1
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Chamness LM, Kuntz CP, McKee AG, Penn WD, Hemmerich CM, Rusch DB, Woods H, Dyotima, Meiler J, Schlebach JP. Divergent folding-mediated epistasis among unstable membrane protein variants. eLife 2024; 12:RP92406. [PMID: 39078397 PMCID: PMC11288631 DOI: 10.7554/elife.92406] [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] [Indexed: 07/31/2024] Open
Abstract
Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency. Though protein stability is known to shape evolution, it is unclear how cotranslational folding constraints modulate the synergistic, epistatic interactions between mutations. We therefore compared the pairwise interactions formed by mutations that disrupt the membrane topology (V276T) or tertiary structure (W107A) of GnRHR. Using deep mutational scanning, we evaluated how the plasma membrane expression of these variants is modified by hundreds of secondary mutations. An analysis of 251 mutants in three genetic backgrounds reveals that V276T and W107A form distinct epistatic interactions that depend on both the severity and the mechanism of destabilization. V276T forms predominantly negative epistatic interactions with destabilizing mutations in soluble loops. In contrast, W107A forms positive interactions with mutations in both loops and transmembrane domains that reflect the diminishing impacts of the destabilizing mutations in variants that are already unstable. These findings reveal how epistasis is remodeled by conformational defects in membrane proteins and in unstable proteins more generally.
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Affiliation(s)
- Laura M Chamness
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - Charles P Kuntz
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue UniversityWest LafayetteUnited States
| | - Andrew G McKee
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - Wesley D Penn
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | | | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana UniversityBloomingtonUnited States
| | - Hope Woods
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
- Chemical and Physical Biology Program, Vanderbilt UniversityNashvilleUnited States
| | - Dyotima
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
- Institute for Drug Discovery, Leipzig UniversityLeipzigGermany
| | - Jonathan P Schlebach
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue UniversityWest LafayetteUnited States
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2
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Ji J, Cui MK, Zou R, Wu MZ, Ge MX, Li J, Zhang ZR. An ATP13A1-assisted topogenesis pathway for folding multi-spanning membrane proteins. Mol Cell 2024; 84:1917-1931.e15. [PMID: 38723633 DOI: 10.1016/j.molcel.2024.04.010] [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: 06/27/2023] [Revised: 02/15/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Many multi-spanning membrane proteins contain poorly hydrophobic transmembrane domains (pTMDs) protected from phospholipid in mature structure. Nascent pTMDs are difficult for translocon to recognize and insert. How pTMDs are discerned and packed into mature, muti-spanning configuration remains unclear. Here, we report that pTMD elicits a post-translational topogenesis pathway for its recognition and integration. Using six-spanning protein adenosine triphosphate-binding cassette transporter G2 (ABCG2) and cultured human cells as models, we show that ABCG2's pTMD2 can pass through translocon into the endoplasmic reticulum (ER) lumen, yielding an intermediate with inserted yet mis-oriented downstream TMDs. After translation, the intermediate recruits P5A-ATPase ATP13A1, which facilitates TMD re-orientation, allowing further folding and the integration of the remaining lumen-exposed pTMD2. Depleting ATP13A1 or disrupting pTMD-characteristic residues arrests intermediates with mis-oriented and exposed TMDs. Our results explain how a "difficult" pTMD is co-translationally skipped for insertion and post-translationally buried into the final correct structure at the late folding stage to avoid excessive lipid exposure.
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Affiliation(s)
- Jia Ji
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Meng-Ke Cui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Rong Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Ming-Zhi Wu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Man-Xi Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Jiqiang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China.
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3
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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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4
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Chamness LM, Kuntz CP, McKee AG, Penn WD, Hemmerich CM, Rusch DB, Woods H, Dyotima, Meiler J, Schlebach JP. Divergent Folding-Mediated Epistasis Among Unstable Membrane Protein Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.25.554866. [PMID: 37662415 PMCID: PMC10473758 DOI: 10.1101/2023.08.25.554866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency. Though protein stability is known to shape evolution, it is unclear how cotranslational folding constraints modulate the synergistic, epistatic interactions between mutations. We therefore compared the pairwise interactions formed by mutations that disrupt the membrane topology (V276T) or tertiary structure (W107A) of GnRHR. Using deep mutational scanning, we evaluated how the plasma membrane expression of these variants is modified by hundreds of secondary mutations. An analysis of 251 mutants in three genetic backgrounds reveals that V276T and W107A form distinct epistatic interactions that depend on both the severity and the mechanism of destabilization. V276T forms predominantly negative epistatic interactions with destabilizing mutations in soluble loops. In contrast, W107A forms positive interactions with mutations in both loops and transmembrane domains that reflect the diminishing impacts of the destabilizing mutations in variants that are already unstable. These findings reveal how epistasis is remodeled by conformational defects in membrane proteins and in unstable proteins more generally.
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Affiliation(s)
- Laura M. Chamness
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Charles P. Kuntz
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Andrew G. McKee
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Wesley D. Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | | | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | - Hope Woods
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Dyotima
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC, Germany
| | - Jonathan P. Schlebach
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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5
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Sun S, Li X, Mariappan M. Signal sequences encode information for protein folding in the endoplasmic reticulum. J Cell Biol 2023; 222:213733. [PMID: 36459117 PMCID: PMC9723807 DOI: 10.1083/jcb.202203070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/22/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
One-third of newly synthesized proteins in mammals are translocated into the endoplasmic reticulum (ER) through the Sec61 translocon. How protein translocation coordinates with chaperone availability in the ER to promote protein folding remains unclear. We find that marginally hydrophobic signal sequences and transmembrane domains cause transient retention at the Sec61 translocon and require the luminal BiP chaperone for efficient protein translocation. Using a substrate-trapping proteomic approach, we identify that nascent proteins bearing marginally hydrophobic signal sequences accumulate on the cytosolic side of the Sec61 translocon. Sec63 is co-translationally recruited to the translocation site and mediates BiP binding to incoming polypeptides. BiP binding not only releases translocationally paused nascent chains but also ensures protein folding in the ER. Increasing hydrophobicity of signal sequences bypasses Sec63/BiP-dependent translocation, but translocated proteins are prone to misfold and aggregate in the ER under limited BiP availability. Thus, the signal sequence-guided protein folding may explain why signal sequences are diverse and use multiple protein translocation pathways.
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Affiliation(s)
- Sha Sun
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
| | - Xia Li
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
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6
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Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022; 23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Protein folding is a fundamental process of life with important implications throughout biology. Indeed, tens of thousands of mutations have been associated with diseases, and most of these mutations are believed to affect protein folding rather than function. Correct folding is also a key element of design. These factors have motivated decades of research on protein folding. Unfortunately, knowledge of membrane protein folding lags that of soluble proteins. This gap is partly caused by the greater technical challenges associated with membrane protein studies, but also because of additional complexities. While soluble proteins fold in a homogenous water environment, membrane proteins fold in a setting that ranges from bulk water to highly charged to apolar. Thus, the forces that drive folding vary in different regions of the protein, and this complexity needs to be incorporated into our understanding of the folding process. Here, we review our understanding of membrane protein folding biophysics. Despite the greater challenge, better model systems and new experimental techniques are starting to unravel the forces and pathways in membrane protein folding.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - James U Bowie
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
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7
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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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8
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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9
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Chamness LM, Zelt NB, Harrington HR, Kuntz CP, Bender BJ, Penn WD, Ziarek JJ, Meiler J, Schlebach JP. Molecular basis for the evolved instability of a human G-protein coupled receptor. Cell Rep 2021; 37:110046. [PMID: 34818554 PMCID: PMC8865034 DOI: 10.1016/j.celrep.2021.110046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 08/06/2021] [Accepted: 11/01/2021] [Indexed: 11/26/2022] Open
Abstract
Membrane proteins are prone to misfolding and degradation. This is particularly true for mammalian forms of the gonadotropin-releasing hormone receptor (GnRHR). Although they function at the plasma membrane, mammalian GnRHRs accumulate within the secretory pathway. Their apparent instability is believed to have evolved through selection for attenuated GnRHR activity. Nevertheless, the molecular basis of this adaptation remains unclear. We show that adaptation coincides with a C-terminal truncation that compromises the translocon-mediated membrane integration of its seventh transmembrane domain (TM7). We also identify a series of polar residues in mammalian GnRHRs that compromise the membrane integration of TM2 and TM6. Reverting a lipid-exposed polar residue in TM6 to an ancestral hydrophobic residue restores expression with no impact on function. Evolutionary trends suggest variations in the polarity of this residue track with reproductive phenotypes. Our findings suggest that the marginal energetics of cotranslational folding can be exploited to tune membrane protein fitness. Integral membrane proteins are prone to misfolding, especially mammalian gonadotropin-releasing hormone receptors (GnRHRs). Chamness et al. show that the evolved instability of mammalian GnRHRs stems from adaptive modifications that disrupt translocon-mediated membrane integration, suggesting that membrane protein misfolding can be exploited to tune fitness.
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Affiliation(s)
- Laura M Chamness
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Nathan B Zelt
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Charles P Kuntz
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Brian J Bender
- Department of Chemistry, Vanderbilt University, Nashville, TN 49795, USA
| | - Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Joshua J Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 49795, USA; Institut for Drug Development, Leipzig University, Leipzig, SAC, Germany
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10
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Efficient integration of transmembrane domains depends on the folding properties of the upstream sequences. Proc Natl Acad Sci U S A 2021; 118:2102675118. [PMID: 34373330 PMCID: PMC8379923 DOI: 10.1073/pnas.2102675118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The topology of membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. For each polypeptide segment of ∼20 residues entering the translocon, their combined hydrophobicities were previously shown to define membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect the hydrophobicity threshold. Sequences that are rapidly folding, intrinsically disordered, very short, or strongly binding chaperones allow efficient integration at low hydrophobicity. Folding deficient mutant domains and artificial sequences not binding chaperones interfered with membrane integration likely by remaining partially unfolded and exposing hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. Rapid folding or strong chaperone binding thus promote efficient integration. The topology of most membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. The translocon provides a pore for the transfer of polypeptide segments across the membrane while giving them lateral access to the lipid. For each polypeptide segment of ∼20 residues, the combined hydrophobicities of its constituent amino acids were previously shown to define the extent of membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect its hydrophobicity requirement for integration. Rapidly folding domains, sequences that are intrinsically disordered or very short or capable of binding chaperones with high affinity, allow for efficient transmembrane integration with low-hydrophobicity thresholds for both orientations in the membrane. In contrast, long protein fragments, folding-deficient mutant domains, and artificial sequences not binding chaperones interfered with membrane integration, requiring higher hydrophobicity. We propose that the latter sequences, as they compact on their hydrophobic residues, partially folded but unable to reach a native state, expose hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. The results suggest that rapid folding or strong chaperone binding is required for efficient transmembrane integration.
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11
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Sun S, Mariappan M. C-terminal tail length guides insertion and assembly of membrane proteins. J Biol Chem 2020; 295:15498-15510. [PMID: 32878985 DOI: 10.1074/jbc.ra120.012992] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/27/2020] [Indexed: 11/06/2022] Open
Abstract
A large number of newly synthesized membrane proteins in the endoplasmic reticulum (ER) are assembled into multiprotein complexes, but little is known about the mechanisms required for assembly membrane proteins. It has been suggested that membrane chaperones might exist, akin to the molecular chaperones that stabilize and direct the assembly of soluble protein complexes, but the mechanisms by which these proteins would bring together membrane protein components is unclear. Here, we have identified that the tail length of the C-terminal transmembrane domains (C-TMDs) determines efficient insertion and assembly of membrane proteins in the ER. We found that membrane proteins with C-TMD tails shorter than ∼60 amino acids are poorly inserted into the ER membrane, which suggests that translation is terminated before they are recognized by the Sec61 translocon for insertion. These C-TMDs with insufficient hydrophobicity are post-translationally recognized and retained by the Sec61 translocon complex, providing a time window for efficient assembly with TMDs from partner proteins. Retained TMDs that fail to assemble with their cognate TMDs are slowly translocated into the ER lumen and are recognized by the ER-associated degradation (ERAD) pathway for removal. In contrast, C-TMDs with sufficient hydrophobicity or tails longer than ∼80 residues are quickly released from the Sec61 translocon into the membrane or the ER lumen, resulting in inefficient assembly with partner TMDs. Thus, our data suggest that C-terminal tails harbor crucial signals for both the insertion and assembly of membrane proteins.
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Affiliation(s)
- Sha Sun
- Frome the Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, Connecticut, USA
| | - Malaiyalam Mariappan
- Frome the Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, Connecticut, USA.
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12
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Ubiquitination of disease-causing CFTR variants in a microsome-based assay. Anal Biochem 2020; 604:113829. [PMID: 32621804 DOI: 10.1016/j.ab.2020.113829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022]
Abstract
Soluble secreted proteins and membrane proteins are subjected to protein quality control pathways during their synthesis in the endoplasmic reticulum (ER) and delivery to other destinations. Foremost among these quality control pathways is the selection of misfolded proteins for ER-associated degradation (ERAD). A growing number of diseases, including Cystic Fibrosis, are linked to the ERAD pathway. In most cases, a membrane protein known as the Cystic Fibrosis Transmembrane Conductance Regulator, or CFTR, is prematurely degraded by ERAD. Cell-based assays and in vitro studies have elucidated factors required for the recognition and degradation of CFTR, yet mechanistic details on how these factors target specific disease-causing variants is limited. Given the possibility that variants might exhibit unique susceptibilities to ubiquitin modification, which is required for proteasome-mediated degradation, we devised an assay that recapitulates this event. Here, we demonstrate that ER-enriched membranes from transfected human cells support CFTR ubiquitination when combined with radiolabeled ubiquitin and isolated enzymes in the ubiquitination cascade. We also show that select disease-causing variants are ubiquitinated more extensively than wild-type channels and to varying degrees. Our system provides a platform to examine how other purified factors impact CFTR ubiquitination and the ubiquitination of additional disease-associated membrane proteins.
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13
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Janezic EM, Lauer SML, Williams RG, Chungyoun M, Lee KS, Navaluna E, Lau HT, Ong SE, Hague C. N-glycosylation of α 1D-adrenergic receptor N-terminal domain is required for correct trafficking, function, and biogenesis. Sci Rep 2020; 10:7209. [PMID: 32350295 PMCID: PMC7190626 DOI: 10.1038/s41598-020-64102-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/09/2020] [Indexed: 01/21/2023] Open
Abstract
G protein-coupled receptor (GPCR) biogenesis, trafficking, and function are regulated by post-translational modifications, including N-glycosylation of asparagine residues. α1D-adrenergic receptors (α1D-ARs) - key regulators of central and autonomic nervous system function - contain two putative N-glycosylation sites within the large N-terminal domain at N65 and N82. However, determining the glycosylation state of this receptor has proven challenging. Towards understanding the role of these putative glycosylation sites, site-directed mutagenesis and lectin affinity purification identified N65 and N82 as bona fide acceptors for N-glycans. Surprisingly, we also report that simultaneously mutating N65 and N82 causes early termination of α1D-AR between transmembrane domain 2 and 3. Label-free dynamic mass redistribution and cell surface trafficking assays revealed that single and double glycosylation deficient mutants display limited function with impaired plasma membrane expression. Confocal microscopy imaging analysis and SNAP-tag sucrose density fractionation assays revealed the dual glycosylation mutant α1D-AR is widely distributed throughout the cytosol and nucleus. Based on these novel findings, we propose α1D-AR transmembrane domain 2 acts as an ER localization signal during active protein biogenesis, and that α1D-AR N-terminal glycosylation is required for complete translation of nascent, functional receptor.
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Affiliation(s)
- Eric M Janezic
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Sophia My-Linh Lauer
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Robert George Williams
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Michael Chungyoun
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Kyung-Soon Lee
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Edelmar Navaluna
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Ho-Tak Lau
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Shao-En Ong
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Chris Hague
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA.
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14
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Bañó-Polo M, Martínez-Gil L, Barrera FN, Mingarro I. Insertion of Bacteriorhodopsin Helix C Variants into Biological Membranes. ACS OMEGA 2020; 5:556-560. [PMID: 31956802 PMCID: PMC6964287 DOI: 10.1021/acsomega.9b03126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
A peptide corresponding to bacteriorhodopsin (bR) helix C, later named pHLIP, inserts across lipid bilayers as a monomeric α-helix at acidic pH, but is an unstructured surface-bound monomer at neutral pH. As a result of such pH-responsiveness, pHLIP targets acidic tumors and has been used as a vehicle for imaging and drug-delivery cargoes. To gain insights about the insertion of bR helix C into biological membranes, we replaced two key aspartic residues that control the topological transition from the aqueous phase into a lipid bilayer. Here, we used an in vitro transcription-translation system to study the translocon-mediated insertion of helix C-derived segments into rough microsomes. Our data provide the first quantitative biological understanding of this effect. Interestingly, replacing the aspartic residues by glutamic residues does not significantly alters the insertion propensity, while replacement by alanines promotes a transmembrane orientation. These results are consistent with mutational data obtained in synthetic liposomes by manipulating pH conditions. Our findings support the notion that the translocon facilitates topogenesis under physiological pH conditions.
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Affiliation(s)
- Manuel Bañó-Polo
- Departament
de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar
en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València. E-46100 Burjassot, Spain
| | - Luis Martínez-Gil
- Departament
de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar
en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València. E-46100 Burjassot, Spain
| | - Francisco N. Barrera
- Department
of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ismael Mingarro
- Departament
de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar
en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València. E-46100 Burjassot, Spain
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15
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Guerriero CJ, Gomez YK, Daskivich GJ, Reutter KR, Augustine AA, Weiberth KF, Nakatsukasa K, Grabe M, Brodsky JL. Harmonizing Experimental Data with Modeling to Predict Membrane Protein Insertion in Yeast. Biophys J 2019; 117:668-678. [PMID: 31399214 DOI: 10.1016/j.bpj.2019.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins must adopt their proper topologies within biological membranes, but achieving the correct topology is compromised by the presence of marginally hydrophobic transmembrane helices (TMHs). In this study, we report on a new model membrane protein in yeast that harbors two TMHs fused to an unstable nucleotide-binding domain. Because the second helix (TMH2) in this reporter has an unfavorable predicted free energy of insertion, we employed established methods to generate variants that alter TMH2 insertion free energy. We first found that altering TMH2 did not significantly affect the extent of protein degradation by the cellular quality control machinery. Next, we correlated predicted insertion free energies from a knowledge-based energy scale with the measured apparent free energies of TMH2 insertion. Although the predicted and apparent insertion energies showed a similar trend, the predicted free-energy changes spanned an unanticipated narrow range. By instead using a physics-based model, we obtained a broader range of free energies that agreed considerably better with the magnitude of the experimentally derived values. Nevertheless, some variants still inserted better in yeast than predicted from energy-based scales. Therefore, molecular dynamics simulations were performed and indicated that the corresponding mutations induced conformational changes within TMH2, which altered the number of stabilizing hydrogen bonds. Together, our results offer insight into the ability of the cellular quality control machinery to recognize conformationally distinct misfolded topomers, provide a model to assess TMH insertion in vivo, and indicate that TMH insertion energy scales may be limited depending on the specific protein and the mutation present.
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Affiliation(s)
| | - Yessica K Gomez
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Grant J Daskivich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Karl-Richard Reutter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew A Augustine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kurt F Weiberth
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kunio Nakatsukasa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
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16
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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: 162] [Impact Index Per Article: 32.4] [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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17
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Roushar FJ, Gruenhagen TC, Penn WD, Li B, Meiler J, Jastrzebska B, Schlebach JP. Contribution of Cotranslational Folding Defects to Membrane Protein Homeostasis. J Am Chem Soc 2018; 141:204-215. [PMID: 30537820 DOI: 10.1021/jacs.8b08243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Membrane proteins are prone to misfolding and degradation within the cell, yet the nature of the conformational defects involved in this process remain poorly understood. The earliest stages of membrane protein folding are mediated by the Sec61 translocon, a molecular machine that facilitates the lateral partitioning of the polypeptide into the membrane. Proper membrane integration is an essential prerequisite for folding of the nascent chain. However, the marginal energetic drivers of this reaction suggest the translocon may operate with modest fidelity. In this work, we employed biophysical modeling in conjunction with quantitative biochemical measurements in order to evaluate the extent to which cotranslational folding defects influence membrane protein homeostasis. Protein engineering was employed to selectively perturb the topological energetics of human rhodopsin, and the expression and cellular trafficking of engineered variants were quantitatively compared. Our results reveal clear relationships between topological energetics and the efficiency of rhodopsin biogenesis, which appears to be limited by the propensity of a polar transmembrane domain to achieve its correct topological orientation. Though the polarity of this segment is functionally constrained, we find that its topology can be stabilized in a manner that enhances biogenesis without compromising the functional properties of rhodopsin. Furthermore, sequence alignments reveal this topological instability has been conserved throughout the course of evolution. These results suggest that topological defects significantly contribute to the inefficiency of membrane protein folding in the cell. Additionally, our findings suggest that the marginal stability of rhodopsin may represent an evolved trait.
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Affiliation(s)
- Francis J Roushar
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Timothy C Gruenhagen
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Wesley D Penn
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Bian Li
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Jens Meiler
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Beata Jastrzebska
- Department of Pharmacology , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Jonathan P Schlebach
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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18
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Patel SJ, Van Lehn RC. Characterizing the Molecular Mechanisms for Flipping Charged Peptide Flanking Loops across a Lipid Bilayer. J Phys Chem B 2018; 122:10337-10348. [PMID: 30376710 DOI: 10.1021/acs.jpcb.8b06613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cell membrane largely prevents the passive diffusion of charged molecules due to the large free energy barrier associated with translocating charged groups across the hydrophobic lipid bilayer core. Despite this barrier, some peptides can interconvert between transmembrane and surface-adsorbed states by "flipping" charged flanking loops across the bilayer on a surprisingly rapid second-minute time scale. The transmembrane helices of some multispanning membrane proteins undergo similar reorientation processes, suggesting that loop-flipping may be a mechanism for regulating membrane protein topology; however, the molecular mechanisms underlying this behavior remain unknown. In this work, we study the loop-flipping behavior exhibited by a peptide with a hydrophobic transmembrane helix, charged flanking loops, and a central, membrane-exposed aspartate residue of varying protonation state. We utilize all-atom temperature accelerated molecular dynamics simulations to predict the likelihood of loop-flipping without predefining specific loop-flipping pathways. We demonstrate that this approach can identify multiple possible flipping pathways, with the prevalence of each pathway depending on the protonation state of the central residue. In particular, we find that a charged central residue facilitates loop-flipping by stabilizing membrane water defects, enabling the "self-catalysis" of charge translocation. These findings provide detailed molecular-level insights into charged loop-flipping pathways that may generalize to other charge translocation processes, such as lipid flip-flop or the large-scale conformational rearrangements of multispanning membrane proteins.
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Affiliation(s)
- Samarthaben J Patel
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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19
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Kida Y, Sakaguchi M. Interaction mapping of the Sec61 translocon identifies two Sec61α regions interacting with hydrophobic segments in translocating chains. J Biol Chem 2018; 293:17050-17060. [PMID: 30213864 DOI: 10.1074/jbc.ra118.003219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/26/2018] [Indexed: 01/09/2023] Open
Abstract
Many proteins in organelles of the secretory pathway, as well as secretory proteins, are translocated across and inserted into the endoplasmic reticulum membrane by the Sec61 translocon, a protein-conducting channel. The channel consists of 10 transmembrane (TM) segments of the Sec61α subunit and possesses an opening between TM2b and TM7, termed the lateral gate. Structural and biochemical analyses of complexes of Sec61 and its ortholog SecY have revealed that the lateral gate is the exit for signal sequences and TM segments of translocating polypeptides to the lipid bilayer and also involved in the recognition of such hydrophobic sequences. Moreover, even marginally hydrophobic (mH) segments insufficient for membrane integration can be transiently stalled in surrounding Sec61α regions and cross-linked to them, but how the Sec61 translocon accommodates these mH segments remains unclear. Here, we used Cys-scanned variants of human Sec61α expressed in cultured 293-H cells to examine which channel regions associate with mH segments. A TM segment in a ribosome-associated polypeptide was mainly cross-linked to positions at the lateral gate, whereas an mH segment in a nascent chain was cross-linked to the Sec61α pore-interior positions at TM5 and TM10, as well as the lateral gate. Of note, cross-linking at position 180 in TM5 of Sec61α was reduced by an I179A substitution. We therefore conclude that at least two Sec61α regions, the lateral gate and the pore-interior site around TM5, interact with mH segments and are involved in accommodating them.
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Affiliation(s)
- Yuichiro Kida
- From the Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
| | - Masao Sakaguchi
- From the Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
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20
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Baker JA, Wong WC, Eisenhaber B, Warwicker J, Eisenhaber F. Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule". BMC Biol 2017; 15:66. [PMID: 28738801 PMCID: PMC5525207 DOI: 10.1186/s12915-017-0404-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022] Open
Abstract
Background Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane’s hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein’s biological functions. Results With statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/negative-outside (NNI/NO) rule). As negative residues are generally rare within or near TMHs, the statistical significance is sensitive with regard to details of TMH alignment and residue frequency normalisation and also to dataset size; therefore, this trend was obscured in previous work. We observe variations amongst taxa as well as for organelles along the secretory pathway. The effect is most pronounced for TMHs from single-pass transmembrane (bitopic) proteins compared to those with multiple TMHs (polytopic proteins) and especially for the class of simple TMHs that evolved for the sole role as membrane anchors. Conclusions The charged-residue flank bias is only one of the TMH sequence features with a role in the anchorage mechanisms, others apparently being the leucine intra-helix propensity skew towards the cytoplasmic side, tryptophan flanking as well as the cysteine and tyrosine inside preference. These observations will stimulate new prediction methods for TMHs and protein topology from a sequence as well as new engineering designs for artificial membrane proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0404-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Alexander Baker
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore.,School of Chemistry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
| | - Wing-Cheong Wong
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore
| | - Jim Warwicker
- School of Chemistry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore. .,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
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21
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Lara P, Öjemalm K, Reithinger J, Holgado A, Maojun Y, Hammed A, Mattle D, Kim H, Nilsson I. Refined topology model of the STT3/Stt3 protein subunit of the oligosaccharyltransferase complex. J Biol Chem 2017; 292:11349-11360. [PMID: 28512128 DOI: 10.1074/jbc.m117.779421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/10/2017] [Indexed: 01/16/2023] Open
Abstract
The oligosaccharyltransferase complex, localized in the endoplasmic reticulum (ER) of eukaryotic cells, is responsible for the N-linked glycosylation of numerous protein substrates. The membrane protein STT3 is a highly conserved part of the oligosaccharyltransferase and likely contains the active site of the complex. However, understanding the catalytic determinants of this system has been challenging, in part because of a discrepancy in the structural topology of the bacterial versus eukaryotic proteins and incomplete information about the mechanism of membrane integration. Here, we use a glycosylation mapping approach to investigate these questions. We measured the membrane integration efficiency of the mouse STT3-A and yeast Stt3p transmembrane domains (TMDs) and report a refined topology of the N-terminal half of the mouse STT3-A. Our results show that most of the STT3 TMDs are well inserted into the ER membrane on their own or in the presence of the natural flanking residues. However, for the mouse STT3-A hydrophobic domains 4 and 6 and yeast Stt3p domains 2, 3a, 3c, and 6 we measured reduced insertion efficiency into the ER membrane. Furthermore, we mapped the first half of the STT3-A protein, finding two extra hydrophobic domains between the third and the fourth TMD. This result indicates that the eukaryotic STT3 has 13 transmembrane domains, consistent with the structure of the bacterial homolog of STT3 and setting the stage for future combined efforts to interrogate this fascinating system.
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Affiliation(s)
- Patricia Lara
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Karin Öjemalm
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Johannes Reithinger
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Aurora Holgado
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - You Maojun
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Abdessalem Hammed
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Daniel Mattle
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
| | - Hyun Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - IngMarie Nilsson
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden and
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22
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Abstract
The insertion and assembly of proteins into the inner membrane of bacteria are crucial for many cellular processes, including cellular respiration, signal transduction, and ion and pH homeostasis. This process requires efficient membrane targeting and insertion of proteins into the lipid bilayer in their correct orientation and proper conformation. Playing center stage in these events are the targeting components, signal recognition particle (SRP) and the SRP receptor FtsY, as well as the insertion components, the Sec translocon and the YidC insertase. Here, we will discuss new insights provided from the recent high-resolution structures of these proteins. In addition, we will review the mechanism by which a variety of proteins with different topologies are inserted into the inner membrane of Gram-negative bacteria. Finally, we report on the energetics of this process and provide information on how membrane insertion occurs in Gram-positive bacteria and Archaea. It should be noted that most of what we know about membrane protein assembly in bacteria is based on studies conducted in Escherichia coli.
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Affiliation(s)
- Andreas Kuhn
- Institute for Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Ross E Dalbey
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
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23
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Ch'ng JH, Sirel M, Zandian A, Del Pilar Quintana M, Chun Leung Chan S, Moll K, Tellgren-Roth A, Nilsson I, Nilsson P, Qundos U, Wahlgren M. Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing. Sci Rep 2017; 7:43190. [PMID: 28233866 PMCID: PMC5324397 DOI: 10.1038/srep43190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/20/2017] [Indexed: 12/28/2022] Open
Abstract
Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.
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Affiliation(s)
- Jun-Hong Ch'ng
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology and Immunology, National University of Singapore, Singapore
| | - Madle Sirel
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Arash Zandian
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Maria Del Pilar Quintana
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Sherwin Chun Leung Chan
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Kirsten Moll
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Asa Tellgren-Roth
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - IngMarie Nilsson
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Ulrika Qundos
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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24
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Buck TM, Jordahl AS, Yates ME, Preston GM, Cook E, Kleyman TR, Brodsky JL. Interactions between intersubunit transmembrane domains regulate the chaperone-dependent degradation of an oligomeric membrane protein. Biochem J 2017; 474:357-376. [PMID: 27903760 PMCID: PMC5423784 DOI: 10.1042/bcj20160760] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 12/22/2022]
Abstract
In the kidney, the epithelial sodium channel (ENaC) regulates blood pressure through control of sodium and volume homeostasis, and in the lung, ENaC regulates the volume of airway and alveolar fluids. ENaC is a heterotrimer of homologous α-, β- and γ-subunits, and assembles in the endoplasmic reticulum (ER) before it traffics to and functions at the plasma membrane. Improperly folded or orphaned ENaC subunits are subject to ER quality control and targeted for ER-associated degradation (ERAD). We previously established that a conserved, ER lumenal, molecular chaperone, Lhs1/GRP170, selects αENaC, but not β- or γ-ENaC, for degradation when the ENaC subunits were individually expressed. We now find that when all three subunits are co-expressed, Lhs1-facilitated ERAD was blocked. To determine which domain-domain interactions between the ENaC subunits are critical for chaperone-dependent quality control, we employed a yeast model and expressed chimeric α/βENaC constructs in the context of the ENaC heterotrimer. We discovered that the βENaC transmembrane domain was sufficient to prevent the Lhs1-dependent degradation of the α-subunit in the context of the ENaC heterotrimer. Our work also found that Lhs1 delivers αENaC for proteasome-mediated degradation after the protein has become polyubiquitinated. These data indicate that the Lhs1 chaperone selectively recognizes an immature form of αENaC, one which has failed to correctly assemble with the other channel subunits via its transmembrane domain.
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Affiliation(s)
- Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, U.S.A
| | - Alexa S Jordahl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, U.S.A
| | - Megan E Yates
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, U.S.A
| | - G Michael Preston
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, U.S.A
| | - Emily Cook
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, U.S.A
| | - Thomas R Kleyman
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh, Pittsburgh, PA, U.S.A
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, U.S.A
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25
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Bañó-Polo M, Martínez-Garay CA, Grau B, Martínez-Gil L, Mingarro I. Membrane insertion and topology of the translocon-associated protein (TRAP) gamma subunit. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:903-909. [PMID: 28132902 DOI: 10.1016/j.bbamem.2017.01.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 12/20/2022]
Abstract
Translocon-associated protein (TRAP) complex is intimately associated with the ER translocon for the insertion or translocation of newly synthesised proteins in eukaryotic cells. The TRAP complex is comprised of three single-spanning and one multiple-spanning subunits. We have investigated the membrane insertion and topology of the multiple-spanning TRAP-γ subunit by glycosylation mapping and green fluorescent protein fusions both in vitro and in cell cultures. Results demonstrate that TRAP-γ has four transmembrane (TM) segments, an Nt/Ct cytosolic orientation and that the less hydrophobic TM segment inserts efficiently into the membrane only in the cellular context of full-length protein.
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Affiliation(s)
- Manuel Bañó-Polo
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València, E-46 100 Burjassot, Spain
| | - Carlos A Martínez-Garay
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València, E-46 100 Burjassot, Spain
| | - Brayan Grau
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València, E-46 100 Burjassot, Spain
| | - Luis Martínez-Gil
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València, E-46 100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València, E-46 100 Burjassot, Spain.
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27
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Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology. Proc Natl Acad Sci U S A 2016; 113:10340-5. [PMID: 27562165 DOI: 10.1073/pnas.1605888113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The energetics of membrane-protein interactions determine protein topology and structure: hydrophobicity drives the insertion of helical segments into the membrane, and positive charges orient the protein with respect to the membrane plane according to the positive-inside rule. Until recently, however, quantifying these contributions met with difficulty, precluding systematic analysis of the energetic basis for membrane-protein topology. We recently developed the dsTβL method, which uses deep sequencing and in vitro selection of segments inserted into the bacterial plasma membrane to infer insertion-energy profiles for each amino acid residue across the membrane, and quantified the insertion contribution from hydrophobicity and the positive-inside rule. Here, we present a topology-prediction algorithm called TopGraph, which is based on a sequence search for minimum dsTβL insertion energy. Whereas the average insertion energy assigned by previous experimental scales was positive (unfavorable), the average assigned by TopGraph in a nonredundant set is -6.9 kcal/mol. By quantifying contributions from both hydrophobicity and the positive-inside rule we further find that in about half of large membrane proteins polar segments are inserted into the membrane to position more positive charges in the cytoplasm, suggesting an interplay between these two energy contributions. Because membrane-embedded polar residues are crucial for substrate binding and conformational change, the results implicate the positive-inside rule in determining the architectures of membrane-protein functional sites. This insight may aid structure prediction, engineering, and design of membrane proteins. TopGraph is available online (topgraph.weizmann.ac.il).
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Kida Y, Ishihara Y, Fujita H, Onishi Y, Sakaguchi M. Stability and flexibility of marginally hydrophobic-segment stalling at the endoplasmic reticulum translocon. Mol Biol Cell 2016; 27:930-40. [PMID: 26823014 PMCID: PMC4791137 DOI: 10.1091/mbc.e15-09-0672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/19/2016] [Indexed: 01/10/2023] Open
Abstract
Many membrane proteins are integrated into the endoplasmic reticulum membrane through the protein-conducting channel, the translocon. Transmembrane segments with insufficient hydrophobicity for membrane integration are frequently found in multispanning membrane proteins, and such marginally hydrophobic (mH) segments should be accommodated, at least transiently, at the membrane. Here we investigated how mH-segments stall at the membrane and their stability. Our findings show that mH-segments can be retained at the membrane without moving into the lipid phase and that such segments flank Sec61α, the core channel of the translocon, in the translational intermediate state. The mH-segments are gradually transferred from the Sec61 channel to the lipid environment in a hydrophobicity-dependent manner, and this lateral movement may be affected by the ribosome. In addition, stalling mH-segments allow for insertion of the following transmembrane segment, forming an Ncytosol/Clumen orientation, suggesting that mH-segments can move laterally to accommodate the next transmembrane segment. These findings suggest that mH-segments may be accommodated at the ER membrane with lateral fluctuation between the Sec61 channel and the lipid phase.
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Affiliation(s)
- Yuichiro Kida
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yudai Ishihara
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Hidenobu Fujita
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yukiko Onishi
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Masao Sakaguchi
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
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29
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Cuviello F, Tellgren-Roth Å, Lara P, Ruud Selin F, Monné M, Bisaccia F, Nilsson I, Ostuni A. Membrane insertion and topology of the amino-terminal domain TMD0 of multidrug-resistance associated protein 6 (MRP6). FEBS Lett 2015; 589:3921-8. [PMID: 26545497 DOI: 10.1016/j.febslet.2015.10.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/20/2015] [Accepted: 10/26/2015] [Indexed: 01/25/2023]
Abstract
The function of the ATP-binding cassette transporter MRP6 is unknown but mutations in its gene cause pseudoxanthoma elasticum. We have investigated the membrane topology of the N-terminal transmembrane domain TMD0 of MRP6 and the membrane integration and orientation propensities of its transmembrane segments (TMs) by glycosylation mapping. Results demonstrate that TMD0 has five TMs, an Nout-Cin topology and that the less hydrophobic TMs have strong preference for their orientation in the membrane that affects the neighboring TMs. Two disease-causing mutations changing the number of positive charges in the loops of TMD0 did not affect the membrane insertion efficiencies of the adjacent TMs.
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Affiliation(s)
- Flavia Cuviello
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy
| | - Åsa Tellgren-Roth
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Patricia Lara
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Frida Ruud Selin
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Magnus Monné
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy
| | - Faustino Bisaccia
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy
| | - IngMarie Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.
| | - Angela Ostuni
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy.
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Van Lehn RC, Zhang B, Miller TF. Regulation of multispanning membrane protein topology via post-translational annealing. eLife 2015; 4. [PMID: 26408961 PMCID: PMC4635508 DOI: 10.7554/elife.08697] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/25/2015] [Indexed: 12/19/2022] Open
Abstract
The canonical mechanism for multispanning membrane protein topogenesis suggests that protein topology is established during cotranslational membrane integration. However, this mechanism is inconsistent with the behavior of EmrE, a dual-topology protein for which the mutation of positively charged loop residues, even close to the C-terminus, leads to dramatic shifts in its topology. We use coarse-grained simulations to investigate the Sec-facilitated membrane integration of EmrE and its mutants on realistic biological timescales. This work reveals a mechanism for regulating membrane-protein topogenesis, in which initially misintegrated configurations of the proteins undergo post-translational annealing to reach fully integrated multispanning topologies. The energetic barriers associated with this post-translational annealing process enforce kinetic pathways that dictate the topology of the fully integrated proteins. The proposed mechanism agrees well with the experimentally observed features of EmrE topogenesis and provides a range of experimentally testable predictions regarding the effect of translocon mutations on membrane protein topogenesis. DOI:http://dx.doi.org/10.7554/eLife.08697.001 Proteins are long chains of smaller molecules called amino acids, and are built inside cells by a molecular machine called the ribosome. Many important proteins must be inserted into the membrane that surrounds each cell in order to carry out their role. As these proteins are being built by the ribosome, they thread their way into a membrane-spanning channel (called the translocon) from the inner side of the membrane. Short segments of these integral membrane proteins (called transmembrane domains) then become embedded in the membrane, while other parts of the protein remain on either side of the membrane. For a membrane protein to work properly, the end of each of its transmembrane domains must be on the correct side of the membrane (i.e., the protein must obtain the correct ‘topology’). The conventional model for this process suggests that topology is fixed when the first transmembrane domain of a protein is initially integrated into the membrane, while the ribosome is still building the protein. This model can explain most integral membrane proteins, which only have a single topology. However, it cannot explain the family of membrane proteins that have an almost equal chance of adopting one of two different topologies (so-called ‘dual-topology proteins’). Van Lehn et al. have now used computer modeling to simulate how a bacterial protein called EmrE (which is a dual-topology protein) integrates into the membrane via the translocon. The results reveal that a few transmembrane domains in EmrE do not fully integrate into the membrane while the ribosome is building the protein. Instead, these transmembrane domains slowly integrate after the ribosome has finished its job. These findings contradict the conventional model and suggest that some membrane proteins only become fully integrated after the protein-building process is complete. The next step in this work is to experimentally test predictions from the computer simulations. DOI:http://dx.doi.org/10.7554/eLife.08697.002
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Affiliation(s)
- Reid C Van Lehn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
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Patterson MA, Bandyopadhyay A, Devaraneni PK, Woodward J, Rooney L, Yang Z, Skach WR. The Ribosome-Sec61 Translocon Complex Forms a Cytosolically Restricted Environment for Early Polytopic Membrane Protein Folding. J Biol Chem 2015; 290:28944-52. [PMID: 26254469 DOI: 10.1074/jbc.m115.672261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/06/2022] Open
Abstract
Transmembrane topology of polytopic membrane proteins (PMPs) is established in the endoplasmic reticulum (ER) by the ribosome Sec61-translocon complex (RTC) through iterative cycles of translocation initiation and termination. It remains unknown, however, whether tertiary folding of transmembrane domains begins after the nascent polypeptide integrates into the lipid bilayer or within a proteinaceous environment proximal to translocon components. To address this question, we used cysteine scanning mutagenesis to monitor aqueous accessibility of stalled translation intermediates to determine when, during biogenesis, hydrophilic peptide loops of the aquaporin-4 (AQP4) water channel are delivered to cytosolic and lumenal compartments. Results showed that following ribosome docking on the ER membrane, the nascent polypeptide was shielded from the cytosol as it emerged from the ribosome exit tunnel. Extracellular loops followed a well defined path through the ribosome, the ribosome translocon junction, the Sec61-translocon pore, and into the ER lumen coincident with chain elongation. In contrast, intracellular loops (ICLs) and C-terminalresidues exited the ribosome into a cytosolically shielded environment and remained inaccessible to both cytosolic and lumenal compartments until translation was terminated. Shielding of ICL1 and ICL2, but not the C terminus, became resistant to maneuvers that disrupt electrostatic ribosome interactions. Thus, the early folding landscape of polytopic proteins is shaped by a spatially restricted environment localized within the assembled ribosome translocon complex.
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Affiliation(s)
- Melissa A Patterson
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Anannya Bandyopadhyay
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Prasanna K Devaraneni
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Josha Woodward
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - LeeAnn Rooney
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - Zhongying Yang
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and
| | - William R Skach
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and the Cystic Fibrosis Foundation Therapeutics (CFFT), Cystic Fibrosis Foundation, Bethesda, Maryland 20814
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32
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De Marothy MT, Elofsson A. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding. Protein Sci 2015; 24:1057-74. [PMID: 25970811 DOI: 10.1002/pro.2698] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/24/2015] [Indexed: 01/12/2023]
Abstract
Cells have developed an incredible machinery to facilitate the insertion of membrane proteins into the membrane. While we have a fairly good understanding of the mechanism and determinants of membrane integration, more data is needed to understand the insertion of membrane proteins with more complex insertion and folding pathways. This review will focus on marginally hydrophobic transmembrane helices and their influence on membrane protein folding. These weakly hydrophobic transmembrane segments are by themselves not recognized by the translocon and therefore rely on local sequence context for membrane integration. How can such segments reside within the membrane? We will discuss this in the light of features found in the protein itself as well as the environment it resides in. Several characteristics in proteins have been described to influence the insertion of marginally hydrophobic helices. Additionally, the influence of biological membranes is significant. To begin with, the actual cost for having polar groups within the membrane may not be as high as expected; the presence of proteins in the membrane as well as characteristics of some amino acids may enable a transmembrane helix to harbor a charged residue. The lipid environment has also been shown to directly influence the topology as well as membrane boundaries of transmembrane helices-implying a dynamic relationship between membrane proteins and their environment.
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Affiliation(s)
- Minttu T De Marothy
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
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33
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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34
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Cymer F, von Heijne G, White SH. Mechanisms of integral membrane protein insertion and folding. J Mol Biol 2014; 427:999-1022. [PMID: 25277655 DOI: 10.1016/j.jmb.2014.09.014] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/13/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
The biogenesis, folding, and structure of α-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, as well as the transport of solutes and signals across membranes. Nearly all MPs require translocons--often referred to as protein-conducting channels--for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here, we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of MP insertion and the folding of polytopic MPs in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion.
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Affiliation(s)
- Florian Cymer
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm.,Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
| | - Stephen H White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems University of California, Irvine Irvine, CA 92697
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35
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Dou D, da Silva DV, Nordholm J, Wang H, Daniels R. Type II transmembrane domain hydrophobicity dictates the cotranslational dependence for inversion. Mol Biol Cell 2014; 25:3363-74. [PMID: 25165139 PMCID: PMC4214783 DOI: 10.1091/mbc.e14-04-0874] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The cellular hydrophobicity threshold for the inversion of Sec-dependent Nin-Cout (type II) transmembrane domains is dictated by whether their membrane integration occurs cotranslationally or posttranslationally. Membrane insertion by the Sec61 translocon in the endoplasmic reticulum (ER) is highly dependent on hydrophobicity. This places stringent hydrophobicity requirements on transmembrane domains (TMDs) from single-spanning membrane proteins. On examining the single-spanning influenza A membrane proteins, we found that the strict hydrophobicity requirement applies to the Nout-Cin HA and M2 TMDs but not the Nin-Cout TMDs from the type II membrane protein neuraminidase (NA). To investigate this discrepancy, we analyzed NA TMDs of varying hydrophobicity, followed by increasing polypeptide lengths, in mammalian cells and ER microsomes. Our results show that the marginally hydrophobic NA TMDs (ΔGapp > 0 kcal/mol) require the cotranslational insertion process for facilitating their inversion during translocation and a positively charged N-terminal flanking residue and that NA inversion enhances its plasma membrane localization. Overall the cotranslational inversion of marginally hydrophobic NA TMDs initiates once ∼70 amino acids past the TMD are synthesized, and the efficiency reaches 50% by ∼100 amino acids, consistent with the positioning of this TMD class in type II human membrane proteins. Inversion of the M2 TMD, achieved by elongating its C-terminus, underscores the contribution of cotranslational synthesis to TMD inversion.
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Affiliation(s)
- Dan Dou
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Diogo V da Silva
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Johan Nordholm
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Hao Wang
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Robert Daniels
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
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36
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Yamagishi M, Onishi Y, Yoshimura S, Fujita H, Imai K, Kida Y, Sakaguchi M. A few positively charged residues slow movement of a polypeptide chain across the endoplasmic reticulum membrane. Biochemistry 2014; 53:5375-83. [PMID: 25093244 DOI: 10.1021/bi500649y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many polypeptide chains are translocated across and integrated into the endoplasmic reticulum membrane through protein-conducting channels. During the process, amino acid sequences of translocating polypeptide chains are scanned by the channels and classified to be retained in the membrane or translocated into the lumen. We established an experimental system with which the kinetic effect of each amino acid residue on the polypeptide chain movement can be analyzed with a time resolution of tens of seconds. Positive charges greatly slow movement; only two lysine residues caused a remarkable slow down, and their effects were additive. The lysine residue was more effective than arginine. In contrast, clusters comprising three residues of each of the other 18 amino acids had little effect on chain movement. We also demonstrated that a four lysine cluster can exert the effect after being fully exposed from the ribosome. We concluded that as few as two to three residues of positively charged amino acids can slow the movement of the nascent polypeptide chain across the endoplasmic reticulum membrane. This effect provides a fundamental basis of the topogenic function of positively charged amino acids.
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Affiliation(s)
- Marifu Yamagishi
- Graduate School of Life Science, University of Hyogo , Kouto Ako-gun, Hyogo 678-1297 Japan
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37
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Jung SJ, Kim JEH, Reithinger JH, Kim H. The Sec62-Sec63 translocon facilitates translocation of the C-terminus of membrane proteins. J Cell Sci 2014; 127:4270-8. [PMID: 25097231 DOI: 10.1242/jcs.153650] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Sec62-Sec63 complex mediates post-translational translocation of a subset of primarily secretory proteins into the endoplasmic reticulum (ER) in yeast. Therefore, it has been thought that membrane proteins, which are mainly co-translationally targeted into the ER, are not handled by the Sec62-Sec63 translocon. By systematic analysis of single and multi-spanning membrane proteins with broad sequence context [with differing hydrophobicity, flanking charged residues and orientation of transmembrane (TM) segments], we show that mutations in the N-terminal cytosolic domain of yeast Sec62 impair its interaction with Sec63 and lead to defects in membrane insertion and translocation of the C-terminus of membrane proteins. These results suggest that there is an unappreciated function of the Sec62-Sec63 translocon in regulating topogenesis of membrane proteins in the eukaryotic cell.
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Affiliation(s)
- Sung-jun Jung
- School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Ji Eun Hani Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Johannes H Reithinger
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Hyun Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
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38
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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Virkki MT, Peters C, Nilsson D, Sörensen T, Cristobal S, Wallner B, Elofsson A. The positive inside rule is stronger when followed by a transmembrane helix. J Mol Biol 2014; 426:2982-91. [PMID: 24927974 DOI: 10.1016/j.jmb.2014.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 11/30/2022]
Abstract
The translocon recognizes transmembrane helices with sufficient level of hydrophobicity and inserts them into the membrane. However, sometimes less hydrophobic helices are also recognized. Positive inside rule, orientational preferences of and specific interactions with neighboring helices have been shown to aid in the recognition of these helices, at least in artificial systems. To better understand how the translocon inserts marginally hydrophobic helices, we studied three naturally occurring marginally hydrophobic helices, which were previously shown to require the subsequent helix for efficient translocon recognition. We find no evidence for specific interactions when we scan all residues in the subsequent helices. Instead, we identify arginines located at the N-terminal part of the subsequent helices that are crucial for the recognition of the marginally hydrophobic transmembrane helices, indicating that the positive inside rule is important. However, in two of the constructs, these arginines do not aid in the recognition without the rest of the subsequent helix; that is, the positive inside rule alone is not sufficient. Instead, the improved recognition of marginally hydrophobic helices can here be explained as follows: the positive inside rule provides an orientational preference of the subsequent helix, which in turn allows the marginally hydrophobic helix to be inserted; that is, the effect of the positive inside rule is stronger if positively charged residues are followed by a transmembrane helix. Such a mechanism obviously cannot aid C-terminal helices, and consequently, we find that the terminal helices in multi-spanning membrane proteins are more hydrophobic than internal helices.
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Affiliation(s)
- Minttu T Virkki
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Christoph Peters
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.
| | - Daniel Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Therese Sörensen
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Health Science, Linköping University, 581 83 Linköping, Sweden; Department of Physiology, IKERBASQUE, Basque Foundation for Science, Faculty of Medicine and Dentistry, University of the Basque Country, 48949 Leioa, Spain.
| | - Björn Wallner
- Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden; Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden.
| | - Arne Elofsson
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.
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40
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Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Reorientation of the first signal-anchor sequence during potassium channel biogenesis at the Sec61 complex. Biochem J 2014; 456:297-309. [PMID: 24015703 PMCID: PMC3898203 DOI: 10.1042/bj20130100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The majority of the polytopic proteins that are synthesized at the ER (endoplasmic reticulum) are integrated co-translationally via the Sec61 translocon, which provides lateral access for their hydrophobic TMs (transmembrane regions) to the phospholipid bilayer. A prolonged association between TMs of the potassium channel subunit, TASK-1 [TWIK (tandem-pore weak inwardly rectifying potassium channel)-related acid-sensitive potassium channel 1], and the Sec61 complex suggests that the ER translocon co-ordinates the folding/assembly of the TMs present in the nascent chain. The N-terminus of both TASK-1 and Kcv (potassium channel protein of chlorella virus), another potassium channel subunit of viral origin, has access to the N-glycosylation machinery located in the ER lumen, indicating that the Sec61 complex can accommodate multiple arrangements/orientations of TMs within the nascent chain, both in vitro and in vivo. Hence the ER translocon can provide the ribosome-bound nascent chain with a dynamic environment in which it can explore a range of different conformations en route to its correct transmembrane topology and final native structure. The Sec61 translocon provides an unexpectedly flexible and dynamic environment within which transmembrane regions of nascent polypeptides can be completely reoriented during the biosynthesis of multiple-spanning membrane proteins.
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The Tobacco mosaic virus movement protein associates with but does not integrate into biological membranes. J Virol 2013; 88:3016-26. [PMID: 24371064 DOI: 10.1128/jvi.03648-13] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED Plant positive-strand RNA viruses require association with plant cell endomembranes for viral translation and replication, as well as for intra- and intercellular movement of the viral progeny. The membrane association and RNA binding of the Tobacco mosaic virus (TMV) movement protein (MP) are vital for orchestrating the macromolecular network required for virus movement. A previously proposed topological model suggests that TMV MP is an integral membrane protein with two putative α-helical transmembrane (TM) segments. Here we tested this model using an experimental system that measured the efficiency with which natural polypeptide segments were inserted into the ER membrane under conditions approximating the in vivo situation, as well as in planta. Our results demonstrated that the two hydrophobic regions (HRs) of TMV MP do not span biological membranes. We further found that mutations to alter the hydrophobicity of the first HR modified membrane association and precluded virus movement. We propose a topological model in which the TMV MP HRs intimately associate with the cellular membranes, allowing maximum exposure of the hydrophilic domains of the MP to the cytoplasmic cellular components. IMPORTANCE To facilitate plant viral infection and spread, viruses encode one or more movement proteins (MPs) that interact with ER membranes. The present work investigated the membrane association of the 30K MP of Tobacco mosaic virus (TMV), and the results challenge the previous topological model, which predicted that the TMV MP behaves as an integral membrane protein. The current data provide greatly needed clarification of the topological model and provide substantial evidence that TMV MP is membrane associated only at the cytoplasmic face of the membrane and that neither of its domains is integrated into the membrane or translocated into the lumen. Understanding the topology of MPs in the ER is vital for understanding the role of the ER in plant virus transport and for predicting interactions with host factors that mediate resistance to plant viruses.
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Feige MJ, Hendershot LM. Quality control of integral membrane proteins by assembly-dependent membrane integration. Mol Cell 2013; 51:297-309. [PMID: 23932713 DOI: 10.1016/j.molcel.2013.07.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/28/2013] [Accepted: 07/09/2013] [Indexed: 02/07/2023]
Abstract
Cell-surface multiprotein complexes are synthesized in the endoplasmic reticulum (ER), where they undergo cotranslational membrane integration and assembly. The quality control mechanisms that oversee these processes remain poorly understood. We show that less hydrophobic transmembrane (TM) regions derived from several single-pass TM proteins can enter the ER lumen completely. Once mislocalized, they are recognized by the Hsp70 chaperone BiP. In a detailed analysis for one of these proteins, the αβT cell receptor (αβTCR), we show that unassembled ER-lumenal subunits are rapidly degraded, whereas specific subunit interactions en route to the native receptor promote membrane integration of the less hydrophobic TM segments, thereby stabilizing the protein. For the TCR α chain, both complete ER import and subunit assembly depend on the same pivotal residue in its TM region. Thus, membrane integration linked to protein assembly allows cellular quality control of membrane proteins and connects the lumenal ER chaperone machinery to membrane protein biogenesis.
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Affiliation(s)
- Matthias J Feige
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Co-translational targeting and translocation of proteins to the endoplasmic reticulum. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2392-402. [DOI: 10.1016/j.bbamcr.2013.02.021] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 12/16/2022]
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Yabuki T, Morimoto F, Kida Y, Sakaguchi M. Membrane translocation of lumenal domains of membrane proteins powered by downstream transmembrane sequences. Mol Biol Cell 2013; 24:3123-32. [PMID: 23924896 PMCID: PMC3784385 DOI: 10.1091/mbc.e13-04-0210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The affinity required for the trapping of translocation of a streptavidin-binding peptide–tagged N-terminal domain of a type I signal anchor sequence is determined. Using the same tagging method, this study also detects the cytosolic stall of lumenal loops of a multispanning membrane protein and the translocation by the following TM sequence. Translocation of the N-terminus of a type I signal anchor (SA-I) sequence across the endoplasmic reticulum membrane can be arrested by tagging with a streptavidin-binding peptide tag (SBP tag) and trapping by streptavidin. In the present study, we first examine the affinity required for the translocation arrest. When the SBP tag is serially truncated, the ability for arrest gradually decreases. Surface plasmon resonance analysis shows that an interaction as strong as 10−8 M or a smaller dissociation constant is required for trapping the topogenesis of a natural SA-I sequence. Such truncated tags, however, become effective by mutating the SA-I sequence, suggesting that the translocation motivation is considerably influenced by the properties of the SA-I sequence. In addition, we introduce the SBP tag into lumenal loops of a multispanning membrane protein, human erythrocyte band 3. Among the tagged loops between transmembrane 1 (TM1) and TM8, three loops are trapped by cytosolic streptavidin. These loops are followed by TM sequences possessing topogenic properties, like the SA-I sequence, and translocation of one loop is diminished by insertion of a proline into the following TM sequence. These findings suggest that the translocation of lumenal loops by SA-I–like TM sequences has a crucial role in topogenesis of multispanning membrane proteins.
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Affiliation(s)
- Takaaki Yabuki
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
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Kang HJ, Lee C, Drew D. Breaking the barriers in membrane protein crystallography. Int J Biochem Cell Biol 2013; 45:636-44. [DOI: 10.1016/j.biocel.2012.12.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 12/03/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
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Charge Pair Interactions in Transmembrane Helices and Turn Propensity of the Connecting Sequence Promote Helical Hairpin Insertion. J Mol Biol 2013; 425:830-40. [DOI: 10.1016/j.jmb.2012.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/25/2012] [Accepted: 12/02/2012] [Indexed: 11/21/2022]
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Tail-extension following the termination codon is critical for release of the nascent chain from membrane-bound ribosomes in a reticulocyte lysate cell-free system. Biochem Biophys Res Commun 2013; 430:567-72. [DOI: 10.1016/j.bbrc.2012.11.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 11/27/2012] [Indexed: 11/20/2022]
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Abstract
The elucidation of the molecular nature of the translocon-assisted protein insertion is a challenging problem due to the complexity of this process. Furthermore, the limited availability of crucial structural information makes it hard to interpret the hints about the insertion mechanism provided by biochemical studies. At present, it is not practical to explore the insertion process by brute force simulation approaches due to the extremely lengthy process and very complex landscape. Thus, this work uses our previously developed coarse-grained model and explores the energetics of the membrane insertion and translocation paths. The trend in the calculated free-energy profiles is verified by evaluating the correlation between the calculated and observed effect of mutations as well as the effect of inverting the signal peptide that reflects the "positive-inside" rule. Furthermore, the effect of the tentative opening induced by the ribosome is found to reduce the kinetic barrier. Significantly, the trend of the forward and backward energy barriers provides a powerful way to analyze key energetics information. Thus, it is concluded that the insertion process is most likely a nonequilibrium process. Moreover, we provided a general formulation for the analysis of the elusive apparent membrane insertion energy, ΔG(app), and conclude that this important parameter is unlikely to correspond to the free-energy difference between the translocon and membrane. Our formulation seems to resolve the controversy about ΔG(app) for Arg.
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Öjemalm K, Watson HR, Roboti P, Cross BCS, Warwicker J, von Heijne G, High S. Positional editing of transmembrane domains during ion channel assembly. J Cell Sci 2012; 126:464-72. [PMID: 23230148 PMCID: PMC3613178 DOI: 10.1242/jcs.111773] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The integration of transmembrane (TM)-spanning regions of many channels and ion transporters is potentially compromised by the presence of polar and charged residues required for biological function. Although the two TMs of the ATP-gated ion channel subunit P2X2 each contain charged/polar amino acids, we found that each TM is efficiently membrane inserted when it is analysed in isolation, and uncovered no evidence for cooperativity between these two TMs during P2X2 integration. However, using minimal N-glycosylation distance mapping, we find that the positioning of TM2 in newly synthesized P2X2 monomers is distinct from that seen in subunits of the high-resolution structures of assembled homologous trimers. We conclude that P2X2 monomers are initially synthesised at the endoplasmic reticulum in a distinct conformation, where the extent of the TM-spanning regions is primarily defined by the thermodynamic cost of their membrane integration at the Sec61 translocon. In this model, TM2 of P2X2 subsequently undergoes a process of positional editing within the membrane that correlates with trimerisation of the monomer, a process requiring specific polar/charged residues in both TM1 and TM2. We postulate that the assembly process offsets any energetic cost of relocating TM2, and find evidence that positional editing of TM2 in the acid-sensing ion channel (ASIC1a) is even more pronounced than that observed for P2X2. Taken together, these data further underline the potential complexities involved in accurately predicting TM domains. We propose that the orchestrated repositioning of TM segments during subunit oligomerisation plays an important role in generating the functional architecture of active ion channels, and suggest that the regulation of this underappreciated biosynthetic step may provide an elegant mechanism for maintaining ER homeostasis.
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Affiliation(s)
- Karin Öjemalm
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden
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