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Tutkus M, Lundgaard CV, Veshaguri S, Tønnesen A, Hatzakis N, Rasmussen SGF, Stamou D. Probing Activation and Conformational Dynamics of the Vesicle-Reconstituted β 2 Adrenergic Receptor at the Single-Molecule Level. J Phys Chem B 2024; 128:2124-2133. [PMID: 38391238 PMCID: PMC10926102 DOI: 10.1021/acs.jpcb.3c08349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
G-protein-coupled receptors (GPCRs) are structurally flexible membrane proteins that mediate a host of physiological responses to extracellular ligands like hormones and neurotransmitters. Fine features of their dynamic structural behavior are hypothesized to encode the functional plasticity seen in GPCR activity, where ligands with different efficacies can direct the same receptor toward different signaling phenotypes. Although the number of GPCR crystal structures is increasing, the receptors are characterized by complex and poorly understood conformational landscapes. Therefore, we employed a fluorescence microscopy assay to monitor conformational dynamics of single β2 adrenergic receptors (β2ARs). To increase the biological relevance of our findings, we decided not to reconstitute the receptor in detergent micelles but rather lipid membranes as proteoliposomes. The conformational dynamics were monitored by changes in the intensity of an environmentally sensitive boron-dipyrromethene (BODIPY 493/503) fluorophore conjugated to an endogenous cysteine (located at the cytoplasmic end of the sixth transmembrane helix of the receptor). Using total internal reflection fluorescence microscopy (TIRFM) and a single small unilamellar liposome assay that we previously developed, we followed the real-time dynamic properties of hundreds of single β2ARs reconstituted in a native-like environment─lipid membranes. Our results showed that β2AR-BODIPY fluctuates between several states of different intensity on a time scale of seconds, compared to BODIPY-lipid conjugates that show almost entirely stable fluorescence emission in the absence and presence of the full agonist BI-167107. Agonist stimulation changes the β2AR dynamics, increasing the population of states with higher intensities and prolonging their durations, consistent with bulk experiments. The transition density plot demonstrates that β2AR-BODIPY, in the absence of the full agonist, interconverts between states of low and moderate intensity, while the full agonist renders transitions between moderate and high-intensity states more probable. This redistribution is consistent with a mechanism of conformational selection and is a promising first step toward characterizing the conformational dynamics of GPCRs embedded in a lipid bilayer.
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Affiliation(s)
- Marijonas Tutkus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio Ave. 7, LT-10257 Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Christian V Lundgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Salome Veshaguri
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Asger Tønnesen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Nikos Hatzakis
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Department of Chemistry and Nanoscience Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience and Pharmacology, Panum, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Dimitrios Stamou
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Center for Geometrically Engineered Cellular Systems, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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2
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Thakur GCN, Uday A, Jurkiewicz P. FRET-GP - A Local Measure of the Impact of Transmembrane Peptide on Lipids. Langmuir 2023; 39:18390-18402. [PMID: 38048524 DOI: 10.1021/acs.langmuir.3c02505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Reconstitution of a transmembrane protein in model lipid systems allows studying its structure and dynamics in isolation from the complexity of the natural environment. This approach also provides a well-defined environment for studying the interactions of proteins with lipids. In this work, we describe the FRET-GP method, which utilizes Förster resonance energy transfer (FRET) to specifically probe the nanoenvironment of a transmembrane domain. The tryptophan residues flanking this domain act as efficient FRET donors, while Laurdan acts as acceptor. The fluorescence of this solvatochromic probe is quantified using generalized polarization (GP) to report on lipid mobility in the vicinity of the transmembrane domain. We applied FRET-GP to study the transmembrane peptide WALP incorporated in liposomes. We found that the direct excitation of Laurdan to its second singlet state strongly contributes to GP values measured in FRET conditions. Removal of this parasitic contribution was essential for proper determination of GPFRET - the local analogue of classical GP parameter. The presence of WALP significantly increased both parameters but the local effects were considerably stronger (GPFRET ≫ GP). We conclude that WALP restricts lipid movement in its vicinity, inducing lateral inhomogeneity in membrane fluidity. WALP was also found to influence lipid phase transition. Our findings demonstrated that FRET-GP simultaneously provides local and global results, thereby enhancing the depth of information obtained from the measurement. We highlight the simplicity and sensitivity of the method, but also discuss its potential and limitations in studying protein-lipid interactions.
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Affiliation(s)
- Garima C N Thakur
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Arunima Uday
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
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3
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Saunders C, de Villiers CA, Stevens MM. Single Particle Chemical Characterisation of Nanoformulations for Cargo Delivery. AAPS J 2023; 25:94. [PMID: 37783923 DOI: 10.1208/s12248-023-00855-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/25/2023] [Indexed: 10/04/2023] Open
Abstract
Nanoparticles can encapsulate a range of therapeutics, from small molecule drugs to sensitive biologics, to significantly improve their biodistribution and biostability. Whilst the regulatory approval of several of these nanoformulations has proven their translatability, there remain several hurdles to the translation of future nanoformulations, leading to a high rate of candidate nanoformulations failing during the drug development process. One barrier is that the difficulty in tightly controlling nanoscale particle synthesis leads to particle-to-particle heterogeneity, which hinders manufacturing and quality control, and regulatory quality checks. To understand and mitigate this heterogeneity requires advancements in nanoformulation characterisation beyond traditional bulk methods to more precise, single particle techniques. In this review, we compare commercially available single particle techniques, with a particular focus on single particle Raman spectroscopy, to provide a guide to adoption of these methods into development workflows, to ultimately reduce barriers to the translation of future nanoformulations.
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Affiliation(s)
- Catherine Saunders
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Camille A de Villiers
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.
- Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK.
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4
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Zhu J, Wu F, Li C, Mao J, Wang Y, Zhou X, Xie H, Wen C. Application of Single Extracellular Vesicle Analysis Techniques. Int J Nanomedicine 2023; 18:5365-5376. [PMID: 37750091 PMCID: PMC10518151 DOI: 10.2147/ijn.s421342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
Extracellular vesicles (EVs) are lipid containers that are actively released by cells and contain complex molecular cargoes. These cargoes include abundant material such as genomes and proteins from cells of origin. They are involved in intercellular communication and various pathological processes, showing excellent potential for diagnosing and treating diseases. Given the significant heterogeneity of EVs in complex physiopathological processes, unveiling their composition is essential to understanding their function. Bulk detection methods have been previously used to analyze EVs, but they often mask their heterogeneity, leading to the loss of valuable information. To overcome this limitation, single extracellular vesicle (SEV) analysis techniques have been developed and advanced. These techniques allow for analyzing EVs' physical information and biometric molecules at the SEV level. This paper reviews recent advances in SEV detection methods and summarizes some clinical applications for SEV detection strategies.
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Affiliation(s)
- Junquan Zhu
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Feifeng Wu
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Cuifang Li
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Jueyi Mao
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Yang Wang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Xin Zhou
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Haotian Xie
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Chuan Wen
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, People’s Republic of China
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5
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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6
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Uchida N, Ryu Y, Takagi Y, Yoshizawa K, Suzuki K, Anraku Y, Ajioka I, Shimokawa N, Takagi M, Hoshino N, Akutagawa T, Matsubara T, Sato T, Higuchi Y, Ito H, Morita M, Muraoka T. Endocytosis-Like Vesicle Fission Mediated by a Membrane-Expanding Molecular Machine Enables Virus Encapsulation for In Vivo Delivery. J Am Chem Soc 2023; 145:6210-6220. [PMID: 36853954 PMCID: PMC10037323 DOI: 10.1021/jacs.2c12348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Biological membranes are functionalized by membrane-associated protein machinery. Membrane-associated transport processes, such as endocytosis, represent a fundamental and universal function mediated by membrane-deforming protein machines, by which small biomolecules and even micrometer-size substances can be transported via encapsulation into membrane vesicles. Although synthetic molecules that induce dynamic membrane deformation have been reported, a molecular approach enabling membrane transport in which membrane deformation is coupled with substance binding and transport remains critically lacking. Here, we developed an amphiphilic molecular machine containing a photoresponsive diazocine core (AzoMEx) that localizes in a phospholipid membrane. Upon photoirradiation, AzoMEx expands the liposomal membrane to bias vesicles toward outside-in fission in the membrane deformation process. Cargo components, including micrometer-size M13 bacteriophages that interact with AzoMEx, are efficiently incorporated into the vesicles through the outside-in fission. Encapsulated M13 bacteriophages are transiently protected from the external environment and therefore retain biological activity during distribution throughout the body via the blood following administration. This research developed a molecular approach using synthetic molecular machinery for membrane functionalization to transport micrometer-size substances and objects via vesicle encapsulation. The molecular design demonstrated in this study to expand the membrane for deformation and binding to a cargo component can lead to the development of drug delivery materials and chemical tools for controlling cellular activities.
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Affiliation(s)
- Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yunosuke Ryu
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yuichiro Takagi
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ken Yoshizawa
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kotono Suzuki
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasutaka Anraku
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Itsuki Ajioka
- Center for Brain Integration Research Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Kanagawa Institute of Industrial Science and Technology, 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Norihisa Hoshino
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Tomoyuki Akutagawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yuji Higuchi
- Institute for Solid State Physics, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8581, Japan
| | - Hiroaki Ito
- Department of Physics, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Masamune Morita
- National Institute of Advanced Industrial Science and Technology, Center 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Kanagawa Institute of Industrial Science and Technology, 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8538, Japan
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Veit S, Paweletz LC, Günther Pomorski T. Determination of membrane protein orientation upon liposomal reconstitution down to the single vesicle level. Biol Chem 2023:hsz-2022-0325. [PMID: 36857289 DOI: 10.1515/hsz-2022-0325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
Reconstitution of membrane proteins into liposomal membranes represents a key technique in enabling functional analysis under well-defined conditions. In this review, we provide a brief introduction to selected methods that have been developed to determine membrane protein orientation after reconstitution in liposomes, including approaches based on proteolytic digestion with proteases, site-specific labeling, fluorescence quenching and activity assays. In addition, we briefly highlight new strategies based on single vesicle analysis to address the problem of sample heterogeneity.
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Affiliation(s)
- Sarina Veit
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Laura Charlotte Paweletz
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany.,Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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8
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Shi Y, Chen L, Zhu M, Zhao Y. The Future of Nanomedicine. Nanomedicine (Lond) 2023. [DOI: 10.1007/978-981-16-8984-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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9
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Kosmidis E, Shuttle CG, Preobraschenski J, Ganzella M, Johnson PJ, Veshaguri S, Holmkvist J, Møller MP, Marantos O, Marcoline F, Grabe M, Pedersen JL, Jahn R, Stamou D. Regulation of the mammalian-brain V-ATPase through ultraslow mode-switching. Nature 2022; 611:827-34. [PMID: 36418452 DOI: 10.1038/s41586-022-05472-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022]
Abstract
Vacuolar-type adenosine triphosphatases (V-ATPases)1-3 are electrogenic rotary mechanoenzymes structurally related to F-type ATP synthases4,5. They hydrolyse ATP to establish electrochemical proton gradients for a plethora of cellular processes1,3. In neurons, the loading of all neurotransmitters into synaptic vesicles is energized by about one V-ATPase molecule per synaptic vesicle6,7. To shed light on this bona fide single-molecule biological process, we investigated electrogenic proton-pumping by single mammalian-brain V-ATPases in single synaptic vesicles. Here we show that V-ATPases do not pump continuously in time, as suggested by observing the rotation of bacterial homologues8 and assuming strict ATP-proton coupling. Instead, they stochastically switch between three ultralong-lived modes: proton-pumping, inactive and proton-leaky. Notably, direct observation of pumping revealed that physiologically relevant concentrations of ATP do not regulate the intrinsic pumping rate. ATP regulates V-ATPase activity through the switching probability of the proton-pumping mode. By contrast, electrochemical proton gradients regulate the pumping rate and the switching of the pumping and inactive modes. A direct consequence of mode-switching is all-or-none stochastic fluctuations in the electrochemical gradient of synaptic vesicles that would be expected to introduce stochasticity in proton-driven secondary active loading of neurotransmitters and may thus have important implications for neurotransmission. This work reveals and emphasizes the mechanistic and biological importance of ultraslow mode-switching.
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10
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Baxani DK, Jamieson WD, Barrow DA, Castell OK. Encapsulated droplet interface bilayers as a platform for high-throughput membrane studies. Soft Matter 2022; 18:5089-5096. [PMID: 35766018 PMCID: PMC9277618 DOI: 10.1039/d1sm01111a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Whilst it is highly desirable to produce artificial lipid bilayer arrays allowing for systematic high-content screening of membrane conditions, it remains a challenge due to the combined requirements of scaled membrane production, simple measurement access, and independent control over individual bilayer experimental conditions. Here, droplet bilayers encapsulated within a hydrogel shell are output individually into multi-well plates for simple, arrayed quantitative measurements. The afforded experimental throughput is used to conduct a 2D concentration screen characterising the synergistic pore-forming peptides Magainin2 and PGLa. Maximal enhanced activity is revealed at equimolar peptide concentrations via a membrane dye leakage assay, a finding consistent with models proposed from NMR data. The versatility of the platform is demonstrated by performing in situ electrophysiology, revealing low conductance pore activity (∼15 to 20 pA with 4.5 pA sub-states). In conclusion, this array platform addresses the aforementioned challenges and provides new and flexible opportunities for high-throughput membrane studies. Furthermore, the ability to engineer droplet networks within each construct paves the way for "lab-in-a-capsule" approaches accommodating multiple assays per construct and allowing for communicative reaction pathways.
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Affiliation(s)
- D K Baxani
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, UK.
| | - W D Jamieson
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, UK.
| | - D A Barrow
- School of Engineering, Cardiff University, 14-17 The Parade, CF4 3AA Cardiff, UK
| | - O K Castell
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, UK.
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11
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Veit S, Paweletz LC, Bohr SSR, Menon AK, Hatzakis NS, Pomorski TG. Single Vesicle Fluorescence-Bleaching Assay for Multi-Parameter Analysis of Proteoliposomes by Total Internal Reflection Fluorescence Microscopy. ACS Appl Mater Interfaces 2022; 14:29659-29667. [PMID: 35748880 DOI: 10.1021/acsami.2c07454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reconstitution of membrane proteins into model membranes is an essential approach for their functional analysis under chemically defined conditions. Established model-membrane systems used in ensemble average measurements are limited by sample heterogeneity and insufficient knowledge of lipid and protein content at the single vesicle level, which limits quantitative analysis of vesicle properties and prevents their correlation with protein activity. Here, we describe a versatile total internal reflection fluorescence microscopy-based bleaching protocol that permits parallel analysis of multiple parameters (physical size, tightness, unilamellarity, membrane protein content, and orientation) of individual proteoliposomes prepared with fluorescently tagged membrane proteins and lipid markers. The approach makes use of commercially available fluorophores including the commonly used nitrobenzoxadiazole dye and may be applied to deduce functional molecular characteristics of many types of reconstituted fluorescently tagged membrane proteins.
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Affiliation(s)
- Sarina Veit
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum 44801, Germany
| | - Laura Charlotte Paweletz
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum 44801, Germany
| | - Søren S-R Bohr
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Nikos S Hatzakis
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen DK-2100, Denmark
- NovoNordisk Foundation Center for Protein Research,Copenhagen DK-2200, Denmark
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum 44801, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen,Frederiksberg C DK-1871, Denmark
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12
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Shi Y, Chen L, Zhu M, Zhao Y. The Future of Nanomedicine. Nanomedicine (Lond) 2022. [DOI: 10.1007/978-981-13-9374-7_24-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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13
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Bordanaba-Florit G, Royo F, Kruglik SG, Falcón-Pérez JM. Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles. Nat Protoc 2021; 16:3163-3185. [PMID: 34135505 DOI: 10.1038/s41596-021-00551-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) are heterogeneous lipid containers with a complex molecular cargo comprising several populations with unique roles in biological processes. These vesicles are closely associated with specific physiological features, which makes them invaluable in the detection and monitoring of various diseases. EVs play a key role in pathophysiological processes by actively triggering genetic or metabolic responses. However, the heterogeneity of their structure and composition hinders their application in medical diagnosis and therapies. This diversity makes it difficult to establish their exact physiological roles, and the functions and composition of different EV (sub)populations. Ensemble averaging approaches currently employed for EV characterization, such as western blotting or 'omics' technologies, tend to obscure rather than reveal these heterogeneities. Recent developments in single-vesicle analysis have made it possible to overcome these limitations and have facilitated the development of practical clinical applications. In this review, we discuss the benefits and challenges inherent to the current methods for the analysis of single vesicles and review the contribution of these approaches to the understanding of EV biology. We describe the contributions of these recent technological advances to the characterization and phenotyping of EVs, examination of the role of EVs in cell-to-cell communication pathways and the identification and validation of EVs as disease biomarkers. Finally, we discuss the potential of innovative single-vesicle imaging and analysis methodologies using microfluidic devices, which promise to deliver rapid and effective basic and practical applications for minimally invasive prognosis systems.
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Affiliation(s)
- Guillermo Bordanaba-Florit
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - Félix Royo
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, Paris, France
| | - Juan M Falcón-Pérez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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14
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Tutkus M, Chmeliov J, Trinkunas G, Akhtar P, Lambrev PH, Valkunas L. Aggregation-related quenching of LHCII fluorescence in liposomes revealed by single-molecule spectroscopy. J Photochem Photobiol B 2021; 218:112174. [PMID: 33799009 DOI: 10.1016/j.jphotobiol.2021.112174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/04/2021] [Accepted: 03/21/2021] [Indexed: 11/20/2022]
Abstract
Incorporation of membrane proteins into reconstituted lipid membranes is a common approach for studying their structure and function relationship in a native-like environment. In this work, we investigated fluorescence properties of liposome-reconstituted major light-harvesting complexes of plants (LHCII). By utilizing liposome labelling with the fluorescent dye molecules and single-molecule microscopy techniques, we were able to study truly liposome-reconstituted LHCII and compare them with bulk measurements and liposome-free LHCII aggregates bound to the surface. Our results showed that fluorescence lifetime obtained in bulk and in single liposome measurements were correlated. The fluorescence lifetimes of LHCII were shorter for liposome-free LHCII than for reconstituted LHCII. In the case of liposome-reconstituted LHCII, fluorescence lifetime showed dependence on the protein density reminiscent to concentration quenching. The dependence of fluorescence lifetime of LHCII on the liposome size was not significant. Our results demonstrated that fluorescence quenching can be induced by LHCII - LHCII interactions in reconstituted membranes, most likely occurring via the same mechanism as photoprotective non-photochemical quenching in vivo.
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15
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Guha A, McGuire ML, Leriche G, Yang J, Mayer M. A single-liposome assay that enables temperature-dependent measurement of proton permeability of extremophile-inspired lipid membranes. Biochim Biophys Acta Biomembr 2021; 1863:183567. [PMID: 33476579 DOI: 10.1016/j.bbamem.2021.183567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Affiliation(s)
- Anirvan Guha
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Melissa L McGuire
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland.
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16
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Poc P, Gutzeit VA, Ast J, Lee J, Jones BJ, D'Este E, Mathes B, Lehmann M, Hodson DJ, Levitz J, Broichhagen J. Interrogating surface versus intracellular transmembrane receptor populations using cell-impermeable SNAP-tag substrates. Chem Sci 2020; 11:7871-7883. [PMID: 34123074 PMCID: PMC8163392 DOI: 10.1039/d0sc02794d] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/02/2020] [Indexed: 01/13/2023] Open
Abstract
Employing self-labelling protein tags for the attachment of fluorescent dyes has become a routine and powerful technique in optical microscopy to visualize and track fused proteins. However, membrane permeability of the dyes and the associated background signals can interfere with the analysis of extracellular labelling sites. Here we describe a novel approach to improve extracellular labelling by functionalizing the SNAP-tag substrate benzyl guanine ("BG") with a charged sulfonate ("SBG"). This chemical manipulation can be applied to any SNAP-tag substrate, improves solubility, reduces non-specific staining and renders the bioconjugation handle impermeable while leaving its cargo untouched. We report SBG-conjugated fluorophores across the visible spectrum, which cleanly label SNAP-fused proteins in the plasma membrane of living cells. We demonstrate the utility of SBG-conjugated fluorophores to interrogate class A, B and C G protein-coupled receptors (GPCRs) using a range of imaging approaches including nanoscopic superresolution imaging, analysis of GPCR trafficking from intra- and extracellular pools, in vivo labelling in mouse brain and analysis of receptor stoichiometry using single molecule pull down.
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Affiliation(s)
- Pascal Poc
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
| | - Vanessa A Gutzeit
- Neuroscience Graduate Program, Weill Cornell Medicine New York NY 10065 USA
| | - Julia Ast
- Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham Birmingham UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners Birmingham UK
| | - Joon Lee
- Department of Biochemistry, Weill Cornell Medicine New York NY 10065 USA
| | - Ben J Jones
- Section of Investigative Medicine, Imperial College London London W12 0NN UK
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research Heidelberg Germany
| | - Bettina Mathes
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Pharmacology and Cell Biology Robert-Rössle-Str. 10 13125 Berlin Germany
| | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham Birmingham UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners Birmingham UK
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine New York NY 10065 USA
- Tri-Institutional PhD Program in Chemical Biology New York NY 10065 USA
| | - Johannes Broichhagen
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Chemical Biology Robert-Rössle-Str. 10 13125 Berlin Germany
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17
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Walsh SM, Mathiasen S, Christensen SM, Fay JF, King C, Provasi D, Borrero E, Rasmussen SGF, Fung JJ, Filizola M, Hristova K, Kobilka B, Farrens DL, Stamou D. Single Proteoliposome High-Content Analysis Reveals Differences in the Homo-Oligomerization of GPCRs. Biophys J 2018; 115:300-12. [PMID: 30021106 DOI: 10.1016/j.bpj.2018.05.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 11/23/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) control vital cellular signaling pathways. GPCR oligomerization is proposed to increase signaling diversity. However, many reports have arrived at disparate conclusions regarding the existence, stability, and stoichiometry of GPCR oligomers, partly because of cellular complexity and ensemble averaging of intrareconstitution heterogeneities that complicate the interpretation of oligomerization data. To overcome these limitations, we exploited fluorescence-microscopy-based high-content analysis of single proteoliposomes. This allowed multidimensional quantification of intrinsic monomer-monomer interactions of three class A GPCRs (β2-adrenergic receptor, cannabinoid receptor type 1, and opsin). Using a billion-fold less protein than conventional assays, we quantified oligomer stoichiometries, association constants, and the influence of two ligands and membrane curvature on oligomerization, revealing key similarities and differences for three GPCRs with decidedly different physiological functions. The assays introduced here will assist with the quantitative experimental observation of oligomerization for transmembrane proteins in general.
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18
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Gutzeit VA, Thibado J, Stor DS, Zhou Z, Blanchard SC, Andersen OS, Levitz J. Conformational dynamics between transmembrane domains and allosteric modulation of a metabotropic glutamate receptor. eLife 2019; 8:45116. [PMID: 31172948 PMCID: PMC6588349 DOI: 10.7554/elife.45116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023] Open
Abstract
Metabotropic glutamate receptors (mGluRs) are class C, synaptic G-protein-coupled receptors (GPCRs) that contain large extracellular ligand binding domains (LBDs) and form constitutive dimers. Despite the existence of a detailed picture of inter-LBD conformational dynamics and structural snapshots of both isolated domains and full-length receptors, it remains unclear how mGluR activation proceeds at the level of the transmembrane domains (TMDs) and how TMD-targeting allosteric drugs exert their effects. Here, we use time-resolved functional and conformational assays to dissect the mechanisms by which allosteric drugs activate and modulate mGluR2. Single-molecule subunit counting and inter-TMD fluorescence resonance energy transfer measurements in living cells reveal LBD-independent conformational rearrangements between TMD dimers during receptor modulation. Using these assays along with functional readouts, we uncover heterogeneity in the magnitude, direction, and the timing of the action of both positive and negative allosteric drugs. Together our experiments lead to a three-state model of TMD activation, which provides a framework for understanding how inter-subunit rearrangements drive class C GPCR activation.
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Affiliation(s)
- Vanessa A Gutzeit
- Neuroscience Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Jordana Thibado
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Daniel Starer Stor
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Scott C Blanchard
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,Tri-Institutional PhD Program in Chemical Biology, New York, United States
| | - Olaf S Andersen
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Joshua Levitz
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, United States.,Tri-Institutional PhD Program in Chemical Biology, New York, United States.,Department of Biochemistry, Weill Cornell Medicine, New York, United States
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19
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Rabanel JM, Adibnia V, Tehrani SF, Sanche S, Hildgen P, Banquy X, Ramassamy C. Nanoparticle heterogeneity: an emerging structural parameter influencing particle fate in biological media? Nanoscale 2019; 11:383-406. [PMID: 30560970 DOI: 10.1039/c8nr04916e] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drug nanocarriers' surface chemistry is often presumed to be uniform. For instance, the polymer surface coverage and distribution of ligands on nanoparticles are described with averaged values obtained from quantification techniques based on particle populations. However, these averaged values may conceal heterogeneities at different levels, either because of the presence of particle sub-populations or because of surface inhomogeneities, such as patchy surfaces on individual particles. The characterization and quantification of chemical surface heterogeneities are tedious tasks, which are rather limited by the currently available instruments and research protocols. However, heterogeneities may contribute to some non-linear effects observed during the nanoformulation optimization process, cause problems related to nanocarrier production scale-up and correlate with unexpected biological outcomes. On the other hand, heterogeneities, while usually unintended and detrimental to nanocarrier performance, may, in some cases, be sought as adjustable properties that provide NPs with unique functionality. In this review, results and processes related to this issue are compiled, and perspectives and possible analytical developments are discussed.
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Affiliation(s)
- Jean-Michel Rabanel
- Centre INRS Institut Armand-Frappier, 531, boul. des Prairies, Laval, QC H7V 1B7, Canada.
| | - Vahid Adibnia
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada.
| | - Soudeh F Tehrani
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada.
| | - Steven Sanche
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada.
| | - Patrice Hildgen
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada.
| | - Xavier Banquy
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada.
| | - Charles Ramassamy
- Centre INRS Institut Armand-Frappier, 531, boul. des Prairies, Laval, QC H7V 1B7, Canada.
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20
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Kim DH, Park S, Kim DK, Jeong MG, Noh J, Kwon Y, Zhou K, Lee NK, Ryu SH. Direct visualization of single-molecule membrane protein interactions in living cells. PLoS Biol 2018; 16:e2006660. [PMID: 30543635 PMCID: PMC6307816 DOI: 10.1371/journal.pbio.2006660] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/27/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Interactions between membrane proteins are poorly understood despite their importance in cell signaling and drug development. Here, we present a co-immunoimmobilization assay (Co-II) enabling the direct observation of membrane protein interactions in single living cells that overcomes the limitations of currently prevalent proximity-based indirect methods. Using Co-II, we investigated the transient homodimerizations of epidermal growth factor receptor (EGFR) and beta-2 adrenergic receptor (β2-AR) in living cells, revealing the differential regulation of these receptors’ dimerizations by molecular conformations and microenvironment in a plasma membrane. Co-II should provide a simple, rapid, and robust platform for visualizing both weak and strong protein interactions in the plasma membrane of living cells. Protein–protein interactions govern cellular processes. The majority of these physical interactions previously identified are strong/permanent interactions, which typically remain unbroken even after purification. The weak/transient interactions between proteins have been implicated in the control of dynamic cellular process that maintain cellular homeostasis and trigger signaling cascades upon environmental changes. However, these interactions are poorly investigated, mainly due to the methodological limitations. Here, we have developed a co-immunoimmobilization assay called Co-II that enables the direct visualization of protein–protein interactions in the membrane of living cells at the single-molecule level. Co-II is based on the intuitive concept that if the protein of interest is immobilized, the interacting protein must be co-immobilized. The use of intrinsic protein diffusivity fundamentally overcomes the limitations of proximity-based methods. Using Co-II, we study the transient homodimerizations of EGFR and β2-AR in living cells, which have been implicated in several types of cancers and heart diseases. We show that the dimerization of these receptors is differently regulated by molecular conformations and the microenvironment in the plasma membrane.
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Affiliation(s)
- Do-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Soyeon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dong-Kyun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Min Gyu Jeong
- Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jungeun Noh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yonghoon Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kai Zhou
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Nam Ki Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- * E-mail: (SHR); (NKL)
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- * E-mail: (SHR); (NKL)
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21
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Tutkus M, Akhtar P, Chmeliov J, Görföl F, Trinkunas G, Lambrev PH, Valkunas L. Fluorescence Microscopy of Single Liposomes with Incorporated Pigment-Proteins. Langmuir 2018; 34:14410-14418. [PMID: 30380887 DOI: 10.1021/acs.langmuir.8b02307] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Reconstitution of transmembrane proteins into liposomes is a widely used method to study their behavior under conditions closely resembling the natural ones. However, this approach does not allow precise control of the liposome size, reconstitution efficiency, and the actual protein-to-lipid ratio in the formed proteoliposomes, which might be critical for some applications and/or interpretation of data acquired during the spectroscopic measurements. Here, we present a novel strategy employing methods of proteoliposome preparation, fluorescent labeling, purification, and surface immobilization that allow us to quantify these properties using fluorescence microscopy at the single-liposome level and for the first time apply it to study photosynthetic pigment-protein complexes LHCII. We show that LHCII proteoliposome samples, even after purification with a density gradient, always contain a fraction of nonreconstituted protein and are extremely heterogeneous in both protein density and liposome sizes. This strategy enables quantitative analysis of the reconstitution efficiency of different protocols and precise fluorescence spectroscopic study of various transmembrane proteins in a controlled nativelike environment.
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Affiliation(s)
- Marijonas Tutkus
- Department of Molecular Compound Physics , Centre for Physical Sciences and Technology , Saulėtekio Avenue 3 , LT-10257 Vilnius , Lithuania
| | - Parveen Akhtar
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári körút 62 , 6726 Szeged , Hungary
| | - Jevgenij Chmeliov
- Department of Molecular Compound Physics , Centre for Physical Sciences and Technology , Saulėtekio Avenue 3 , LT-10257 Vilnius , Lithuania
- Institute of Chemical Physics, Faculty of Physics , Vilnius University , Saulėtekio Avenue 9-III , LT-10222 Vilnius , Lithuania
| | - Fanni Görföl
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári körút 62 , 6726 Szeged , Hungary
| | - Gediminas Trinkunas
- Department of Molecular Compound Physics , Centre for Physical Sciences and Technology , Saulėtekio Avenue 3 , LT-10257 Vilnius , Lithuania
| | - Petar H Lambrev
- Biological Research Centre , Hungarian Academy of Sciences , Temesvári körút 62 , 6726 Szeged , Hungary
| | - Leonas Valkunas
- Department of Molecular Compound Physics , Centre for Physical Sciences and Technology , Saulėtekio Avenue 3 , LT-10257 Vilnius , Lithuania
- Institute of Chemical Physics, Faculty of Physics , Vilnius University , Saulėtekio Avenue 9-III , LT-10222 Vilnius , Lithuania
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22
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Schwamborn M, Schumacher J, Sibold J, Teiwes NK, Steinem C. Monitoring ATPase induced pH changes in single proteoliposomes with the lipid-coupled fluorophore Oregon Green 488. Analyst 2018; 142:2670-2677. [PMID: 28616949 DOI: 10.1039/c7an00215g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monitoring the proton pumping activity of proteins such as ATPases in reconstituted single proteoliposomes is key to quantify the function of proteins as well as potential proton pump inhibitors. However, most pH-detecting assays available are either not quantitative, require well-adapted reconstitution protocols or are not appropriate for single vesicle studies. Here, we describe the quantitative and time-resolved detection of F-type ATPase-induced pH changes across vesicular membranes doped with the commercially available pH sensitive fluorophore Oregon Green 488 DHPE. This dye is shown to be well suited to monitor acidification of lipid vesicles not only in bulk but also at the single vesicle level. The pKa value of Oregon Green 488 DHPE embedded in a lipid environment was determined to be 6.1 making the fluorophore well suited for a variety of physiologically relevant proton pumps. The TFOF1-ATPase from a thermophilic bacterium was reconstituted into large unilamellar vesicles and the bulk acidification assay clearly reveals the overall activity of the F-type ATPase in the vesicle ensemble with an average pH change of 0.45. However, monitoring the pH changes in individual vesicles attached to a substrate demonstrates that the fraction of vesicles with a significant observable pH change is only about 5%, a number that cannot be gathered from bulk experiments and which is considerably lower than expected.
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Affiliation(s)
- Miriam Schwamborn
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany.
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23
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Belardi B, Son S, Vahey MD, Wang J, Hou J, Fletcher DA. Claudin-4 reconstituted in unilamellar vesicles is sufficient to form tight interfaces that partition membrane proteins. J Cell Sci 2018; 132:jcs.221556. [PMID: 30209136 DOI: 10.1242/jcs.221556] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/01/2018] [Indexed: 01/05/2023] Open
Abstract
Tight junctions have been hypothesized to act as molecular fences in the plasma membrane of epithelial cells, helping to form differentiated apical and basolateral domains. While this fence function is believed to arise from the interaction of four-pass transmembrane claudins, the complexity of tight junctions has made direct evidence of their role as a putative diffusion barrier difficult to obtain. Here, we address this challenge by reconstituting claudin-4 into giant unilamellar vesicles using microfluidic jetting. We find that reconstituted claudin-4 alone can form adhesive membrane interfaces without the accessory proteins that are present in vivo By controlling the molecular composition of the inner and outer leaflets of jetted vesicle membranes, we show that claudin-4-mediated interfaces can drive partitioning of extracellular membrane proteins with ectodomains as small as 5 nm but not of inner or outer leaflet lipids. Our findings indicate that homotypic interactions of claudins and their small size can contribute to the polarization of epithelial cells.
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Affiliation(s)
- Brian Belardi
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA
| | - Sungmin Son
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA
| | - Michael D Vahey
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA
| | - Jinzhi Wang
- Department of Internal Medicine & Center for Investigation of Membrane Excitability Disease, Washington University Medical School, St. Louis, MO 63110, USA
| | - Jianghui Hou
- Department of Internal Medicine & Center for Investigation of Membrane Excitability Disease, Washington University Medical School, St. Louis, MO 63110, USA
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720, USA .,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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24
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Pick H, Alves AC, Vogel H. Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications. Chem Rev 2018; 118:8598-8654. [PMID: 30153012 DOI: 10.1021/acs.chemrev.7b00777] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.
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Affiliation(s)
- Horst Pick
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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25
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Jiang WY, Li Y, Li ZY, Cui ZJ. Permanent Photodynamic Cholecystokinin 1 Receptor Activation: Dimer-to-Monomer Conversion. Cell Mol Neurobiol 2018; 38:1283-1292. [PMID: 29869099 DOI: 10.1007/s10571-018-0596-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/30/2018] [Indexed: 02/07/2023]
Abstract
The G protein-coupled cholecystokinin 1 receptor (CCK1R) is activated permanently by type II photodynamic action (i.e., by singlet oxygen) in the freshly isolated rat pancreatic acini, in contrast to reversible activation by CCK. But how CCK1R is photodynamically activated is not known. Therefore, in the present work, we subjected membrane proteins extracted from isolated rat pancreatic acini to photodynamic action with photosensitiser sulphonated aluminium phthalocyanine (SALPC), and used reducing gel electrophoresis and Western blot to detect possible changes in CCK1R oligomerization status. Photodynamic action (SALPC 1 µM, light 36.7 mW cm- 2 × 10 min) was found to convert dimeric CCK1R nearly quantitatively to monomers. Such conversion was dependent on both irradiance (8.51-36.7 mW cm- 2) and irradiation time (1-20 min). Minimum effective irradiance was found to be 11.1 mW cm- 2 (× 10 min, with SALPC 1 µM), and brief photodynamic action (SALPC 1 µM, 36.7 mW cm- 2 × 1 min) was effective. Whilst CCK stimulation of purified membrane proteins alone had no effect on CCK1R dimer/monomer balance, sub-threshold photodynamic action (SALPC 100 nM, 36.7 mW cm- 2 × 10 min) plus CCK revealed a bell-shaped CCK dose response curve for CCK1R monomerization, which was remarkably similar to the dose response curve for CCK-stimulated amylase secretion in isolated rat pancreatic acini. These two lines of evidence together suggest that during photodynamic CCK1R activation, CCK1R is permanently monomerized, thus providing a unique approach for permanent G protein-coupled receptor (GPCR) activation which has not been achieved before.
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Affiliation(s)
- Wen Yi Jiang
- Institute of Cell Biology, Beijing Normal University, Beijing, 100875, China
| | - Yuan Li
- Institute of Cell Biology, Beijing Normal University, Beijing, 100875, China
| | - Zhi Ying Li
- Institute of Cell Biology, Beijing Normal University, Beijing, 100875, China
| | - Zong Jie Cui
- Institute of Cell Biology, Beijing Normal University, Beijing, 100875, China.
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26
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Diederichs T, Nguyen QH, Urban M, Tampé R, Tornow M. Transparent Nanopore Cavity Arrays Enable Highly Parallelized Optical Studies of Single Membrane Proteins on Chip. Nano Lett 2018; 18:3901-3910. [PMID: 29741381 DOI: 10.1021/acs.nanolett.8b01252] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Membrane proteins involved in transport processes are key targets for pharmaceutical research and industry. Despite continuous improvements and new developments in the field of electrical readouts for the analysis of transport kinetics, a well-suited methodology for high-throughput characterization of single transporters with nonionic substrates and slow turnover rates is still lacking. Here, we report on a novel architecture of silicon chips with embedded nanopore microcavities, based on a silicon-on-insulator technology for high-throughput optical readouts. Arrays containing more than 14 000 inverted-pyramidal cavities of 50 femtoliter volumes and 80 nm circular pore openings were constructed via high-resolution electron-beam lithography in combination with reactive ion etching and anisotropic wet etching. These cavities feature both, an optically transparent bottom and top cap. Atomic force microscopy analysis reveals an overall extremely smooth chip surface, particularly in the vicinity of the nanopores, which exhibits well-defined edges. Our unprecedented transparent chip design provides parallel and independent fluorescent readout of both cavities and buffer reservoir for unbiased single-transporter recordings. Spreading of large unilamellar vesicles with efficiencies up to 96% created nanopore-supported lipid bilayers, which are stable for more than 1 day. A high lipid mobility in the supported membrane was determined by fluorescent recovery after photobleaching. Flux kinetics of α-hemolysin were characterized at single-pore resolution with a rate constant of 0.96 ± 0.06 × 10-3 s-1. Here, we deliver an ideal chip platform for pharmaceutical research, which features high parallelism and throughput, synergistically combined with single-transporter resolution.
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Affiliation(s)
- Tim Diederichs
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany
| | - Quoc Hung Nguyen
- Molecular Electronics , Technical University of Munich , Theresienstrasse 90 , 80333 Munich , Germany
| | - Michael Urban
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany
- Cluster of Excellence Frankfurt (CEF) Macromolecular Complexes ; Goethe University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt/M. , Germany
| | - Marc Tornow
- Molecular Electronics , Technical University of Munich , Theresienstrasse 90 , 80333 Munich , Germany
- Fraunhofer Research Institution for Microsystems and Solid State Technologies (EMFT) , Hansastrasse 27d , 80686 Munich , Germany
- Center for NanoScience (CeNS) , Ludwig-Maximilians-University , Geschwister-Scholl Platz 1 , 80539 Munich , Germany
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27
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Lundgren A, Fast BJ, Block S, Agnarsson B, Reimhult E, Gunnarsson A, Höök F. Affinity Purification and Single-Molecule Analysis of Integral Membrane Proteins from Crude Cell-Membrane Preparations. Nano Lett 2018; 18:381-385. [PMID: 29231738 DOI: 10.1021/acs.nanolett.7b04227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The function of integral membrane proteins is critically dependent on their naturally surrounding lipid membrane. Detergent-solubilized and purified membrane proteins are therefore often reconstituted into cell-membrane mimics and analyzed for their function with single-molecule microscopy. Expansion of this approach toward a broad range of pharmaceutically interesting drug targets and biomarkers however remains hampered by the fact that these proteins have low expression levels, and that detergent solubilization and reconstitution often cause protein conformational changes and loss of membrane-specific cofactors, which may impair protein function. To overcome this limitation, we here demonstrate how antibody-modified nanoparticles can be used to achieve affinity purification and enrichment of selected integral membrane proteins directly from cell membrane preparations. Nanoparticles were first bound to the ectodomain of β-secretase 1 (BACE1) contained in cell-derived membrane vesicles. In a subsequent step, these were merged into a continuous supported membrane in a microfluidic channel. Through the extended nanoparticle tag, a weak (∼fN) hydrodynamic force could be applied, inducing directed in-membrane movement of targeted BACE1 exclusively. This enabled selective thousand-fold enrichment of the targeted membrane protein while preserving a natural lipid environment. In addition, nanoparticle-targeting also enabled simultaneous tracking analysis of each individual manipulated protein, revealing how their mobility changed when moved from one lipid environment to another. We therefore believe this approach will be particularly useful for separation in-line with single-molecule analysis, eventually opening up for membrane-protein sorting devices analogous to fluorescence-activated cell sorting.
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Affiliation(s)
- Anders Lundgren
- Department of Physics, Chalmers University of Technology , 41296 Göteborg, Sweden
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences , 1190 Vienna, Austria
| | - Björn Johansson Fast
- Department of Physics, Chalmers University of Technology , 41296 Göteborg, Sweden
| | - Stephan Block
- Department of Physics, Chalmers University of Technology , 41296 Göteborg, Sweden
| | - Björn Agnarsson
- Department of Physics, Chalmers University of Technology , 41296 Göteborg, Sweden
| | - Erik Reimhult
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences , 1190 Vienna, Austria
| | - Anders Gunnarsson
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , 43183 Mölndal, Sweden
| | - Fredrik Höök
- Department of Physics, Chalmers University of Technology , 41296 Göteborg, Sweden
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28
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Chadda R, Cliff L, Brimberry M, Robertson JL. A model-free method for measuring dimerization free energies of CLC-ec1 in lipid bilayers. J Gen Physiol 2018; 150:355-365. [PMID: 29321261 PMCID: PMC5806674 DOI: 10.1085/jgp.201711893] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/30/2017] [Indexed: 11/20/2022] Open
Abstract
The thermodynamic reasons why membrane proteins form stable complexes inside the hydrophobic lipid bilayer remain poorly understood. This is largely because of a lack of membrane-protein systems amenable for equilibrium studies and a limited number of methods for measuring these reactions. Recently, we reported the equilibrium dimerization of the CLC-ec1 Cl-/H+ transporter in lipid bilayers (Chadda et al. 2016. eLife https://doi.org/10.7554/eLife.17438), which provided a new type of model system for studying protein association in membranes. The measurement was conducted using the subunit-capture approach, involving passive dilution of the protein in large multilamellar vesicles, followed by single-molecule photobleaching analysis of the Poisson distribution describing protein encapsulation into extruded liposomes. To estimate the fraction of dimers (FDimer ) as a function of protein density, the photobleaching distributions for the nonreactive, ideal monomer and dimer species must be known so that random co-capture probabilities can be accounted for. Previously, this was done by simulating the Poisson process of protein reconstitution into a known size distribution of liposomes composed of Escherichia coli polar lipids (EPLs). In the present study, we investigate the dependency of FDimer and ΔG° on the modeling through a comparison of different liposome size distributions (EPL versus 2:1 POPE/POPG). The results show that the estimated FDimer values are comparable, except at higher densities when liposomes become saturated with protein. We then develop empirical controls to directly measure the photobleaching distributions of the nonreactive monomer (CLC-ec1 I201W/I422W) and ideal dimer (WT CLC-ec1 cross-linked by glutaraldehyde or CLC-ec1 R230C/L249C cross-linked by a disulfide bond). The measured equilibrium constants do not depend on the correction method used, indicating the robustness of the subunit-capture approach. This strategy therefore presents a model-free way to quantify protein dimerization in lipid bilayers, offering a simplified strategy in the ongoing effort to characterize equilibrium membrane-protein reactions in membranes.
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Affiliation(s)
- Rahul Chadda
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA
| | - Lucy Cliff
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Department of Chemistry, The University of Bath, Bath, England, UK
| | - Marley Brimberry
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA
| | - Janice L Robertson
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA
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29
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Dyla M, Terry DS, Kjaergaard M, Sørensen TLM, Lauwring Andersen J, Andersen JP, Rohde Knudsen C, Altman RB, Nissen P, Blanchard SC. Dynamics of P-type ATPase transport revealed by single-molecule FRET. Nature 2017; 551:346-351. [PMID: 29144454 DOI: 10.1038/nature24296] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023]
Abstract
Phosphorylation-type (P-type) ATPases are ubiquitous primary transporters that pump cations across cell membranes through the formation and breakdown of a phosphoenzyme intermediate. Structural investigations suggest that the transport mechanism is defined by conformational changes in the cytoplasmic domains of the protein that are allosterically coupled to transmembrane helices so as to expose ion binding sites to alternate sides of the membrane. Here, we have used single-molecule fluorescence resonance energy transfer to directly observe conformational changes associated with the functional transitions in the Listeria monocytogenes Ca2+-ATPase (LMCA1), an orthologue of eukaryotic Ca2+-ATPases. We identify key intermediates with no known crystal structures and show that Ca2+ efflux by LMCA1 is rate-limited by phosphoenzyme formation. The transport process involves reversible steps and an irreversible step that follows release of ADP and extracellular release of Ca2+.
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Affiliation(s)
- Mateusz Dyla
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
| | - Magnus Kjaergaard
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Thomas L-M Sørensen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Jacob Lauwring Andersen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jens P Andersen
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Roger B Altman
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
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30
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Bolean M, Simão AMS, Barioni MB, Favarin BZ, Sebinelli HG, Veschi EA, Janku TAB, Bottini M, Hoylaerts MF, Itri R, Millán JL, Ciancaglini P. Biophysical aspects of biomineralization. Biophys Rev 2017; 9:747-60. [PMID: 28852989 DOI: 10.1007/s12551-017-0315-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
During the process of endochondral bone formation, chondrocytes and osteoblasts mineralize their extracellular matrix (ECM) by promoting the synthesis of hydroxyapatite (HA) seed crystals in the sheltered interior of membrane-limited matrix vesicles (MVs). Several lipid and proteins present in the membrane of the MVs mediate the interactions of MVs with the ECM and regulate the initial mineral deposition and posterior propagation. Among the proteins of MV membranes, ion transporters control the availability of phosphate and calcium needed for initial HA deposition. Phosphatases (orphan phosphatase 1, ectonucleotide pyrophosphatase/phosphodiesterase 1 and tissue-nonspecific alkaline phosphatase) play a crucial role in controlling the inorganic pyrophosphate/inorganic phosphate ratio that allows MV-mediated initiation of mineralization. The lipidic microenvironment can help in the nucleation process of first crystals and also plays a crucial physiological role in the function of MV-associated enzymes and transporters (type III sodium-dependent phosphate transporters, annexins and Na+/K+ ATPase). The whole process is mediated and regulated by the action of several molecules and steps, which make the process complex and highly regulated. Liposomes and proteoliposomes, as models of biological membranes, facilitate the understanding of lipid-protein interactions with emphasis on the properties of physicochemical and biochemical processes. In this review, we discuss the use of proteoliposomes as multiple protein carrier systems intended to mimic the various functions of MVs during the initiation and propagation of mineral growth in the course of biomineralization. We focus on studies applying biophysical tools to characterize the biomimetic models in order to gain an understanding of the importance of lipid-protein and lipid-lipid interfaces throughout the process.
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31
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Abstract
The human cannabinoid receptor, CB1, has been difficult to purify in a functional form, hampering structural and biophysical studies. Here, we present our approaches for obtaining pure, detergent solubilized, functional CB1. We also discuss our site-directed fluorescence labeling (SDFL) methods for identifying different structural changes that CB1 can undergo upon binding different cannabinoid ligands. To identify optimal CB1 constructs for these studies (those with the best expression levels, solubility in detergent and function), we first screened various CB1-green fluorescent protein chimeras in a mammalian expression system. Once identified, we then tagged the best candidates with the 1D4 epitope (the C-terminus of rhodopsin) and purified them using a single-step immunoaffinity process. The resulting, highly pure proteins retain their ability to activate G-protein, and are ~85% functional, as assessed by radioligand binding studies. The SDFL studies involve introducing single cysteine residues at key places in the receptor, then labeling them with a small fluorophore, bimane. The spectral properties of the bimane probe are then monitored before and after addition of cannabinoid ligands. Changes in fluorescence of the attached probe indicate regions of the receptor undergoing conformational changes upon ligand binding. Together, these approaches set the stage for a deeper understanding of the structure and function of CB1. Access to pure, functional CB1 makes subsequent structural studies possible (such as crystallography and single-particle EM analysis), and the SDFL studies enable a better structural and mechanistic understanding of this key receptor and the dynamic changes it undergoes during activation and attenuation.
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32
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Flagmeier P, De S, Wirthensohn DC, Lee SF, Vincke C, Muyldermans S, Knowles TPJ, Gandhi S, Dobson CM, Klenerman D. Ultrasensitive Measurement of Ca 2+
Influx into Lipid Vesicles Induced by Protein Aggregates. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick Flagmeier
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Suman De
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - David C. Wirthensohn
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Steven F. Lee
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology; Vrije Universiteit Brussel; Brussels Belgium
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology; Vrije Universiteit Brussel; Brussels Belgium
| | - Tuomas P. J. Knowles
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Sonia Gandhi
- Department of Molecular Neuroscience; Institute of Neurology; University College London; Queen Square London WC1N 3BG UK
| | - Christopher M. Dobson
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - David Klenerman
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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33
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Jefferson RE, Min D, Corin K, Wang JY, Bowie JU. Applications of Single-Molecule Methods to Membrane Protein Folding Studies. J Mol Biol 2017; 430:424-437. [PMID: 28549924 DOI: 10.1016/j.jmb.2017.05.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 02/07/2023]
Abstract
Protein folding is a fundamental life process with many implications throughout biology and medicine. Consequently, there have been enormous efforts to understand how proteins fold. Almost all of this effort has focused on water-soluble proteins, however, leaving membrane proteins largely wandering in the wilderness. The neglect has occurred not because membrane proteins are unimportant but rather because they present many theoretical and technical complications. Indeed, quantitative membrane protein folding studies are generally restricted to a handful of well-behaved proteins. Single-molecule methods may greatly alter this picture, however, because the ability to work at or near infinite dilution removes aggregation problems, one of the main technical challenges of membrane protein folding studies.
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Affiliation(s)
- Robert E Jefferson
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Duyoung Min
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Karolina Corin
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Jing Yang Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA.
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34
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Rosholm KR, Leijnse N, Mantsiou A, Tkach V, Pedersen SL, Wirth VF, Oddershede LB, Jensen KJ, Martinez KL, Hatzakis NS, Bendix PM, Callan-Jones A, Stamou D. Membrane curvature regulates ligand-specific membrane sorting of GPCRs in living cells. Nat Chem Biol 2017; 13:724-729. [DOI: 10.1038/nchembio.2372] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 02/02/2017] [Indexed: 11/09/2022]
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35
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Flagmeier P, De S, Wirthensohn DC, Lee SF, Vincke C, Muyldermans S, Knowles TPJ, Gandhi S, Dobson CM, Klenerman D. Ultrasensitive Measurement of Ca 2+ Influx into Lipid Vesicles Induced by Protein Aggregates. Angew Chem Int Ed Engl 2017; 56:7750-7754. [PMID: 28474754 PMCID: PMC5615231 DOI: 10.1002/anie.201700966] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/23/2017] [Indexed: 12/15/2022]
Abstract
To quantify and characterize the potentially toxic protein aggregates associated with neurodegenerative diseases, a high‐throughput assay based on measuring the extent of aggregate‐induced Ca2+ entry into individual lipid vesicles has been developed. This approach was implemented by tethering vesicles containing a Ca2+ sensitive fluorescent dye to a passivated surface and measuring changes in the fluorescence as a result of membrane disruption using total internal reflection microscopy. Picomolar concentrations of Aβ42 oligomers could be observed to induce Ca2+ influx, which could be inhibited by the addition of a naturally occurring chaperone and a nanobody designed to bind to the Aβ peptide. We show that the assay can be used to study aggregates from other proteins, such as α‐synuclein, and to probe the effects of complex biofluids, such as cerebrospinal fluid, and thus has wide applicability.
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Affiliation(s)
- Patrick Flagmeier
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Suman De
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David C Wirthensohn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sonia Gandhi
- Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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36
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Bilkova E, Pleskot R, Rissanen S, Sun S, Czogalla A, Cwiklik L, Róg T, Vattulainen I, Cremer PS, Jungwirth P, Coskun Ü. Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition. J Am Chem Soc 2017; 139:4019-4024. [PMID: 28177616 PMCID: PMC5364432 DOI: 10.1021/jacs.6b11760] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The orchestrated recognition of phosphoinositides and concomitant intracellular release of Ca2+ is pivotal to almost every aspect of cellular processes, including membrane homeostasis, cell division and growth, vesicle trafficking, as well as secretion. Although Ca2+ is known to directly impact phosphoinositide clustering, little is known about the molecular basis for this or its significance in cellular signaling. Here, we study the direct interaction of Ca2+ with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), the main lipid marker of the plasma membrane. Electrokinetic potential measurements of PI(4,5)P2 containing liposomes reveal that Ca2+ as well as Mg2+ reduce the zeta potential of liposomes to nearly background levels of pure phosphatidylcholine membranes. Strikingly, lipid recognition by the default PI(4,5)P2 lipid sensor, phospholipase C delta 1 pleckstrin homology domain (PLC δ1-PH), is completely inhibited in the presence of Ca2+, while Mg2+ has no effect with 100 nm liposomes and modest effect with giant unilamellar vesicles. Consistent with biochemical data, vibrational sum frequency spectroscopy and atomistic molecular dynamics simulations reveal how Ca2+ binding to the PI(4,5)P2 headgroup and carbonyl regions leads to confined lipid headgroup tilting and conformational rearrangements. We rationalize these findings by the ability of calcium to block a highly specific interaction between PLC δ1-PH and PI(4,5)P2, encoded within the conformational properties of the lipid itself. Our studies demonstrate the possibility that switchable phosphoinositide conformational states can serve as lipid recognition and controlled cell signaling mechanisms.
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Affiliation(s)
- Eva Bilkova
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research (DZD e.V.) , Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Roman Pleskot
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,Institute of Experimental Botany, Academy of Sciences of the Czech Republic , v.v.i., Rozvojová 263, 16502 Prague 6, Czech Republic
| | - Sami Rissanen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | | | - Aleksander Czogalla
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław , Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Lukasz Cwiklik
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014, Helsinki, Finland.,MEMPHYS- Center for Biomembrane Physics, University of Southern Denmark , DK-5230 Odense, Denmark
| | | | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research (DZD e.V.) , Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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37
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Friedrich R, Block S, Alizadehheidari M, Heider S, Fritzsche J, Esbjörner EK, Westerlund F, Bally M. A nano flow cytometer for single lipid vesicle analysis. Lab Chip 2017; 17:830-841. [PMID: 28128381 DOI: 10.1039/c6lc01302c] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 μl sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.
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Affiliation(s)
- Remo Friedrich
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Stephan Block
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | | | - Susanne Heider
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Marta Bally
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Institut Curie, Centre de Recherche, CNRS, UMR168, Physico-Chimie Curie, Paris, France
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38
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King C, Raicu V, Hristova K. Understanding the FRET Signatures of Interacting Membrane Proteins. J Biol Chem 2017; 292:5291-5310. [PMID: 28188294 DOI: 10.1074/jbc.m116.764282] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 02/07/2017] [Indexed: 12/30/2022] Open
Abstract
FRET is an indispensable experimental tool for studying membrane proteins. Currently, two models are available for researchers to determine the oligomerization state of membrane proteins in a static quenching FRET experiment: the model of Veatch and Stryer, derived in 1977, and the kinetic theory-based model for intraoligomeric FRET, derived in 2007. Because of confinement in two dimensions, a substantial amount of FRET is generated by energy transfer between fluorophores located in separate oligomers in the two-dimensional bilayer. This interoligomeric FRET (also known as stochastic, bystander, or proximity FRET) is not accounted for in either model. Here, we use the kinetic theory formalism to describe the dependence of the FRET efficiency measured in an experiment (i.e. the "total apparent FRET efficiency") on the interoligomeric FRET due to random proximity within the bilayer and the intraoligomeric FRET resulting from protein-protein interactions. We find that data analysis with both models without consideration of the proximity FRET leads to incorrect conclusions about the oligomeric state of the protein. We show that knowledge of the total surface densities of fluorophore-labeled membrane proteins is essential for correctly interpreting the measured total apparent FRET efficiency. We also find that bulk, two-color, static quenching FRET experiments are best suited for the study of monomeric, dimerizing, or dimeric proteins but have limitations in discerning the order of larger oligomers. The theory and methodology described in this work will allow researchers to extract meaningful parameters from static quenching FRET measurements in biological membranes.
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Affiliation(s)
- Christopher King
- the Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 and
| | - Valerica Raicu
- the Department of Physics, University of Wisconsin, Milwaukee, Wisconsin 53211
| | - Kalina Hristova
- the Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 and .,From the Department of Materials Science and Engineering and
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39
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Abstract
Dimerization of membrane protein interfaces occurs during membrane protein folding and cell receptor signaling. Here, we summarize a method that allows for measurement of equilibrium dimerization reactions of membrane proteins in lipid bilayers, by measuring the Poisson distribution of subunit capture into liposomes by single-molecule photobleaching analysis. This strategy is grounded in the fact that given a comparable labeling efficiency, monomeric or dimeric forms of a membrane protein will give rise to distinctly different photobleaching probability distributions. These methods have been used to verify the dimer stoichiometry of the Fluc F- ion channel and the dimerization equilibrium constant of the ClC-ec1 Cl-/H+ antiporter in lipid bilayers. This approach can be applied to any membrane protein system provided it can be purified, fluorescently labeled in a quantitative manner, and verified to be correctly folded by functional assays, even if the structure is not yet known.
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Affiliation(s)
- R Chadda
- The University of Iowa, Iowa City, IA, United States
| | - J L Robertson
- The University of Iowa, Iowa City, IA, United States.
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40
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Scott A, Noga MJ, de Graaf P, Westerlaken I, Yildirim E, Danelon C. Cell-Free Phospholipid Biosynthesis by Gene-Encoded Enzymes Reconstituted in Liposomes. PLoS One 2016; 11:e0163058. [PMID: 27711229 DOI: 10.1371/journal.pone.0163058] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/01/2016] [Indexed: 11/19/2022] Open
Abstract
The goal of bottom-up synthetic biology culminates in the assembly of an entire cell from separate biological building blocks. One major challenge resides in the in vitro production and implementation of complex genetic and metabolic pathways that can support essential cellular functions. Here, we show that phospholipid biosynthesis, a multiple-step process involved in cell membrane homeostasis, can be reconstituted starting from the genes encoding for all necessary proteins. A total of eight E. coli enzymes for acyl transfer and headgroup modifications were produced in a cell-free gene expression system and were co-translationally reconstituted in liposomes. Acyl-coenzyme A and glycerol-3-phosphate were used as canonical precursors to generate a variety of important bacterial lipids. Moreover, this study demonstrates that two-step acyl transfer can occur from enzymes synthesized inside vesicles. Besides clear implications for growth and potentially division of a synthetic cell, we postulate that gene-based lipid biosynthesis can become instrumental for ex vivo and protein purification-free production of natural and non-natural lipids.
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41
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Block S, Fast BJ, Lundgren A, Zhdanov VP, Höök F. Two-dimensional flow nanometry of biological nanoparticles for accurate determination of their size and emission intensity. Nat Commun 2016; 7:12956. [PMID: 27658367 DOI: 10.1038/ncomms12956] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/18/2016] [Indexed: 01/07/2023] Open
Abstract
Biological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging. Optical microscopy allows precise determination of fluorescence/scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. Here, we show that by attaching BNPs to a supported lipid bilayer, subjecting them to hydrodynamic flows and tracking their motion via surface-sensitive optical imaging enable determination of their diffusion coefficients and flow-induced drifts, from which accurate quantification of both BNP size and emission intensity can be made. For vesicles, the accuracy of this approach is demonstrated by resolving the expected radius-squared dependence of their fluorescence intensity for radii down to 15 nm.
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42
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Chadda R, Krishnamani V, Mersch K, Wong J, Brimberry M, Chadda A, Kolmakova-Partensky L, Friedman LJ, Gelles J, Robertson JL. The dimerization equilibrium of a ClC Cl(-)/H(+) antiporter in lipid bilayers. eLife 2016; 5. [PMID: 27484630 PMCID: PMC5010387 DOI: 10.7554/elife.17438] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/29/2016] [Indexed: 12/20/2022] Open
Abstract
Interactions between membrane protein interfaces in lipid bilayers play an important role in membrane protein folding but quantification of the strength of these interactions has been challenging. Studying dimerization of ClC-type transporters offers a new approach to the problem, as individual subunits adopt a stable and functionally verifiable fold that constrains the system to two states - monomer or dimer. Here, we use single-molecule photobleaching analysis to measure the probability of ClC-ec1 subunit capture into liposomes during extrusion of large, multilamellar membranes. The capture statistics describe a monomer to dimer transition that is dependent on the subunit/lipid mole fraction density and follows an equilibrium dimerization isotherm. This allows for the measurement of the free energy of ClC-ec1 dimerization in lipid bilayers, revealing that it is one of the strongest membrane protein complexes measured so far, and introduces it as new type of dimerization model to investigate the physical forces that drive membrane protein association in membranes.
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Affiliation(s)
- Rahul Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Kacey Mersch
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Jason Wong
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States.,Department of Natural Sciences, University of Bath, Bath, United Kingdom
| | - Marley Brimberry
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Ankita Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Janice L Robertson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
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43
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Iijima M, Yoshimoto N, Niimi T, Maturana AD, Kuroda S. Bio-nanocapsule-based scaffold improves the sensitivity and ligand-binding capacity of mammalian receptors on the sensor chip. Biotechnol J 2016; 11:805-13. [DOI: 10.1002/biot.201500443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/13/2016] [Accepted: 04/08/2016] [Indexed: 12/19/2022]
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44
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Veshaguri S, Christensen SM, Kemmer GC, Ghale G, Møller MP, Lohr C, Christensen AL, Justesen BH, Jørgensen IL, Schiller J, Hatzakis NS, Grabe M, Pomorski TG, Stamou D. Direct observation of proton pumping by a eukaryotic P-type ATPase. Science 2016; 351:1469-73. [PMID: 27013734 DOI: 10.1126/science.aad6429] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/23/2016] [Indexed: 12/12/2022]
Abstract
In eukaryotes, P-type adenosine triphosphatases (ATPases) generate the plasma membrane potential and drive secondary transport systems; however, despite their importance, their regulation remains poorly understood. We monitored at the single-molecule level the activity of the prototypic proton-pumping P-type ATPase Arabidopsis thaliana isoform 2 (AHA2). Our measurements, combined with a physical nonequilibrium model of vesicle acidification, revealed that pumping is stochastically interrupted by long-lived (~100 seconds) inactive or leaky states. Allosteric regulation by pH gradients modulated the switch between these states but not the pumping or leakage rates. The autoinhibitory regulatory domain of AHA2 reduced the intrinsic pumping rates but increased the dwell time in the active pumping state. We anticipate that similar functional dynamics underlie the operation and regulation of many other active transporters.
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Affiliation(s)
- Salome Veshaguri
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Sune M Christensen
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Gerdi C Kemmer
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg Denmark
| | - Garima Ghale
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Mads P Møller
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina Lohr
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Andreas L Christensen
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Bo H Justesen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg Denmark
| | - Ida L Jørgensen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg Denmark
| | - Jürgen Schiller
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Nikos S Hatzakis
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Thomas Günther Pomorski
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg Denmark
| | - Dimitrios Stamou
- Bionanotecnology and Nanomedicine Laboratory, University of Copenhagen, Copenhagen, Denmark. Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark
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45
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Deller MC, Kong L, Rupp B. Protein stability: a crystallographer's perspective. Acta Crystallogr F Struct Biol Commun 2016; 72:72-95. [PMID: 26841758 PMCID: PMC4741188 DOI: 10.1107/s2053230x15024619] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.
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Affiliation(s)
- Marc C Deller
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125, USA
| | - Leopold Kong
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084, USA
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46
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Moses M, Hedegård P, Hatzakis N. Quantification of Functional Dynamics of Membrane Proteins Reconstituted in Nanodiscs Membranes by Single Turnover Functional Readout. Methods Enzymol 2016; 581:227-256. [DOI: 10.1016/bs.mie.2016.08.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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47
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Li M, Jørgensen SK, McMillan DGG, Krzemiński Ł, Daskalakis NN, Partanen RH, Tutkus M, Tuma R, Stamou D, Hatzakis NS, Jeuken LJC. Single Enzyme Experiments Reveal a Long-Lifetime Proton Leak State in a Heme-Copper Oxidase. J Am Chem Soc 2015; 137:16055-63. [PMID: 26618221 PMCID: PMC4697922 DOI: 10.1021/jacs.5b08798] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Heme-copper oxidases (HCOs) are key
enzymes in prokaryotes and
eukaryotes for energy production during aerobic respiration. They
catalyze the reduction of the terminal electron acceptor, oxygen,
and utilize the Gibbs free energy to transport protons across a membrane
to generate a proton (ΔpH) and electrochemical gradient termed
proton motive force (PMF), which provides the driving force for the
adenosine triphosphate (ATP) synthesis. Excessive PMF is known to
limit the turnover of HCOs, but the molecular mechanism of this regulatory
feedback remains relatively unexplored. Here we present a single-enzyme
study that reveals that cytochrome bo3 from Escherichia coli, an HCO closely homologous
to Complex IV in human mitochondria, can enter a rare, long-lifetime
leak state during which proton flow is reversed. The probability of
entering the leak state is increased at higher ΔpH. By rapidly
dissipating the PMF, we propose that this leak state may enable cytochrome bo3, and possibly other HCOs, to maintain a suitable
ΔpH under extreme redox conditions.
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Affiliation(s)
- Mengqiu Li
- School of Biomedical Sciences, University of Leeds , LS2 9JT Leeds, U.K
| | - Sune K Jørgensen
- Department of Chemistry, Nano-Science Center and Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen , 2100 Copenhagen, Denmark
| | | | - Łukasz Krzemiński
- School of Biomedical Sciences, University of Leeds , LS2 9JT Leeds, U.K
| | | | - Riitta H Partanen
- School of Biomedical Sciences, University of Leeds , LS2 9JT Leeds, U.K
| | - Marijonas Tutkus
- Department of Chemistry, Nano-Science Center and Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen , 2100 Copenhagen, Denmark
| | - Roman Tuma
- School of Molecular and Cellular Biology, University of Leeds , LS2 9JT Leeds, U.K
| | - Dimitrios Stamou
- Department of Chemistry, Nano-Science Center and Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen , 2100 Copenhagen, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry, Nano-Science Center and Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen , 2100 Copenhagen, Denmark
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds , LS2 9JT Leeds, U.K
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48
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Sušac L, O'Connor C, Stevens RC, Wüthrich K. In-Membrane Chemical Modification (IMCM) for Site-Specific Chromophore Labeling of GPCRs. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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49
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Sušac L, O'Connor C, Stevens RC, Wüthrich K. In-Membrane Chemical Modification (IMCM) for Site-Specific Chromophore Labeling of GPCRs. Angew Chem Int Ed Engl 2015; 54:15246-9. [PMID: 26545333 DOI: 10.1002/anie.201508506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 11/08/2022]
Abstract
We present in-membrane chemical modification (IMCM) for obtaining selective chromophore labeling of intracellular surface cysteines in G-protein-coupled receptors (GPCRs) with minimal mutagenesis. This method takes advantage of the natural protection of most cysteines by the membrane environment. Practical use of IMCM is illustrated with the site-specific introduction of chromophores for NMR and fluorescence spectroscopy in the human κ-opioid receptor (KOR) and the human A2A adenosine receptor (A2A AR). IMCM is applicable to a wide range of in vitro studies of GPCRs, including single-molecule spectroscopy, and is a promising platform for in-cell spectroscopy experiments.
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Affiliation(s)
- Lukas Sušac
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Casey O'Connor
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA).,Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, Los Angeles, CA 90089 (USA)
| | - Raymond C Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, Los Angeles, CA 90089 (USA)
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA). .,Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA). .,Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich (Switzerland).
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50
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Wahlsten O, Gunnarsson A, Simonsson Nyström L, Pace H, Geschwindner S, Höök F. Equilibrium-fluctuation analysis for interaction studies between natural ligands and single G protein-coupled receptors in native lipid vesicles. Langmuir 2015; 31:10774-10780. [PMID: 26347379 DOI: 10.1021/acs.langmuir.5b02463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
G protein-coupled receptors (GPCRs) constitute the most versatile family of cell-membrane receptors and have been increasingly identified as important mediators of many physiological functions. They also belong to one of the most central drug target classes, but current screening technologies are limited by the requirements of overexpression and stabilization of GPCRs. This calls for sensitivity-increased detection strategies preferably meeting single-molecule detection limits. This challenge is here addressed by employing total internal reflection fluorescence microscopy to characterize the interaction kinetics between CXCR3, a GPCR involved in inflammatory responses, and two of its chemokine ligands, CXCL10 and CXCL11. Fluorescence labeling of the lipid membrane, rather than the membrane protein itself, of GPCR-containing native vesicles, and immobilization of the corresponding ligand on the surface, enabled determination of the interaction kinetics using single-molecule equilibrium-fluctuation analysis. With a limit of detection of GPCR-containing vesicles in the low picomolar concentration regime, the results demonstrate the possibility to use inhibition in solution screening of high affinity ligands/drug candidates, which due to target-binding depletion of the inhibiting compounds is demanding using assays with more moderate detection limits.
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Affiliation(s)
- Olov Wahlsten
- Department of Applied Physics, Chalmers University of Technology , SE 41296 Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, AstraZeneca R&D Mölndal , S-43183 Mölndal, Sweden
| | - Lisa Simonsson Nyström
- Department of Applied Physics, Chalmers University of Technology , SE 41296 Gothenburg, Sweden
| | - Hudson Pace
- Department of Applied Physics, Chalmers University of Technology , SE 41296 Gothenburg, Sweden
| | | | - Fredrik Höök
- Department of Applied Physics, Chalmers University of Technology , SE 41296 Gothenburg, Sweden
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