1
|
Hirst IJ, Thomas WJR, Davies RA, Muench SP. CryoEM grid preparation: a closer look at advancements and impact of preparation mode and new approaches. Biochem Soc Trans 2024; 52:1529-1537. [PMID: 38864435 DOI: 10.1042/bst20231553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
Sample preparation can present a significant hurdle within single particle cryo-electron microscopy (cryoEM), resulting in issues with reproducibility, data quality or an inability to visualise the sample. There are several factors which can influence this, including sample or buffer composition, grid type, route of sample preparation and interactions with the air-water interface (AWI). Here, we review some of the current routes for sample preparation and the associated challenges. We discuss a range of approaches for overcoming these challenges, such as minimising the grid preparation time, surfactants, grid type and biochemical approaches such as nanomagnetic beads. Finally, we discuss how a set of commercially available protein samples may serve as a benchmark suite for future technologies. This provides a route to compare techniques' abilities not just to generate high-resolution structures but also to overcome the challenges traditionally associated with cryoEM. As the field continues to produce new approaches to sample preparation and we start to better understand the underlying principles behind the behaviour of proteins within a thin film and in response to different environments, especially grid composition, it is hoped that more universal solutions can be provided that make the intractable systems tractable, improve resolution and, importantly, speed up data collection and reduce the currently required dataset sizes.
Collapse
Affiliation(s)
- Isobel J Hirst
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - William J R Thomas
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Rhiannon A Davies
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| |
Collapse
|
2
|
Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman JE, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579775. [PMID: 38405833 PMCID: PMC10888908 DOI: 10.1101/2024.02.10.579775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The intricate molecular environment of the native membrane profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergent-like molecules that disrupt and remove this vital local membrane context. This severely impedes our ability to quantitatively decipher the local molecular context and comprehend its regulatory role in the structure, function, and biogenesis of MPs. Using a library of membrane-active polymers we have developed a platform for the high-throughput analysis of the membrane proteome. The platform enables near-complete spatially resolved extraction of target MPs directly from their endogenous membranes into native nanodiscs that maintain the local membrane context. We accompany this advancement with an open-access quantitative database that provides the most efficient extraction conditions of 2065 unique mammalian MPs. Our method enables rapid and near-complete extraction and purification of target MPs directly from their endogenous organellar membranes at physiological expression levels while maintaining the nanoscale local membrane environment. Going beyond the plasma membrane proteome, our platform enables extraction from any target organellar membrane including the endoplasmic reticulum, mitochondria, lysosome, Golgi, and even transient organelles such as the autophagosome. To further validate this platform we took several independent MPs and demonstrated how our resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, taking two synaptic vesicle MPs, we show how the database can be extended to capture multiprotein complexes between overexpressed MPs. We expect these publicly available resources to empower researchers across disciplines to capture membrane 'nano-scoops' containing a target MP efficiently and interface with structural, functional, and other bioanalytical approaches. We demonstrate an example of this by combining our extraction platform with single-molecule TIRF imaging to demonstrate how it can enable rapid determination of homo-oligomeric states of target MPs in native cell membranes.
Collapse
Affiliation(s)
- Caroline Brown
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Snehasish Ghosh
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Rachel McAllister
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Mukesh Kumar
- F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gerard Walker
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Eric Sun
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Talat Aman
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Shailesh Kumar
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Jeff Coleman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - James E Rothman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| |
Collapse
|
3
|
Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling Difficult Cryo-ET Samples: A Study with Primary Neurons from Drosophila melanogaster. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2127-2148. [PMID: 37966978 PMCID: PMC11168236 DOI: 10.1093/micmic/ozad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons having been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
Collapse
Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA
| |
Collapse
|
4
|
Pettersen JM, Yang Y, Robinson AS. Advances in nanodisc platforms for membrane protein purification. Trends Biotechnol 2023; 41:1041-1054. [PMID: 36935323 DOI: 10.1016/j.tibtech.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023]
Abstract
Membrane scaffold protein nanodiscs (MSPNDs) are an invaluable tool for improving purified membrane protein (MP) stability and activity compared to traditional micellar methods, thus enabling an increase in high-resolution MP structures, particularly in concert with cryogenic electron microscopy (cryo-EM) approaches. In this review we highlight recent advances and breakthroughs in MSPND methodology and applications. We also introduce and discuss saposin-lipoprotein nanoparticles (salipros) and copolymer nanodiscs which have recently emerged as authentic MSPND alternatives. We compare the advantages and disadvantages of MSPNDs, salipros, and copolymer nanodisc technologies to highlight potential opportunities for using each platform for MP purification and characterization.
Collapse
Affiliation(s)
- John M Pettersen
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yaxin Yang
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Anne S Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
| |
Collapse
|
5
|
Dhankhar P, Trinh TKH, Qiu W, Guo Y. Characterization of Ca 2+-ATPase, LMCA1, with native cell membrane nanoparticles system. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184143. [PMID: 36863681 PMCID: PMC10375462 DOI: 10.1016/j.bbamem.2023.184143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 03/04/2023]
Abstract
Ca2+-ATPases are membrane pumps that transport calcium ions across the cell membrane and are dependent on ATP. The mechanism of Listeria monocytogenes Ca2+-ATPase (LMCA1) in its native environment remains incompletely understood. LMCA1 has been investigated biochemically and biophysically with detergents in the past. This study characterizes LMCA1 using the detergent-free Native Cell Membrane Nanoparticles (NCMNP) system. As demonstrated by ATPase activity assays, the NCMNP7-25 polymer is compatible with a broad pH range and Ca2+ ions. This result suggests that NCMNP7-25 may have a wider array of applications in membrane protein research.
Collapse
Affiliation(s)
- Poonam Dhankhar
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA.
| |
Collapse
|
6
|
Seneviratne R, Coates G, Xu Z, Cornell CE, Thompson RF, Sadeghpour A, Maskell DP, Jeuken LJC, Rappolt M, Beales PA. High Resolution Membrane Structures within Hybrid Lipid-Polymer Vesicles Revealed by Combining X-Ray Scattering and Electron Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206267. [PMID: 36866488 DOI: 10.1002/smll.202206267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/26/2023] [Indexed: 06/02/2023]
Abstract
Hybrid vesicles consisting of phospholipids and block-copolymers are increasingly finding applications in science and technology. Herein, small angle X-ray scattering (SAXS) and cryo-electron tomography (cryo-ET) are used to obtain detailed structural information about hybrid vesicles with different ratios of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and poly(1,2-butadiene-block-ethylene oxide) (PBd22 -PEO14 , Ms = 1800 g mol-1 ). Using single particle analysis (SPA) the authors are able to further interpret the information gained from SAXS and cryo-ET experiments, showing that increasing PBd22 -PEO14 mole fraction increases the membrane thickness from 52 Å for a pure lipid system to 97 Å for pure PBd22 -PEO14 vesicles. Two vesicle populations with different membrane thicknesses in hybrid vesicle samples are found. As these lipids and polymers are reported to homogeneously mix, bistability is inferred between weak and strong interdigitation regimes of PBd22 -PEO14 within the hybrid membranes. It is hypothesized that membranes of intermediate structure are not energetically favorable. Therefore, each vesicle exists in one of these two membrane structures, which are assumed to have comparable free energies. The authors conclude that, by combining biophysical methods, accurate determination of the influence of composition on the structural properties of hybrid membranes is achieved, revealing that two distinct membranes structures can coexist in homogeneously mixed lipid-polymer hybrid vesicles.
Collapse
Affiliation(s)
- Rashmi Seneviratne
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Georgina Coates
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Zexi Xu
- School of Food Science and Nutrition, School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Caitlin E Cornell
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Rebecca F Thompson
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Amin Sadeghpour
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK
| | - Daniel P Maskell
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Lars J C Jeuken
- Leiden Institute of Chemistry, Leiden University, PC Box 9502, Leiden, 2300 RA, Netherlands
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul A Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| |
Collapse
|
7
|
Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
Collapse
Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| |
Collapse
|
8
|
Sawczyc H, Heit S, Watts A. A comparative characterisation of commercially available lipid-polymer nanoparticles formed from model membranes. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:39-51. [PMID: 36786921 PMCID: PMC10039845 DOI: 10.1007/s00249-023-01632-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/15/2023]
Abstract
From the discovery of the first membrane-interacting polymer, styrene maleic-acid (SMA), there has been a rapid development of membrane solubilising polymers. These new polymers can solubilise membranes under a wide range of conditions and produce varied sizes of nanoparticles, yet there has been a lack of broad comparison between the common polymer types and solubilising conditions. Here, we present a comparative study on the three most common commercial polymers: SMA 3:1, SMA 2:1, and DIBMA. Additionally, this work presents, for the first time, a comparative characterisation of polymethacrylate copolymer (PMA). Absorbance and dynamic light scattering measurements were used to evaluate solubilisation across key buffer conditions in a simple, adaptable assay format that looked at pH, salinity, and divalent cation concentration. Lipid-polymer nanoparticles formed from SMA variants were found to be the most susceptible to buffer effects, with nanoparticles from either zwitterionic DMPC or POPC:POPG (3:1) bilayers only forming in low to moderate salinity (< 600 mM NaCl) and above pH 6. DIBMA-lipid nanoparticles could be formed above a pH of 5 and were stable in up to 4 M NaCl. Similarly, PMA-lipid nanoparticles were stable in all NaCl concentrations tested (up to 4 M) and a broad pH range (3-10). However, for both DIBMA and PMA nanoparticles there is a severe penalty observed for bilayer solubilisation in non-optimal conditions or when using a charged membrane. Additionally, lipid fluidity of the DMPC-polymer nanoparticles was analysed through cw-EPR, showing no cooperative gel-fluid transition as would be expected for native-like lipid membranes.
Collapse
Affiliation(s)
- Henry Sawczyc
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Sabine Heit
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| |
Collapse
|
9
|
Heterologous (Over) Expression of Human SoLute Carrier (SLC) in Yeast: A Well-Recognized Tool for Human Transporter Function/Structure Studies. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081206. [PMID: 36013385 PMCID: PMC9410066 DOI: 10.3390/life12081206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022]
Abstract
For more than 20 years, yeast has been a widely used system for the expression of human membrane transporters. Among them, more than 400 are members of the largest transporter family, the SLC superfamily. SLCs play critical roles in maintaining cellular homeostasis by transporting nutrients, ions, and waste products. Based on their involvement in drug absorption and in several human diseases, they are considered emerging therapeutic targets. Despite their critical role in human health, a large part of SLCs' is 'orphans' for substrate specificity or function. Moreover, very few data are available concerning their 3D structure. On the basis of the human health benefits of filling these knowledge gaps, an understanding of protein expression in systems that allow functional production of these proteins is essential. Among the 500 known yeast species, S. cerevisiae and P. pastoris represent those most employed for this purpose. This review aims to provide a comprehensive state-of-the-art on the attempts of human SLC expression performed by exploiting yeast. The collected data will hopefully be useful for guiding new attempts in SLCs expression with the aim to reveal new fundamental data that could lead to potential effects on human health.
Collapse
|
10
|
Krishnarjuna B, Ramamoorthy A. Detergent-Free Isolation of Membrane Proteins and Strategies to Study Them in a Near-Native Membrane Environment. Biomolecules 2022; 12:1076. [PMID: 36008970 PMCID: PMC9406181 DOI: 10.3390/biom12081076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
Collapse
Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
11
|
Nishimura T, Hatatani Y, Ando M, Sasaki Y, Akiyoshi K. Single-component nanodiscs via the thermal folding of amphiphilic graft copolymers with the adjusted flexibility of the main chain. Chem Sci 2022; 13:5243-5251. [PMID: 35655565 PMCID: PMC9093194 DOI: 10.1039/d2sc01674e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 12/26/2022] Open
Abstract
Nanodiscs have attracted considerable attention as structural scaffolds for membrane-protein research and as biomaterials in e.g. drug-delivery systems. However, conventional disc-fabrication methods are usually laborious, and disc fabrication via the self-assembly of amphiphiles is difficult. Herein, we report the formation of polymer nanodiscs based on the self-assembly of amphiphilic graft copolymers by adjusting the persistence length of the main chain. Amphiphilic graft copolymers with a series of different main-chain persistence lengths were prepared and these formed, depending on the persistence length, either rods, discs, or vesicles. Notably, polymer nanodiscs were formed upon heating a chilled polymer solution without the need for any additives, and the thus obtained nanodiscs were used to solubilize a membrane protein during cell-free protein synthesis. Given the simplicity of this disc-fabrication method and the ability of these discs to solubilize membrane proteins, this study considerably expands the fundamental and practical scope of graft-copolymer nanodiscs and demonstrates their utility as tools for studying the structure and function of membrane proteins.
Collapse
Affiliation(s)
- Tomoki Nishimura
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University 3-15-1, Tokida Ueda Nagano 386-8567 Japan
| | - Yusuke Hatatani
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Mitsuru Ando
- Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University Shogoin Kawahara-cho, Sakyo-ku Kyoto 606-8507 Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| |
Collapse
|
12
|
Formation of styrene maleic acid lipid nanoparticles (SMALPs) using SMA thin film on a substrate. Anal Biochem 2022; 647:114692. [DOI: 10.1016/j.ab.2022.114692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022]
|
13
|
Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. NANOMATERIALS 2022; 12:nano12030361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
Collapse
Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (P.S.O.); (K.V.S.)
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Correspondence: (P.S.O.); (K.V.S.)
| |
Collapse
|
14
|
Kopf AH, Lijding O, Elenbaas BOW, Koorengevel MC, Dobruchowska JM, van Walree CA, Killian JA. Synthesis and Evaluation of a Library of Alternating Amphipathic Copolymers to Solubilize and Study Membrane Proteins. Biomacromolecules 2022; 23:743-759. [PMID: 34994549 PMCID: PMC8924871 DOI: 10.1021/acs.biomac.1c01166] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Amphipathic copolymers
such as poly(styrene-maleic acid) (SMA)
are promising tools for the facile extraction of membrane proteins
(MPs) into native nanodiscs. Here, we designed and synthesized a library
of well-defined alternating copolymers of SMA analogues in order to
elucidate polymer properties that are important for MP solubilization
and stability. MP extraction efficiency was determined using KcsA
from E. coli membranes, and general solubilization
efficiency was investigated via turbidimetry experiments on membranes
of E. coli, yeast mitochondria, and synthetic
lipids. Remarkably, halogenation of SMA copolymers dramatically improved
solubilization efficiency in all systems, while substituents on the
copolymer backbone improved resistance to Ca2+. Relevant
polymer properties were found to include hydrophobic balance, size
and positioning of substituents, rigidity, and electronic effects.
The library thus contributes to the rational design of copolymers
for the study of MPs.
Collapse
Affiliation(s)
- Adrian H Kopf
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Odette Lijding
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Barend O W Elenbaas
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Justyna M Dobruchowska
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
15
|
Higgins AJ, Flynn AJ, Marconnet A, Musgrove LJ, Postis VLG, Lippiat JD, Chung CW, Ceska T, Zoonens M, Sobott F, Muench SP. Cycloalkane-modified amphiphilic polymers provide direct extraction of membrane proteins for CryoEM analysis. Commun Biol 2021; 4:1337. [PMID: 34824357 PMCID: PMC8617058 DOI: 10.1038/s42003-021-02834-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/27/2021] [Indexed: 12/30/2022] Open
Abstract
Membrane proteins are essential for cellular growth, signalling and homeostasis, making up a large proportion of therapeutic targets. However, the necessity for a solubilising agent to extract them from the membrane creates challenges in their structural and functional study. Although amphipols have been very effective for single-particle electron cryo-microscopy (cryoEM) and mass spectrometry, they rely on initial detergent extraction before exchange into the amphipol environment. Therefore, circumventing this pre-requirement would be a big advantage. Here we use an alternative type of amphipol: a cycloalkane-modified amphiphile polymer (CyclAPol) to extract Escherichia coli AcrB directly from the membrane and demonstrate that the protein can be isolated in a one-step purification with the resultant cryoEM structure achieving 3.2 Å resolution. Together this work shows that cycloalkane amphipols provide a powerful approach for the study of membrane proteins, allowing native extraction and high-resolution structure determination by cryoEM.
Collapse
Affiliation(s)
- Anna J Higgins
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Anaïs Marconnet
- Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le dévelopement de la recherche scientifique, F-75005, Paris, France
| | - Laura J Musgrove
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Vincent L G Postis
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Wellcome Centre for Anti-Infectives Research, Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, UK
| | - Jonathan D Lippiat
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Chun-Wa Chung
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | | | - Manuela Zoonens
- Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, F-75005, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le dévelopement de la recherche scientifique, F-75005, Paris, France.
| | - Frank Sobott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
16
|
Kacher YG, Karlova MG, Glukhov GS, Zhang H, Zaklyazminskaya EV, Loussouarn G, Sokolova OS. The Integrative Approach to Study of the Structure and Functions of Cardiac Voltage-Dependent Ion Channels. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Grime RL, Logan RT, Nestorow SA, Sridhar P, Edwards PC, Tate CG, Klumperman B, Dafforn TR, Poyner DR, Reeves PJ, Wheatley M. Differences in SMA-like polymer architecture dictate the conformational changes exhibited by the membrane protein rhodopsin encapsulated in lipid nano-particles. NANOSCALE 2021; 13:13519-13528. [PMID: 34477756 PMCID: PMC8359648 DOI: 10.1039/d1nr02419a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Membrane proteins are of fundamental importance to cellular processes and nano-encapsulation strategies that preserve their native lipid bilayer environment are particularly attractive for studying and exploiting these proteins. Poly(styrene-co-maleic acid) (SMA) and related polymers poly(styrene-co-(N-(3-N',N'-dimethylaminopropyl)maleimide)) (SMI) and poly(diisobutylene-alt-maleic acid) (DIBMA) have revolutionised the study of membrane proteins by spontaneously solubilising membrane proteins direct from cell membranes within nanoscale discs of native bilayer called SMA lipid particles (SMALPs), SMILPs and DIBMALPs respectively. This systematic study shows for the first time, that conformational changes of the encapsulated protein are dictated by the solubilising polymer. The photoactivation pathway of rhodopsin (Rho), a G-protein-coupled receptor (GPCR), comprises structurally-defined intermediates with characteristic absorbance spectra that revealed conformational restrictions with styrene-containing SMA and SMI, so that photoactivation proceeded only as far as metarhodopsin-I, absorbing at 478 nm, in a SMALP or SMILP. In contrast, full attainment of metarhodopsin-II, absorbing at 382 nm, was observed in a DIBMALP. Consequently, different intermediate states of Rho could be generated readily by simply employing different SMA-like polymers. Dynamic light-scattering and analytical ultracentrifugation revealed differences in size and thermostability between SMALP, SMILP and DIBMALP. Moreover, encapsulated Rho exhibited different stability in a SMALP, SMILP or DIBMALP. Overall, we establish that SMA, SMI and DIBMA constitute a 'toolkit' of solubilising polymers, so that selection of the appropriate solubilising polymer provides a spectrum of useful attributes for studying membrane proteins.
Collapse
Affiliation(s)
- Rachael L Grime
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Janson K, Zierath J, Kyrilis FL, Semchonok DA, Hamdi F, Skalidis I, Kopf AH, Das M, Kolar C, Rasche M, Vargas C, Keller S, Kastritis PL, Meister A. Solubilization of artificial mitochondrial membranes by amphiphilic copolymers of different charge. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183725. [PMID: 34384757 DOI: 10.1016/j.bbamem.2021.183725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/21/2021] [Accepted: 08/02/2021] [Indexed: 01/19/2023]
Abstract
Certain amphiphilic copolymers form lipid-bilayer nanodiscs from artificial and natural membranes, thereby rendering incorporated membrane proteins optimal for structural analysis. Recent studies have shown that the amphiphilicity of a copolymer strongly determines its solubilization efficiency. This is especially true for highly negatively charged membranes, which experience pronounced Coulombic repulsion with polyanionic polymers. Here, we present a systematic study on the solubilization of artificial multicomponent lipid vesicles that mimic inner mitochondrial membranes, which harbor essential membrane-protein complexes. In particular, we compared the lipid-solubilization efficiencies of established anionic with less densely charged or zwitterionic and even cationic copolymers in low- and high-salt concentrations. The nanodiscs formed under these conditions were characterized by dynamic light scattering and negative-stain electron microscopy, pointing to a bimodal distribution of nanodisc diameters with a considerable fraction of nanodiscs engaging in side-by-side interactions through their polymer rims. Overall, our results show that some recent, zwitterionic copolymers are best suited to solubilize negatively charged membranes at high ionic strengths even at low polymer/lipid ratios.
Collapse
Affiliation(s)
- Kevin Janson
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany
| | - Jennifer Zierath
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany
| | - Ioannis Skalidis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany
| | - Adrian H Kopf
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany
| | - Cenek Kolar
- GLYCON Biochemicals GmbH, Im Biotechnologie Park TGZ 1, 14943 Luckenwalde, Germany
| | - Marie Rasche
- GLYCON Biochemicals GmbH, Im Biotechnologie Park TGZ 1, 14943 Luckenwalde, Germany
| | - Carolyn Vargas
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany; Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale, Germany.
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle/Saale, Germany.
| |
Collapse
|
19
|
Guo Y. Detergent-free systems for structural studies of membrane proteins. Biochem Soc Trans 2021; 49:1361-1374. [PMID: 34110369 PMCID: PMC8276625 DOI: 10.1042/bst20201080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022]
Abstract
Membrane proteins play vital roles in living organisms, serving as targets for most currently prescribed drugs. Membrane protein structural biology aims to provide accurate structural information to understand their mechanisms of action. The advance of membrane protein structural biology has primarily relied on detergent-based methods over the past several decades. However, detergent-based approaches have significant drawbacks because detergents often damage the native protein-lipid interactions, which are often crucial for maintaining the natural structure and function of membrane proteins. Detergent-free methods recently have emerged as alternatives with a great promise, e.g. for high-resolution structure determinations of membrane proteins in their native cell membrane lipid environments. This minireview critically examines the current status of detergent-free methods by a comparative analysis of five groups of membrane protein structures determined using detergent-free and detergent-based methods. This analysis reveals that current detergent-free systems, such as the styrene-maleic acid lipid particles (SMALP), the diisobutyl maleic acid lipid particles (DIBMALP), and the cycloalkane-modified amphiphile polymer (CyclAPol) technologies are not better than detergent-based approaches in terms of maintenance of native cell membrane lipids on the transmembrane domain and high-resolution structure determination. However, another detergent-free technology, the native cell membrane nanoparticles (NCMN) system, demonstrated improved maintenance of native cell membrane lipids with the studied membrane proteins, and produced particles that were suitable for high-resolution structural analysis. The ongoing development of new membrane-active polymers and their optimization will facilitate the maturation of these new detergent-free systems.
Collapse
Affiliation(s)
- Youzhong Guo
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
| |
Collapse
|
20
|
Biological insights from SMA-extracted proteins. Biochem Soc Trans 2021; 49:1349-1359. [PMID: 34110372 PMCID: PMC8286838 DOI: 10.1042/bst20201067] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
In the twelve years since styrene maleic acid (SMA) was first used to extract and purify a membrane protein within a native lipid bilayer, this technological breakthrough has provided insight into the structural and functional details of protein–lipid interactions. Most recently, advances in cryo-EM have demonstrated that SMA-extracted membrane proteins are a rich-source of structural data. For example, it has been possible to resolve the details of annular lipids and protein–protein interactions within complexes, the nature of lipids within central cavities and binding pockets, regions involved in stabilising multimers, details of terminal residues that would otherwise remain unresolved and the identification of physiologically relevant states. Functionally, SMA extraction has allowed the analysis of membrane proteins that are unstable in detergents, the characterization of an ultrafast component in the kinetics of electron transfer that was not possible in detergent-solubilised samples and quantitative, real-time measurement of binding assays with low concentrations of purified protein. While the use of SMA comes with limitations such as its sensitivity to low pH and divalent cations, its major advantage is maintenance of a protein's lipid bilayer. This has enabled researchers to view and assay proteins in an environment close to their native ones, leading to new structural and mechanistic insights.
Collapse
|
21
|
Plant transporters involved in combating boron toxicity: beyond 3D structures. Biochem Soc Trans 2021; 48:1683-1696. [PMID: 32779723 PMCID: PMC7458394 DOI: 10.1042/bst20200164] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Membrane transporters control the movement and distribution of solutes, including the disposal or compartmentation of toxic substances that accumulate in plants under adverse environmental conditions. In this minireview, in the light of the approaching 100th anniversary of unveiling the significance of boron to plants (K. Warington, 1923; Ann. Bot.37, 629) we discuss the current state of the knowledge on boron transport systems that plants utilise to combat boron toxicity. These transport proteins include: (i) nodulin-26-like intrinsic protein-types of aquaporins, and (ii) anionic efflux (borate) solute carriers. We describe the recent progress made on the structure–function relationships of these transport proteins and point out that this progress is integral to quantitative considerations of the transporter's roles in tissue boron homeostasis. Newly acquired knowledge at the molecular level has informed on the transport mechanics and conformational states of boron transport systems that can explain their impact on cell biology and whole plant physiology. We expect that this information will form the basis for engineering transporters with optimised features to alleviate boron toxicity tolerance in plants exposed to suboptimal soil conditions for sustained food production.
Collapse
|
22
|
Klenotic PA, Moseng MA, Morgan CE, Yu EW. Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters. Chem Rev 2021; 121:5378-5416. [PMID: 33211490 PMCID: PMC8119314 DOI: 10.1021/acs.chemrev.0c00621] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multidrug resistant (MDR) bacteria are a global threat with many common infections becoming increasingly difficult to eliminate. While significant effort has gone into the development of potent biocides, the effectiveness of many first-line antibiotics has been diminished due to adaptive resistance mechanisms. Bacterial membrane proteins belonging to the resistance-nodulation-cell division (RND) superfamily play significant roles in mediating bacterial resistance to antimicrobials. They participate in multidrug efflux and cell wall biogenesis to transform bacterial pathogens into "superbugs" that are resistant even to last resort antibiotics. In this review, we summarize the RND superfamily of efflux transporters with a primary focus on the assembly and function of the inner membrane pumps. These pumps are critical for extrusion of antibiotics from the cell as well as the transport of lipid moieties to the outer membrane to establish membrane rigidity and stability. We analyze recently solved structures of bacterial inner membrane efflux pumps as to how they bind and transport their substrates. Our cumulative data indicate that these RND membrane proteins are able to utilize different oligomerization states to achieve particular activities, including forming MDR pumps and cell wall remodeling machineries, to ensure bacterial survival. This mechanistic insight, combined with simulated docking techniques, allows for the design and optimization of new efflux pump inhibitors to more effectively treat infections that today are difficult or impossible to cure.
Collapse
Affiliation(s)
- Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| |
Collapse
|
23
|
Di Mauro GM, La Rosa C, Condorelli M, Ramamoorthy A. Benchmarks of SMA-Copolymer Derivatives and Nanodisc Integrity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3113-3121. [PMID: 33645999 DOI: 10.1021/acs.langmuir.0c03554] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Poly(styrene-co-maleic acid) or SMA and its derivatives, a family of synthetic amphipathic copolymers, are increasingly used to directly solubilize cell membranes to functionally reconstitute membrane proteins in native-like copolymer-lipid nanodiscs. Although these copolymers act, de facto, like a "macromolecular detergent", the polymer-based lipid-nanodiscs has been demonstrated to be an excellent membrane mimetic for structural and functional studies of membrane proteins and their complexes by a variety of biophysical and biochemical approaches. In many studies reported in the literature, the choice of the right SMA formulation can depend on a number of factors, and the experimental conditions are typically developed according to a trial-and-error process since each studied system requires adapted protocols. While increasing number of nanodisc-forming copolymers are reported to be useful and they provide flexibilities in optimizing the sample preparation conditions, it is important to develop a systematic protocol that can be used for various applications. In this context, there is a vital necessity of benchmarking the performances of existing copolymer formulations, assessing crucial parameters for the successful extraction, isolation, and stabilization of membrane proteins. In this study, we compare both copolymers and copolymer-lipid nanodiscs obtained by SMA-EA with a set of anionic XIRAN copolymer formulations commercially available under the names of SL25010 P, SL30010 P, and SL40005 P. The reported results show how the critical micellar concentration (c.m.c.) of each copolymer is significantly altered in the presence of lipids and confirms the existence of an equilibrium between nanodisc-bound and "free" or "micellar" copolymer chains in the solution. We believe that these findings can be exploited to optimize studies that involve the necessity of special copolymers, which would not only simplify the applications but also broaden the scope of polymer-based nanodiscs.
Collapse
Affiliation(s)
- Giacomo M Di Mauro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Carmelo La Rosa
- Department of Chemistry, University of Catania, Catania 95125, Italy
| | | | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Biophysics and Chemistry Department, Macromolecular Science and Engineering, and Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
24
|
Lipid Dynamics in Diisobutylene-Maleic Acid (DIBMA) Lipid Particles in Presence of Sensory Rhodopsin II. Int J Mol Sci 2021; 22:ijms22052548. [PMID: 33806280 PMCID: PMC7961963 DOI: 10.3390/ijms22052548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/01/2023] Open
Abstract
Amphiphilic diisobutylene/maleic acid (DIBMA) copolymers extract lipid-encased membrane proteins from lipid bilayers in a detergent-free manner, yielding nanosized, discoidal DIBMA lipid particles (DIBMALPs). Depending on the DIBMA/lipid ratio, the size of DIBMALPs can be broadly varied which makes them suitable for the incorporation of proteins of different sizes. Here, we examine the influence of the DIBMALP sizes and the presence of protein on the dynamics of encased lipids. As shown by a set of biophysical methods, the stability of DIBMALPs remains unaffected at different DIBMA/lipid ratios. Coarse-grained molecular dynamics simulations confirm the formation of viable DIBMALPs with an overall size of up to 35 nm. Electron paramagnetic resonance spectroscopy of nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels reveals that the dynamics of enclosed lipids are not altered by the DIBMALP size. The presence of the membrane protein sensory rhodopsin II from Natronomonas pharaonis (NpSRII) results in a slight increase in the lipid dynamics compared to empty DIBMALPs. The light-induced photocycle shows full functionality of DIBMALPs-embedded NpSRII and a significant effect of the protein-to-lipid ratio during preparation on the NpSRII dynamics. This study indicates a possible expansion of the applicability of the DIBMALP technology on studies of membrane protein–protein interaction and oligomerization in a constraining environment.
Collapse
|
25
|
Korotych OI, Nguyen TT, Reagan BC, Burch-Smith TM, Bruce BD. Poly(styrene-co-maleic acid)-mediated isolation of supramolecular membrane protein complexes from plant thylakoids. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148347. [PMID: 33253667 DOI: 10.1016/j.bbabio.2020.148347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/09/2020] [Accepted: 11/21/2020] [Indexed: 12/25/2022]
Abstract
Derivatives of poly(styrene-co-maleic acid) (pSMA), have recently emerged as effective reagents for extracting membrane protein complexes from biological membranes. Despite recent progress in using SMAs to study artificial and bacterial membranes, very few reports have addressed their use in studying the highly abundant and well characterized thylakoid membranes. Recently, we tested the ability of twelve commercially available SMA copolymers with different physicochemical properties to extract membrane protein complexes (MPCs) from spinach thylakoid membrane. Based on the efficacy of both protein and chlorophyll extraction, we have found five highly efficient SMA copolymers: SMA® 1440, XIRAN® 25010, XIRAN® 30010, SMA® 17352, and SMA® PRO 10235, that show promise in extracting MPCs from chloroplast thylakoids. To further advance the application of these polymers for studying biomembrane organization, we have examined the composition of thylakoid supramolecular protein complexes extracted by the five SMA polymers mentioned above. Two commonly studied plants, spinach (Spinacia oleracea) and pea (Pisum sativum), were used for extraction as model biomembranes. We found that the pSMAs differentially extract protein complexes from spinach and pea thylakoids. Based on their differential activity, which correlates with the polymer chemical structure, pSMAs can be divided into two groups: unfunctionalized polymers and ester derivatives.
Collapse
Affiliation(s)
- Olena I Korotych
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, TN 37996, United States of America
| | - Thao T Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, TN 37996, United States of America
| | - Brandon C Reagan
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, TN 37996, United States of America
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, TN 37996, United States of America
| | - Barry D Bruce
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville, TN 37996, United States of America; Department of Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, TN 37996, United States of America.
| |
Collapse
|
26
|
Klenotic PA, Morgan CE, Yu EW. Cryo-EM as a tool to study bacterial efflux systems and the membrane proteome. Fac Rev 2021; 10:24. [PMID: 33718941 PMCID: PMC7946387 DOI: 10.12703/r/10-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance is an emerging threat to global health. Current treatment regimens for these types of bacterial infections are becoming increasingly inadequate. Thus, new innovative technologies are needed to help identify and characterize novel drugs and drug targets which are critical in order to combat multidrug-resistant bacterial strains. Bacterial efflux systems have emerged as an attractive target for drug design, as blocking their export function significantly increases the potency of administered antibiotics. However, in order to develop potent and tolerable efflux pump inhibitors with high efficacy, detailed structural information is required for both the apo- and substrate-bound forms of these membrane proteins. The emergence of cryo-electron microscopy (cryo-EM) has greatly advanced the field of membrane protein structural biology. It has significantly enhanced the ability to solve large multi-protein complexes as well as extract meaningful data from a heterogeneous sample, such as identification of several assembly states of the bacterial ribosome, from a single data set. This technique can be expanded to solve the structures of substrate-bound efflux pumps and entire efflux systems from previously unusable membrane protein sample preparations. Subsequently, cryo-EM combined with other biophysical techniques has the potential to markedly advance the field of membrane protein structural biology. The ability to discern complete transport machineries, enzymatic signal transduction pathways, and other membrane-associated complexes will help us fully understand the complexities of the membrane proteome.
Collapse
Affiliation(s)
- Philip A Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106-4965, USA
| |
Collapse
|
27
|
PELDOR/DEER: An Electron Paramagnetic Resonance Method to Study Membrane Proteins in Lipid Bilayers. Methods Mol Biol 2021. [PMID: 33582999 DOI: 10.1007/978-1-0716-0724-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Every membrane protein is involved in close interactions with the lipid environment of cellular membranes. The annular lipids, that are in direct contact with the polypeptide, can in principle be seen as an integral part of its structure, akin to the first hydration shell of soluble proteins. It is therefore desirable to investigate the structure of membrane proteins and especially their conformational flexibility under conditions that are as close as possible to their native state. This can be achieved by reconstituting the protein into proteoliposomes, nanodiscs, or bicelles. In recent years, PELDOR/DEER spectroscopy has proved to be a very useful method to study the structure and function of membrane proteins in such artificial membrane environments. The technique complements both X-ray crystallography and cryo-EM and can be used in combination with virtually any artificial membrane environment and under certain circumstances even in native membranes. Of the above-mentioned membrane mimics, bicelles are currently the least often used for PELDOR studies, although they offer some advantages, especially their ease of use. Here, we provide a step-by-step protocol for studying a bicelle reconstituted membrane protein with PELDOR/DEER spectroscopy.
Collapse
|
28
|
A Three-Dimensional Model of the Yeast Transmembrane Sensor Wsc1 Obtained by SMA-Based Detergent-Free Purification and Transmission Electron Microscopy. J Fungi (Basel) 2021; 7:jof7020118. [PMID: 33562593 PMCID: PMC7915640 DOI: 10.3390/jof7020118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022] Open
Abstract
The cell wall sensor Wsc1 belongs to a small family of transmembrane proteins, which are crucial to sustain cell integrity in yeast and other fungi. Wsc1 acts as a mechanosensor of the cell wall integrity (CWI) signal transduction pathway which responds to external stresses. Here we report on the purification of Wsc1 by its trapping in water-soluble polymer-stabilized lipid nanoparticles, obtained with an amphipathic styrene-maleic acid (SMA) copolymer. The latter was employed to transfer tagged sensors from their native yeast membranes into SMA/lipid particles (SMALPs), which allows their purification in a functional state, i.e., avoiding denaturation. The SMALPs composition was characterized by fluorescence correlation spectroscopy, followed by two-dimensional image acquisition from single particle transmission electron microscopy to build a three-dimensional model of the sensor. The latter confirms that Wsc1 consists of a large extracellular domain connected to a smaller intracellular part by a single transmembrane domain, which is embedded within the hydrophobic moiety of the lipid bilayer. The successful extraction of a sensor from the yeast plasma membrane by a detergent-free procedure into a native-like membrane environment provides new prospects for in vitro structural and functional studies of yeast plasma proteins which are likely to be applicable to other fungi, including plant and human pathogens.
Collapse
|
29
|
Ball LE, Riley LJ, Hadasha W, Pfukwa R, Smith CJI, Dafforn TR, Klumperman B. Influence of DIBMA Polymer Length on Lipid Nanodisc Formation and Membrane Protein Extraction. Biomacromolecules 2020; 22:763-772. [PMID: 33373193 DOI: 10.1021/acs.biomac.0c01538] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polymer-based lipid nanoparticles like styrene-maleic acid lipid particles have revolutionized the study of membrane proteins. More recently, alternative polymers such as poly(diisobutylene-alt-maleic acid) (DIBMA) have been used in this field. DIBMA is commonly synthesized via conventional radical copolymerization. In order to study the influence of its chain length on lipid nanodisc formation and membrane protein extraction, we synthesized DIBMA with molar masses varying from 1.2-12 kDa via RAFT-mediated polymerization. For molar masses in the range of 3-7 kDa, the rate of lipid nanodisc formation was the highest and similar to those of poly(styrene-co-maleic acid) (SMA) and commercially available DIBMA. ZipA solubilization efficiency was significantly higher than for commercially available DIBMA and similar to SMA (circa 75%). Furthermore, RAFT-made DIBMA with a molar mass of 1.2-3.9 kDa showed a much cleaner separation on SDS-PAGE, without the smearing that is typically seen for SMA and commercially available DIBMA.
Collapse
Affiliation(s)
- Lauren E Ball
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Liam J Riley
- School of Life Sciences, The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, United Kingdom.,School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Waled Hadasha
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Rueben Pfukwa
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Corinne J I Smith
- School of Life Sciences, The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, United Kingdom
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Bert Klumperman
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| |
Collapse
|
30
|
A 10-year meta-analysis of membrane protein structural biology: Detergents, membrane mimetics, and structure determination techniques. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183533. [PMID: 33340490 DOI: 10.1016/j.bbamem.2020.183533] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022]
Abstract
Structure determination of membrane proteins is critical to the molecular understanding of many life processes, yet it has historically been a technically challenging endeavor. This past decade has given rise to a number of technological advancements, techniques, and reagents, which have facilitated membrane protein structural biology, resulting in an ever-growing number of membrane protein structures determined. To collate these advances, we have mined available literature to analyze the purification and structure determination specifics for all uniquely solved membrane protein structures from 2010 to 2019. Our analyses demonstrate the strong impact of single-particle cryo-electron microscopy on the field and illustrate how this technique has affected detergent and membrane mimetic usage. Furthermore, we detail how different structure determination methods, taxonomic domains and protein classes have unique detergent/membrane mimetic profiles, highlighting the importance of tailoring their selection. Our analyses provide a quantitative overview of where the field of membrane protein structural biology stands and how it has developed over time. We anticipate that these will serve as a useful tool to streamline future membrane protein structure determination by guiding the choice of detergent/membrane mimetic.
Collapse
|
31
|
Flegler VJ, Rasmussen A, Rao S, Wu N, Zenobi R, Sansom MSP, Hedrich R, Rasmussen T, Böttcher B. The MscS-like channel YnaI has a gating mechanism based on flexible pore helices. Proc Natl Acad Sci U S A 2020; 117:28754-28762. [PMID: 33148804 PMCID: PMC7682570 DOI: 10.1073/pnas.2005641117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanosensitive channel of small conductance (MscS) is the prototype of an evolutionarily diversified large family that fine-tunes osmoregulation but is likely to fulfill additional functions. Escherichia coli has six osmoprotective paralogs with different numbers of transmembrane helices. These helices are important for gating and sensing in MscS but the role of the additional helices in the paralogs is not understood. The medium-sized channel YnaI was extracted and delivered in native nanodiscs in closed-like and open-like conformations using the copolymer diisobutylene/maleic acid (DIBMA) for structural studies. Here we show by electron cryomicroscopy that YnaI has an extended sensor paddle that during gating relocates relative to the pore concomitant with bending of a GGxGG motif in the pore helices. YnaI is the only one of the six paralogs that has this GGxGG motif allowing the sensor paddle to move outward. Access to the pore is through a vestibule on the cytosolic side that is fenestrated by side portals. In YnaI, these portals are obstructed by aromatic side chains but are still fully hydrated and thus support conductance. For comparison with large-sized channels, we determined the structure of YbiO, which showed larger portals and a wider pore with no GGxGG motif. Further in silico comparison of MscS, YnaI, and YbiO highlighted differences in the hydrophobicity and wettability of their pores and vestibule interiors. Thus, MscS-like channels of different sizes have a common core architecture but show different gating mechanisms and fine-tuned conductive properties.
Collapse
Affiliation(s)
- Vanessa Judith Flegler
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
| | - Akiko Rasmussen
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
- Lehrstuhl für Botanik I, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom
| | - Na Wu
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom
| | - Rainer Hedrich
- Lehrstuhl für Botanik I, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Tim Rasmussen
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany;
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
| | - Bettina Böttcher
- Biocenter, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany;
- Rudolf-Virchow-Center, Julius-Maximilians-Universität Würzburg, 97080 Würzburg, Germany
| |
Collapse
|
32
|
Chen A, Majdinasab EJ, Fiori MC, Liang H, Altenberg GA. Polymer-Encased Nanodiscs and Polymer Nanodiscs: New Platforms for Membrane Protein Research and Applications. Front Bioeng Biotechnol 2020; 8:598450. [PMID: 33304891 PMCID: PMC7701119 DOI: 10.3389/fbioe.2020.598450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
Membrane proteins (MPs) are essential to many organisms’ major functions. They are notorious for being difficult to isolate and study, and mimicking native conditions for studies in vitro has proved to be a challenge. Lipid nanodiscs are among the most promising platforms for MP reconstitution, but they contain a relatively labile lipid bilayer and their use requires previous protein solubilization in detergent. These limitations have led to the testing of copolymers in new types of nanodisc platforms. Polymer-encased nanodiscs and polymer nanodiscs support functional MPs and address some of the limitations present in other MP reconstitution platforms. In this review, we provide a summary of recent developments in the use of polymers in nanodiscs.
Collapse
Affiliation(s)
- Angela Chen
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Elleana J Majdinasab
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Mariana C Fiori
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Hongjun Liang
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Guillermo A Altenberg
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| |
Collapse
|
33
|
|
34
|
Rajapaksha P, Pandeya A, Wei Y. Probing the Dynamics of AcrB Through Disulfide Bond Formation. ACS OMEGA 2020; 5:21844-21852. [PMID: 32905396 PMCID: PMC7469415 DOI: 10.1021/acsomega.0c02921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
The resistant-nodulation-division (RND) superfamily member tripartite AcrA-AcrB-TolC efflux pump is a major contributor to the multidrug resistance in Escherichia coli. AcrB is the inner membrane protein of the efflux complex and is responsible for the recognition and binding of compounds before their transportation out of the cell. Understanding the dynamics of AcrB during functional rotation in the process of drug efflux is the focus of this study. For this purpose, we introduced six inter-subunit disulfide bonds into the periplasmic domain of AcrB using site-directed mutagenesis to study the importance of the relative flexibility at the inter-subunit interface. Western blot analysis revealed the formation of disulfide bond-linked AcrB oligomers, which were reduced into monomers under reducing conditions. The impact of mutation and formation of disulfide bond on efflux were evaluated via comparison of the minimum inhibitory concentration (MIC) of an acrB knockout strain expressing different mutants. The double Cys mutants tested led to equal or higher susceptibility to AcrB substrates compared to their corresponding single mutants. To determine if the reduction of activity in a double mutant is due to restriction on conformational changes by the disulfide bond formation, ethidium bromide accumulation assays were conducted utilizing dithiothreitol (DTT) as the reducing agent. In two cases, the activities of the double Cys mutants were partially restored by DTT reduction, confirming the importance of relative movement in the respective location for function. These findings provide new insights into the dynamics of the AcrAB-TolC efflux pump in E. coli.
Collapse
|
35
|
Hothersall JD, Jones AY, Dafforn TR, Perrior T, Chapman KL. Releasing the technical 'shackles' on GPCR drug discovery: opportunities enabled by detergent-free polymer lipid particle (PoLiPa) purification. Drug Discov Today 2020; 25:S1359-6446(20)30337-8. [PMID: 32835806 DOI: 10.1016/j.drudis.2020.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/04/2020] [Accepted: 08/13/2020] [Indexed: 12/19/2022]
Abstract
G-protein-coupled receptor (GPCR) drug research is presently hindered by the technical challenges associated with generating purified receptors. Consequently, the application of critical modern discovery technologies has been limited, and the vast untapped opportunity for new GPCR-directed medicines is not being realised. A simple but transformative solution is to purify receptors without removing them from their native phospholipid environment by using polymer lipid particle (PoLiPa) technology, with reagents such as styrene-maleic acid co-polymer (SMA). Compared with contemporary detergent-based and stabilising mutagenesis methods, the PoLiPa approach is simple and generic and, therefore, offers huge advantages, with the potential to revolutionise GPCR research by facilitating the availability of the purified receptors that are required for structural biology, biophysical, and panning technologies.
Collapse
Affiliation(s)
- J Daniel Hothersall
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK.
| | - Andrew Y Jones
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Trevor Perrior
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK
| | - Kathryn L Chapman
- Domainex Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK
| |
Collapse
|
36
|
Pellowe G, Findlay HE, Lee K, Gemeinhardt TM, Blackholly LR, Reading E, Booth PJ. Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies. Biochemistry 2020; 59:2764-2775. [PMID: 32627541 PMCID: PMC7551657 DOI: 10.1021/acs.biochem.0c00423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/02/2020] [Indexed: 01/02/2023]
Abstract
Co-translational folding studies of membrane proteins lag behind cytosolic protein investigations largely due to the technical difficulty in maintaining membrane lipid environments for correct protein folding. Stalled ribosome-bound nascent chain complexes (RNCs) can give snapshots of a nascent protein chain as it emerges from the ribosome during biosynthesis. Here, we demonstrate how SecM-facilitated nascent chain stalling and native nanodisc technologies can be exploited to capture in vivo-generated membrane protein RNCs within their native lipid compositions. We reveal that a polytopic membrane protein can be successfully stalled at various stages during its synthesis and the resulting RNC extracted within either detergent micelles or diisobutylene-maleic acid co-polymer native nanodiscs. Our approaches offer tractable solutions for the structural and biophysical interrogation of nascent membrane proteins of specified lengths, as the elongating nascent chain emerges from the ribosome and inserts into its native lipid milieu.
Collapse
Affiliation(s)
- Grant
A. Pellowe
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Heather E. Findlay
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Karen Lee
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Tim M. Gemeinhardt
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Laura R. Blackholly
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Eamonn Reading
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Paula J. Booth
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| |
Collapse
|
37
|
Cunningham RD, Kopf AH, Elenbaas BOW, Staal BB, Pfukwa R, Killian JA, Klumperman B. Iterative RAFT-Mediated Copolymerization of Styrene and Maleic Anhydride toward Sequence- and Length-Controlled Copolymers and Their Applications for Solubilizing Lipid Membranes. Biomacromolecules 2020; 21:3287-3300. [DOI: 10.1021/acs.biomac.0c00736] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Randy D. Cunningham
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Adrian H. Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Barend O. W. Elenbaas
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Bastiaan B.P. Staal
- BASF SE, RAA/AC, E210, Carl-Bosch-Strasse 38, Ludwigshafen am Rhein 67056, Germany
| | - Rueben Pfukwa
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - J. Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Bert Klumperman
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| |
Collapse
|
38
|
Kroeck KG, Qiu W, Catalano C, Trinh TKH, Guo Y. Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis. J Vis Exp 2020. [PMID: 32744521 DOI: 10.3791/61298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal transduction; from sensing environmental signals to biological response; from metabolic regulation to developmental control. Accurate structural information of protein-protein interactions is crucial for understanding the molecular mechanisms of membrane protein complexes and for the design of highly specific molecules to modulate these proteins. Many in vivo and in vitro approaches have been developed for the detection and analysis of protein-protein interactions. Among them the structural biology approach is unique in that it can provide direct structural information of protein-protein interactions at the atomic level. However, current membrane protein structural biology is still largely limited to detergent-based methods. The major drawback of detergent-based methods is that they often dissociate or denature membrane protein complexes once their native lipid bilayer environment is removed by detergent molecules. We have been developing a native cell membrane nanoparticle system for membrane protein structural biology. Here, we demonstrate the use of this system in the analysis of protein-protein interactions on the cell membrane with a case study of the oligomeric state of AcrB.
Collapse
Affiliation(s)
- Kyle G Kroeck
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Claudio Catalano
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University;
| |
Collapse
|
39
|
Johnson RM, Fais C, Parmar M, Cheruvara H, Marshall RL, Hesketh SJ, Feasey MC, Ruggerone P, Vargiu AV, Postis VLG, Muench SP, Bavro VN. Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella. Microorganisms 2020; 8:E943. [PMID: 32585951 PMCID: PMC7355581 DOI: 10.3390/microorganisms8060943] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Accepted: 06/20/2020] [Indexed: 12/31/2022] Open
Abstract
Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.
Collapse
Affiliation(s)
- Rachel M. Johnson
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Chiara Fais
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Mayuriben Parmar
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds LS1 3HE, UK; (M.P.); (V.L.G.P.)
| | - Harish Cheruvara
- Diamond Light Source, Membrane Protein Laboratory (MPL), Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK;
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Robert L. Marshall
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Sophie J. Hesketh
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Matthew C. Feasey
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Vincent L. G. Postis
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds LS1 3HE, UK; (M.P.); (V.L.G.P.)
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| |
Collapse
|
40
|
Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies. Methods 2020; 180:111-126. [PMID: 32422249 DOI: 10.1016/j.ymeth.2020.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning helices, encompass families of proteins which are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels and transporters. Although these proteins have typically been targeted by small molecule drugs and peptides, the high specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. However, it remains the case that isolation of antibodies with desired pharmacological function(s) has proven difficult due to technical challenges in preparing membrane protein antigens suitable to support antibody drug discovery. In this review recent progress in defining strategies for generation of membrane protein antigens is outlined. We also highlight antibody isolation strategies which have generated antibodies which bind the membrane protein and modulate the protein function.
Collapse
|
41
|
Chorev DS, Tang H, Rouse SL, Bolla JR, von Kügelgen A, Baker LA, Wu D, Gault J, Grünewald K, Bharat TAM, Matthews SJ, Robinson CV. The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes. Nat Protoc 2020; 15:1690-1706. [PMID: 32238951 PMCID: PMC7305028 DOI: 10.1038/s41596-020-0303-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/23/2020] [Indexed: 12/28/2022]
Abstract
Recent applications of mass spectrometry (MS) to study membrane protein complexes are yielding valuable insights into the binding of lipids and their structural and functional roles. To date, most native MS experiments with membrane proteins are based on detergent solubilization. Many insights into the structure and function of membrane proteins have been obtained using detergents; however, these can promote local lipid rearrangement and can cause fluctuations in the oligomeric state of protein complexes. To overcome these problems, we developed a method that does not use detergents or other chemicals. Here we report a detailed protocol that enables direct ejection of protein complexes from membranes for analysis by native MS. Briefly, lipid vesicles are prepared directly from membranes of different sources and subjected to sonication pulses. The resulting destabilized vesicles are concentrated, introduced into a mass spectrometer and ionized. The mass of the observed protein complexes is determined and this information, in conjunction with 'omics'-based strategies, is used to determine subunit stoichiometry as well as cofactor and lipid binding. Within this protocol, we expand the applications of the method to include peripheral membrane proteins of the S-layer and amyloid protein export machineries overexpressed in membranes from which the most abundant components have been removed. The described experimental procedure takes approximately 3 d from preparation to MS. The time required for data analysis depends on the complexity of the protein assemblies embedded in the membrane under investigation.
Collapse
Affiliation(s)
- Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Haiping Tang
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, London, UK
| | - Jani Reddy Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Microscopy Imaging Centre, Oxford, UK
| | - Lindsay A Baker
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Kay Grünewald
- Division of Structural Biology, University of Oxford, Oxford, UK
- Heinrich Pette Institute, Leibniz-Institut für Experimentelle Virologie, Centre for Structural Systems Biology, c/o DESY, Hamburg, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Microscopy Imaging Centre, Oxford, UK
| | | | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
| |
Collapse
|
42
|
Hall SCL, Clifton LA, Tognoloni C, Morrison KA, Knowles TJ, Kinane CJ, Dafforn TR, Edler KJ, Arnold T. Adsorption of a styrene maleic acid (SMA) copolymer-stabilized phospholipid nanodisc on a solid-supported planar lipid bilayer. J Colloid Interface Sci 2020; 574:272-284. [PMID: 32330753 PMCID: PMC7276985 DOI: 10.1016/j.jcis.2020.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022]
Abstract
Over recent years, there has been a rapid development of membrane-mimetic systems to encapsulate and stabilize planar segments of phospholipid bilayers in solution. One such system has been the use of amphipathic copolymers to solubilize lipid bilayers into nanodiscs. The attractiveness of this system, in part, stems from the capability of these polymers to solubilize membrane proteins directly from the host cell membrane. The assumption has been that the native lipid annulus remains intact, with nanodiscs providing a snapshot of the lipid environment. Recent studies have provided evidence that phospholipids can exchange from the nanodiscs with either lipids at interfaces, or with other nanodiscs in bulk solution. Here we investigate kinetics of lipid exchange between three recently studied polymer-stabilized nanodiscs and supported lipid bilayers at the silicon-water interface. We show that lipid and polymer exchange occurs in all nanodiscs tested, although the rate and extent differs between different nanodisc types. Furthermore, we observe adsorption of nanodiscs to the supported lipid bilayer for one nanodisc system which used a polymer made using reversible addition-fragmentation chain transfer polymerization. These results have important implications in applications of polymer-stabilized nanodiscs, such as in the fabrication of solid-supported films containing membrane proteins.
Collapse
Affiliation(s)
- Stephen C L Hall
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Cecilia Tognoloni
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Kerrie A Morrison
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Christian J Kinane
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Karen J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Thomas Arnold
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK; ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK; Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK; European Spallation Source ERIC, P.O Box 176, SE-221 00 Lund, Sweden.
| |
Collapse
|
43
|
Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
|
44
|
Akbar S, Mozumder S, Sengupta J. Retrospect and Prospect of Single Particle Cryo-Electron Microscopy: The Class of Integral Membrane Proteins as an Example. J Chem Inf Model 2020; 60:2448-2457. [DOI: 10.1021/acs.jcim.9b01015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shirin Akbar
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
45
|
Abstract
The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.
Collapse
|
46
|
Factors influencing the solubilization of membrane proteins from Escherichia coli membranes by styrene–maleic acid copolymers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183125. [DOI: 10.1016/j.bbamem.2019.183125] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/17/2019] [Accepted: 11/10/2019] [Indexed: 12/21/2022]
|
47
|
Guo Y. Be Cautious with Crystal Structures of Membrane Proteins or Complexes Prepared in Detergents. CRYSTALS 2020; 10:86. [PMID: 32494365 PMCID: PMC7269168 DOI: 10.3390/cryst10020086] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Membrane proteins are an important class of macromolecules found in all living organisms and many of them serve as important drug targets. In order to understand their biological and biochemical functions and to exploit them for structure-based drug design, high-resolution and accurate structures of membrane proteins are needed, but are still rarely available, e.g., predominantly from X-ray crystallography, and more recently from single particle cryo-EM - an increasingly powerful tool for membrane protein structure determination. However, while protein-lipid interactions play crucial roles for the structural and functional integrity of membrane proteins, for historical reasons and due to technological limitations, until recently, the primary method for membrane protein crystallization has relied on detergents. Bicelle and lipid cubic phase (LCP) methods have also been used for membrane protein crystallization, but the first step requires detergent extraction of the protein from its native cell membrane. The resulting, crystal structures have been occasionally questioned, but such concerns were generally dismissed as accidents or ignored. However, even a hint of controversy indicates that methodological drawbacks in such structural research may exist. In the absence of caution, structures determined using these methods are often assumed to be correct, which has led to surprising hypotheses for their mechanisms of action. In this communication, several examples of structural studies on membrane proteins or complexes will be discussed: Resistance-Nodulation-Division (RND) family transporters, microbial rhodopsins, Tryptophan-rich Sensory Proteins (TSPO), and Energy-Coupling Factor (ECF) type ABC transporters. These analyses should focus the attention of membrane protein structural biologists on the potential problems in structure determination relying on detergent-based methods. Furthermore, careful examination of membrane proteins in their native cell environments by biochemical and biophysical techniques is warranted, and completely detergent-free systems for membrane protein research are crucially needed.
Collapse
Affiliation(s)
- Youzhong Guo
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
| |
Collapse
|
48
|
Styrene maleic-acid lipid particles (SMALPs) into detergent or amphipols: An exchange protocol for membrane protein characterisation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183192. [PMID: 31945320 PMCID: PMC7086155 DOI: 10.1016/j.bbamem.2020.183192] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/06/2019] [Accepted: 01/10/2020] [Indexed: 12/24/2022]
Abstract
Membrane proteins are traditionally extracted and purified in detergent for biochemical and structural characterisation. This process is often costly and laborious, and the stripping away of potentially stabilising lipids from the membrane protein of interest can have detrimental effects on protein integrity. Recently, styrene-maleic acid (SMA) co-polymers have offered a solution to this problem by extracting membrane proteins directly from their native membrane, while retaining their naturally associated lipids in the form of stable SMA lipid particles (SMALPs). However, the inherent nature and heterogeneity of the polymer renders their use challenging for some downstream applications – particularly mass spectrometry (MS). While advances in cryo-electron microscopy (cryo-EM) have enhanced our understanding of membrane protein:lipid interactions in both SMALPs and detergent, the resolution obtained with this technique is often insufficient to accurately identify closely associated lipids within the transmembrane annulus. Native-MS has the power to fill this knowledge gap, but the SMA polymer itself remains largely incompatible with this technique. To increase sample homogeneity and allow characterisation of membrane protein:lipid complexes by native-MS, we have developed a novel SMA-exchange method; whereby the membrane protein of interest is first solubilised and purified in SMA, then transferred into amphipols or detergents. This allows the membrane protein and endogenously associated lipids extracted by SMA co-polymer to be identified and examined by MS, thereby complementing results obtained by cryo-EM and creating a better understanding of how the lipid bilayer directly affects membrane protein structure and function. First reported exchange protocol for transferring membrane proteins solubilised in SMALPs, into detergent or amphipols. Purification of protein:lipid complexes without detergent for mass spectrometry and subsequent lipid identification. Cost effective membrane protein purification requiring only minimal amounts of detergents in the exchange process.
Collapse
|
49
|
Kalienkova V, Alvadia C, Clerico Mosina V, Paulino C. Single-Particle Cryo-EM of Membrane Proteins in Lipid Nanodiscs. Methods Mol Biol 2020; 2127:245-273. [PMID: 32112327 DOI: 10.1007/978-1-0716-0373-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single-particle cryo-electron microscopy has become an indispensable technique in structural biology. In particular when studying membrane proteins, it allows the use of membrane-mimicking tools, which can be crucial for a comprehensive understanding of the structure-function relationship of the protein in its native environment. In this chapter we focus on the application of nanodiscs and use our recent studies on the TMEM16 family as an example.
Collapse
Affiliation(s)
- Valeria Kalienkova
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Carolina Alvadia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Vanessa Clerico Mosina
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
50
|
Bada Juarez JF, Muñoz-García JC, Inácio Dos Reis R, Henry A, McMillan D, Kriek M, Wood M, Vandenplas C, Sands Z, Castro L, Taylor R, Watts A. Detergent-free extraction of a functional low-expressing GPCR from a human cell line. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183152. [PMID: 31843475 DOI: 10.1016/j.bbamem.2019.183152] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/21/2019] [Accepted: 12/05/2019] [Indexed: 01/02/2023]
Abstract
Dopamine receptors (DRs) are class A G-Protein Coupled Receptors (GPCRs) prevalent in the central nervous system (CNS). These receptors mediate physiological functions ranging from voluntary movement and reward recognition to hormonal regulation and hypertension. Drugs targeting dopaminergic neurotransmission have been employed to treat several neurological and psychiatric disorders, including Parkinson's disease, schizophrenia, Huntington's disease, attention deficit hyperactivity disorder (ADHD), and Tourette's syndrome. In vivo, incorporation of GPCRs into lipid membranes is known to be key to their biological function and, by inference, maintenance of their tertiary structure. A further significant challenge in the structural and biochemical characterization of human DRs is their low levels of expression in mammalian cells. Thus, the purification and enrichment of DRs whilst retaining their structural integrity and function is highly desirable for biophysical studies. A promising new approach is the use of styrene-maleic acid (SMA) copolymer to solubilize GPCRs directly in their native environment, to produce polymer-assembled Lipodisqs (LQs). We have developed a novel methodology to yield detergent-free D1-containing Lipodisqs directly from HEK293f cells expressing wild-type human dopamine receptor 1 (D1). We demonstrate that D1 in the Lipodisq retains activity comparable to that in the native environment and report, for the first time, the affinity constant for the interaction of the peptide neurotransmitter neurotensin (NT) with D1, in the native state.
Collapse
Affiliation(s)
| | - Juan C Muñoz-García
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, UK; School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | | | | | | | - Marco Kriek
- UCB Celltech, 216 Bath Road, Slough SL1 3WE, UK
| | - Martyn Wood
- UCB BioPharma SPRL, Braine-l'Alleud, Belgium
| | | | - Zara Sands
- UCB Celltech, 216 Bath Road, Slough SL1 3WE, UK
| | - Luis Castro
- UCB Celltech, 216 Bath Road, Slough SL1 3WE, UK
| | | | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|