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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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2
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Frotscher E, Krainer G, Hartmann A, Schlierf M, Keller S. Conformational Dynamics Govern the Free-Energy Landscape of a Membrane-Interacting Protein. ACS OMEGA 2018; 3:12026-12032. [PMID: 31459283 PMCID: PMC6690567 DOI: 10.1021/acsomega.8b01609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 05/08/2023]
Abstract
The equilibrium stabilities and the folding rates of membrane-bound proteins are determined by hydrophobic and polar intermolecular contacts with their environment as well as by intramolecular packing and conformational dynamics. The contributions of these factors, however, remain elusive and might vary considerably among proteins. Mistic from Bacillus subtilis is a particularly intriguing example of an α-helical protein that associates with membranes in spite of its unusual hydrophilicity. In micelles, Mistic is stabilized by hydrophobic and polar interactions with detergents, but it is unclear whether and how these intermolecular contacts are coupled to structural and dynamic adaptations of the protein itself. Here, we investigated the packing and the conformational dynamics of Mistic as functions of detergent headgroup chemistry and chain length, employing single-molecule Förster resonance energy transfer spectroscopy and time-resolved intrinsic tryptophan fluorescence spectroscopy. Surprisingly, in nonionic detergents, more effective hydrophobic burial and, thus, greater protein stability with increasing hydrophobic micellar thickness were accompanied by a gradual loosening of the helical bundle. By contrast, Mistic was found to assume a stable, compact fold in zwitterionic detergents that allowed faster dynamics on the nanosecond timescale. Thus, intramolecular packing per se is insufficient for conferring high protein stability; instead, enhanced nanosecond dynamics and, consequently, greater conformational entropy in the compact folded state account for Mistic's high equilibrium stability and fast folding rates in zwitterionic micelles even at the expense of less effective hydrophobic burial.
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Affiliation(s)
- Erik Frotscher
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Georg Krainer
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Andreas Hartmann
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Michael Schlierf
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
- E-mail: (M.S.)
| | - Sandro Keller
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- E-mail: (S.K.)
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3
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Lee SC, Knowles TJ, Postis VLG, Jamshad M, Parslow RA, Lin YP, Goldman A, Sridhar P, Overduin M, Muench SP, Dafforn TR. A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc 2016; 11:1149-62. [PMID: 27254461 DOI: 10.1038/nprot.2016.070] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the great importance of membrane proteins, structural and functional studies of these proteins present major challenges. A significant hurdle is the extraction of the functional protein from its natural lipid membrane. Traditionally achieved with detergents, purification procedures can be costly and time consuming. A critical flaw with detergent approaches is the removal of the protein from the native lipid environment required to maintain functionally stable protein. This protocol describes the preparation of styrene maleic acid (SMA) co-polymer to extract membrane proteins from prokaryotic and eukaryotic expression systems. Successful isolation of membrane proteins into SMA lipid particles (SMALPs) allows the proteins to remain with native lipid, surrounded by SMA. We detail procedures for obtaining 25 g of SMA (4 d); explain the preparation of protein-containing SMALPs using membranes isolated from Escherichia coli (2 d) and control protein-free SMALPS using E. coli polar lipid extract (1-2 h); investigate SMALP protein purity by SDS-PAGE analysis and estimate protein concentration (4 h); and detail biophysical methods such as circular dichroism (CD) spectroscopy and sedimentation velocity analytical ultracentrifugation (svAUC) to undertake initial structural studies to characterize SMALPs (∼2 d). Together, these methods provide a practical tool kit for those wanting to use SMALPs to study membrane proteins.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Tim J Knowles
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Vincent L G Postis
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds, UK
| | | | | | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Pooja Sridhar
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Michael Overduin
- School of Biosciences, University of Birmingham, Birmingham, UK.,Department of Biochemistry, Faculty of Medicine &Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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4
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Klein N, Hellmann N, Schneider D. Anionic Lipids Modulate the Activity of the Aquaglyceroporin GlpF. Biophys J 2016; 109:722-31. [PMID: 26287624 DOI: 10.1016/j.bpj.2015.06.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 01/30/2023] Open
Abstract
The structure and composition of a biological membrane can severely influence the activity of membrane-embedded proteins. Here, we show that the E. coli aquaglyceroporin GlpF has only little activity in lipid bilayers formed from native E. coli lipids. Thus, at first glance, GlpF appears to not be optimized for its natural membrane environment. In fact, we found that GlpF activity was severely affected by negatively charged lipids regardless of the exact chemical nature of the lipid headgroup, whereas GlpF was not sensitive to changes in the lateral membrane pressure. These observations illustrate a potential mechanism by which the activity of an α-helical membrane protein is modulated by the negative charge density around the protein.
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Affiliation(s)
- Noreen Klein
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Nadja Hellmann
- Institut für Molekulare Biophysik, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany.
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Textor M, Vargas C, Keller S. Calorimetric quantification of linked equilibria in cyclodextrin/lipid/detergent mixtures for membrane-protein reconstitution. Methods 2015; 76:183-193. [DOI: 10.1016/j.ymeth.2015.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 12/30/2014] [Accepted: 01/02/2015] [Indexed: 10/24/2022] Open
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6
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Marino J, Bordag N, Keller S, Zerbe O. Mistic's membrane association and its assistance in overexpression of a human GPCR are independent processes. Protein Sci 2014; 24:38-48. [PMID: 25297828 DOI: 10.1002/pro.2582] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/15/2014] [Accepted: 10/06/2014] [Indexed: 01/19/2023]
Abstract
The interaction of the Bacillus subtilis protein Mistic with the bacterial membrane and its role in promoting the overexpression of other membrane proteins are still matters of debate. In this study, we aimed to determine whether individual helical fragments of Mistic are sufficient for its interaction with membranes in vivo and in vitro. To this end, fragments encompassing each of Mistic's helical segments and combinations of them were produced as GFP-fusions, and their cellular localization was studied in Escherichia coli. Furthermore, peptides corresponding to the four helical fragments were synthesized by solid-phase peptide synthesis, and their ability to acquire secondary structure in a variety of lipids and detergents was studied by circular dichroism spectroscopy. Both types of experiments demonstrate that the third helical fragment of Mistic interacts only with LDAO micelles but does not partition into lipid bilayers. Interestingly, the other three helices interact with membranes in vivo and in vitro. Nevertheless, all of these short sequences can replace full-length Mistic as N-terminal fusions to achieve overexpression of a human G-protein-coupled receptor in E. coli, although with different effects on quantity and quality of the protein produced. A bioinformatic analysis of the Mistic family expanded the number of homologs from 4 to 20, including proteins outside the genus Bacillus. This information allowed us to discover a highly conserved Shine-Dalgarno sequence in the operon mstX-yugO that is important for downstream translation of the potassium ion channel yugO.
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Affiliation(s)
- Jacopo Marino
- Department of Chemistry, University of Zürich, Switzerland
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7
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Broecker J, Fiedler S, Gimpl K, Keller S. Polar Interactions Trump Hydrophobicity in Stabilizing the Self-Inserting Membrane Protein Mistic. J Am Chem Soc 2014; 136:13761-8. [DOI: 10.1021/ja5064795] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jana Broecker
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
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8
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Jacso T, Bardiaux B, Broecker J, Fiedler S, Baerwinkel T, Mainz A, Fink U, Vargas C, Oschkinat H, Keller S, Reif B. The Mechanism of Denaturation and the Unfolded State of the α-Helical Membrane-Associated Protein Mistic. J Am Chem Soc 2013; 135:18884-91. [DOI: 10.1021/ja408644f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tomas Jacso
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Benjamin Bardiaux
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Jana Broecker
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Tom Baerwinkel
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Andi Mainz
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Uwe Fink
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Carolyn Vargas
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Sandro Keller
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Bernd Reif
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
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