - Lucrezia Caselli
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Firenze, Italy; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Firenze, Italy
| | - Costanza Montis
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Firenze, Italy; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Firenze, Italy
| | - Tommy Nylander
- Physical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden; Lund Institute of Advanced Neutron and X-ray Science - LINXS, SE- 223 70 Lund, Sweden; NanoLund, Lund University, SE-221 00 Lund, Sweden
| | - Debora Berti
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Firenze, Italy; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Firenze, Italy
| | - Marco Brucale
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Firenze, Italy; Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati, 40129 Bologna, Italy
| | - Francesco Valle
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Firenze, Italy; Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati, 40129 Bologna, Italy
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32
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NMR spectroscopy of lipidic cubic phases. Biophys Rev 2021; 14:67-74. [DOI: 10.1007/s12551-021-00900-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
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33
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Abrahams G, Newman J. Data- and diversity-driven development of a Shotgun crystallization screen using the Protein Data Bank. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1437-1450. [PMID: 34726171 DOI: 10.1107/s2059798321009724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/17/2021] [Indexed: 11/10/2022]
Abstract
Protein crystallization has for decades been a critical and restrictive step in macromolecular structure determination via X-ray diffraction. Crystallization typically involves a multi-stage exploration of the available chemical space, beginning with an initial sampling (screening) followed by iterative refinement (optimization). Effective screening is important for reducing the number of optimization rounds required, reducing the cost and time required to determine a structure. Here, an initial screen (Shotgun II) derived from analysis of the up-to-date Protein Data Bank (PDB) is proposed and compared with the previously derived (2014) Shotgun I screen. In an update to that analysis, it is clarified that the Shotgun approach entails finding the crystallization conditions that cover the most diverse space of proteins by sequence found in the PDB, which can be mapped to the well known maximum coverage problem in computer science. With this realization, it was possible to apply a more effective algorithm for selecting conditions. In-house data demonstrate that compared with alternatives, the Shotgun I screen has been remarkably successful over the seven years that it has been in use, indicating that Shotgun II is also likely to be a highly effective screen.
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Affiliation(s)
- Gabriel Abrahams
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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34
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Healey RD, Basu S, Humm AS, Leyrat C, Cong X, Golebiowski J, Dupeux F, Pica A, Granier S, Márquez JA. An automated platform for structural analysis of membrane proteins through serial crystallography. CELL REPORTS METHODS 2021; 1:None. [PMID: 34723237 PMCID: PMC8545655 DOI: 10.1016/j.crmeth.2021.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 09/22/2021] [Indexed: 11/01/2022]
Abstract
Membrane proteins are central to many pathophysiological processes, yet remain very difficult to analyze structurally. Moreover, high-throughput structure-based drug discovery has not yet been exploited for membrane proteins because of lack of automation. Here, we present a facile and versatile platform for in meso membrane protein crystallization, enabling rapid atomic structure determination at both cryogenic and room temperatures. We apply this approach to human integral membrane proteins, which allowed us to identify different conformational states of intramembrane enzyme-product complexes and analyze by molecular dynamics simulations the structural dynamics of the ADIPOR2 integral membrane protein. Finally, we demonstrate an automated pipeline combining high-throughput microcrystal soaking, automated laser-based harvesting, and serial crystallography, enabling screening of small-molecule libraries with membrane protein crystals grown in meso. This approach brings needed automation to this important class of drug targets and enables high-throughput structure-based ligand discovery with membrane proteins.
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Affiliation(s)
- Robert D. Healey
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Shibom Basu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Anne-Sophie Humm
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Cedric Leyrat
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Xiaojing Cong
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Jérôme Golebiowski
- Institute of Chemistry of Nice UMR7272, Université Côte d’Azur, CNRS, 28 Avenue Valrose, 06108 Nice, France
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Technology, 711-873 Daegu, South Korea
| | - Florine Dupeux
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Andrea Pica
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- ALPX S.A.S. 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sébastien Granier
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - José Antonio Márquez
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- ALPX S.A.S. 71 Avenue des Martyrs, 38000 Grenoble, France
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35
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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36
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Ehsan M, Wang H, Cecchetti C, Mortensen JS, Du Y, Hariharan P, Nygaard A, Lee HJ, Ghani L, Guan L, Loland CJ, Byrne B, Kobilka BK, Chae PS. Maltose-bis(hydroxymethyl)phenol (MBPs) and Maltose-tris(hydroxymethyl)phenol (MTPs) Amphiphiles for Membrane Protein Stability. ACS Chem Biol 2021; 16:1779-1790. [PMID: 34445864 DOI: 10.1021/acschembio.1c00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Membrane protein structures provide a fundamental understanding of their molecular actions and are of importance for drug development. Detergents are widely used to solubilize, stabilize, and crystallize membrane proteins, but membrane proteins solubilized in conventional detergents are prone to denaturation and aggregation. Thus, developing novel detergents with enhanced efficacy for protein stabilization remains important. We report herein the design and synthesis of a class of phenol-derived maltoside detergents. Using two different linkers, we prepared two sets of new detergents, designated maltose-bis(hydroxymethyl)phenol (MBPs) and maltose-tris(hydroxymethyl)phenol (MTPs). The evaluation of these detergents with three transporters and two G-protein coupled receptors allowed us to identify a couple of new detergents (MBP-C9 and MTP-C12) that consistently conferred enhanced stability to all tested proteins compared to a gold standard detergent (DDM). Furthermore, the data analysis based on the detergent structures provides key detergent features responsible for membrane protein stabilization that together will facilitate the future design of novel detergents.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jonas S. Mortensen
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ho Jin Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Lubna Ghani
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Pil Seok Chae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
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37
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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38
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Zhao J, Xu H, Lebrette H, Carroni M, Taberman H, Högbom M, Zou X. A simple pressure-assisted method for MicroED specimen preparation. Nat Commun 2021; 12:5036. [PMID: 34413316 PMCID: PMC8377027 DOI: 10.1038/s41467-021-25335-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
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Affiliation(s)
- Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Helena Taberman
- Max Delbrück Centrum for Molecular Medicine, Berlin, Germany
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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39
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Cholesterol in GPCR Structures: Prevalence and Relevance. J Membr Biol 2021; 255:99-106. [PMID: 34365520 DOI: 10.1007/s00232-021-00197-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022]
Abstract
Bound cholesterol molecules are emerging as important hallmarks of GPCR structures. In this commentary, we analyze their statistical prevalence and biological relevance.
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Sarkar P, Chattopadhyay A. Cholesterol footprint in high-resolution structures of serotonin receptors: Where are we now and what does it mean? Chem Phys Lipids 2021; 239:105120. [PMID: 34332970 DOI: 10.1016/j.chemphyslip.2021.105120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/24/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
An emerging feature of several high-resolution GPCR structures is the presence of closely bound cholesterol molecules. In this Perspective, we share the excitement of the recent advancements in GPCR structural biology. We further highlight our laboratory's journey in comprehensively elucidating functional sensitivity of GPCRs (using the serotonin1A receptor as a representative neurotransmitter GPCR) to membrane cholesterol and validation using a variety of assays and molecular dynamics simulations. Although high-resolution structures of many GPCRs have been reported in the last few years, the structure of the serotoin1A receptor proved to be elusive for a long time. Very recently the cryo-EM structure of the serotoin1A receptor displaying 10 bound cholesterol molecules has been reported. We conclude by providing a critical analysis of caveats involved in GPCR structure determination.
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Affiliation(s)
- Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
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Olatunji S, Bowen K, Huang CY, Weichert D, Singh W, Tikhonova IG, Scanlan EM, Olieric V, Caffrey M. Structural basis of the membrane intramolecular transacylase reaction responsible for lyso-form lipoprotein synthesis. Nat Commun 2021; 12:4254. [PMID: 34253723 PMCID: PMC8275575 DOI: 10.1038/s41467-021-24475-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/08/2021] [Indexed: 11/08/2022] Open
Abstract
Lipoproteins serve diverse functions in the bacterial cell and some are essential for survival. Some lipoproteins are adjuvants eliciting responses from the innate immune system of the host. The growing list of membrane enzymes responsible for lipoprotein synthesis includes the recently discovered lipoprotein intramolecular transacylase, Lit. Lit creates a lipoprotein that is less immunogenic, possibly enabling the bacteria to gain a foothold in the host by stealth. Here, we report the crystal structure of the Lit enzyme from Bacillus cereus and describe its mechanism of action. Lit consists of four transmembrane helices with an extracellular cap. Conserved residues map to the cap-membrane interface. They include two catalytic histidines that function to effect unimolecular transacylation. The reaction involves acyl transfer from the sn-2 position of the glyceryl moiety to the amino group on the N-terminal cysteine of the substrate via an 8-membered ring intermediate. Transacylation takes place in a confined aromatic residue-rich environment that likely evolved to bring distant moieties on the substrate into proximity and proper orientation for catalysis.
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Affiliation(s)
- Samir Olatunji
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Katherine Bowen
- School of Chemistry, Trinity College Dublin, Dublin, Ireland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Dietmar Weichert
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Warispreet Singh
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
- Hub for Biotechnology in Build Environment, Newcastle upon Tyne, United Kingdom
| | - Irina G Tikhonova
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Eoin M Scanlan
- School of Chemistry, Trinity College Dublin, Dublin, Ireland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
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Esmaili M, Eldeeb MA, Moosavi-Movahedi AA. Current Developments in Native Nanometric Discoidal Membrane Bilayer Formed by Amphipathic Polymers. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1771. [PMID: 34361157 PMCID: PMC8308186 DOI: 10.3390/nano11071771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Unlike cytosolic proteins, membrane proteins (MPs) are embedded within the plasma membrane and the lipid bilayer of intracellular organelles. MPs serve in various cellular processes and account for over 65% of the current drug targets. The development of membrane mimetic systems such as bicelles, short synthetic polymers or amphipols, and membrane scaffold proteins (MSP)-based nanodiscs has facilitated the accommodation of synthetic lipids to stabilize MPs, yet the preparation of these membrane mimetics remains detergent-dependent. Bio-inspired synthetic polymers present an invaluable tool for excision and liberation of superstructures of MPs and their surrounding annular lipid bilayer in the nanometric discoidal assemblies. In this article, we discuss the significance of self-assembling process in design of biomimetic systems, review development of multiple series of amphipathic polymers and the significance of these polymeric "belts" in biomedical research in particular in unraveling the structures, dynamics and functions of several high-value membrane protein targets.
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Affiliation(s)
- Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mohamed A. Eldeeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Chemistry, Faculty of Science, Cairo University, Cairo 12613, Egypt
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Abstract
Rhodopsins, most of which are proton pumps generating transmembrane electrochemical proton gradients, span all three domains of life, are abundant in the biosphere, and could play a crucial role in the early evolution of life on earth. Whereas archaeal and bacterial proton pumps are among the best structurally characterized proteins, rhodopsins from unicellular eukaryotes have not been well characterized. To fill this gap in the current understanding of the proton pumps and to gain insight into the evolution of rhodopsins using a structure-based approach, we performed a structural and functional analysis of the light-driven proton pump LR (Mac) from the pathogenic fungus Leptosphaeria maculans. The first high-resolution structure of fungi rhodopsin and its functional properties reveal the striking similarity of its membrane part to archaeal but not to bacterial rhodopsins. We show that an unusually long N-terminal region stabilizes the protein through direct interaction with its extracellular loop (ECL2). We compare to our knowledge all available structures and sequences of outward light-driven proton pumps and show that eukaryotic and archaeal proton pumps, most likely, share a common ancestor. Zabelskii et al. present a structural and functional analysis of the lightdriven proton pump LR (Mac) from the fungus Leptosphaeria maculans. Their findings indicate that the archaeal ancestry of eukaryotic type 1 rhodopsins, and that the archaeal host of the proto-mitochondrial endosymbiont was capable of light-driven proton pumping.
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Bagatolli LA, Stock RP. Lipids, membranes, colloids and cells: A long view. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183684. [PMID: 34166642 DOI: 10.1016/j.bbamem.2021.183684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/01/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022]
Abstract
This paper revisits long-standing ideas about biological membranes in the context of an equally long-standing, but hitherto largely unappreciated, perspective of the cell based on concepts derived from the physics and chemistry of colloids. Specifically, we discuss important biophysical aspects of lipid supramolecular structure to understand how the intracellular milieu may constrain lipid self-assembly. To this end we will develop four lines of thought: first, we will look at the historical development of the current view of cellular structure and physiology, considering also the plurality of approaches that influenced its formative period. Second, we will review recent basic research on the structural and dynamical properties of lipid aggregates as well as the role of phase transitions in biophysical chemistry and cell biology. Third, we will present a general overview of contemporary studies into cellular compartmentalization in the context of a very rich and mostly forgotten general theory of cell physiology called the Association-Induction Hypothesis, which was developed around the time that the current view of cells congealed into its present form. Fourth, we will examine some recent developments in cellular studies, mostly from our laboratory, that raise interesting issues about the dynamical aspects of cell structure and compartmentalization. We will conclude by suggesting what we consider are relevant questions about the nature of cellular processes as emergent phenomena.
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Affiliation(s)
- Luis A Bagatolli
- Instituto de Investigación Médica Mercedes y Martín Ferreyra - INIMEC (CONICET)-Universidad Nacional de Córdoba, Friuli 2434, 5016 Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; MEMPHYS - International and Interdisciplinary research network, Denmark.
| | - Roberto P Stock
- MEMPHYS - International and Interdisciplinary research network, Denmark
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Bicontinuous Gyroid Phase of a Water-Swollen Wedge-Shaped Amphiphile: Studies with In-Situ Grazing-Incidence X-ray Scattering and Atomic Force Microscopy. MATERIALS 2021; 14:ma14112892. [PMID: 34071178 PMCID: PMC8198821 DOI: 10.3390/ma14112892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022]
Abstract
We report on formation of a bicontinuous double gyroid phase by a wedge-shaped amphiphilic mesogen, pyridinium 4′-[3″,4″,5″-tris-(octyloxy)benzoyloxy]azobenzene-4-sulfonate. It is found that this compound can self-organize in zeolite-like structures adaptive to environmental conditions (e.g., temperature, humidity, solvent vapors). Depending on the type of the phase, the structure contains 1D, 2D, or 3D networks of nanometer-sized ion channels. Of particular interest are bicontinuous phases, such as the double gyroid phase, as they hold promise for applications in separation and energy. Specially designed environmental cells compatible with grazing-incidence X-ray scattering and atomic force microscopy enable simultaneous measurements of structural parameters/morphology during vapor-annealing treatment at different temperatures. Such in-situ approach allows finding the environmental conditions at which the double gyroid phase can be formed and provide insights on the supramolecular structure of thin films at different spatial levels.
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Taghon GJ, Rowe JB, Kapolka NJ, Isom DG. Predictable cholesterol binding sites in GPCRs lack consensus motifs. Structure 2021; 29:499-506.e3. [PMID: 33508215 PMCID: PMC9162085 DOI: 10.1016/j.str.2021.01.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/17/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022]
Abstract
A rich diversity of transmembrane G protein-coupled receptors (GPCRs) are used by eukaryotes to sense physical and chemical signals. In humans alone, 800 GPCRs comprise the largest and most therapeutically targeted receptor class. Recent advances in GPCR structural biology have produced hundreds of GPCR structures solved by X-ray diffraction and increasingly, cryo-electron microscopy (cryo-EM). Many of these structures are stabilized by site-specific cholesterol binding, but it is unclear whether these interactions are a product of recurring cholesterol-binding motifs and if observed patterns of cholesterol binding differ by experimental technique. Here, we comprehensively analyze the location and composition of cholesterol binding sites in the current set of 473 human GPCR structural chains. Our findings establish that cholesterol binds similarly in cryo-EM and X-ray structures and show that 92% of cholesterol molecules on GPCR surfaces reside in predictable locations that lack discernable cholesterol-binding motifs.
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Affiliation(s)
- Geoffrey J Taghon
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, RMSB 6078A, Miami, FL 33136, USA
| | - Jacob B Rowe
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, RMSB 6078A, Miami, FL 33136, USA
| | - Nicholas J Kapolka
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, RMSB 6078A, Miami, FL 33136, USA
| | - Daniel G Isom
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, RMSB 6078A, Miami, FL 33136, USA; University of Miami Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA; University of Miami Institute for Data Science and Computing, Miami, FL 33136, USA.
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Klenotic PA, Morgan CE, Yu EW. Cryo-EM as a tool to study bacterial efflux systems and the membrane proteome. Fac Rev 2021; 10:24. [PMID: 33718941 PMCID: PMC7946387 DOI: 10.12703/r/10-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance is an emerging threat to global health. Current treatment regimens for these types of bacterial infections are becoming increasingly inadequate. Thus, new innovative technologies are needed to help identify and characterize novel drugs and drug targets which are critical in order to combat multidrug-resistant bacterial strains. Bacterial efflux systems have emerged as an attractive target for drug design, as blocking their export function significantly increases the potency of administered antibiotics. However, in order to develop potent and tolerable efflux pump inhibitors with high efficacy, detailed structural information is required for both the apo- and substrate-bound forms of these membrane proteins. The emergence of cryo-electron microscopy (cryo-EM) has greatly advanced the field of membrane protein structural biology. It has significantly enhanced the ability to solve large multi-protein complexes as well as extract meaningful data from a heterogeneous sample, such as identification of several assembly states of the bacterial ribosome, from a single data set. This technique can be expanded to solve the structures of substrate-bound efflux pumps and entire efflux systems from previously unusable membrane protein sample preparations. Subsequently, cryo-EM combined with other biophysical techniques has the potential to markedly advance the field of membrane protein structural biology. The ability to discern complete transport machineries, enzymatic signal transduction pathways, and other membrane-associated complexes will help us fully understand the complexities of the membrane proteome.
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Affiliation(s)
- Philip A Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
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PELDOR/DEER: An Electron Paramagnetic Resonance Method to Study Membrane Proteins in Lipid Bilayers. Methods Mol Biol 2021. [PMID: 33582999 DOI: 10.1007/978-1-0716-0724-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Every membrane protein is involved in close interactions with the lipid environment of cellular membranes. The annular lipids, that are in direct contact with the polypeptide, can in principle be seen as an integral part of its structure, akin to the first hydration shell of soluble proteins. It is therefore desirable to investigate the structure of membrane proteins and especially their conformational flexibility under conditions that are as close as possible to their native state. This can be achieved by reconstituting the protein into proteoliposomes, nanodiscs, or bicelles. In recent years, PELDOR/DEER spectroscopy has proved to be a very useful method to study the structure and function of membrane proteins in such artificial membrane environments. The technique complements both X-ray crystallography and cryo-EM and can be used in combination with virtually any artificial membrane environment and under certain circumstances even in native membranes. Of the above-mentioned membrane mimics, bicelles are currently the least often used for PELDOR studies, although they offer some advantages, especially their ease of use. Here, we provide a step-by-step protocol for studying a bicelle reconstituted membrane protein with PELDOR/DEER spectroscopy.
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Conn CE, de Campo L, Whitten AE, Garvey CJ, Krause-Heuer AM, van 't Hag L. Membrane Protein Structures in Lipid Bilayers; Small-Angle Neutron Scattering With Contrast-Matched Bicontinuous Cubic Phases. Front Chem 2021; 8:619470. [PMID: 33644002 PMCID: PMC7903247 DOI: 10.3389/fchem.2020.619470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/02/2020] [Indexed: 01/12/2023] Open
Abstract
This perspective describes advances in determining membrane protein structures in lipid bilayers using small-angle neutron scattering (SANS). Differentially labeled detergents with a homogeneous scattering length density facilitate contrast matching of detergent micelles; this has previously been used successfully to obtain the structures of membrane proteins. However, detergent micelles do not mimic the lipid bilayer environment of the cell membrane in vivo. Deuterated vesicles can be used to obtain the radius of gyration of membrane proteins, but protein-protein interference effects within the vesicles severely limits this method such that the protein structure cannot be modeled. We show herein that different membrane protein conformations can be distinguished within the lipid bilayer of the bicontinuous cubic phase using contrast-matching. Time-resolved studies performed using SANS illustrate the complex phase behavior in lyotropic liquid crystalline systems and emphasize the importance of this development. We believe that studying membrane protein structures and phase behavior in contrast-matched lipid bilayers will advance both biological and pharmaceutical applications of membrane-associated proteins, biosensors and food science.
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Affiliation(s)
- Charlotte E. Conn
- School of Science, STEM College, RMIT University, Melbourne, VIC, Australia
| | - Liliana de Campo
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Andrew E. Whitten
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Christopher J. Garvey
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
- Lund Institute for Advanced Neutron and X-Ray Science, Lund, Sweden
- Biolfim-Research Center for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | - Anwen M. Krause-Heuer
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Leonie van 't Hag
- Department of Chemical Engineering, Monash University, Clayton, VIC, Australia
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Sarkar P, Chattopadhyay A. Insights into cellular signaling from membrane dynamics. Arch Biochem Biophys 2021; 701:108794. [PMID: 33571482 DOI: 10.1016/j.abb.2021.108794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/20/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022]
Abstract
Biological membranes allow morphological compartmentalization of cells and represent complex micro-heterogeneous fluids exhibiting a range of dynamics. The plasma membrane occupies a central place in cellular signaling which allows the cell to perform a variety of functions. In this review, we analyze cellular signaling in a dynamic biophysical framework guided by the "mobile receptor hypothesis". We describe a variety of examples from literature in which lateral diffusion of signaling membrane proteins acts as an important determinant in the efficiency of signaling. A major focus in our review is on membrane-embedded G protein-coupled receptors (GPCRs) which act as cellular signaling hubs for diverse cellular functions. Taken together, we describe a dynamics-based signaling paradigm with chosen examples from literature to elucidate how such a paradigm helps us understand signaling by GPCRs, maintenance of cellular polarity in yeast and infection by pathogens. We envision that with further technological advancement, it would be possible to explore cellular signaling more holistically as cells undergo development, differentiation and aging, thereby providing us a robust window into the dynamics of the cellular interior and its functional correlates.
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Affiliation(s)
- Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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