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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: 0] [Impact Index Per Article: 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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Petrosyan R, Narayan A, Woodside MT. Single-Molecule Force Spectroscopy of Protein Folding. J Mol Biol 2021; 433:167207. [PMID: 34418422 DOI: 10.1016/j.jmb.2021.167207] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
The use of force probes to induce unfolding and refolding of single molecules through the application of mechanical tension, known as single-molecule force spectroscopy (SMFS), has proven to be a powerful tool for studying the dynamics of protein folding. Here we provide an overview of what has been learned about protein folding using SMFS, from small, single-domain proteins to large, multi-domain proteins. We highlight the ability of SMFS to measure the energy landscapes underlying folding, to map complex pathways for native and non-native folding, to probe the mechanisms of chaperones that assist with native folding, to elucidate the effects of the ribosome on co-translational folding, and to monitor the folding of membrane proteins.
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Affiliation(s)
- Rafayel Petrosyan
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Abhishek Narayan
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
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4
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Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy. Proc Natl Acad Sci U S A 2021; 118:2020083118. [PMID: 33753487 DOI: 10.1073/pnas.2020083118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Single amino acid mutations provide quantitative insight into the energetics that underlie the dynamics and folding of membrane proteins. Chemical denaturation is the most widely used assay and yields the change in unfolding free energy (ΔΔG). It has been applied to >80 different residues of bacteriorhodopsin (bR), a model membrane protein. However, such experiments have several key limitations: 1) a nonnative lipid environment, 2) a denatured state with significant secondary structure, 3) error introduced by extrapolation to zero denaturant, and 4) the requirement of globally reversible refolding. We overcame these limitations by reversibly unfolding local regions of an individual protein with mechanical force using an atomic-force-microscope assay optimized for 2 μs time resolution and 1 pN force stability. In this assay, bR was unfolded from its native bilayer into a well-defined, stretched state. To measure ΔΔG, we introduced two alanine point mutations into an 8-amino-acid region at the C-terminal end of bR's G helix. For each, we reversibly unfolded and refolded this region hundreds of times while the rest of the protein remained folded. Our single-molecule-derived ΔΔG for mutant L223A (-2.3 ± 0.6 kcal/mol) quantitatively agreed with past chemical denaturation results while our ΔΔG for mutant V217A was 2.2-fold larger (-2.4 ± 0.6 kcal/mol). We attribute the latter result, in part, to contact between Val217 and a natively bound squalene lipid, highlighting the contribution of membrane protein-lipid contacts not present in chemical denaturation assays. More generally, we established a platform for determining ΔΔG for a fully folded membrane protein embedded in its native bilayer.
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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Yu H, Jacobson DR, Luo H, Perkins TT. Quantifying the Native Energetics Stabilizing Bacteriorhodopsin by Single-Molecule Force Spectroscopy. PHYSICAL REVIEW LETTERS 2020; 125:068102. [PMID: 32845671 DOI: 10.1103/physrevlett.125.068102] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
We quantified the equilibrium (un)folding free energy ΔG_{0} of an eight-amino-acid region starting from the fully folded state of the model membrane-protein bacteriorhodopsin using single-molecule force spectroscopy. Analysis of equilibrium and nonequilibrium data yielded consistent, high-precision determinations of ΔG_{0} via multiple techniques (force-dependent kinetics, Crooks fluctuation theorem, and inverse Boltzmann analysis). We also deduced the full 1D projection of the free-energy landscape in this region. Importantly, ΔG_{0} was determined in bacteriorhodopsin's native bilayer, an advance over traditional results obtained by chemical denaturation in nonphysiological detergent micelles.
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Affiliation(s)
- Hao Yu
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - David R Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
| | - Hao Luo
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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7
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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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Ritzmann N, Thoma J. Mechanical Unfolding and Refolding of Single Membrane Proteins by Atomic Force Microscopy. Methods Mol Biol 2020; 2127:359-372. [PMID: 32112333 DOI: 10.1007/978-1-0716-0373-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Atomic force microscopy (AFM)-based single-molecule force spectroscopy allows direct physical manipulation of single membrane proteins under near-physiological conditions. It can be applied to study mechanical properties and molecular interactions as well as unfolding and folding pathways of membrane proteins. Here, we describe the basic procedure to study membrane proteins by single-molecule force spectroscopy and discuss general requirements of the experimental setup as well as common pitfalls typically encountered when working with membrane proteins in AFM.
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Affiliation(s)
- Noah Ritzmann
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel, Switzerland
| | - Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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Nash MA. Zig Zag AFM Protocol Reveals New Intermediate Folding States of Bacteriorhodopsin. Biophys J 2019; 118:538-540. [PMID: 32023441 DOI: 10.1016/j.bpj.2019.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/12/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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10
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Jacobson DR, Uyetake L, Perkins TT. Membrane-Protein Unfolding Intermediates Detected with Enhanced Precision Using a Zigzag Force Ramp. Biophys J 2019; 118:667-675. [PMID: 31882249 DOI: 10.1016/j.bpj.2019.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 01/15/2023] Open
Abstract
Precise quantification of the energetics and interactions that stabilize membrane proteins in a lipid bilayer is a long-sought goal. Toward this end, atomic force microscopy has been used to unfold individual membrane proteins embedded in their native lipid bilayer, typically by retracting the cantilever at a constant velocity. Recently, unfolding intermediates separated by as few as two amino acids were detected using focused-ion-beam-modified ultrashort cantilevers. However, unambiguously discriminating between such closely spaced states remains challenging, in part because any individual unfolding trajectory only occupies a subset of the total number of intermediates. Moreover, structural assignment of these intermediates via worm-like-chain analysis is hindered by brief dwell times compounded with thermal and instrumental noise. To overcome these issues, we moved the cantilever in a sawtooth pattern of 6-12 nm, offset by 0.25-1 nm per cycle, generating a "zigzag" force ramp of alternating positive and negative loading rates. We applied this protocol to the model membrane protein bacteriorhodopsin (bR). In contrast to conventional studies that extract bR's photoactive retinal along with the first transmembrane helix, we unfolded bR in the presence of its retinal. To do so, we introduced a previously developed enzymatic-cleavage site between helices E and F and pulled from the top of the E helix using a site-specific, covalent attachment. The resulting zigzag unfolding trajectories occupied 40% more states per trajectory and occupied those states for longer times than traditional constant-velocity records. In total, we identified 31 intermediates during the unfolding of five helices of EF-cleaved bR. These included a previously reported, mechanically robust intermediate located between helices C and B that, with our enhanced resolution, is now shown to be two distinct states separated by three amino acids. Interestingly, another intermediate directly interacted with the retinal, an interaction confirmed by removing the retinal.
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Affiliation(s)
- David R Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado.
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11
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Wang Z, Jumper JM, Freed KF, Sosnick TR. On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations. Biophys J 2019; 117:1429-1441. [PMID: 31587831 DOI: 10.1016/j.bpj.2019.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 08/25/2019] [Accepted: 09/12/2019] [Indexed: 11/25/2022] Open
Abstract
Single-molecule force spectroscopy has proven extremely beneficial in elucidating folding pathways for membrane proteins. Here, we simulate these measurements, conducting hundreds of unfolding trajectories using our fast Upside algorithm for slow enough speeds to reproduce key experimental features that may be missed using all-atom methods. The speed also enables us to determine the logarithmic dependence of pulling velocities on the rupture levels to better compare to experimental values. For simulations of atomic force microscope measurements in which force is applied vertically to the C-terminus of bacteriorhodopsin, we reproduce the major experimental features including even the back-and-forth unfolding of single helical turns. When pulling laterally on GlpG to mimic the experiment, we observe quite different behavior depending on the stiffness of the spring. With a soft spring, as used in the experimental studies with magnetic tweezers, the force remains nearly constant after the initial unfolding event, and a few pathways and a high degree of cooperativity are observed in both the experiment and simulation. With a stiff spring, however, the force drops to near zero after each major unfolding event, and numerous intermediates are observed along a wide variety of pathways. Hence, the mode of force application significantly alters the perception of the folding landscape, including the number of intermediates and the degree of folding cooperativity, important issues that should be considered when designing experiments and interpreting unfolding data.
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Affiliation(s)
- Zongan Wang
- Department of Chemistry, James Franck Institute, The University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - John M Jumper
- Department of Chemistry, James Franck Institute, The University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Karl F Freed
- Department of Chemistry, James Franck Institute, The University of Chicago, Chicago, Illinois.
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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12
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Heenan PR, Yu H, Siewny MGW, Perkins TT. Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy. J Chem Phys 2018; 148:123313. [PMID: 29604885 DOI: 10.1063/1.5009108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG0) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.
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Affiliation(s)
- Patrick R Heenan
- JILA, National Institute of Standard and Technology and University of Colorado, Boulder, Colorado 80309, USA
| | - Hao Yu
- JILA, National Institute of Standard and Technology and University of Colorado, Boulder, Colorado 80309, USA
| | - Matthew G W Siewny
- JILA, National Institute of Standard and Technology and University of Colorado, Boulder, Colorado 80309, USA
| | - Thomas T Perkins
- JILA, National Institute of Standard and Technology and University of Colorado, Boulder, Colorado 80309, USA
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13
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Yu H, Siewny MGW, Edwards DT, Sanders AW, Perkins TT. Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins. Science 2017; 355:945-950. [PMID: 28254940 DOI: 10.1126/science.aah7124] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/06/2017] [Indexed: 12/27/2022]
Abstract
Protein folding occurs as a set of transitions between structural states within an energy landscape. An oversimplified view of the folding process emerges when transiently populated states are undetected because of limited instrumental resolution. Using force spectroscopy optimized for 1-microsecond resolution, we reexamined the unfolding of individual bacteriorhodopsin molecules in native lipid bilayers. The experimental data reveal the unfolding pathway in unprecedented detail. Numerous newly detected intermediates-many separated by as few as two or three amino acids-exhibited complex dynamics, including frequent refolding and state occupancies of <10 μs. Equilibrium measurements between such states enabled the folding free-energy landscape to be deduced. These results sharpen the picture of the mechanical unfolding of membrane proteins and, more broadly, enable experimental access to previously obscured protein dynamics.
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Affiliation(s)
- Hao Yu
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
| | - Matthew G W Siewny
- 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
| | - Aric W Sanders
- Radio Frequency Technology Division, National Institute of Standards and Technology, Boulder, CO 80305, 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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14
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Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1512-1521. [PMID: 28844743 DOI: 10.1016/j.bbapap.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022]
Abstract
Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.
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15
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Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics. Biophys J 2017; 111:2086-2098. [PMID: 27851934 DOI: 10.1016/j.bpj.2016.09.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 12/18/2022] Open
Abstract
Developments in atomic force microscopy have opened up a new path toward single-molecular phenomena; in particular, during the process of pulling a membrane protein out of a lipid bilayer. However, the characteristic features of the force-distance (F-D) curve of a bacteriorhodopsin in purple membrane, for instance, have not yet been fully elucidated in terms of physicochemical principles. To address the issue, we performed a computer simulation of bacteriorhodopsin with, to our knowledge, a novel coarse-grained (C-G) model. Peptide planes are represented as rigid spheres, while the surrounding environment consisting of water solvents and lipid bilayers is represented as an implicit continuum. Force-field parameters were determined on the basis of auxiliary simulations and experimental values of transfer free energy of each amino acid from water to membrane. According to Popot's two-stage model, we separated molecular interactions involving membrane proteins into two parts: I) affinity of each amino acid to the membrane and intrahelical hydrogen bonding between main chain peptide bonds; and II) interhelix interactions. Then, only part I was incorporated into the C-G model because we assumed that the part plays a dominant role in the forced unfolding process. As a result, the C-G simulation has successfully reproduced the key features, including peak positions, of the experimental F-D curves in the literature, indicating that the peak positions are essentially determined by the residue-lipid and intrahelix interactions. Furthermore, we investigated the relationships between the energy barrier formation on the forced unfolding pathways and the force peaks of the F-D curves.
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16
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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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17
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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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Lei H, He C, Hu C, Li J, Hu X, Hu X, Li H. Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hai Lei
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chengzhi He
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chunguang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Jinliang Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Xiaodong Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Hongbin Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
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Lei H, He C, Hu C, Li J, Hu X, Hu X, Li H. Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2. Angew Chem Int Ed Engl 2016; 56:6117-6121. [DOI: 10.1002/anie.201610648] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Hai Lei
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chengzhi He
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Chunguang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Jinliang Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Xiaodong Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
| | - Hongbin Li
- Department of Chemistry; University of British Columbia; 2036 Main Mall Vancouver BC V6T 1Z1 Canada
- State Key Laboratory of Precision Measurements Technology and Instruments; School of Precision Instrument and Optoelectronics Engineering; Tianjin University; Tianjin 300072 China
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20
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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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21
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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22
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Baumann A, Kerruth S, Fitter J, Büldt G, Heberle J, Schlesinger R, Ataka K. In-Situ Observation of Membrane Protein Folding during Cell-Free Expression. PLoS One 2016; 11:e0151051. [PMID: 26978519 PMCID: PMC4792443 DOI: 10.1371/journal.pone.0151051] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/23/2016] [Indexed: 12/31/2022] Open
Abstract
Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando) at molecular resolution.
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Affiliation(s)
- Axel Baumann
- Forschungszentrum Jülich, Institute of Complex Systems, Molecular Biophysics (ICS-5), 52425 Jülich, Germany
| | - Silke Kerruth
- Freie Universität Berlin, Department of Physics, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Fitter
- Forschungszentrum Jülich, Institute of Complex Systems, Molecular Biophysics (ICS-5), 52425 Jülich, Germany
- Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
| | - Georg Büldt
- Forschungszentrum Jülich, Institute of Complex Systems, Molecular Biophysics (ICS-5), 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, Laboratory for Advanced Studies of Membrane Proteins, 141700 Dolgoprudniy, Russia
| | - Joachim Heberle
- Freie Universität Berlin, Department of Physics, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Ramona Schlesinger
- Freie Universität Berlin, Department of Physics, Genetic Biophysics, Arnimallee 14, 14195 Berlin, Germany
- * E-mail: (KA); (RS)
| | - Kenichi Ataka
- Freie Universität Berlin, Department of Physics, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
- * E-mail: (KA); (RS)
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23
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Czajkowsky DM, Sun J, Shao Z. Single molecule compression reveals intra-protein forces drive cytotoxin pore formation. eLife 2015; 4:e08421. [PMID: 26652734 PMCID: PMC4714976 DOI: 10.7554/elife.08421] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/12/2015] [Indexed: 11/13/2022] Open
Abstract
Perfringolysin O (PFO) is a prototypical member of a large family of pore-forming proteins that undergo a significant reduction in height during the transition from the membrane-assembled prepore to the membrane-inserted pore. Here, we show that targeted application of compressive forces can catalyze this conformational change in individual PFO complexes trapped at the prepore stage, recapitulating this critical step of the spontaneous process. The free energy landscape determined from these measurements is in good agreement with that obtained from molecular dynamics simulations showing that an equivalent internal force is generated by the interaction of the exposed hydrophobic residues with the membrane. This hydrophobic force is transmitted across the entire structure to produce a compressive stress across a distant, otherwise stable domain, catalyzing its transition from an extended to compact conformation. Single molecule compression is likely to become an important tool to investigate conformational transitions in membrane proteins. DOI:http://dx.doi.org/10.7554/eLife.08421.001 Proteins are made up of chains of amino acids that need to fold into intricate three-dimensional shapes to work correctly. But some proteins also have to change their shape drastically when they work. Mechanical forces that change the shape of a protein can therefore be used to determine how a protein folds and how it changes its structure when working. Although researchers have developed techniques to analyze the effect of force on single proteins, most studies carried out so far have investigated the effect of stretching (or tensile forces) to understand structural changes that naturally involve an extension within the protein. However, many proteins undergo structural changes that involve a compaction in their shape. How these changes occur remains poorly understood because, for these, methods to apply compressive forces to single proteins are required. Perfringolysin O (PFO for short) is a protein that is made by a bacterium that causes food poisoning in humans. PFO makes pores in the membrane that surrounds cells. This causes the cell’s contents to leak out, killing the cell. When inserting into the membrane, PFO changes from an elongated “prepore” state to a compact pore-forming state. Czajkowsky et al. now use a combination of single molecule techniques and computer simulations to investigate how PFO undergoes this compaction. Previous work had identified a mutant PFO protein that arrests at the prepore state. Applying a compressive force to the top of this prepore-trapped PFO as it sits on the membrane transmitted forces across the entire PFO protein. This ultimately produced a compressive force across a distant part of the protein that caused the protein to change from the elongated prepore state to the compact, pore-like shape. If a compressive force was not applied, the PFO protein remained in the prepore state. Czajkowsky et al. further found that this compressive force is naturally produced by distant water-repellent parts of the naturally occurring protein interacting with the cell membrane. Therefore, internal forces can transmit across proteins to drive shape changes in distant regions. In the future, the methods developed in this study could be applied to analyze other naturally occurring changes in proteins where shape compaction happens when working. DOI:http://dx.doi.org/10.7554/eLife.08421.002
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Affiliation(s)
- Daniel M Czajkowsky
- State Key Laboratory of Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jielin Sun
- State Key Laboratory of Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhifeng Shao
- State Key Laboratory of Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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24
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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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25
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Scholl ZN, Yang W, Marszalek PE. Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization. ACS NANO 2015; 9:1189-97. [PMID: 25639698 DOI: 10.1021/nn504686f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Understanding how protein oligomerization affects the stability of monomers in self-assembled structures is crucial to the development of new protein-based nanomaterials and protein cages for drug delivery. Here, we use single-molecule force spectroscopy (AFM-SMFS), protein engineering, and computer simulations to evaluate how dimerization and tetramerization affects the stability of the monomer of Streptavidin, a model homotetrameric protein. The unfolding force directly relates to the folding stability, and we find that monomer of Streptavidin is mechanically stabilized by 40% upon dimerization, and that it is stabilized an additional 24% upon tetramerization. We also find that biotin binding increases stability by another 50% as compared to the apo-tetrameric form. We used the distribution of unfolding forces to extract properties of the underlying energy landscape and found that the distance to the transition state is decreased and the barrier height is increased upon multimerization. Finally, we investigated the origin of the strengthening by ligand binding. We found that, rather than being strengthened through intramolecular contacts, it is strengthened due to the contacts provided by the biotin-binding loop that crosses the interface between the dimers.
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Affiliation(s)
- Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Duke University , Durham, North Carolina 27708, United States
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26
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Chen Y, Radford SE, Brockwell DJ. Force-induced remodelling of proteins and their complexes. Curr Opin Struct Biol 2015; 30:89-99. [PMID: 25710390 PMCID: PMC4499843 DOI: 10.1016/j.sbi.2015.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 11/23/2022]
Abstract
Force can drive conformational changes in proteins, as well as modulate their stability and the affinity of their complexes, allowing a mechanical input to be converted into a biochemical output. These properties have been utilised by nature and force is now recognised to be widely used at the cellular level. The effects of force on the biophysical properties of biological systems can be large and varied. As these effects are only apparent in the presence of force, studies on the same proteins using traditional ensemble biophysical methods can yield apparently conflicting results. Where appropriate, therefore, force measurements should be integrated with other experimental approaches to understand the physiological context of the system under study.
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Affiliation(s)
- Yun Chen
- 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.
| | - 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.
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27
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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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28
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Pfreundschuh M, Martinez-Martin D, Mulvihill E, Wegmann S, Muller DJ. Multiparametric high-resolution imaging of native proteins by force-distance curve–based AFM. Nat Protoc 2014; 9:1113-30. [DOI: 10.1038/nprot.2014.070] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Scholl ZN, Li Q, Marszalek PE. Single molecule mechanical manipulation for studying biological properties of proteins,
DNA
, and sugars. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 6:211-29. [DOI: 10.1002/wnan.1253] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/10/2013] [Accepted: 10/17/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Zackary N. Scholl
- Department of Computational Biology and Bioinformatics Duke University Durham NC USA
| | - Qing Li
- Department of Mechanical Engineering and Materials Science Duke University Durham NC USA
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems Duke University Durham NC USA
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30
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Van Lehn RC, Atukorale PU, Carney RP, Yang YS, Stellacci F, Irvine DJ, Alexander-Katz A. Effect of particle diameter and surface composition on the spontaneous fusion of monolayer-protected gold nanoparticles with lipid bilayers. NANO LETTERS 2013; 13:4060-7. [PMID: 23915118 PMCID: PMC4177149 DOI: 10.1021/nl401365n] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Anionic, monolayer-protected gold nanoparticles (AuNPs) have been shown to nondisruptively penetrate cellular membranes. Here, we show that a critical first step in the penetration process is potentially the fusion of such AuNPs with lipid bilayers. Free energy calculations, experiments on unilamellar and multilamellar vesicles, and cell studies all support this hypothesis. Furthermore, we show that fusion is only favorable for AuNPs with core diameters below a critical size that depends on the monolayer composition.
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Affiliation(s)
- Reid C. Van Lehn
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Prabhani U. Atukorale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Randy P. Carney
- Institute of Materials, École Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Yu-Sang Yang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Darrell J. Irvine
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Corresponding Author
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31
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Scholl ZN, Marszalek PE. Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions. Ultramicroscopy 2013; 136:7-14. [PMID: 24001740 DOI: 10.1016/j.ultramic.2013.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/17/2013] [Accepted: 07/25/2013] [Indexed: 12/30/2022]
Abstract
The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age.
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Affiliation(s)
- Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
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32
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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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33
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Heyden M, Freites JA, Ulmschneider MB, White SH, Tobias DJ. Assembly and Stability of α-Helical Membrane Proteins. SOFT MATTER 2012; 8:7742-7752. [PMID: 23166562 PMCID: PMC3500387 DOI: 10.1039/c2sm25402f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Grease to grease - this is how one might begin to describe the tendency of hydrophobic stretches in protein amino acid sequences to form transmembrane domains. While this simple rule contains a lot of truth, the mechanisms of membrane protein folding, the insertion of hydrophobic protein domains into the lipid bilayer, and the apparent existence of highly polar residues in some proteins in the hydrophobic membrane core are subjects of lively debate - an indication that many details remain unresolved. Here, we present a historical survey of recent insights from experiments and computational studies into the rules and mechanisms of α-helical membrane protein assembly and stability.
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Affiliation(s)
- Matthias Heyden
- Department of Chemistry, University of California, Irvine, CA 92697, U.S.A
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34
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Booth PJ. A successful change of circumstance: a transition state for membrane protein folding. Curr Opin Struct Biol 2012; 22:469-75. [DOI: 10.1016/j.sbi.2012.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/09/2012] [Accepted: 03/14/2012] [Indexed: 01/02/2023]
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35
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Churnside AB, Sullan RMA, Nguyen DM, Case SO, Bull MS, King GM, Perkins TT. Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy. NANO LETTERS 2012; 12:3557-61. [PMID: 22694769 PMCID: PMC3397142 DOI: 10.1021/nl301166w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Force drift is a significant, yet unresolved, problem in atomic force microscopy (AFM). We show that the primary source of force drift for a popular class of cantilevers is their gold coating, even though they are coated on both sides to minimize drift. Drift of the zero-force position of the cantilever was reduced from 900 nm for gold-coated cantilevers to 70 nm (N = 10; rms) for uncoated cantilevers over the first 2 h after wetting the tip; a majority of these uncoated cantilevers (60%) showed significantly less drift (12 nm, rms). Removing the gold also led to ∼10-fold reduction in reflected light, yet short-term (0.1-10 s) force precision improved. Moreover, improved force precision did not require extended settling; most of the cantilevers tested (9 out of 15) achieved sub-pN force precision (0.54 ± 0.02 pN) over a broad bandwidth (0.01-10 Hz) just 30 min after loading. Finally, this precision was maintained while stretching DNA. Hence, removing gold enables both routine and timely access to sub-pN force precision in liquid over extended periods (100 s). We expect that many current and future applications of AFM can immediately benefit from these improvements in force stability and precision.
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Affiliation(s)
| | | | - Duc M. Nguyen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, 80309, USA
| | | | - Matthew S. Bull
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA
| | | | - Thomas T. Perkins
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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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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Damaghi M, Köster S, Bippes CA, Yildiz Ö, Müller DJ. One β Hairpin Follows the Other: Exploring Refolding Pathways and Kinetics of the Transmembrane β-Barrel Protein OmpG. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101450] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Damaghi M, Köster S, Bippes CA, Yildiz Ö, Müller DJ. One β Hairpin Follows the Other: Exploring Refolding Pathways and Kinetics of the Transmembrane β-Barrel Protein OmpG. Angew Chem Int Ed Engl 2011; 50:7422-4. [DOI: 10.1002/anie.201101450] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 05/10/2011] [Indexed: 11/10/2022]
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Andreopoulos B, Labudde D. Efficient unfolding pattern recognition in single molecule force spectroscopy data. Algorithms Mol Biol 2011; 6:16. [PMID: 21645400 PMCID: PMC3126767 DOI: 10.1186/1748-7188-6-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 06/06/2011] [Indexed: 11/20/2022] Open
Abstract
Background Single-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D) curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived. Results In the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR). We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise unfolding of the transmembrane helices. In contrast, a side peak is an unfolding event in the alpha-helix or other secondary structural element. The algorithm is capable of detecting side peaks along with main peaks. Therefore, we can detect the individual unfolding pathway as the sequence of events labeled with their occurrences and co-occurrences special to bR's unfolding pathway. We find that side peaks do not co-occur with one another in curves as frequently as main peaks do, which may imply a synergistic effect occurring between helices. While main peaks co-occur as pairs in at least 50% of curves, the side peaks co-occur with one another in less than 10% of curves. Moreover, the algorithm runtime scales well as the dataset size increases. Conclusions Our algorithm satisfies the requirements of an automated methodology that combines high accuracy with efficiency in analyzing SMFS datasets. The algorithm tackles the force spectroscopy analysis bottleneck leading to more consistent and reproducible results.
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Kinetic folding mechanism of an integral membrane protein examined by pulsed oxidative labeling and mass spectrometry. J Mol Biol 2011; 410:146-58. [PMID: 21570983 DOI: 10.1016/j.jmb.2011.04.074] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/26/2011] [Accepted: 04/29/2011] [Indexed: 11/21/2022]
Abstract
We report the application of pulsed oxidative labeling for deciphering the folding mechanism of a membrane protein. SDS-denatured bacteriorhodopsin (BR) was refolded by mixing with bicelles in the presence of free retinal. At various time points (20 ms to 1 day), the protein was exposed to a microsecond ·OH pulse that induces oxidative modifications at solvent-accessible methionine side chains. The extent of labeling was determined by mass spectrometry. These measurements were complemented by stopped-flow spectroscopy. Major time-dependent changes in solvent accessibility were detected for M20 (helix A) and M118 (helix D). Our kinetic data indicate a sequential folding mechanism, consistent with models previously suggested by others on the basis of optical data. Yet, ·OH labeling provides additional structural insights. An initial folding intermediate I(1) gets populated within 20 ms, concomitantly with formation of helix A. Subsequent structural consolidation leads to a transient species I(2). Noncovalent retinal binding to I(2) induces folding of helix D, thereby generating an intermediate I(R). In the absence of retinal, the latter transition does not take place. Hence, formation of helix D depends on retinal binding, whereas this is not the case for helix A. As the cofactor settles deeper into its binding pocket, a final transient species I(R) is generated. This intermediate converts into native BR within minutes by formation of the retinal-K216 Schiff base linkage. The combination of pulsed covalent labeling and optical spectroscopy employed here should also be suitable for exploring the folding mechanisms of other membrane proteins.
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Velocity-dependent mechanical unfolding of bacteriorhodopsin is governed by a dynamic interaction network. Biophys J 2011; 100:1109-19. [PMID: 21320457 DOI: 10.1016/j.bpj.2011.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/03/2011] [Accepted: 01/05/2011] [Indexed: 12/17/2022] Open
Abstract
Bacteriorhodopsin is a model system for membrane proteins. This seven transmembrane helical protein is embedded within a membrane structure called purple membrane. Its structural stability against mechanical stress was recently investigated by atomic force microscopy experiments, in which single proteins were extracted from the purple membrane. Here, we study this process by all-atom molecular dynamics simulations, in which single bacteriorhodopsin molecules were extracted and unfolded from an atomistic purple membrane model. In our simulations, key features from the experiments like force profiles and location of key residues that resist mechanical unfolding were reproduced. These key residues were seen to be stabilized by a dynamic network of intramolecular interactions. Further, the unfolding pathway was found to be velocity-dependent. Simulations in which the mechanical stress was released during unfolding revealed relaxation motions that allowed characterization of the nonequilibrium processes during fast extraction.
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Last JA, Russell P, Nealey PF, Murphy CJ. The applications of atomic force microscopy to vision science. Invest Ophthalmol Vis Sci 2011; 51:6083-94. [PMID: 21123767 DOI: 10.1167/iovs.10-5470] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The atomic force microscope (AFM) is widely used in materials science and has found many applications in biological sciences but has been limited in use in vision science. The AFM can be used to image the topography of soft biological materials in their native environments. It can also be used to probe the mechanical properties of cells and extracellular matrices, including their intrinsic elastic modulus and receptor-ligand interactions. In this review, the operation of the AFM is described along with a review of how it has been thus far used in vision science. It is hoped that this review will serve to stimulate vision scientists to consider incorporating AFM as part of their research toolkit.
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Affiliation(s)
- Julie A Last
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Lee W, Zeng X, Zhou HX, Bennett V, Yang W, Marszalek PE. Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. J Biol Chem 2010; 285:38167-72. [PMID: 20870713 DOI: 10.1074/jbc.m110.179697] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
During co-translational folding, the nascent polypeptide chain is extruded sequentially from the ribosome exit tunnel and is [corrected] under severe conformational constraints [corrected] dictated by the one-dimensional geometry of the tunnel. [corrected] How do such vectorial constraints impact the folding pathway? Here, we combine single-molecule atomic force spectroscopy and steered molecular dynamics simulations to examine protein folding in the presence of one-dimensional constraints that are similar to those imposed on the nascent polypeptide chain. The simulations exquisitely reproduced the experimental unfolding and refolding force extension relationships and led to the full reconstruction of the vectorial folding pathway of a large polypeptide, the 253-residue consensus ankyrin repeat protein, NI6C. We show that fully stretched and then relaxed NI6C starts folding by the formation of local secondary structures, followed by the nucleation of three N-terminal repeats. This rate-limiting step is then followed by the vectorial and sequential folding of the remaining repeats. However, after partial unfolding, when allowed to refold, the C-terminal repeats successively regain structures without any nucleation step by using the intact N-terminal repeats as a template. These results suggest a pathway for the co-translational folding of repeat proteins and have implications for mechanotransduction.
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Affiliation(s)
- Whasil Lee
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
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Wright CJ, Shah MK, Powell LC, Armstrong I. Application of AFM from microbial cell to biofilm. SCANNING 2010; 32:134-49. [PMID: 20648545 DOI: 10.1002/sca.20193] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Atomic Force Microscopy (AFM) has proven itself over recent years as an essential tool for the analysis of microbial systems. This article will review how AFM has been used to study microbial systems to provide unique insight into their behavior and relationship with their environment. Immobilization of live cells has enabled AFM imaging and force measurement to provide understanding of the structure and function of numerous microbial cells. At the macromolecular level AFM investigation into the properties of surface macromolecules and the energies associated with their mechanical conformation and functionality has helped unravel the complex interactions of microbial cells. At the level of the whole cell AFM has provided an integrated analysis of how the microbial cell exploits its environment through its selective, adaptable interface, the cell surface. In addition to these areas of study the AFM investigation of microbial biofilms has been vital for industrial and medical process analysis. There exists a tremendous potential for the future application of AFM to microbial systems and this has been strengthened by the trend to use AFM in combination with other characterization methods, such as confocal microscopy and Raman spectroscopy, to elucidate dynamic cellular processes.
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Affiliation(s)
- Chris J Wright
- Multidisciplinary Nanotechnology Centre, School of Engineering, Swansea University, Swansea, United Kingdom.
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45
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Evidence for a Broad Transition-State Ensemble in Calmodulin Folding from Single-Molecule Force Spectroscopy. Angew Chem Int Ed Engl 2010; 49:3306-9. [DOI: 10.1002/anie.200905747] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Junker J, Rief M. Nachweis für ein breites Ensemble von Übergangszuständen bei der Faltung von Calmodulin durch Einzelmolekül-Kraftspektroskopie. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Sapra KT, Damaghi M, Köster S, Yildiz O, Kühlbrandt W, Muller DJ. One beta hairpin after the other: exploring mechanical unfolding pathways of the transmembrane beta-barrel protein OmpG. Angew Chem Int Ed Engl 2010; 48:8306-8. [PMID: 19787673 DOI: 10.1002/anie.200904361] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- K Tanuj Sapra
- Department of Cellular Machines, Biotechnology Center, University of Technology Dresden, 01307 Dresden, Germany
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48
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Pan Y, Konermann L. Membrane protein structural insights from chemical labeling and mass spectrometry. Analyst 2010; 135:1191-200. [DOI: 10.1039/b924805f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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49
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Pan Y, Brown L, Konermann L. Mapping the Structure of an Integral Membrane Protein under Semi-Denaturing Conditions by Laser-Induced Oxidative Labeling and Mass Spectrometry. J Mol Biol 2009; 394:968-81. [DOI: 10.1016/j.jmb.2009.09.063] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 09/28/2009] [Accepted: 09/28/2009] [Indexed: 12/23/2022]
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50
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Neumann J, Gottschalk KE. The effect of different force applications on the protein-protein complex Barnase-Barstar. Biophys J 2009; 97:1687-99. [PMID: 19751674 DOI: 10.1016/j.bpj.2009.01.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 01/09/2009] [Accepted: 01/13/2009] [Indexed: 12/16/2022] Open
Abstract
Steered molecular dynamics simulations are a tool to examine the energy landscape of protein-protein complexes by applying external forces. Here, we analyze the influence of the velocity and geometry of the probing forces on a protein complex using this tool. With steered molecular dynamics, we probe the stability of the protein-protein complex Barnase-Barstar. The individual proteins are mechanically labile. The Barnase-Barstar binding site is more stable than the folds of the individual proteins. By using different force protocols, we observe a variety of responses of the system to the applied tension.
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Affiliation(s)
- Jan Neumann
- Angewandte Physik und Biophysik, Ludwig-Maximilians Universität, Munich, Germany
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