1
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Blaimschein N, Parameswaran H, Nagler G, Manioglu S, Helenius J, Ardelean C, Kuhn A, Guan L, Müller DJ. The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini. Structure 2023; 31:1419-1430.e5. [PMID: 37708891 PMCID: PMC10840855 DOI: 10.1016/j.str.2023.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/22/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023]
Abstract
The insertion and folding of proteins into membranes is crucial for cell viability. Yet, the detailed contributions of insertases remain elusive. Here, we monitor how the insertase YidC guides the folding of the polytopic melibiose permease MelB into membranes. In vivo experiments using conditionally depleted E. coli strains show that MelB can insert in the absence of SecYEG if YidC resides in the cytoplasmic membrane. In vitro single-molecule force spectroscopy reveals that the MelB substrate itself forms two folding cores from which structural segments insert stepwise into the membrane. However, misfolding dominates, particularly in structural regions that interface the pseudo-symmetric α-helical domains of MelB. Here, YidC takes an important role in accelerating and chaperoning the stepwise insertion and folding process of both MelB folding cores. Our findings reveal a great flexibility of the chaperoning and insertase activity of YidC in the multifaceted folding processes of complex polytopic membrane proteins.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Hariharan Parameswaran
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Gisela Nagler
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Jonne Helenius
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | | | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland.
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2
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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3
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Viljoen A, Dufrêne YF. Force-induced unfolding of an antibiotic-bound outer-membrane protein. Structure 2022; 30:321-323. [PMID: 35245432 DOI: 10.1016/j.str.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this issue of Structure, Ritzmann et al. characterize the unfolding of the β-barrel assembly machinery component BamA with single-molecule force spectroscopy and reveal how an antibiotic changes BamA's mechanical properties and inhibits its activity. This work helps us understand the effects antibiotics have on Gram-negative outer membrane proteins.
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Affiliation(s)
- Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium.
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium.
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4
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Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. Methods Mol Biol 2020. [PMID: 31218616 DOI: 10.1007/978-1-4939-9512-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.
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5
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Rath P, Sharpe T, Kohl B, Hiller S. Two‐State Folding of the Outer Membrane Protein X into a Lipid Bilayer Membrane. Angew Chem Int Ed Engl 2019; 58:2665-2669. [DOI: 10.1002/anie.201812321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Parthasarathi Rath
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Timothy Sharpe
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Bastian Kohl
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Sebastian Hiller
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
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6
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Rath P, Sharpe T, Kohl B, Hiller S. Two‐State Folding of the Outer Membrane Protein X into a Lipid Bilayer Membrane. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Parthasarathi Rath
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Timothy Sharpe
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Bastian Kohl
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Sebastian Hiller
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
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7
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Yu H, Heenan PR, Edwards DT, Uyetake L, Perkins TT. Quantifying the Initial Unfolding of Bacteriorhodopsin Reveals Retinal Stabilization. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hao Yu
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
- Present address: School of Physics Huazhong University of Science and Technology Wuhan China
| | - Patrick R. Heenan
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
- Department of Physics University of Colorado Boulder CO 80309 USA
| | - Devin T. Edwards
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
| | - Thomas T. Perkins
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
- Department of Molecular, Cellular, and Developmental Biology University of Colorado Boulder CO 80309 USA
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8
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Yu H, Heenan PR, Edwards DT, Uyetake L, Perkins TT. Quantifying the Initial Unfolding of Bacteriorhodopsin Reveals Retinal Stabilization. Angew Chem Int Ed Engl 2019; 58:1710-1713. [DOI: 10.1002/anie.201812072] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Hao Yu
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
- Present address: School of Physics Huazhong University of Science and Technology Wuhan China
| | - Patrick R. Heenan
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
- Department of Physics University of Colorado Boulder CO 80309 USA
| | - Devin T. Edwards
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
| | - Thomas T. Perkins
- JILA, National Institute of Standards and Technology and University of Colorado Boulder CO 80309 USA
- Department of Molecular, Cellular, and Developmental Biology University of Colorado Boulder CO 80309 USA
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9
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Thoma J, Sapra KT, Müller DJ. Single-Molecule Force Spectroscopy of Transmembrane β-Barrel Proteins. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:375-395. [PMID: 29894225 DOI: 10.1146/annurev-anchem-061417-010055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule force spectroscopy (SMFS) has been widely applied to study the mechanical unfolding and folding of transmembrane proteins. Here, we review the recent progress in characterizing bacterial and human transmembrane β-barrel proteins by SMFS. First, we describe the mechanical unfolding of transmembrane β-barrels, which follows a general mechanism dictated by the sequential unfolding and extraction of individual β-strands and β-hairpins from membranes. Upon force relaxation, the unfolded polypeptide can insert stepwise into the membrane as single β-strands or β-hairpins to fold as the native β-barrel. The refolding can be followed at a high spatial and temporal resolution, showing that small β-barrels are able to fold without assistance, whereas large and complex β-barrels require chaperone cofactors. Applied in the dynamic mode, SMFS can quantify the kinetic and mechanical properties of single β-hairpins and reveal complementary insight into the membrane protein structure and function relationship. We further outline the challenges that SMFS experiments must overcome for a comprehensive understanding of the folding and function of transmembrane β-barrel proteins.
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Affiliation(s)
- Johannes Thoma
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland;
| | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland;
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10
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Protein-enriched outer membrane vesicles as a native platform for outer membrane protein studies. Commun Biol 2018; 1:23. [PMID: 30271910 PMCID: PMC6123736 DOI: 10.1038/s42003-018-0027-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/20/2018] [Indexed: 01/15/2023] Open
Abstract
Most studies characterizing the folding, structure, and function of membrane proteins rely on solubilized or reconstituted samples. Whereas solubilized membrane proteins lack the functionally important lipid membrane, reconstitution embeds them into artificial lipid bilayers, which lack characteristic features of cellular membranes including lipid diversity, composition and asymmetry. Here, we utilize outer membrane vesicles (OMVs) released from Escherichia coli to study outer membrane proteins (Omps) in the native membrane environment. Enriched in the native membrane of the OMV we characterize the assembly, folding, and structure of OmpG, FhuA, Tsx, and BamA. Comparing Omps in OMVs to those reconstituted into artificial lipid membranes, we observe different unfolding pathways for some Omps. This observation highlights the importance of the native membrane environment to maintain the native structure and function relationship of Omps. Our fast and easy approach paves the way for functional and structural studies of Omps in the native membrane. Johannes Thoma et al. overexpress outer membrane proteins (Omps) in Escherichia coli and collect the expelled outer membrane vesicles (OMVs) to study Omp assembly, folding and structure. They find that Omps in OMVs show different unfolding pathways compared to Omps reconstituted in artificial lipid membranes.
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11
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Thoma J, Ritzmann N, Wolf D, Mulvihill E, Hiller S, Müller DJ. Maltoporin LamB Unfolds β Hairpins along Mechanical Stress-Dependent Unfolding Pathways. Structure 2017. [DOI: 10.1016/j.str.2017.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Affiliation(s)
- Daniel J. Müller
- Department of Biosystems Science and Engineering, ETH
Zürich, 4058 Basel, Switzerland
| | - Hermann E. Gaub
- Department of Physics, Ludwig-Maximilians-Universität,
80799 München, Germany
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13
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Serdiuk T, Balasubramaniam D, Sugihara J, Mari SA, Kaback HR, Müller DJ. YidC assists the stepwise and stochastic folding of membrane proteins. Nat Chem Biol 2016; 12:911-917. [PMID: 27595331 PMCID: PMC5069129 DOI: 10.1038/nchembio.2169] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Abstract
How chaperones, insertases and translocases facilitate insertion and folding of complex cytoplasmic proteins into cellular membranes is not fully understood. Here we utilize single-molecule force spectroscopy to observe YidC, a transmembrane chaperone and insertase, sculpting the folding trajectory of the polytopic α-helical membrane protein lactose permease (LacY). In the absence of YidC, unfolded LacY inserts individual structural segments into the membrane; however, misfolding dominates the process so that folding cannot be completed. YidC prevents LacY from misfolding by stabilizing the unfolded state from which LacY inserts structural segments stepwise into the membrane until folding is completed. During stepwise insertion, YidC and the membrane together stabilize the transient folds. Remarkably, the order of insertion of structural segments is stochastic, indicating that LacY can fold along variable pathways toward the native structure. Since YidC is essential in membrane protein biogenesis and LacY is a model for the major facilitator superfamily, our observations have general relevance.
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Affiliation(s)
- Tetiana Serdiuk
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | - Junichi Sugihara
- Department of Physiology, University of California-Los Angeles, Los Angeles, USA
| | - Stefania A. Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - H. Ronald Kaback
- Department of Physiology, University of California-Los Angeles, Los Angeles, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California-Los Angeles, Los Angeles, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, USA
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
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14
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Oh KI, Smith-Dupont KB, Markiewicz BN, Gai F. Kinetics of peptide folding in lipid membranes. Biopolymers 2016; 104:281-90. [PMID: 25808575 DOI: 10.1002/bip.22640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/12/2015] [Accepted: 02/14/2015] [Indexed: 12/31/2022]
Abstract
Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Kathryn B Smith-Dupont
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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15
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Raschle T, Rios Flores P, Opitz C, Müller DJ, Hiller S. Monitoring Backbone Hydrogen‐Bond Formation in β‐Barrel Membrane Protein Folding. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Raschle
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Perla Rios Flores
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Christian Opitz
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Sebastian Hiller
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
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16
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Raschle T, Rios Flores P, Opitz C, Müller DJ, Hiller S. Monitoring Backbone Hydrogen‐Bond Formation in β‐Barrel Membrane Protein Folding. Angew Chem Int Ed Engl 2016; 55:5952-5. [DOI: 10.1002/anie.201509910] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Raschle
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Perla Rios Flores
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Christian Opitz
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Sebastian Hiller
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
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17
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Impact of holdase chaperones Skp and SurA on the folding of β-barrel outer-membrane proteins. Nat Struct Mol Biol 2015; 22:795-802. [PMID: 26344570 DOI: 10.1038/nsmb.3087] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 08/13/2015] [Indexed: 12/27/2022]
Abstract
Chaperones increase the folding yields of soluble proteins by suppressing misfolding and aggregation, but how they modulate the folding of integral membrane proteins is not well understood. Here we use single-molecule force spectroscopy and NMR spectroscopy to observe the periplasmic holdase chaperones SurA and Skp shaping the folding trajectory of the large β-barrel outer-membrane receptor FhuA from Escherichia coli. Either chaperone prevents FhuA from misfolding by stabilizing a dynamic, unfolded state, thus allowing the substrate to search for structural intermediates. During this search, the SurA-chaperoned FhuA polypeptide inserts β-hairpins into the membrane in a stepwise manner until the β-barrel is folded. The membrane acts as a free-energy sink for β-hairpin insertion and physically separates transient folds from chaperones. This stabilization of dynamic unfolded states and the trapping of folding intermediates funnel the FhuA polypeptide toward the native conformation.
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18
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McMorran LM, Brockwell DJ, Radford SE. Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 2014; 564:265-80. [PMID: 24613287 PMCID: PMC4262575 DOI: 10.1016/j.abb.2014.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/16/2014] [Accepted: 02/20/2014] [Indexed: 11/17/2022]
Abstract
Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
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Affiliation(s)
- Lindsay M McMorran
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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19
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Folding membrane proteins in vitro: A table and some comments. Arch Biochem Biophys 2014; 564:314-26. [DOI: 10.1016/j.abb.2014.06.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/17/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
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20
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Folding and stability of integral membrane proteins in amphipols. Arch Biochem Biophys 2014; 564:327-43. [PMID: 25449655 DOI: 10.1016/j.abb.2014.10.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/11/2014] [Accepted: 10/22/2014] [Indexed: 11/23/2022]
Abstract
Amphipols (APols) are a family of amphipathic polymers designed to keep transmembrane proteins (TMPs) soluble in aqueous solutions in the absence of detergent. APols have proven remarkably efficient at (i) stabilizing TMPs, as compared to detergent solutions, and (ii) folding them from a denatured state to a native, functional one. The underlying physical-chemical mechanisms are discussed.
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21
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Selkrig J, Leyton DL, Webb CT, Lithgow T. Assembly of β-barrel proteins into bacterial outer membranes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1542-50. [DOI: 10.1016/j.bbamcr.2013.10.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/05/2013] [Accepted: 10/08/2013] [Indexed: 12/30/2022]
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22
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Hausrath AC. Model for coupled insertion and folding of membrane-spanning proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022707. [PMID: 25215758 DOI: 10.1103/physreve.90.022707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 06/03/2023]
Abstract
Current understanding of the forces directing the folding of integral membrane proteins is very limited compared to the detailed picture available for water-soluble proteins. While mechanistic studies of the folding process in vitro have been conducted for only a small number of membrane proteins, the available evidence indicates that their folding process is thermodynamically driven like that of soluble proteins. In vivo, however, the majority of integral membrane proteins are installed in membranes by dedicated machinery, suggesting that the cellular systems may act to facilitate and regulate the spontaneous physical process of folding. Both the in vitro folding process and the in vivo pathway must navigate an energy landscape dominated by the energetically favorable burial of hydrophobic segments in the membrane interior and the opposition to folding due to the need for passage of polar segments across the membrane. This manuscript describes a simple, exactly solvable model which incorporates these essential features of membrane protein folding. The model is used to compare the folding time under conditions which depict both the in vitro and in vivo pathways. It is proposed that the cellular complexes responsible for insertion of membrane proteins act by lowering the energy barrier for passage of polar regions through the membrane, thereby allowing the chain to more rapidly achieve the folded state.
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Affiliation(s)
- Andrew C Hausrath
- Department of Chemistry and Biochemistry and Program in Applied Mathematics, University of Arizona, Tucson, Arizona 85721, USA
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Zhuang T, Tamm LK. Control of the conductance of engineered protein nanopores through concerted loop motions. Angew Chem Int Ed Engl 2014; 53:5897-902. [PMID: 24777684 PMCID: PMC4091679 DOI: 10.1002/anie.201400400] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/12/2014] [Indexed: 11/11/2022]
Abstract
Protein nanopores have attracted much interest for nucleic acid sequencing, chemical sensing, and protein folding at the single molecule level. The outer membrane protein OmpG from E. coli stands out because it forms a nanopore from a single polypeptide chain. This property allows the separate engineering of each of the seven extracellular loops that control access to the pore. The longest of these loops, loop 6, has been recognized as the main gating loop that closes the pore at low pH values and opens it at high pH values. A method was devised to pin each of the loops to the embedding membrane and measure the single-pore conductances of the resulting constructs. The electrophysiological and complementary NMR measurements show that the pinning of individual loops alters the structure and dynamics of neighboring and distant loops in a correlated fashion. Pinning loop 6 generates a constitutively open pore and patterns of concerted loop motions control access to the OmpG nanopore.
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Affiliation(s)
- Tiandi Zhuang
- Department of Molecular Physiology and Biological Physics and Center for Membrane Biology, University of Virginia School of Medicine, P.O. Box 800886, Charlottesville, VA 22908, U.S.A. Homepage: http://tammlab.medicine.virginia.edu/
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane Biology, University of Virginia School of Medicine, P.O. Box 800886, Charlottesville, VA 22908, U.S.A. Homepage: http://tammlab.medicine.virginia.edu/
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24
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Control of the Conductance of Engineered Protein Nanopores through Concerted Loop Motions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Mechanistic Explanation of Different Unfolding Behaviors Observed for Transmembrane and Soluble β-Barrel Proteins. Structure 2013; 21:1317-24. [DOI: 10.1016/j.str.2013.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/01/2013] [Accepted: 06/05/2013] [Indexed: 01/31/2023]
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26
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Gao X, Qin M, Yin P, Liang J, Wang J, Cao Y, Wang W. Single-molecule experiments reveal the flexibility of a Per-ARNT-Sim domain and the kinetic partitioning in the unfolding pathway under force. Biophys J 2012; 102:2149-57. [PMID: 22824279 DOI: 10.1016/j.bpj.2012.03.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/21/2012] [Accepted: 03/20/2012] [Indexed: 10/28/2022] Open
Abstract
Per-ARNT-Sim (PAS) domains serve as versatile binding motifs in many signal-transduction proteins and are able to respond to a wide spectrum of chemical or physical signals. Despite their diverse functions, PAS domains share a conserved structure. It has been suggested that the structure of PAS domains is flexible and thus adaptable to many binding partners. However, direct measurement of the flexibility of PAS domains has not yet been provided. Here, we quantitatively measure the mechanical unfolding of a PAS domain, ARNT PAS-B, using single-molecule atomic force microscopy. Our force spectroscopy results indicate that the structure of ARNT PAS-B can be unraveled under mechanical forces as low as ~30 pN due to its broad potential well for the mechanical unfolding transition of ~2 nm. This allows the PAS-B domain to extend by up to 75% of its resting end-to-end distance without unfolding. Moreover, we found that the ARNT PAS-B domain unfolds in two distinct pathways via a kinetic partitioning mechanism. Sixty-seven percent of ARNT PAS-B unfolds through a simple two-state pathway, whereas the other 33% unfolds with a well-defined intermediate state in which the C-terminal β-hairpin is detached. We propose that the structural flexibility and force-induced partial unfolding of PAS-B domains may provide a unique mechanism for them to recruit diverse binding partners and lower the free-energy barrier for the formation of the binding interface.
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Affiliation(s)
- Xiang Gao
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing, People's Republic of China
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27
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Thoma J, Bosshart P, Pfreundschuh M, Müller D. Out but Not In: The Large Transmembrane β-Barrel Protein FhuA Unfolds but Cannot Refold via β-Hairpins. Structure 2012; 20:2185-90. [DOI: 10.1016/j.str.2012.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 10/15/2012] [Accepted: 10/19/2012] [Indexed: 12/19/2022]
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28
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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29
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Lv C, Tan C, Qin M, Zou D, Cao Y, Wang W. Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation. Biophys J 2012; 102:1944-51. [PMID: 22768951 DOI: 10.1016/j.bpj.2012.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/08/2012] [Accepted: 03/14/2012] [Indexed: 10/28/2022] Open
Abstract
Some small proteins, such as HP35, fold at submicrosecond timescale with low folding cooperativity. Although these proteins have been extensively investigated, still relatively little is known about their folding mechanism. Here, using single-molecule force spectroscopy and steered molecule dynamics simulation, we study the unfolding of HP35 under external force. Our results show that HP35 unfolds at extremely low forces without a well-defined unfolding transition state. Subsequently, we probe the structure of unfolded HP35 using the persistence length obtained in the force spectroscopy. We found that the persistence length of unfolded HP35 is around 0.72 nm, >40% longer than typical unstructured proteins, suggesting that there are a significant amount of residual secondary structures in the unfolded HP35. Molecular dynamics simulation further confirmed this finding and revealed that many native contacts are preserved in HP35, even its two ends have been extended up to 8 nm. Our results therefore suggest that retaining a significant amount of secondary structures in the unfolded state of HP35 may be an efficient way to reduce the entropic cost for the formation of tertiary structure and increase the folding speed, although the folding cooperativity is compromised. Moreover, we anticipate that the methods we used in this work can be extended to the study of other proteins with complex folding behaviors and even intrinsically disordered ones.
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Affiliation(s)
- Chunmei Lv
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing, People's Republic of China
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30
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Bosshart PD, Iordanov I, Garzon-Coral C, Demange P, Engel A, Milon A, Müller DJ. The transmembrane protein KpOmpA anchoring the outer membrane of Klebsiella pneumoniae unfolds and refolds in response to tensile load. Structure 2012; 20:121-7. [PMID: 22244761 DOI: 10.1016/j.str.2011.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/20/2011] [Accepted: 11/04/2011] [Indexed: 10/14/2022]
Abstract
In Klebsiella pneumoniae the transmembrane β-barrel forming outer membrane protein KpOmpA mediates adhesion to a wide range of immune effector cells, thereby promoting respiratory tract and urinary infections. As major transmembrane protein OmpA stabilizes Gram-negative bacteria by anchoring their outer membrane to the peptidoglycan layer. Adhesion, osmotic pressure, hydrodynamic flow, and structural deformation apply mechanical stress to the bacterium. This stress can generate tensile load to the peptidoglycan-binding domain (PGBD) of KpOmpA. To investigate how KpOmpA reacts to mechanical stress, we applied a tensile load to the PGBD and observed a detailed unfolding pathway of the transmembrane β-barrel. Each step of the unfolding pathway extended the polypeptide connecting the bacterial outer membrane to the peptidoglycan layer and absorbed mechanical energy. After relieving the tensile load, KpOmpA reversibly refolded back into the membrane. These results suggest that bacteria may reversibly unfold transmembrane proteins in response to mechanical stress.
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Affiliation(s)
- Patrick D Bosshart
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
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