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Yao J, Hong H. Steric trapping strategy for studying the folding of helical membrane proteins. Methods 2024; 225:1-12. [PMID: 38428472 PMCID: PMC11107808 DOI: 10.1016/j.ymeth.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024] Open
Abstract
Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This is not a trivial task because the reversible control of folding is inherently difficult in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions. In a nutshell, steric trapping exploits the coupling of spontaneous denaturation of a doubly biotinylated protein to the simultaneous binding of bulky monovalent streptavidin molecules. This strategy has been evolved to investigate key elements of membrane protein folding such as thermodynamic stability, spontaneous denaturation rates, conformational features of the denatured states, and cooperativity of stabilizing interactions. In this review, we describe the critical methodological advancement, limitation, and outlook of the steric trapping strategy.
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Affiliation(s)
- Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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2
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Moochickal Assainar B, Ragunathan K, Baldridge RD. Direct observation of autoubiquitination for an integral membrane ubiquitin ligase in ERAD. Nat Commun 2024; 15:1340. [PMID: 38351109 PMCID: PMC10864399 DOI: 10.1038/s41467-024-45541-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
The endoplasmic reticulum associated degradation (ERAD) pathway regulates protein quality control at the endoplasmic reticulum. ERAD of lumenal and membrane proteins requires a conserved E3 ubiquitin ligase, called Hrd1. We do not understand the molecular configurations of Hrd1 that enable autoubiquitination and the subsequent retrotranslocation of misfolded protein substrates from the ER to the cytosol. Here, we have established a generalizable, single-molecule platform that enables high-efficiency labeling, stoichiometry determination, and functional assays for any integral membrane protein. Using this approach, we directly count Hrd1 proteins reconstituted into individual proteoliposomes. We report that Hrd1 assembles in different oligomeric configurations with mostly monomers and dimers detected at limiting dilution. By correlating oligomeric states with ubiquitination in vitro, we conclude that Hrd1 monomers are inefficient in autoubiquitination while dimers efficiently assemble polyubiquitin chains. Therefore, our results reveal the minimal composition of a Hrd1 oligomer that is capable of autoubiquitination. Our methods are broadly applicable to studying other complex membrane protein functions using reconstituted bilayer systems.
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Affiliation(s)
- Basila Moochickal Assainar
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Kaushik Ragunathan
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Ryan D Baldridge
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
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3
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Yen HY, Abramsson ML, Agasid MT, Lama D, Gault J, Liko I, Kaldmäe M, Saluri M, Qureshi AA, Suades A, Drew D, Degiacomi MT, Marklund EG, Allison TM, Robinson CV, Landreh M. Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Adv 2022; 12:9671-9680. [PMID: 35424940 PMCID: PMC8972943 DOI: 10.1039/d2ra01282k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Electrospray ionization mass spectrometry is increasingly applied to study the structures and interactions of membrane protein complexes. However, the charging mechanism is complicated by the presence of detergent micelles during ionization. Here, we show that the final charge of membrane proteins can be predicted by their molecular weight when released from the non-charge reducing saccharide detergents. Our data indicate that PEG detergents lower the charge depending on the number of detergent molecules in the surrounding micelle, whereas fos-choline detergents may additionally participate in ion–ion reactions after desolvation. The supercharging reagent sulfolane, on the other hand, has no discernible effect on the charge of detergent-free membrane proteins. Taking our observations into the context of protein-detergent interactions in the gas phase, we propose a charge equilibration model for the generation of native-like membrane protein ions. During ionization of the protein-detergent complex, the ESI charges are distributed between detergent and protein according to proton affinity of the detergent, number of detergent molecules, and surface area of the protein. Charge equilibration influenced by detergents determines the final charge state of membrane proteins. This process likely contributes to maintaining a native-like fold after detergent release and can be harnessed to stabilize particularly labile membrane protein complexes in the gas phase. The electrospray ionization mechanism contributes to preserving the structures and interactions of membrane protein complexes in native mass spectrometry.![]()
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Affiliation(s)
- Hsin-Yung Yen
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Institute of Biological Chemistry, Academia Sinica 128, Academia Road Sec. 2, Nankang Taipei 115 Taiwan
| | - Mia L Abramsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mark T Agasid
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Joseph Gault
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Idlir Liko
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Margit Kaldmäe
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mihkel Saluri
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Abdul Aziz Qureshi
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - Albert Suades
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | | | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University Box 576 75123 Uppsala Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury Christchurch 8140 New Zealand
| | - Carol V Robinson
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
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Hong H, Choi HK, Yoon TY. Untangling the complexity of membrane protein folding. Curr Opin Struct Biol 2022; 72:237-247. [PMID: 34995926 DOI: 10.1016/j.sbi.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/15/2022]
Abstract
Delineating the folding steps of helical-bundle membrane proteins has been a challenging task. Many questions remain unanswered, including the conformation and stability of the states populated during folding, the shape of the energy barriers between the states, and the role of lipids as a solvent in mediating the folding. Recently, theoretical frames have matured to a point that permits detailed dissection of the folding steps, and advances in experimental techniques at both single-molecule and ensemble levels enable selective modulation of specific steps for quantitative determination of the folding energy landscapes. We also discuss how lipid molecules would play an active role in shaping the folding energy landscape of membrane proteins, and how folding of multi-domain membrane proteins can be understood based on our current knowledge. We conclude this review by offering an outlook for emerging questions in the study of membrane protein folding.
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Affiliation(s)
- Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
| | - Hyun-Kyu Choi
- Wallace H. Coulter Department of Biomedical Engineering and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.
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Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Rep 2021; 37:109840. [PMID: 34686332 PMCID: PMC8641752 DOI: 10.1016/j.celrep.2021.109840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/19/2021] [Accepted: 09/27/2021] [Indexed: 01/13/2023] Open
Abstract
Nearly one-third of proteins are initially targeted to the endoplasmic reticulum (ER) membrane, where they are correctly folded and then delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) moves these clients from the ER membrane to the cytosol, a process known as retrotranslocation. Our recent work in Saccharomyces cerevisiae reveals a derlin rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated ERAD membrane substrates. In this study, we identify conserved residues of Dfm1 that are critical for retrotranslocation. We find several retrotranslocation-deficient Loop 1 mutants that display impaired binding to membrane substrates. Furthermore, Dfm1 possesses lipid thinning function to facilitate in the removal of ER membrane substrates, and this feature is conserved in its human homolog, Derlin-1, further implicating that derlin-mediated retrotranslocation is a well-conserved process.
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Affiliation(s)
- Anahita Nejatfard
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Wauer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Satarupa Bhaduri
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam Conn
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Saroj Gourkanti
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Narinderbir Singh
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Tiffany Kuo
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Kandel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
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Mihaljević L, Urban S. Decoding the Functional Evolution of an Intramembrane Protease Superfamily by Statistical Coupling Analysis. Structure 2020; 28:1329-1336.e4. [PMID: 32795403 DOI: 10.1016/j.str.2020.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/12/2020] [Accepted: 07/24/2020] [Indexed: 11/18/2022]
Abstract
How evolution endowed membrane enzymes with specific abilities, and then tuned them to the needs of different cells, is poorly understood. We examined whether statistical coupling analysis (SCA) can be applied to rhomboid proteases, the most widely distributed membrane proteins, to identify amino acid "sectors" that evolved independently to acquire a specific function. SCA revealed three coevolving residue networks that form two sectors. Sector 1 determines substrate specificity, but is paradoxically scattered across the protein, consistent with dynamics driving rhomboid-substrate interactions. Sector 2 is hierarchically composed of a subgroup that maintains the catalytic site, and another that maintains the overall fold, forecasting evolution of rhomboid pseudoproteases. Changing only sector 1 residues of a "recipient" rhomboid converted its substrate specificity and catalytic efficiency to that of the "donor." While used only twice over a decade ago, SCA should be generally applicable to membrane proteins, and our sector grafting approach provides an efficient strategy for designing enzymes.
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Affiliation(s)
- Ljubica Mihaljević
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Siniša Urban
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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Škerle J, Humpolíčková J, Johnson N, Rampírová P, Poláchová E, Fliegl M, Dohnálek J, Suchánková A, Jakubec D, Strisovsky K. Membrane Protein Dimerization in Cell-Derived Lipid Membranes Measured by FRET with MC Simulations. Biophys J 2020; 118:1861-1875. [PMID: 32246901 DOI: 10.1016/j.bpj.2020.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/06/2020] [Accepted: 03/13/2020] [Indexed: 11/19/2022] Open
Abstract
Many membrane proteins are thought to function as dimers or higher oligomers, but measuring membrane protein oligomerization in lipid membranes is particularly challenging. Förster resonance energy transfer (FRET) and fluorescence cross-correlation spectroscopy are noninvasive, optical methods of choice that have been applied to the analysis of dimerization of single-spanning membrane proteins. However, the effects inherent to such two-dimensional systems, such as the excluded volume of polytopic transmembrane proteins, proximity FRET, and rotational diffusion of fluorophore dipoles, complicate interpretation of FRET data and have not been typically accounted for. Here, using FRET and fluorescence cross-correlation spectroscopy, we introduce a method to measure surface protein density and to estimate the apparent Förster radius, and we use Monte Carlo simulations of the FRET data to account for the proximity FRET effect occurring in confined two-dimensional environments. We then use FRET to analyze the dimerization of human rhomboid protease RHBDL2 in giant plasma membrane vesicles. We find no evidence for stable oligomers of RHBDL2 in giant plasma membrane vesicles of human cells even at concentrations that highly exceed endogenous expression levels. This indicates that the rhomboid transmembrane core is intrinsically monomeric. Our findings will find use in the application of FRET and fluorescence correlation spectroscopy for the analysis of oligomerization of transmembrane proteins in cell-derived lipid membranes.
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Affiliation(s)
- Jan Škerle
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Humpolíčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.
| | - Nicholas Johnson
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Petra Rampírová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Edita Poláchová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic; First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Monika Fliegl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Jan Dohnálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic; University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Anna Suchánková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.
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Kreutzberger AJB, Ji M, Aaron J, Mihaljević L, Urban S. Rhomboid distorts lipids to break the viscosity-imposed speed limit of membrane diffusion. Science 2019; 363:363/6426/eaao0076. [PMID: 30705155 DOI: 10.1126/science.aao0076] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/30/2018] [Accepted: 12/07/2018] [Indexed: 12/25/2022]
Abstract
Enzymes that cut proteins inside membranes regulate diverse cellular events, including cell signaling, homeostasis, and host-pathogen interactions. Adaptations that enable catalysis in this exceptional environment are poorly understood. We visualized single molecules of multiple rhomboid intramembrane proteases and unrelated proteins in living cells (human and Drosophila) and planar lipid bilayers. Notably, only rhomboid proteins were able to diffuse above the Saffman-Delbrück viscosity limit of the membrane. Hydrophobic mismatch with the irregularly shaped rhomboid fold distorted surrounding lipids and propelled rhomboid diffusion. The rate of substrate processing in living cells scaled with rhomboid diffusivity. Thus, intramembrane proteolysis is naturally diffusion-limited, but cells mitigate this constraint by using the rhomboid fold to overcome the "speed limit" of membrane diffusion.
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Affiliation(s)
- Alex J B Kreutzberger
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Ming Ji
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jesse Aaron
- Howard Hughes Medical Institute, Advanced Imaging Center, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Ljubica Mihaljević
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Siniša Urban
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA. .,Howard Hughes Medical Institute, Advanced Imaging Center, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
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