1
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Dadsena S, Cuevas Arenas R, Vieira G, Brodesser S, Melo MN, García-Sáez AJ. Lipid unsaturation promotes BAX and BAK pore activity during apoptosis. Nat Commun 2024; 15:4700. [PMID: 38830851 PMCID: PMC11148036 DOI: 10.1038/s41467-024-49067-6] [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: 07/07/2023] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
BAX and BAK are proapoptotic members of the BCL2 family that directly mediate mitochondrial outer membrane permeabilition (MOMP), a central step in apoptosis execution. However, the molecular architecture of the mitochondrial apoptotic pore remains a key open question and especially little is known about the contribution of lipids to MOMP. By performing a comparative lipidomics analysis of the proximal membrane environment of BAK isolated in lipid nanodiscs, we find a significant enrichment of unsaturated species nearby BAK and BAX in apoptotic conditions. We then demonstrate that unsaturated lipids promote BAX pore activity in model membranes, isolated mitochondria and cellular systems, which is further supported by molecular dynamics simulations. Accordingly, the fatty acid desaturase FADS2 not only enhances apoptosis sensitivity, but also the activation of the cGAS/STING pathway downstream mtDNA release. The correlation of FADS2 levels with the sensitization to apoptosis of different lung and kidney cancer cell lines by co-treatment with unsaturated fatty acids supports the relevance of our findings. Altogether, our work provides an insight on how local lipid environment affects BAX and BAK function during apoptosis.
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Affiliation(s)
- Shashank Dadsena
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Rodrigo Cuevas Arenas
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CG, Utrecht, The Netherlands
| | - Gonçalo Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susanne Brodesser
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana J García-Sáez
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne, Germany.
- Department of Membrane Dynamics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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2
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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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3
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Blazhynska M, Gumbart JC, Chen H, Tajkhorshid E, Roux B, Chipot C. A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes. J Chem Theory Comput 2023; 19:9077-9092. [PMID: 38091976 PMCID: PMC11145395 DOI: 10.1021/acs.jctc.3c00941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for understanding the mechanisms by which they recognize one another and reversibly associate. The glycophorin A (GpA) homodimer, composed of two α-helical segments, has long served as a model system for studying TM protein reversible association. The present work establishes a methodological framework for calculating the binding affinity of the GpA homodimer in the heterogeneous environment of a membrane. Our investigation carefully considered a variety of protocols, including the appropriate choice of the force field, rigorous standardization reflecting the experimental conditions, sampling algorithm, anisotropic environment, and collective variables, to accurately describe GpA dimerization via molecular dynamics-based approaches. Specifically, two strategies were explored: (i) an unrestrained potential mean force (PMF) calculation, which merely enhances sampling along the separation of the two binding partners without any restraint, and (ii) a so-called "geometrical route", whereby the α-helices are progressively separated with imposed restraints on their orientational, positional, and conformational degrees of freedom to accelerate convergence. Our simulations reveal that the simplified, unrestrained PMF approach is inadequate for the description of GpA dimerization. Instead, the geometrical route, tailored specifically to GpA in a membrane environment, yields excellent agreement with experimental data within a reasonable computational time. A dimerization free energy of -10.7 kcal/mol is obtained, in fairly good agreement with available experimental data. The geometrical route further helps elucidate how environmental forces drive association before helical interactions stabilize it. Our simulations also brought to light a distinct, long-lived spatial arrangement that potentially serves as an intermediate state during dimer formation. The methodological advances in the generalized geometrical route provide a powerful tool for accurate and efficient binding-affinity calculations of intricate TM protein complexes in inhomogeneous environments.
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Affiliation(s)
- Marharyta Blazhynska
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332, United States
| | - Haochuan Chen
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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4
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Situ AJ, Ulmer TS. Comparison of Integrin αIIbβ3 Transmembrane Association in Vesicles and Bicelles. Biochemistry 2023. [PMID: 37279176 DOI: 10.1021/acs.biochem.3c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Membrane proteins are commonly reconstituted in membrane mimics exhibiting discontinuous lipid bilayers. In contrast, the continuous membranes of cells are conceptually best represented by large unilamellar vesicles (LUVs). Here, we compared the thermodynamic stability of the integrin αIIbβ3 transmembrane (TM) complex between vesicles and bicelles to assess the consequence of this simplification. In LUVs, we further evaluated the strength of the αIIb(G972S)-β3(V700T) interaction that corresponds to the hydrogen bond interaction postulated for β2 integrins. An upper limit of 0.9 kcal/mol was estimated for superior TM complex stabilization in LUVs relative to bicelles. Compared to the αIIbβ3 TM complex stability in LUVs of 5.6 ± 0.2 kcal/mol, this limit is modest, indicating that bicelles performed well relative to LUVs. The implementation of β3(V700T) alleviated αIIb(G972S) destabilization by 0.4 ± 0.2 kcal/mol in confirmation of relatively weak hydrogen bonding. Interestingly, the hydrogen bond adjusts the TM complex stability to a level that is not achievable by merely varying the residue corresponding to αIIb(Gly972).
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Affiliation(s)
- Alan J Situ
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
| | - Tobias S Ulmer
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
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5
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Muhammednazaar S, Yao J, Guo R, Rhee MS, Kim KH, Kang SG, Hong H. Lipid Bilayer Strengthens the Cooperative Network of a Membrane-Integral Enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542905. [PMID: 37398072 PMCID: PMC10312574 DOI: 10.1101/2023.05.30.542905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Lipid bilayer provides a two-dimensional hydrophobic solvent milieu for membrane proteins in cells. Although the native bilayer is widely recognized as an optimal environment for folding and function of membrane proteins, the underlying physical basis remains elusive. Here, employing the intramembrane protease GlpG of Escherichia coli as a model, we elucidate how the bilayer stabilizes a membrane protein and engages the protein's residue interaction network compared to the nonnative hydrophobic medium, micelles. We find that the bilayer enhances GlpG stability by promoting residue burial in the protein interior compared to micelles. Strikingly, while the cooperative residue interactions cluster into multiple distinct regions in micelles, the whole packed regions of the protein act as a single cooperative unit in the bilayer. Molecular dynamics (MD) simulation indicates that lipids less efficiently solvate GlpG than detergents. Thus, the bilayerinduced enhancement of stability and cooperativity likely stems from the dominant intraprotein interactions outcompeting the weak lipid solvation. Our findings reveal a foundational mechanism in the folding, function, and quality control of membrane proteins. The enhanced cooperativity benefits function facilitating propagation of local structural perturbation across the membrane. However, the same phenomenon can render the proteins' conformational integrity vulnerable to missense mutations causing conformational diseases1,2.
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Affiliation(s)
| | - Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ruiqiong Guo
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - May S Rhee
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kelly H Kim
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Seung-Gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, 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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6
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Díaz Vázquez G, Cui Q, Senes A. Thermodynamic analysis of the GAS right transmembrane motif supports energetic model of dimerization. Biophys J 2023; 122:143-155. [PMID: 36371634 PMCID: PMC9822795 DOI: 10.1016/j.bpj.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/12/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
The GASright motif, best known as the fold of the glycophorin A transmembrane dimer, is one of the most common dimerization motifs in membrane proteins, characterized by its hallmark GxxxG-like sequence motifs (GxxxG, AxxxG, GxxxS, and similar). Structurally, GASright displays a right-handed crossing angle and short interhelical distance. Contact between the helical backbones favors the formation of networks of weak hydrogen bonds between Cα-H carbon donors and carbonyl acceptors on opposing helices (Cα-H···O=C). To understand the factors that modulate the stability of GASright, we previously presented a computational and experimental structure-based analysis of 26 predicted dimers. We found that the contributions of van der Waals packing and Cα-H hydrogen bonding to stability, as inferred from the structural models, correlated well with relative dimerization propensities estimated experimentally with the in vivo assay TOXCAT. Here we test this model with a quantitative thermodynamic analysis. We used Förster resonance energy transfer (FRET) to determine the free energy of dimerization of a representative subset of seven of the 26 original TOXCAT dimers using FRET. To overcome the technical issue arising from limited sampling of the dimerization isotherm, we introduced a globally fitting strategy across a set of constructs comprising a wide range of stabilities. This strategy yielded precise thermodynamic data that show strikingly good agreement between the original propensities and ΔG° of association in detergent, suggesting that TOXCAT is a thermodynamically driven process. From the correlation between TOXCAT and thermodynamic stability, the predicted free energy for all the 26 GASright dimers was calculated. These energies correlate with the in silico ΔE scores of dimerization that were computed on the basis of their predicted structure. These findings corroborate our original model with quantitative thermodynamic evidence, strengthening the hypothesis that van der Waals and Cα-H hydrogen bond interactions are the key modulators of GASright stability.
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Affiliation(s)
- Gladys Díaz Vázquez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin.
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7
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Hellmann N, Schneider D. Hydrophobic mismatch and sequence specificity compete when transmembrane helix-helix interactions are measured with the TOXCAT assay. Front Chem 2022; 10:1049310. [DOI: 10.3389/fchem.2022.1049310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
Genetic assays capable of measuring the propensity of transmembrane helices to oligomerize within the cytoplasmic membrane of the bacterium E. coli are frequently used when sequence-specificity in transmembrane helix-helix interactions is investigated. In the present study, dimerization of the well-investigated wild-type and G83I-mutated transmembrane helix of the human glycophorin A protein was studied. Gradual prolongation of the transmembrane helix at the C-terminus with Leu residues lead to pronounced changes in the dimerization propensity when measured with the TOXCAT assay. Thus, besides sequence specificity, hydrophobic mismatch between the hydrophobic core of a studied transmembrane helix and the E. coli membrane can impact the oligomerization propensity of a transmembrane helix. This suggests that the results of genetic assays aiming at determining interactions of heterologous transmembrane helices within the E. coli membrane do not necessarily solely reflect sequence specificity in transmembrane helix-helix interactions, but might be additionally modulated by topological and structural effects caused by hydrophobic mismatch.
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8
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Jackson V, Hermann J, Tynan CJ, Rolfe DJ, Corey RA, Duncan AL, Noriega M, Chu A, Kalli AC, Jones EY, Sansom MSP, Martin-Fernandez ML, Seiradake E, Chavent M. The guidance and adhesion protein FLRT2 dimerizes in cis via dual small-X 3-small transmembrane motifs. Structure 2022; 30:1354-1365.e5. [PMID: 35700726 DOI: 10.1016/j.str.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/03/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
Fibronectin Leucine-rich Repeat Transmembrane (FLRT 1-3) proteins are a family of broadly expressed single-spanning transmembrane receptors that play key roles in development. Their extracellular domains mediate homotypic cell-cell adhesion and heterotypic protein interactions with other receptors to regulate cell adhesion and guidance. These in trans FLRT interactions determine the formation of signaling complexes of varying complexity and function. Whether FLRTs also interact at the surface of the same cell, in cis, remains unknown. Here, molecular dynamics simulations reveal two dimerization motifs in the FLRT2 transmembrane helix. Single particle tracking experiments show that these Small-X3-Small motifs synergize with a third dimerization motif encoded in the extracellular domain to permit the cis association and co-diffusion patterns of FLRT2 receptors on cells. These results may point to a competitive switching mechanism between in cis and in trans interactions, which suggests that homotypic FLRT interaction mirrors the functionalities of classic adhesion molecules.
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Affiliation(s)
- Verity Jackson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Julia Hermann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Christopher J Tynan
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Daniel J Rolfe
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Maxime Noriega
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Amy Chu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine and Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, LS2 9NL, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK.
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France.
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9
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Alavizargar A, Elting A, Wedlich-Söldner R, Heuer A. Lipid-Mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes. J Phys Chem B 2022; 126:3240-3256. [PMID: 35446028 DOI: 10.1021/acs.jpcb.2c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane (PM) such as receptor activation, lateral domain formation, and mechanotransduction. The self-association of the respective transmembrane domains (TMDs) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast PM. However, the underlying interplay between the local lipid composition and the TMD identity is still not mechanistically understood. In this work, we combined coarse-grained molecular dynamics simulations of simplified bilayer systems with high-resolution live-cell microscopy to analyze the distribution of a representative helical yeast TMD from the PM sensor Slg1 within different lipid environments. In our simulations, we specifically evaluated the effects of acyl chain saturation and anionic lipid head groups on the association of two TMDs. We found that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids (PLs) strongly reduced the helix-helix interaction, while the presence of anionic phosphatidylserine (PS) hardly affected the dimer formation. We could experimentally confirm this surprising lack of effect of PS using the network factor, a mesoscopic measure of PM pattern formation in yeast cells. Simulations also showed that the formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization. In summary, our results shed new light on the mechanisms of lipid-mediated dimerization of TMDs in complex lipid mixtures.
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Affiliation(s)
- Azadeh Alavizargar
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
| | - Annegret Elting
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Roland Wedlich-Söldner
- Institute of Cell Dynamics and Imaging, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
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10
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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: 1] [Impact Index Per Article: 0.5] [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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11
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Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein. Proc Natl Acad Sci U S A 2022; 119:2109169119. [PMID: 34969836 PMCID: PMC8740594 DOI: 10.1073/pnas.2109169119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/19/2022] Open
Abstract
Defining the denatured state ensemble (DSE) and disordered proteins is essential to understanding folding, chaperone action, degradation, and translocation. As compared with water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we measure the DSE of the helical membrane protein GlpG of Escherichia coli (E. coli) in native-like lipid bilayers. The DSE was obtained using our steric trapping method, which couples denaturation of doubly biotinylated GlpG to binding of two streptavidin molecules. The helices and loops are probed using limited proteolysis and mass spectrometry, while the dimensions are determined using our paramagnetic biotin derivative and double electron-electron resonance spectroscopy. These data, along with our Upside simulations, identify the DSE as being highly dynamic, involving the topology changes and unfolding of some of the transmembrane (TM) helices. The DSE is expanded relative to the native state but only to 15 to 75% of the fully expanded condition. The degree of expansion depends on the local protein packing and the lipid composition. E. coli's lipid bilayer promotes the association of TM helices in the DSE and, probably in general, facilitates interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.
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12
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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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13
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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
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14
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Ernst M, Robertson JL. The Role of the Membrane in Transporter Folding and Activity. J Mol Biol 2021; 433:167103. [PMID: 34139219 PMCID: PMC8756397 DOI: 10.1016/j.jmb.2021.167103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
The synthesis, folding, and function of membrane transport proteins are critical factors for defining cellular physiology. Since the stability of these proteins evolved amidst the lipid bilayer, it is no surprise that we are finding that many of these membrane proteins demonstrate coupling of their structure or activity in some way to the membrane. More and more transporter structures are being determined with some information about the surrounding membrane, and computational modeling is providing further molecular details about these solvation structures. Thus, the field is moving towards identifying which molecular mechanisms - lipid interactions, membrane perturbations, differential solvation, and bulk membrane effects - are involved in linking membrane energetics to transporter stability and function. In this review, we present an overview of these mechanisms and the growing evidence that the lipid bilayer is a major determinant of the fold, form, and function of membrane transport proteins in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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15
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Marx DC, Fleming KG. Membrane proteins enter the fold. Curr Opin Struct Biol 2021; 69:124-130. [PMID: 33975156 DOI: 10.1016/j.sbi.2021.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 11/19/2022]
Abstract
Membrane proteins have historically been recalcitrant to biophysical folding studies. However, recent adaptations of methods from the soluble protein folding field have found success in their applications to transmembrane proteins composed of both α-helical and β-barrel conformations. Avoiding aggregation is critical for the success of these experiments. Altogether these studies are leading to discoveries of folding trajectories, foundational stabilizing forces and better-defined endpoints that enable more accurate interpretation of thermodynamic data. Increased information on membrane protein folding in the cell shows that the emerging biophysical principles are largely recapitulated even in the complex biological environment.
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Affiliation(s)
- Dagan C Marx
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States
| | - Karen G Fleming
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States.
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16
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Yano Y, Watanabe Y, Matsuzaki K. Thermodynamic and kinetic stabilities of transmembrane helix bundles as revealed by single-pair FRET analysis: Effects of the number of membrane-spanning segments and cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183532. [PMID: 33316240 DOI: 10.1016/j.bbamem.2020.183532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022]
Abstract
The tertiary structures and conformational dynamics of transmembrane (TM) helical proteins are maintained by the interhelical interaction network in membranes, although it is complicated to analyze the underlying driving forces because the amino acid sequences can involve multiple and various types of interactions. To obtain insights into basal and common effects of the number of membrane-spanning segments and membrane cholesterol, we measured stabilities of helix bundles composed of simple TM helices (AALALAA)3 (1TM) and (AALALAA)3-G5-(AALALAA)3 (2TM). Association-dissociation dynamics for 1TM-1TM, 1TM-2TM, and 2TM-2TM pairs were monitored to compare stabilities of 2-, 3-, and 4-helical bundles, respectively, with single-pair fluorescence resonance energy transfer (sp-FRET) in liposome membranes. Both thermodynamic and kinetic stabilities of the helix bundles increased with a greater number of membrane-spanning segments in POPC. The presence of 30 mol% cholesterol strongly enhanced the formation of 1TM-1TM and 1TM-2TM bundles (~ - 9 kJ mol-1), whereas it only weakly stabilized the 2TM-2TM bundle (~ - 3 kJ mol-1). Fourier transform infrared-polarized attenuated total reflection (ATR-FTIR) spectroscopy revealed an ~30° tilt of the helix axis relative to bilayer normal for the 1TM-2TM pair in the presence of cholesterol, suggesting the formation of a tilted helix bundle to release high lateral pressure at the center of cholesterol-containing membranes. These results demonstrate that the number of membrane-spanning segments affects the stability and structure of the helix bundle, and their cholesterol-dependences. Such information is useful to understand the basics of folding and assembly of multispanning TM proteins.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuta Watanabe
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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17
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Corin K, Bowie JU. How bilayer properties influence membrane protein folding. Protein Sci 2020; 29:2348-2362. [PMID: 33058341 DOI: 10.1002/pro.3973] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/24/2023]
Abstract
The question of how proteins manage to organize into a unique three-dimensional structure has been a major field of study since the first protein structures were determined. For membrane proteins, the question is made more complex because, unlike water-soluble proteins, the solvent is not homogenous or even unique. Each cell and organelle has a distinct lipid composition that can change in response to environmental stimuli. Thus, the study of membrane protein folding requires not only understanding how the unfolded chain navigates its way to the folded state, but also how changes in bilayer properties can affect that search. Here we review what we know so far about the impact of lipid composition on bilayer physical properties and how those properties can affect folding. A better understanding of the lipid bilayer and its effects on membrane protein folding is not only important for a theoretical understanding of the folding process, but can also have a practical impact on our ability to work with and design membrane proteins.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, California, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, California, USA
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18
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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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19
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Gopal SM, Pawar AB, Wassenaar TA, Sengupta D. Lipid-dependent conformational landscape of the ErbB2 growth factor receptor dimers. Chem Phys Lipids 2020; 230:104911. [PMID: 32353357 DOI: 10.1016/j.chemphyslip.2020.104911] [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: 12/11/2019] [Revised: 03/04/2020] [Accepted: 03/27/2020] [Indexed: 01/31/2023]
Abstract
Altered lipid metabolism has been linked to cancer development and progression. Several roles have been attributed to the increased saturation and length of lipid acyl tails observed in tumors, but its effect on signaling receptors is still emerging. In this work, we have analyzed the lipid dependence of the ErbB2 growth factor receptor dimerization that plays an important role in the pathogenesis of breast cancer. We have performed coarse-grain ensemble molecular dynamics simulations to comprehensively sample the ErbB2 monomer-dimer association. Our results indicate a dynamic dimer state with a complex conformational landscape that is modulated with increasing lipid tail length. We resolve the native N-terminal "active" and C-terminal "inactive" conformations in all membrane compositions. However, the relative population of the N-terminal and C-terminal conformers is dependent on length of the saturated lipid tails. In short-tail membranes, additional non-specific dimers are observed which are reduced or absent in long-tailed bilayers. Our results indicate that the relative population as well as the structure of the dimer state is modulated by membrane composition. We have correlated these differences to local perturbations of the membrane around the receptor. Our work is an important step in characterizing ErbB dimers in healthy and diseased states and emphasize the importance of sampling lipid dynamics in understanding receptor association.
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Affiliation(s)
- Srinivasa M Gopal
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; Lehrstuhl fur Theoretische Chemie, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Aiswarya B Pawar
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; AcSIR, Mathura Road, New Delhi, 110 025, India
| | - Tsjerk A Wassenaar
- Molecular Dynamics, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; AcSIR, Mathura Road, New Delhi, 110 025, India.
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20
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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: 153] [Impact Index Per Article: 30.6] [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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21
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Yano Y, Matsuzaki K. [Fluorescent Peptide Tools for Studying the Self-association of Membrane Proteins]. YAKUGAKU ZASSHI 2019; 139:273-276. [PMID: 30713239 DOI: 10.1248/yakushi.18-00174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Detecting the behaviors of proteins in membranes is often challenging; we need to develop new methods to better understand the mechanisms involved. We have developed two types of peptide-based experimental systems that can detect the self-association of proteins in bilayer environments: 1) a single-pair fluorescence detection system for studying the self-association of transmembrane helices in model membranes; and 2) live-cell fluorescence labeling and analysis of the oligomeric state of membrane proteins using a coiled-coil labeling method. By using these methods, we show that membrane cholesterol significantly affects the self-association of transmembrane helices.
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Affiliation(s)
- Yoshiaki Yano
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Katsumi Matsuzaki
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University
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22
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Reißer S, Strandberg E, Steinbrecher T, Elstner M, Ulrich AS. Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR. J Chem Theory Comput 2018; 14:6002-6014. [PMID: 30289704 DOI: 10.1021/acs.jctc.8b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane alignment of helical amphiphilic peptides in oriented phospholipid bilayers can be obtained as ensemble and time averages from solid state 2H NMR by fitting the quadrupolar splittings to ideal α-helices. At the same time, molecular dynamics (MD) simulations can provide atomistic insight into peptide-membrane systems. Here, we evaluate the potential of MD simulations to complement the experimental NMR data that is available on three exemplary systems: the natural antimicrobial peptide PGLa and the two designer-made peptides MSI-103 and KIA14, whose sequences were derived from PGLa. Each peptide was simulated for 1 μs in a DMPC lipid bilayer. We calculated from the MD simulations the local angles which define the side chain geometry with respect to the peptide helix. The peptide orientation was then calculated (i) directly from the simulation, (ii) from back-calculated MD-derived NMR splittings, and (iii) from experimental 2H NMR splittings. Our findings are that (1) the membrane orientation and secondary structure of the peptides found in the NMR analysis are generally well reproduced by the simulations; (2) the geometry of the side chains with respect to the helix backbone can deviate significantly from the ideal structure depending on the specific residue, but on average all side chains have the same orientation; and (3) for all of our peptides, the azimuthal rotation angle found from the MD-derived splittings is about 15° smaller than the experimental value.
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Affiliation(s)
- Sabine Reißer
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
| | - Thomas Steinbrecher
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Anne S Ulrich
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany.,Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
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23
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Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Proteins 2018; 86:581-591. [PMID: 29427530 PMCID: PMC5912992 DOI: 10.1002/prot.25479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/06/2018] [Indexed: 12/26/2022]
Abstract
We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.
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Affiliation(s)
- J C Gaines
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
| | - S Acebes
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - A Virrueta
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - M Butler
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, 90007
| | - L Regan
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, 06520
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520
| | - C S O'Hern
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
- Department of Physics, Yale University, New Haven, Connecticut, 06520
- Department of Applied Physics, Yale University, New Haven, Connecticut, 06520
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24
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GHSR-D2R heteromerization modulates dopamine signaling through an effect on G protein conformation. Proc Natl Acad Sci U S A 2018; 115:4501-4506. [PMID: 29632174 DOI: 10.1073/pnas.1712725115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The growth hormone secretagogue receptor (GHSR) and dopamine receptor (D2R) have been shown to oligomerize in hypothalamic neurons with a significant effect on dopamine signaling, but the molecular processes underlying this effect are still obscure. We used here the purified GHSR and D2R to establish that these two receptors assemble in a lipid environment as a tetrameric complex composed of two each of the receptors. This complex further recruits G proteins to give rise to an assembly with only two G protein trimers bound to a receptor tetramer. We further demonstrate that receptor heteromerization directly impacts on dopamine-mediated Gi protein activation by modulating the conformation of its α-subunit. Indeed, association to the purified GHSR:D2R heteromer triggers a different active conformation of Gαi that is linked to a higher rate of GTP binding and a faster dissociation from the heteromeric receptor. This is an additional mechanism to expand the repertoire of GPCR signaling modulation that could have implications for the control of dopamine signaling in normal and physiopathological conditions.
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25
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Lipid bilayer composition modulates the unfolding free energy of a knotted α-helical membrane protein. Proc Natl Acad Sci U S A 2018; 115:E1799-E1808. [PMID: 29432185 DOI: 10.1073/pnas.1714668115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
α-Helical membrane proteins have eluded investigation of their thermodynamic stability in lipid bilayers. Reversible denaturation curves have enabled some headway in determining unfolding free energies. However, these parameters have been limited to detergent micelles or lipid bicelles, which do not possess the same mechanical properties as lipid bilayers that comprise the basis of natural membranes. We establish reversible unfolding of the membrane transporter LeuT in lipid bilayers, enabling the comparison of apparent unfolding free energies in different lipid compositions. LeuT is a bacterial ortholog of neurotransmitter transporters and contains a knot within its 12-transmembrane helical structure. Urea is used as a denaturant for LeuT in proteoliposomes, resulting in the loss of up to 30% helical structure depending upon the lipid bilayer composition. Urea unfolding of LeuT in liposomes is reversible, with refolding in the bilayer recovering the original helical structure and transport activity. A linear dependence of the unfolding free energy on urea concentration enables the free energy to be extrapolated to zero denaturant. Increasing lipid headgroup charge or chain lateral pressure increases the thermodynamic stability of LeuT. The mechanical and charge properties of the bilayer also affect the ability of urea to denature the protein. Thus, we not only gain insight to the long-sought-after thermodynamic stability of an α-helical protein in a lipid bilayer but also provide a basis for studies of the folding of knotted proteins in a membrane environment.
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26
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Pawar AB, Sengupta D. Effect of Membrane Composition on Receptor Association: Implications of Cancer Lipidomics on ErbB Receptors. J Membr Biol 2018; 251:359-368. [DOI: 10.1007/s00232-018-0015-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
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27
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Jefferson RE, Min D, Corin K, Wang JY, Bowie JU. Applications of Single-Molecule Methods to Membrane Protein Folding Studies. J Mol Biol 2017; 430:424-437. [PMID: 28549924 DOI: 10.1016/j.jmb.2017.05.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 02/07/2023]
Abstract
Protein folding is a fundamental life process with many implications throughout biology and medicine. Consequently, there have been enormous efforts to understand how proteins fold. Almost all of this effort has focused on water-soluble proteins, however, leaving membrane proteins largely wandering in the wilderness. The neglect has occurred not because membrane proteins are unimportant but rather because they present many theoretical and technical complications. Indeed, quantitative membrane protein folding studies are generally restricted to a handful of well-behaved proteins. Single-molecule methods may greatly alter this picture, however, because the ability to work at or near infinite dilution removes aggregation problems, one of the main technical challenges of membrane protein folding studies.
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Affiliation(s)
- Robert E Jefferson
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Duyoung Min
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Karolina Corin
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - Jing Yang Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, 90095, CA, USA.
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28
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Schneider D. Border controls: Lipids control proteins and proteins control lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:507-508. [DOI: 10.1016/j.bbamem.2016.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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29
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Dubey V, Prasanna X, Sengupta D. Estimating the Lipophobic Contributions in Model Membranes. J Phys Chem B 2017; 121:2111-2120. [DOI: 10.1021/acs.jpcb.6b09863] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Vikas Dubey
- Physical Chemistry Division, National Chemical Laboratory, Pune 411008, India
| | - Xavier Prasanna
- Physical Chemistry Division, National Chemical Laboratory, Pune 411008, India
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune 411008, India
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30
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Yano Y, Kondo K, Watanabe Y, Zhang TO, Ho JJ, Oishi S, Fujii N, Zanni MT, Matsuzaki K. GXXXG-Mediated Parallel and Antiparallel Dimerization of Transmembrane Helices and Its Inhibition by Cholesterol: Single-Pair FRET and 2D IR Studies. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Kotaro Kondo
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Yuta Watanabe
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Tianqi O. Zhang
- Department of Chemistry; University of Wisconsin; Madison WI 53706 USA
| | - Jia-Jung Ho
- Department of Chemistry; University of Wisconsin; Madison WI 53706 USA
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Martin T. Zanni
- Department of Chemistry; University of Wisconsin; Madison WI 53706 USA
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
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31
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Yano Y, Furukawa N, Ono S, Takeda Y, Matsuzaki K. Selective amine labeling of cell surface proteins guided by coiled-coil assembly. Biopolymers 2017; 106:484-90. [PMID: 26285787 DOI: 10.1002/bip.22715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/30/2015] [Accepted: 08/09/2015] [Indexed: 01/17/2023]
Abstract
Covalent labeling of target proteins in living cells is useful for both fluorescence live-cell imaging and the subsequent biochemical analyses of the proteins. Here, we report an efficient method for the amine labeling of membrane proteins on the cell surface, guided by a noncovalent coiled-coil interaction. A carboxyl sulfosuccinimidyl ester introduced at the C-terminus of the coiled-coil probe reacted with target proteins under mild labeling conditions ([probe] = 150 nM, pH 7.4, 25°C) for 20 min. Various fluorescent moieties with different hydrophobicities are available for covalent labeling with high signal/background labeling ratios. Using this method, oligomeric states of glycophorin A (GpA) were compared in mammalian CHO-K1 cells and sodium dodecyl sulfate (SDS) micelles. In the cell membranes, no significant self-association of GpA was detected, whereas SDS-PAGE suggested partial dimerization of the proteins. Membrane cholesterol was found to be an important factor that suppressed the dimerization of GpA. Thus, the covalent functionality enables direct comparison of the oligomeric state of membrane proteins under various conditions. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 484-490, 2016.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Nami Furukawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Satoshi Ono
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Yuki Takeda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
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32
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Yano Y, Kondo K, Watanabe Y, Zhang TO, Ho JJ, Oishi S, Fujii N, Zanni MT, Matsuzaki K. GXXXG-Mediated Parallel and Antiparallel Dimerization of Transmembrane Helices and Its Inhibition by Cholesterol: Single-Pair FRET and 2D IR Studies. Angew Chem Int Ed Engl 2017; 56:1756-1759. [PMID: 28071848 DOI: 10.1002/anie.201609708] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/05/2016] [Indexed: 02/06/2023]
Abstract
Small-residue-mediated interhelical packings are ubiquitously found in helical membrane proteins, although their interaction dynamics and lipid dependence remain mostly uncharacterized. We used a single-pair FRET technique to examine the effect of a GXXXG motif on the association of de novo designed (AALALAA)3 helices in liposomes. Dimerization occurred with sub-second lifetimes, which was abolished by cholesterol. Utilizing the nearly instantaneous time-resolution of 2D IR spectroscopy, parallel and antiparallel helix associations were identified by vibrational couplings across helices at their interface. Taken together, the data illustrate that the GXXXG motif controls helix packing but still allows for a dynamic and lipid-regulated oligomeric state.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Kotaro Kondo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuta Watanabe
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Tianqi O Zhang
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
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33
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Bocharov EV, Mineev KS, Pavlov KV, Akimov SA, Kuznetsov AS, Efremov RG, Arseniev AS. Helix-helix interactions in membrane domains of bitopic proteins: Specificity and role of lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:561-576. [PMID: 27884807 DOI: 10.1016/j.bbamem.2016.10.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/18/2016] [Accepted: 10/20/2016] [Indexed: 12/23/2022]
Abstract
Interaction between transmembrane helices often determines biological activity of membrane proteins. Bitopic proteins, a broad subclass of membrane proteins, form dimers containing two membrane-spanning helices. Some aspects of their structure-function relationship cannot be fully understood without considering the protein-lipid interaction, which can determine the protein conformational ensemble. Experimental and computer modeling data concerning transmembrane parts of bitopic proteins are reviewed in the present paper. They highlight the importance of lipid-protein interactions and resolve certain paradoxes in the behavior of such proteins. Besides, some properties of membrane organization provided a clue to understanding of allosteric interactions between distant parts of proteins. Interactions of these kinds appear to underlie a signaling mechanism, which could be widely employed in the functioning of many membrane proteins. Treatment of membrane proteins as parts of integrated fine-tuned proteolipid system promises new insights into biological function mechanisms and approaches to drug design. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; National Research Centre "Kurchatov Institute", Akad. Kurchatova pl. 1, Moscow, 123182, Russian Federation.
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation
| | - Sergey A Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation; National University of Science and Technology "MISiS", Leninskiy prospect 4, Moscow, 119049, Russian Federation
| | - Andrey S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; Higher School of Economics, Myasnitskaya ul. 20, Moscow, 101000, Russian Federation
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation.
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34
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Hedger G, Rouse SL, Domański J, Chavent M, Koldsø H, Sansom MSP. Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes. Biochemistry 2016; 55:6238-6249. [PMID: 27786441 PMCID: PMC5120876 DOI: 10.1021/acs.biochem.6b00751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
The exchange of ADP
and ATP across the inner mitochondrial membrane
is a fundamental cellular process. This exchange is facilitated by
the adenine nucleotide translocase, the structure and function of
which are critically dependent on the signature phospholipid of mitochondria,
cardiolipin (CL). Here we employ multiscale molecular dynamics simulations
to investigate CL interactions within a membrane environment. Using
simulations at both coarse-grained and atomistic resolutions, we identify
three CL binding sites on the translocase, in agreement with those
seen in crystal structures and inferred from nuclear magnetic resonance
measurements. Characterization of the free energy landscape for lateral
lipid interaction via potential of mean force calculations demonstrates
the strength of interaction compared to those of binding sites on
other mitochondrial membrane proteins, as well as their selectivity
for CL over other phospholipids. Extending the analysis to other members
of the family, yeast Aac2p and mouse uncoupling protein 2, suggests
a degree of conservation. Simulation of large patches of a model mitochondrial
membrane containing multiple copies of the translocase shows that
CL interactions persist in the presence of protein–protein
interactions and suggests CL may mediate interactions between translocases.
This study provides a key example of how computational microscopy
may be used to shed light on regulatory lipid–protein interactions.
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Affiliation(s)
- George Hedger
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Sarah L Rouse
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - Jan Domański
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,D. E. Shaw Research , 120 West 45th Street, 39th Floor, New York, New York 10036, United States
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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35
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Chadda R, Krishnamani V, Mersch K, Wong J, Brimberry M, Chadda A, Kolmakova-Partensky L, Friedman LJ, Gelles J, Robertson JL. The dimerization equilibrium of a ClC Cl(-)/H(+) antiporter in lipid bilayers. eLife 2016; 5. [PMID: 27484630 PMCID: PMC5010387 DOI: 10.7554/elife.17438] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/29/2016] [Indexed: 12/20/2022] Open
Abstract
Interactions between membrane protein interfaces in lipid bilayers play an important role in membrane protein folding but quantification of the strength of these interactions has been challenging. Studying dimerization of ClC-type transporters offers a new approach to the problem, as individual subunits adopt a stable and functionally verifiable fold that constrains the system to two states - monomer or dimer. Here, we use single-molecule photobleaching analysis to measure the probability of ClC-ec1 subunit capture into liposomes during extrusion of large, multilamellar membranes. The capture statistics describe a monomer to dimer transition that is dependent on the subunit/lipid mole fraction density and follows an equilibrium dimerization isotherm. This allows for the measurement of the free energy of ClC-ec1 dimerization in lipid bilayers, revealing that it is one of the strongest membrane protein complexes measured so far, and introduces it as new type of dimerization model to investigate the physical forces that drive membrane protein association in membranes.
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Affiliation(s)
- Rahul Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Kacey Mersch
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Jason Wong
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States.,Department of Natural Sciences, University of Bath, Bath, United Kingdom
| | - Marley Brimberry
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Ankita Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Janice L Robertson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
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36
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Bugge K, Lindorff-Larsen K, Kragelund BB. Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing? FEBS J 2016; 283:4424-4451. [PMID: 27350538 DOI: 10.1111/febs.13793] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Abstract
Single-pass transmembrane receptors are involved in essential processes of both physiological and pathological nature and represent more than 1300 proteins in the human genome. Despite the high biological relevance of these receptors, the mechanisms of the signal transductions they facilitate are incompletely understood. One major obstacle is the lack of structures of the transmembrane domains that connect the extracellular ligand-binding domains to the intracellular signaling platforms. Over a period of almost 20 years since the first structure was reported, only 21 of these receptors have become represented by a transmembrane domain structure. This scarceness stands in strong contrast to the significance of these transmembrane α-helices for receptor functionality. In this review, we explore the properties and qualities of the current set of structures, as well as the methodological difficulties associated with their characterization and the challenges left to be overcome. Without an increased and focused effort to bring this class of proteins on par with the remaining membrane protein field, a serious lag in their biological understanding looms. Design of pharmaceutical agents, prediction of mutational affects in relation to disease, and deciphering of functional mechanisms require high-resolution structural information, especially when dealing with a domain carrying so much functionality in so few residues.
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Affiliation(s)
- Katrine Bugge
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Birthe B Kragelund
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
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37
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Tong S, Lin Y, Lu S, Wang M, Bogdanov M, Zheng L. Structural Insight into Substrate Selection and Catalysis of Lipid Phosphate Phosphatase PgpB in the Cell Membrane. J Biol Chem 2016; 291:18342-52. [PMID: 27405756 DOI: 10.1074/jbc.m116.737874] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 12/19/2022] Open
Abstract
PgpB belongs to the lipid phosphate phosphatase protein family and is one of three bacterial integral membrane phosphatases catalyzing dephosphorylation of phosphatidylglycerol phosphate (PGP) to generate phosphatidylglycerol. Although the structure of its apo form became recently available, the mechanisms of PgpB substrate binding and catalysis are still unclear. We found that PgpB was inhibited by phosphatidylethanolamine (PE) in a competitive mode in vitro Here we report the crystal structure of the lipid-bound form of PgpB. The structure shows that a PE molecule is stabilized in a membrane-embedded tunnel formed by TM3 and the "PSGH" fingerprint peptide near the catalytic site, providing structural insight into PgpB substrate binding mechanism. Noteworthy, in silico docking of varied lipid phosphates exhibited similar substrate binding modes to that of PE, and the residues in the lipid tunnel appear to be important for PgpB catalysis. The catalytic triad in the active site is essential for dephosphorylating substrates lysophosphatidic acid, phosphatidic acid, or sphingosine-1-phosphate but surprisingly not for the native substrate PGP. Remarkably, residue His-207 alone is sufficient to hydrolyze PGP, indicating a specific catalytic mechanism for PgpB in PG biosynthesis. We also identified two novel sensor residues, Lys-93 and Lys-97, on TM3. Our data show that Lys-97 is essential for the recognition of lyso-form substrates. Modification at the Lys-93 position may alter substrate specificity of lipid phosphate phosphatase proteins in prokaryotes versus eukaryotes. These studies reveal new mechanisms of lipid substrate selection and catalysis by PgpB and suggest that the enzyme rests in a PE-stabilized state in the bilayer.
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Affiliation(s)
- Shuilong Tong
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Yibin Lin
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Shuo Lu
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Mikhail Bogdanov
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Lei Zheng
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
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38
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Klein N, Hellmann N, Schneider D. Anionic Lipids Modulate the Activity of the Aquaglyceroporin GlpF. Biophys J 2016; 109:722-31. [PMID: 26287624 DOI: 10.1016/j.bpj.2015.06.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 01/30/2023] Open
Abstract
The structure and composition of a biological membrane can severely influence the activity of membrane-embedded proteins. Here, we show that the E. coli aquaglyceroporin GlpF has only little activity in lipid bilayers formed from native E. coli lipids. Thus, at first glance, GlpF appears to not be optimized for its natural membrane environment. In fact, we found that GlpF activity was severely affected by negatively charged lipids regardless of the exact chemical nature of the lipid headgroup, whereas GlpF was not sensitive to changes in the lateral membrane pressure. These observations illustrate a potential mechanism by which the activity of an α-helical membrane protein is modulated by the negative charge density around the protein.
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Affiliation(s)
- Noreen Klein
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Nadja Hellmann
- Institut für Molekulare Biophysik, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany.
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39
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Guo R, Gaffney K, Yang Z, Kim M, Sungsuwan S, Huang X, Hubbell WL, Hong H. Steric trapping reveals a cooperativity network in the intramembrane protease GlpG. Nat Chem Biol 2016; 12:353-360. [PMID: 26999782 PMCID: PMC4837050 DOI: 10.1038/nchembio.2048] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 01/22/2016] [Indexed: 12/21/2022]
Abstract
Membrane proteins are assembled through balanced interactions among protein, lipids and water. Studying their folding while maintaining the native lipid environment is necessary but challenging. Here we present methods for analyzing key elements in membrane protein folding including thermodynamic stability, compactness of the unfolded state and folding cooperativity under native conditions. The methods are based on steric trapping which couples unfolding of a doubly-biotinylated protein to binding of monovalent streptavidin (mSA). We further advanced this technology for general application by developing versatile biotin probes possessing spectroscopic reporters that are sensitized by mSA binding or protein unfolding. By applying these methods to an intramembrane protease GlpG of Escherichia coli, we elucidated a widely unraveled unfolded state, subglobal unfolding of the region encompassing the active site, and a network of cooperative and localized interactions to maintain the stability. These findings provide crucial insights into the folding energy landscape of membrane proteins.
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Affiliation(s)
- Ruiqiong Guo
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kristen Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Miyeon Kim
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Suttipun Sungsuwan
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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40
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Mori T, Miyashita N, Im W, Feig M, Sugita Y. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1635-51. [PMID: 26766517 DOI: 10.1016/j.bbamem.2015.12.032] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Takaharu Mori
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Miyashita
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Faculty of Biology-Oriented Science and Technology, KINDAI University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Wonpil Im
- Department of Molecular Sciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, United States
| | - Michael Feig
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States
| | - Yuji Sugita
- iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States; Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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41
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Kuznetsov AS, Polyansky AA, Fleck M, Volynsky PE, Efremov RG. Adaptable Lipid Matrix Promotes Protein–Protein Association in Membranes. J Chem Theory Comput 2015; 11:4415-26. [DOI: 10.1021/acs.jctc.5b00206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrey S. Kuznetsov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Anton A. Polyansky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Markus Fleck
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Roman G. Efremov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Higher School of Economics, Myasnitskaya Str., 20, Moscow 101000, Russia
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42
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Abstract
Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. It is therefore tempting to use the presence of these simple motifs as an indicator of TM helix interactions. In this Current Topic review, we point out that these motifs are quite common, with more than 50% of single-pass TM domains containing a (small)xxx(small) motif. However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane.
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Affiliation(s)
- Mark G Teese
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München , 85354 Freising, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München , 85354 Freising, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany
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43
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BRET evidence that β2 adrenergic receptors do not oligomerize in cells. Sci Rep 2015; 5:10166. [PMID: 25955971 PMCID: PMC4424835 DOI: 10.1038/srep10166] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/01/2015] [Indexed: 11/29/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) is often used to study association of membrane proteins, and in particular oligomerization of G protein-coupled receptors (GPCRs). Oligomerization of class A GPCRs is controversial, in part because the methods used to study this question are not completely understood. Here we reconsider oligomerization of the class A β2 adrenergic receptor (β2AR), and reevaluate BRET titration as a method to study membrane protein association. Using inducible expression of the energy acceptor at multiple levels of donor expression we find that BRET between β2AR protomers is directly proportional to the density of the acceptor up to ~3,000 acceptors μm−2, and does not depend on the density of the donor or on the acceptor:donor (A:D) stoichiometry. In contrast, BRET between tightly-associating control proteins does not depend on the density of the acceptor, but does depend on the density of the donor and on the A:D ratio. We also find that the standard frameworks used to interpret BRET titration experiments rely on simplifying assumptions that are frequently invalid. These results suggest that β2ARs do not oligomerize in cells, and demonstrate a reliable method of assessing membrane protein association with BRET.
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Sarabipour S, Hristova K. FGFR3 unliganded dimer stabilization by the juxtamembrane domain. J Mol Biol 2015; 427:1705-14. [PMID: 25688803 PMCID: PMC4380549 DOI: 10.1016/j.jmb.2015.02.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/12/2015] [Accepted: 02/11/2015] [Indexed: 11/22/2022]
Abstract
Receptor tyrosine kinases (RTKs) conduct biochemical signals upon dimerization in the membrane plane. While RTKs are generally known to be activated in response to ligand binding, many of these receptors are capable of forming unliganded dimers that are likely important intermediates in the signaling process. All 58 RTKs consist of an extracellular (EC) domain, a transmembrane (TM) domain, and an intracellular domain that includes a juxtamembrane (JM) sequence and a kinase domain. Here we investigate directly the effect of the JM domain on unliganded dimer stability of FGFR3, a receptor that is critically important for skeletal development. The data suggest that FGFR3 unliganded dimers are stabilized by receptor-receptor contacts that involve the JM domains. The contribution is significant, as it is similar in magnitude to the stabilizing contribution of a pathogenic mutation and the repulsive contribution of the EC domain. Furthermore, we show that the effects of the JM domain and a TM pathogenic mutation on unliganded FGFR3 dimer stability are additive. We observe that the JM-mediated dimer stabilization occurs when the JM domain is linked to FGFR3 TM domain and not simply anchored to the plasma membrane. These results point to a coordinated stabilization of the unliganded dimeric state of FGFR3 by its JM and TM domains via a mechanism that is distinctly different from the case of another well studied receptor, EGFR.
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Affiliation(s)
- Sarvenaz Sarabipour
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21212, USA.
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Abstract
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Whole human genome sequencing of
individuals is becoming rapid
and inexpensive, enabling new strategies for using personal genome
information to help diagnose, treat, and even prevent human disorders
for which genetic variations are causative or are known to be risk
factors. Many of the exploding number of newly discovered genetic
variations alter the structure, function, dynamics, stability, and/or
interactions of specific proteins and RNA molecules. Accordingly,
there are a host of opportunities for biochemists and biophysicists
to participate in (1) developing tools to allow accurate and sometimes
medically actionable assessment of the potential pathogenicity of
individual variations and (2) establishing the mechanistic linkage
between pathogenic variations and their physiological consequences,
providing a rational basis for treatment or preventive care. In this
review, we provide an overview of these opportunities and their associated
challenges in light of the current status of genomic science and personalized
medicine, the latter often termed precision medicine.
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Affiliation(s)
- Brett M Kroncke
- †Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,‡Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Carlos G Vanoye
- §Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Jens Meiler
- ‡Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States.,∥Departments of Chemistry, Pharmacology, and Bioinformatics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Alfred L George
- §Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Charles R Sanders
- †Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,‡Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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Nadeau VG, Gao A, Deber CM. Design and characterization of a membrane protein unfolding platform in lipid bilayers. PLoS One 2015; 10:e0120253. [PMID: 25799099 PMCID: PMC4370600 DOI: 10.1371/journal.pone.0120253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/20/2015] [Indexed: 11/29/2022] Open
Abstract
Accurate measurement of membrane protein stability—and particularly how it may vary as a result of disease-phenotypic mutations—ideally requires a denaturant that can unfold a membrane-embedded structure while leaving the solubilizing environment unaffected. The steric trap method fulfills this requirement by using monovalent streptavidin (mSA) molecules to unfold membrane proteins engineered with two spatially close biotin tags. Here we adapted this method to an 87-residue helix-loop-helix (hairpin) construct derived from helices 3 and 4 in the transmembrane domain of the human cystic fibrosis transmembrane conductance regulator (CFTR), wherein helix-helix tertiary interactions are anticipated to confer a portion of construct stability. The wild type CFTR TM3/4 hairpin construct was modified with two accessible biotin tags for mSA-induced unfolding, along with two helix-terminal pyrene labels to monitor loss of inter-helical contacts by pyrene excimer fluorescence. A series of eight constructs with biotin tags at varying distances from the helix-terminal pyrene labels were expressed, purified and labeled appropriately; all constructs exhibited largely helical circular dichroism spectra. We found that addition of mSA to an optimized construct in lipid vesicles led to a complete and reversible loss in pyrene excimer fluorescence and mSA binding, and hence hairpin unfolding—results further supported by SDS-PAGE visualization of mSA bound and unbound species. While some dimeric/oligomeric populations persist that may affect quantitation of the unfolding step, our characterization of the design yields a promising prototype of a future platform for the systematic study of membrane protein folding in a lipid bilayer environment.
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Affiliation(s)
- Vincent G. Nadeau
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Anqi Gao
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- * E-mail:
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47
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Stangl M, Schneider D. Functional competition within a membrane: Lipid recognition vs. transmembrane helix oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1886-96. [PMID: 25791349 DOI: 10.1016/j.bbamem.2015.03.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/27/2022]
Abstract
Binding of specific lipids to large, polytopic membrane proteins is well described, and it is clear that such lipids are crucial for protein stability and activity. In contrast, binding of defined lipid species to individual transmembrane helices and regulation of transmembrane helix monomer-oligomer equilibria by binding of distinct lipids is a concept, which has emerged only lately. Lipids bind to single-span membrane proteins, both in the juxta-membrane region as well as in the hydrophobic membrane core. While some interactions counteract transmembrane helix oligomerization, in other cases lipid binding appears to enhance oligomerization. As reversible oligomerization is involved in activation of many membrane proteins, binding of defined lipids to single-span transmembrane proteins might be a mechanism to regulate and/or fine-tune the protein activity. But how could lipid binding trigger the activity of a protein? How can binding of a single lipid molecule to a transmembrane helix affect the structure of a transmembrane helix oligomer, and consequently its signaling state? These questions are discussed in the present article based on recent results obtained with simple, single-span transmembrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Michael Stangl
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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Zuber J, Danial SA, Connelly SM, Naider F, Dumont ME. Identification of destabilizing and stabilizing mutations of Ste2p, a G protein-coupled receptor in Saccharomyces cerevisiae. Biochemistry 2015; 54:1787-806. [PMID: 25647246 DOI: 10.1021/bi501314t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The isolation of mutations affecting the stabilities of transmembrane proteins is useful for enhancing the suitability of proteins for structural characterization and identification of determinants of membrane protein stability. We have pursued a strategy for the identification of stabilized variants of the yeast α-factor receptor Ste2p. Because it was not possible to screen directly for mutations providing thermal stabilization, we first isolated a battery of destabilized temperature-sensitive variants, based on loss of signaling function and decreased levels of binding of the fluorescent ligand, and then screened for intragenic second-site suppressors of these phenotypes. The initial screens recovered singly and multiply substituted mutations conferring temperature sensitivity throughout the predicted transmembrane helices of the receptor. All of the singly substituted variants exhibit decreases in cell-surface expression. We then screened randomly mutagenized libraries of clones expressing temperature-sensitive variants for second-site suppressors that restore elevated levels of binding sites for fluorescent ligand. To determine whether any of these were global suppressors, and thus likely stabilizing mutations, they were combined with different temperature-sensitive mutations. Eight of the suppressors exhibited the ability to reverse the defect in ligand binding of multiple temperature-sensitive mutations. Combining certain suppressors into a single allele resulted in levels of suppression greater than that seen with either suppressor alone. Solubilized receptors containing suppressor mutations in the absence of temperature-sensitive mutations exhibit a reduced tendency to aggregate during immobilization on an affinity matrix. Several of the suppressors also exhibit allele-specific behavior indicative of specific intramolecular interactions in the receptor.
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Affiliation(s)
- Jeffrey Zuber
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , P.O. Box 712, Rochester, New York 14642, United States
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Yano Y, Kondo K, Kitani R, Yamamoto A, Matsuzaki K. Cholesterol-Induced Lipophobic Interaction between Transmembrane Helices Using Ensemble and Single-Molecule Fluorescence Resonance Energy Transfer. Biochemistry 2015; 54:1371-9. [DOI: 10.1021/bi501528e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kotaro Kondo
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryota Kitani
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Arisa Yamamoto
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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50
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Hong H. Role of Lipids in Folding, Misfolding and Function of Integral Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:1-31. [DOI: 10.1007/978-3-319-17344-3_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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