1
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McKenzie DM, Wirth D, Pogorelov TV, Hristova K. Utility of FRET in studies of membrane protein oligomerization: The concept of the effective dissociation constant. Biophys J 2023; 122:4113-4120. [PMID: 37735871 PMCID: PMC10598290 DOI: 10.1016/j.bpj.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/07/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
The activity of many membrane receptors is controlled through their lateral association into dimers or higher-order oligomers. Although Förster resonance energy transfer (FRET) measurements have been used extensively to characterize the stability of receptor dimers, the utility of FRET in studies of larger oligomers has been limited. Here we introduce an effective equilibrium dissociation constant that can be extracted from FRET measurements for EphA2, a receptor tyrosine kinase (RTK) known to form active oligomers of heterogeneous distributions in response to its ligand ephrinA1-Fc. The newly introduced effective equilibrium dissociation constant has a well-defined physical meaning and biological significance. It denotes the receptor concentration for which half of the receptors are monomeric and inactive, and the other half are associated into oligomers and are active, irrespective of the exact oligomer size. This work introduces a new dimension to the utility of FRET in studies of membrane receptor association and signaling in the plasma membrane.
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Affiliation(s)
- Daniel M McKenzie
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, Maryland
| | - Daniel Wirth
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, Maryland
| | - Taras V Pogorelov
- Department of Chemistry, Center for Biophysics and Quantitative Biology, School of Chemical Sciences, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, Maryland.
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2
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Ionic liquids as protein stabilizers for biological and biomedical applications: A review. Biotechnol Adv 2022; 61:108055. [DOI: 10.1016/j.biotechadv.2022.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022]
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3
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Ernst M, Robertson JL. The Role of the Membrane in Transporter Folding and Activity. J Mol Biol 2021; 433:167103. [PMID: 34139219 PMCID: PMC8756397 DOI: 10.1016/j.jmb.2021.167103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
The synthesis, folding, and function of membrane transport proteins are critical factors for defining cellular physiology. Since the stability of these proteins evolved amidst the lipid bilayer, it is no surprise that we are finding that many of these membrane proteins demonstrate coupling of their structure or activity in some way to the membrane. More and more transporter structures are being determined with some information about the surrounding membrane, and computational modeling is providing further molecular details about these solvation structures. Thus, the field is moving towards identifying which molecular mechanisms - lipid interactions, membrane perturbations, differential solvation, and bulk membrane effects - are involved in linking membrane energetics to transporter stability and function. In this review, we present an overview of these mechanisms and the growing evidence that the lipid bilayer is a major determinant of the fold, form, and function of membrane transport proteins in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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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: 5] [Impact Index Per Article: 1.7] [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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5
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Paul MD, Rainwater R, Zuo Y, Gu L, Hristova K. Probing Membrane Protein Association Using Concentration‐Dependent Number and Brightness. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael D. Paul
- Program in Molecular Biophysics Johns Hopkins University Baltimore MD 21218 USA
| | - Randall Rainwater
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Yi Zuo
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Luo Gu
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA
- Program in Molecular Biophysics Johns Hopkins University Baltimore MD 21218 USA
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6
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Paul MD, Rainwater R, Zuo Y, Gu L, Hristova K. Probing Membrane Protein Association Using Concentration-Dependent Number and Brightness. Angew Chem Int Ed Engl 2021; 60:6503-6508. [PMID: 33351993 DOI: 10.1002/anie.202010049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/11/2020] [Indexed: 01/13/2023]
Abstract
We introduce concentration-dependent number and brightness (cdN&B), a fluorescence fluctuation technique that can be implemented on a standard confocal microscope and can report on the thermodynamics of membrane protein association in the native plasma membrane. It uses transient transfection to enable measurements of oligomer size as a function of receptor concentration over a broad range, yielding the association constant. We discuss artifacts in cdN&B that are concentration-dependent and can distort the oligomerization curves, and we outline procedures that can correct for them. Using cdN&B, we characterize the association of neuropilin 1 (NRP1), a protein that plays a critical role in the development of the embryonic cardiovascular and nervous systems. We show that NRP1 associates into a tetramer in a concentration-dependent manner, and we quantify the strength of the association. This work demonstrates the utility of cdN&B as a powerful tool in biophysical chemistry.
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Affiliation(s)
- Michael D Paul
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Randall Rainwater
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yi Zuo
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Luo Gu
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
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7
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Cho CH, Park SI, Ciniglia C, Yang EC, Graf L, Bhattacharya D, Yoon HS. Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta). BMC Evol Biol 2020; 20:112. [PMID: 32892741 PMCID: PMC7487498 DOI: 10.1186/s12862-020-01677-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/20/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). RESULTS To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. CONCLUSIONS The high divergence of G-type mitogenomes was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.
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Affiliation(s)
- Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Claudia Ciniglia
- Department of Environmental, Biological and Pharmaceutical Science and Technologies, University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Eun Chan Yang
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, 49111, South Korea
| | - Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea.
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8
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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: 9] [Impact Index Per Article: 2.3] [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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9
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Solid-state NMR spectroscopy based atomistic view of a membrane protein unfolding pathway. Nat Commun 2019; 10:3867. [PMID: 31455771 PMCID: PMC6711998 DOI: 10.1038/s41467-019-11849-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/06/2019] [Indexed: 01/17/2023] Open
Abstract
Membrane protein folding, structure, and function strongly depend on a cell membrane environment, yet detailed characterization of folding within a lipid bilayer is challenging. Studies of reversible unfolding yield valuable information on the energetics of folding and on the hierarchy of interactions contributing to protein stability. Here, we devise a methodology that combines hydrogen-deuterium (H/D) exchange and solid-state NMR (SSNMR) to follow membrane protein unfolding in lipid membranes at atomic resolution through detecting changes in the protein water-accessible surface, and concurrently monitoring the reversibility of unfolding. We obtain atomistic description of the reversible part of a thermally induced unfolding pathway of a seven-helical photoreceptor. The pathway is visualized through SSNMR-detected snapshots of H/D exchange patterns as a function of temperature, revealing the unfolding intermediate and its stabilizing factors. Our approach is transferable to other membrane proteins, and opens additional ways to characterize their unfolding and stabilizing interactions with atomic resolution.
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10
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Joh NH, Grigoryan G, Wu Y, DeGrado WF. Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630154 DOI: 10.1098/rstb.2016.0214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Ion transporters and channels are able to identify and act on specific substrates among myriads of ions and molecules critical to cellular processes, such as homeostasis, cell signalling, nutrient influx and drug efflux. Recently, we designed Rocker, a minimalist model for Zn2+/H+ co-transport. The success of this effort suggests that de novo membrane protein design has now come of age so as to serve a key approach towards probing the determinants of membrane protein folding, assembly and function. Here, we review general principles that can be used to design membrane proteins, with particular reference to helical assemblies with transport function. We also provide new functional and NMR data that probe the dynamic mechanism of conduction through Rocker.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Nathan H Joh
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
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11
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González Flecha FL. Kinetic stability of membrane proteins. Biophys Rev 2017; 9:563-572. [PMID: 28921106 DOI: 10.1007/s12551-017-0324-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Although membrane proteins constitute an important class of biomolecules involved in key cellular processes, study of the thermodynamic and kinetic stability of their structures is far behind that of soluble proteins. It is known that many membrane proteins become unstable when removed by detergent extraction from the lipid environment. In addition, most of them undergo irreversible denaturation, even under mild experimental conditions. This process was found to be associated with partial unfolding of the polypeptide chain exposing hydrophobic regions to water, and it was proposed that the formation of kinetically trapped conformations could be involved. In this review, we will describe some of the efforts toward understanding the irreversible inactivation of membrane proteins. Furthermore, its modulation by phospholipids, ligands, and temperature will be herein discussed.
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Affiliation(s)
- F Luis González Flecha
- Universidad de Buenos Aires, CONICET, Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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12
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Del Piccolo N, Hristova K. Quantifying the Interaction between EGFR Dimers and Grb2 in Live Cells. Biophys J 2017; 113:1353-1364. [PMID: 28734476 DOI: 10.1016/j.bpj.2017.06.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/19/2017] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Adaptor proteins are a class of cytoplasmic proteins that bind to phosphorylated residues in receptor tyrosine kinases and trigger signaling cascades that control critically important cellular processes, such as cell survival, growth, differentiation, and motility. Here, we seek to characterize the interaction between epidermal growth factor receptor (EGFR) and the cytoplasmic adaptor protein growth factor receptor-bound protein 2 (Grb2) in a cellular context. To do so, we explore the utility of a highly biologically relevant model system, mammalian cells under reversible osmotic stress, and a recently introduced Förster resonance energy transfer microscopy method, fully quantified spectral imaging. We present a method that allows us to quantify the stoichiometry and the association constant of the EGFR-Grb2 binding interaction in the plasma membrane, in the presence and absence of activating ligand. The method that we introduce can have broad utility in membrane protein research, as it can be applied to different membrane protein-cytoplasmic protein pairs.
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Affiliation(s)
- Nuala Del Piccolo
- Department of Materials Science and Engineering and Institute for NanoBio Technology, Johns Hopkins University, Baltimore, Maryland
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBio Technology, Johns Hopkins University, Baltimore, Maryland.
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13
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Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1180-1189. [PMID: 28341438 DOI: 10.1016/j.bbamem.2017.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/20/2017] [Accepted: 03/18/2017] [Indexed: 12/12/2022]
Abstract
β-Barrelmembrane proteins (βMPs) form barrel-shaped pores in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Because of the robustness of their barrel structures, βMPs have great potential as nanosensors for single-molecule detection. However, natural βMPs currently employed have inflexible biophysical properties and are limited in their pore geometry, hindering their applications in sensing molecules of different sizes and properties. Computational engineering has the promise to generate βMPs with desired properties. Here we report a method for engineering novel βMPs based on the discovery of sequence motifs that predominantly interact with the cell membrane and appear in more than 75% of transmembrane strands. By replacing β1-β6 strands of the protein OmpF that lack these motifs with β1-β6 strands of OmpG enriched with these motifs and computational verification of increased stability of its transmembrane section, we engineered a novel βMP called OmpGF. OmpGF is predicted to form a monomer with a stable transmembrane region. Experimental validations showed that OmpGF could refold in vitro with a predominant β-sheet structure, as confirmed by circular dichroism. Evidence of OmpGF membrane insertion was provided by intrinsic tryptophan fluorescence spectroscopy, and its pore-forming property was determined by a dye-leakage assay. Furthermore, single-channel conductance measurements confirmed that OmpGF function as a monomer and exhibits increased conductance than OmpG and OmpF. These results demonstrated that a novel and functional βMP can be successfully engineered through strand replacement based on sequence motif analysis and stability calculation.
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14
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Del Piccolo N, Sarabipour S, Hristova K. A New Method to Study Heterodimerization of Membrane Proteins and Its Application to Fibroblast Growth Factor Receptors. J Biol Chem 2016; 292:1288-1301. [PMID: 27927983 DOI: 10.1074/jbc.m116.755777] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 12/05/2016] [Indexed: 12/30/2022] Open
Abstract
The activity of receptor tyrosine kinases (RTKs) is controlled through their lateral association in the plasma membrane. RTKs are believed to form both homodimers and heterodimers, and the different dimers are believed to play unique roles in cell signaling. However, RTK heterodimers remain poorly characterized, as compared with homodimers, because of limitations in current experimental methods. Here, we develop a FRET-based methodology to assess the thermodynamics of hetero-interactions in the plasma membrane. To demonstrate the utility of the methodology, we use it to study the hetero-interactions between three fibroblast growth factor receptors-FGFR1, FGFR2, and FGFR3-in the absence of ligand. Our results show that all possible FGFR heterodimers form, suggesting that the biological roles of FGFR heterodimers may be as significant as the homodimer roles. We further investigate the effect of two pathogenic point mutations in FGFR3 (A391E and G380R) on heterodimerization. We show that each of these mutations stabilize most of the heterodimers, with the largest effects observed for FGFR3 wild-type/mutant heterodimers. We thus demonstrate that the methodology presented here can yield new knowledge about RTK interactions and can further our understanding of signal transduction across the plasma membrane.
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Affiliation(s)
- Nuala Del Piccolo
- From the Department of Materials Science & Engineering, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Sarvenaz Sarabipour
- From the Department of Materials Science & Engineering, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Kalina Hristova
- From the Department of Materials Science & Engineering, The Johns Hopkins University, Baltimore, Maryland 21218
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15
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King C, Stoneman M, Raicu V, Hristova K. Fully quantified spectral imaging reveals in vivo membrane protein interactions. Integr Biol (Camb) 2016; 8:216-29. [PMID: 26787445 DOI: 10.1039/c5ib00202h] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Here we introduce the fully quantified spectral imaging (FSI) method as a new tool to probe the stoichiometry and stability of protein complexes in biological membranes. The FSI method yields two dimensional membrane concentrations and FRET efficiencies in native plasma membranes. It can be used to characterize the association of membrane proteins: to differentiate between monomers, dimers, or oligomers, to produce binding (association) curves, and to measure the free energies of association in the membrane. We use the FSI method to study the lateral interactions of Vascular Endothelial Growth Factor Receptor 2 (VEGFR2), a member of the receptor tyrosine kinase (RTK) superfamily, in plasma membranes, in vivo. The knowledge gained through the use of the new method challenges the current understanding of VEGFR2 signaling.
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Affiliation(s)
- Christopher King
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
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16
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Tanaka K, Caaveiro JMM, Tsumoto K. Bidirectional Transformation of a Metamorphic Protein between the Water-Soluble and Transmembrane Native States. Biochemistry 2015; 54:6863-6. [DOI: 10.1021/acs.biochem.5b01112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Koji Tanaka
- Department of Chemistry and Biotechnology and ‡Department of
Bioengineering, School
of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jose M. M. Caaveiro
- Department of Chemistry and Biotechnology and ‡Department of
Bioengineering, School
of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology and ‡Department of
Bioengineering, School
of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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17
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Sarabipour S, Del Piccolo N, Hristova K. Characterization of membrane protein interactions in plasma membrane derived vesicles with quantitative imaging Förster resonance energy transfer. Acc Chem Res 2015; 48:2262-9. [PMID: 26244699 PMCID: PMC4841635 DOI: 10.1021/acs.accounts.5b00238] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Here we describe an experimental tool, termed quantitative imaging Förster resonance energy transfer (QI-FRET), that enables the quantitative characterization of membrane protein interactions. The QI-FRET methodology allows us to acquire binding curves and calculate association constants for complex membrane proteins in the native plasma membrane environment. The method utilizes FRET detection, and thus requires that the proteins of interest are labeled with florescent proteins, either FRET donors or FRET acceptors. Since plasma membranes of cells have complex topologies precluding the acquisition of two-dimensional binding curves, the FRET measurements are performed in plasma membrane derived vesicles that bud off cells as a result of chemical or osmotic stress. The results overviewed here are acquired in vesicles produced with an osmotic vesiculation buffer developed in our laboratory, which does not utilize harsh chemicals. The concentrations of the donor-labeled and the acceptor-labeled proteins are determined, along with the FRET efficiencies, in each vesicle. The experiments utilize transient transfection, such that a wide variety of concentrations is sampled. Then, data from hundreds of vesicles are combined to yield dimerization curves. Here we discuss recent findings about the dimerization of receptor tyrosine kinases (RTKs), membrane proteins that control cell growth and differentiation via lateral dimerization in the plasma membrane. We focus on the dimerization of fibroblast growth factor receptor 3 (FGFR3), a RTK that plays a critically important role in skeletal development. We study the role of different FGFR3 domains in FGFR3 dimerization in the absence of ligand, and we show that FGFR3 extracellular domains inhibit unliganded dimerization, while contacts between the juxtamembrane domains, which connect the transmembrane domains to the kinase domains, stabilize the unliganded FGFR3 dimers. Since FGFR3 has been documented to harbor many pathogenic single amino acid mutations that cause skeletal and cranial dysplasias, as well as cancer, we also study the effects of these mutations on dimerization. First, we show that the A391E mutation, linked to Crouzon syndrome with acanthosis nigricans and to bladder cancer, significantly enhances FGFR3 dimerization in the absence of ligand and thus induces aberrant receptor interactions. Second, we present results about the effect of three cysteine mutations that cause thanatophoric dysplasia, a lethal phenotype. Such cysteine mutations have been hypothesized previously to cause constitutive dimerization, but we find instead that they have a surprisingly modest effect on dimerization. Most of the studied pathogenic mutations also altered FGFR3 dimer structure, suggesting that both increases in dimerization propensities and changes in dimer structure contribute to the pathological phenotypes. The results acquired with the QI-FRET method further our understanding of the interactions between FGFR3 molecules and RTK molecules in general. Since RTK dimerization regulates RTK signaling, our findings advance our knowledge of RTK activity in health and disease. The utility of the QI-FRET method is not restricted to RTKs, and we thus hope that in the future the QI-FRET method will be applied to other classes of membrane proteins, such as channels and G protein-coupled receptors.
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MESH Headings
- Acanthosis Nigricans/etiology
- Acanthosis Nigricans/genetics
- Cell Membrane/chemistry
- Cell Membrane/metabolism
- Craniofacial Dysostosis/etiology
- Craniofacial Dysostosis/genetics
- Dimerization
- Fluorescence Resonance Energy Transfer
- Humans
- Mutagenesis, Site-Directed
- Protein Structure, Tertiary
- Receptor, Fibroblast Growth Factor, Type 3/chemistry
- Receptor, Fibroblast Growth Factor, Type 3/deficiency
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Thanatophoric Dysplasia/etiology
- Thanatophoric Dysplasia/genetics
- Transport Vesicles/chemistry
- Transport Vesicles/metabolism
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Affiliation(s)
- Sarvenaz Sarabipour
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Nuala Del Piccolo
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218
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18
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Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops. Proc Natl Acad Sci U S A 2015; 112:7978-83. [PMID: 26056273 DOI: 10.1073/pnas.1424751112] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2-3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3-6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state-level structure in the transition state. We propose that loops 1-3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated.
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19
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Wang Z, Ye C, Zhang X, Wei Y. Cysteine residue is not essential for CPM protein thermal-stability assay. Anal Bioanal Chem 2015; 407:3683-91. [PMID: 25772562 DOI: 10.1007/s00216-015-8587-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/10/2015] [Accepted: 02/20/2015] [Indexed: 11/29/2022]
Abstract
A popular thermal-stability assay developed especially for the study of membrane proteins uses a thiol-specific probe, 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). The fluorescence emission of CPM surges when it forms a covalent bond with the side chain of a free Cys, which becomes more readily accessible upon protein thermal denaturation. Interestingly, the melting temperatures of membrane proteins determined using the CPM assay in literature are closely clustered in the temperature range 45-55 °C. A thorough understanding of the mechanism behind the observed signal change is critical for the accurate interpretation of the protein unfolding. Here we used two α-helical membrane proteins, AqpZ and AcrB, as model systems to investigate the nature of the fluorescence surge in the CPM assay. We found that the transition temperatures measured using circular-dichroism (CD) spectroscopy and the CPM assay were significantly different. To eliminate potential artifact that might arise from the presence of detergent, we monitored the unfolding of two soluble proteins. We found that, contrary to current understanding, the presence of a sulfhydryl group was not a prerequisite for the CPM thermal-stability assay. The observed fluorescence increase is probably caused by binding of the fluorophore to hydrophobic patches exposed upon protein unfolding.
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Affiliation(s)
- Zhaoshuai Wang
- Department of Chemistry, University of Kentucky, 305 Chemistry-Physics Building, Lexington, KY, 40506, USA
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20
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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21
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The safety dance: biophysics of membrane protein folding and misfolding in a cellular context. Q Rev Biophys 2014; 48:1-34. [PMID: 25420508 DOI: 10.1017/s0033583514000110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Most biological processes require the production and degradation of proteins, a task that weighs heavily on the cell. Mutations that compromise the conformational stability of proteins place both specific and general burdens on cellular protein homeostasis (proteostasis) in ways that contribute to numerous diseases. Efforts to elucidate the chain of molecular events responsible for diseases of protein folding address one of the foremost challenges in biomedical science. However, relatively little is known about the processes by which mutations prompt the misfolding of α-helical membrane proteins, which rely on an intricate network of cellular machinery to acquire and maintain their functional structures within cellular membranes. In this review, we summarize the current understanding of the physical principles that guide membrane protein biogenesis and folding in the context of mammalian cells. Additionally, we explore how pathogenic mutations that influence biogenesis may differ from those that disrupt folding and assembly, as well as how this may relate to disease mechanisms and therapeutic intervention. These perspectives indicate an imperative for the use of information from structural, cellular, and biochemical studies of membrane proteins in the design of novel therapeutics and in personalized medicine.
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22
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Cymer F, von Heijne G, White SH. Mechanisms of integral membrane protein insertion and folding. J Mol Biol 2014; 427:999-1022. [PMID: 25277655 DOI: 10.1016/j.jmb.2014.09.014] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/13/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
The biogenesis, folding, and structure of α-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, as well as the transport of solutes and signals across membranes. Nearly all MPs require translocons--often referred to as protein-conducting channels--for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here, we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of MP insertion and the folding of polytopic MPs in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion.
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Affiliation(s)
- Florian Cymer
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm.,Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
| | - Stephen H White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems University of California, Irvine Irvine, CA 92697
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23
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Broecker J, Fiedler S, Gimpl K, Keller S. Polar Interactions Trump Hydrophobicity in Stabilizing the Self-Inserting Membrane Protein Mistic. J Am Chem Soc 2014; 136:13761-8. [DOI: 10.1021/ja5064795] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jana Broecker
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
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24
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Laganowsky A, Reading E, Allison TM, Ulmschneider MB, Degiacomi MT, Baldwin AJ, Robinson CV. Membrane proteins bind lipids selectively to modulate their structure and function. Nature 2014; 510:172-175. [PMID: 24899312 PMCID: PMC4087533 DOI: 10.1038/nature13419] [Citation(s) in RCA: 568] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/28/2014] [Indexed: 01/04/2023]
Abstract
Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane protein structure and/or function. We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding.
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Affiliation(s)
- Arthur Laganowsky
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Eamonn Reading
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Timothy M. Allison
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Matteo T. Degiacomi
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Andrew J. Baldwin
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
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25
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Ye C, Wang Z, Lu W, Zhong M, Chai Q, Wei Y. Correlation between AcrB trimer association affinity and efflux activity. Biochemistry 2014; 53:3738-46. [PMID: 24854514 PMCID: PMC4067148 DOI: 10.1021/bi5000838] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The majority of membrane proteins
function as oligomers. However,
it remains largely unclear how the oligomer stability of protein complexes
correlates with their function. Understanding the relationship between
oligomer stability and activity is essential to protein research and
to virtually all cellular processes that depend on the function of
protein complexes. Proteins make lasting or transient interactions
as they perform their functions. Obligate oligomeric proteins exist
and function exclusively at a specific oligomeric state. Although
oligomerization is clearly critical for such proteins to function,
a direct correlation between oligomer affinity and biological activity
has not yet been reported. Here, we used an obligate trimeric membrane
transporter protein, AcrB, as a model to investigate the correlation
between its relative trimer affinity and efflux activity. AcrB is
a component of the major multidrug efflux system in Escherichia coli. We created six AcrB constructs
with mutations at the transmembrane intersubunit interface, and we
determined their activities using both a drug susceptibility assay
and an ethidium bromide accumulation assay. The relative trimer affinities
of these mutants in detergent micelles were obtained using blue native
polyacrylamide gel electrophoresis. A correlation between the relative
trimer affinity and substrate efflux activity was observed, in which
a threshold trimer stability was required to maintain efflux activity.
The trimer affinity of the wild-type protein was approximately 3 kcal/mol
more stable than the threshold value. Once the threshold was reached,
an additional increase of stability in the range observed had no observable
effect on protein activity.
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Affiliation(s)
- Cui Ye
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
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26
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Ye C, Wang Z, Lu W, Wei Y. Unfolding study of a trimeric membrane protein AcrB. Protein Sci 2014; 23:897-905. [PMID: 24715637 DOI: 10.1002/pro.2471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 01/18/2023]
Abstract
The folding of a multi-domain trimeric α-helical membrane protein, Escherichia coli inner membrane protein AcrB, was investigated. AcrB contains both a transmembrane domain and a large periplasmic domain. Protein unfolding in sodium dodecyl sulfate (SDS) and urea was monitored using the intrinsic fluorescence and circular dichroism spectroscopy. The SDS denaturation curve displayed a sigmoidal profile, which could be fitted with a two-state unfolding model. To investigate the unfolding of separate domains, a triple mutant was created, in which all three Trp residues in the transmembrane domain were replaced with Phe. The SDS unfolding profile of the mutant was comparable to that of the wild type AcrB, suggesting that the observed signal change was largely originated from the unfolding of the soluble domain. Strengthening of trimer association through the introduction of an inter-subunit disulfide bond had little effect on the unfolding profile, suggesting that trimer dissociation was not the rate-limiting step in unfolding monitored by fluorescence emission. Under our experimental condition, AcrB unfolding was not reversible. Furthermore, we experimented with the refolding of a monomeric mutant, AcrBΔloop , from the SDS unfolded state. The CD spectrum of the refolded AcrBΔloop superimposed well onto the spectra of the original folded protein, while the fluorescence spectrum was not fully recovered. In summary, our results suggested that the unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild-type AcrB.
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Affiliation(s)
- Cui Ye
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, 40506
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27
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Roman EA, González Flecha FL. Kinetics and thermodynamics of membrane protein folding. Biomolecules 2014; 4:354-73. [PMID: 24970219 PMCID: PMC4030980 DOI: 10.3390/biom4010354] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/19/2014] [Accepted: 02/23/2014] [Indexed: 02/06/2023] Open
Abstract
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.
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Affiliation(s)
- Ernesto A Roman
- Laboratory of Molecular Biophysics, Institute of Biochemistry and Biophysical Chemistry, University of Buenos Aires-CONICET, Buenos Aires 1113, Argentina.
| | - F Luis González Flecha
- Laboratory of Molecular Biophysics, Institute of Biochemistry and Biophysical Chemistry, University of Buenos Aires-CONICET, Buenos Aires 1113, Argentina.
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28
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Tastan O, Dutta A, Booth P, Klein-Seetharaman J. Retinal proteins as model systems for membrane protein folding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:656-63. [PMID: 24333783 DOI: 10.1016/j.bbabio.2013.11.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/19/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
Abstract
Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins-You can teach an old dog new tricks.
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Affiliation(s)
- Oznur Tastan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Arpana Dutta
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, USA
| | - Paula Booth
- School of Biochemistry, University of Bristol, UK
| | - Judith Klein-Seetharaman
- Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry, UK.
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29
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Yu L, Lu W, Ye C, Wang Z, Zhong M, Chai Q, Sheetz M, Wei Y. Role of a conserved residue R780 in Escherichia coli multidrug transporter AcrB. Biochemistry 2013; 52:6790-6. [PMID: 24007302 DOI: 10.1021/bi400452v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multidrug efflux pumps play important roles in bacteria drug resistance. A major multidrug efflux system in Gram-negative bacteria is composed of the inner membrane transporter AcrB, outer membrane protein channel TolC, and membrane fusion protein AcrA. These three proteins form a large complex that spans both layers of cell membranes and the periplasmic space. AcrB exists and functions as a homotrimer. To identify residues at the trimer interface that play important roles in AcrB function, we conducted site directed mutagenesis and discovered a key residue, R780. Although R780K was partially functional, all other R780 mutants tested were completely nonfunctional. Replacement of R780 by other residues disrupted trimer association. However, a decrease of trimer stability was not the lone cause for the observed loss of activity, because the activity loss could not be restored by strengthening trimer interaction. Using both heat and chemical denaturation methods, we found that the mutation decreased protein stability. Finally, we identified a repressor mutation, M774K, through random mutagenesis. It restored the activity of AcrBR780A to a level close to that of the wild-type protein. To examine the mechanism of activity restoration, we monitored denaturation of AcrBR780A/M774K and found that the repressor mutation improved protein stability. These results suggest that R780 is critical for AcrB stability. When R780 was replaced by Ala, the protein retained the overall structure, still trimerized in the cell membrane, and interacted with AcrA. However, local structural rearrangement might have occurred and lead to the decrease of protein stability and loss of substrate efflux activity.
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Affiliation(s)
- Linliang Yu
- Department of Chemistry, University of Kentucky ,Lexington, Kentucky 40506, United States
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30
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Schlebach JP, Peng D, Kroncke BM, Mittendorf KF, Narayan M, Carter BD, Sanders CR. Reversible folding of human peripheral myelin protein 22, a tetraspan membrane protein. Biochemistry 2013; 52:3229-41. [PMID: 23639031 DOI: 10.1021/bi301635f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Misfolding of the α-helical membrane protein peripheral myelin protein 22 (PMP22) has been implicated in the pathogenesis of the common neurodegenerative disease known as Charcot-Marie-Tooth disease (CMTD) and also several other related peripheral neuropathies. Emerging evidence suggests that the propensity of PMP22 to misfold in the cell may be due to an intrinsic lack of conformational stability. Therefore, quantitative studies of the conformational equilibrium of PMP22 are needed to gain insight into the molecular basis of CMTD. In this work, we have investigated the folding and unfolding of wild type (WT) human PMP22 in mixed micelles. Both kinetic and thermodynamic measurements demonstrate that the denaturation of PMP22 by n-lauroyl sarcosine (LS) in dodecylphosphocholine (DPC) micelles is reversible. Assessment of the conformational equilibrium indicates that a significant fraction of unfolded PMP22 persists even in the absence of the denaturing detergent. However, we find the stability of PMP22 is increased by glycerol, which facilitates quantitation of thermodynamic parameters. To our knowledge, this work represents the first report of reversible unfolding of a eukaryotic multispan membrane protein. The results indicate that WT PMP22 possesses minimal conformational stability in micelles, which parallels its poor folding efficiency in the endoplasmic reticulum. Folding equilibrium measurements for PMP22 in micelles may provide an approach to assess the effects of cellular metabolites or potential therapeutic agents on its stability. Furthermore, these results pave the way for future investigation of the effects of pathogenic mutations on the conformational equilibrium of PMP22.
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Affiliation(s)
- Jonathan P Schlebach
- Department of Biochemistry and ‡Center for Structural Biology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States
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31
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The stability of 2-state, 3-state and more-state proteins from simple spectroscopic techniques... plus the structure of the equilibrium intermediates at the same time. Arch Biochem Biophys 2013; 531:4-13. [DOI: 10.1016/j.abb.2012.10.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/22/2012] [Accepted: 10/28/2012] [Indexed: 11/20/2022]
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32
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Hong H, Chang YC, Bowie JU. Measuring transmembrane helix interaction strengths in lipid bilayers using steric trapping. Methods Mol Biol 2013; 1063:37-56. [PMID: 23975771 DOI: 10.1007/978-1-62703-583-5_3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have developed a method to measure strong transmembrane (TM) helix interaction affinities in lipid bilayers that are difficult to measure by traditional dilution methods. The method, called steric trapping, couples dissociation of biotinylated TM helices to a competitive binding by monovalent streptavidin (mSA), so that dissociation is driven by the affinity of mSA for biotin and mSA concentration. By adjusting the binding affinity of mSA through mutation, the method can obtain dissociation constants of TM helix dimers (K d,dimer) over a range of six orders of magnitudes. The K d,dimer limit of measurable target interaction is extended 3-4 orders of magnitude lower than possible by dilution methods. Thus, steric trapping opens up new opportunities to study the folding and assembly of α-helical membrane proteins in lipid bilayer environments. Here we provide detailed methods for applying steric trapping to a TM helix dimer.
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Affiliation(s)
- Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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33
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Tol MB, Deluz C, Hassaine G, Graff A, Stahlberg H, Vogel H. Thermal unfolding of a mammalian pentameric ligand-gated ion channel proceeds at consecutive, distinct steps. J Biol Chem 2012; 288:5756-69. [PMID: 23275379 DOI: 10.1074/jbc.m112.422287] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pentameric ligand-gated ion channels (LGICs) play an important role in fast synaptic signal transduction. Binding of agonists to the β-sheet-structured extracellular domain opens an ion channel in the transmembrane α-helical region of the LGIC. How the structurally distinct and distant domains are functionally coupled for such central transmembrane signaling processes remains an open question. To obtain detailed information about the stability of and the coupling between these different functional domains, we analyzed the thermal unfolding of a homopentameric LGIC, the 5-hydroxytryptamine receptor (ligand binding, secondary structure, accessibility of Trp and Cys residues, and aggregation), in plasma membranes as well as during detergent extraction, purification, and reconstitution into artificial lipid bilayers. We found a large loss in thermostability correlating with the loss of the lipid bilayer during membrane solubilization and purification. Thermal unfolding of the 5-hydroxytryptamine receptor occurred in consecutive steps at distinct protein locations. A loss of ligand binding was detected first, followed by formation of different transient low oligomeric states of receptor pentamers, followed by partial unfolding of helical parts of the protein, which finally lead to the formation receptor aggregates. Structural destabilization of the receptor in detergents could be partially reversed by reconstituting the receptor into lipid bilayers. Our results are important because they quantify the stability of LGICs during detergent extraction and purification and can be used to create stabilized receptor proteins for structural and functional studies.
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Affiliation(s)
- Menno B Tol
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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34
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Del Piccolo N, Placone J, He L, Agudelo SC, Hristova K. Production of plasma membrane vesicles with chloride salts and their utility as a cell membrane mimetic for biophysical characterization of membrane protein interactions. Anal Chem 2012; 84:8650-5. [PMID: 22985263 DOI: 10.1021/ac301776j] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plasma membrane derived vesicles are used as a model system for the biochemical and biophysical investigations of membrane proteins and membrane organization. The most widely used vesiculation procedure relies on formaldehyde and dithiothreitol (DTT), but these active chemicals may introduce artifacts in the experimental results. Here we describe a procedure to vesiculate Chinese hamster ovary (CHO) cells, widely used for the expression of recombinant proteins, using a hypertonic vesiculation buffer containing chloride salts and no formaldehyde or DTT. We characterize the size distribution of the produced vesicles. We also show that these vesicles can be used for the biophysical characterization of interactions between membrane proteins.
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Affiliation(s)
- Nuala Del Piccolo
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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35
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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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36
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Architectural and thermodynamic principles underlying intramembrane protease function. Nat Chem Biol 2012; 8:759-68. [PMID: 22797666 PMCID: PMC4028635 DOI: 10.1038/nchembio.1021] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 06/07/2012] [Indexed: 12/18/2022]
Abstract
Intramembrane proteases hydrolyze peptide bonds within the membrane as a signaling paradigm universal to all life forms and with implications in disease. Deciphering the architectural strategies supporting intramembrane proteolysis is an essential but unattained goal. We integrated a new, quantitative and high-throughput thermal light-scattering technology, reversible equilibrium un/refolding, and quantitative protease assays to interrogate rhomboid architecture with 151 purified variants. Rhomboid proteases maintain low intrinsic thermodynamic stability (ΔG=2.1-4.5kcal/mol) resulting from a multitude of generally-weak transmembrane packing interactions, making them highly-responsive to their environment. Stability is consolidated by two buried glycines and several packing leucines, with a few multifaceted hydrogen bonds strategically-deployed to two peripheral regions. Opposite these regions lie transmembrane segment 5 and connected loops that are notably exempt of structural responsibility, suggesting intramembrane proteolysis involves considerable but localized protein dynamics. Our analyses provide a comprehensive ‘heat map’ of the physio-chemical anatomy underlying membrane-immersed enzyme function at unprecedented resolution.
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37
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Abstract
Of great interest to the academic and pharmaceutical research communities, helical transmembrane proteins are characterized by their ability to dissolve and fold in lipid bilayers—properties conferred by polypeptide spans termed transmembrane domains (TMDs). The apolar nature of TMDs necessitates the use of membrane-mimetic solvents for many structure and folding studies. This review examines the relationship between TMD structure and solvent environment, focusing on principles elucidated largely in membrane-mimetic environments with single-TMD protein and peptide models. Following a brief description of TMD sequence and conformational characteristics gleaned from the structural database, we present an overview of the conceptual models used to study folding in vitro. The impact of sequence and solvent context on the incorporation of TMDs into membranes, and its role in measurements of TMD self-assembly strengths, is then described. We conclude with a discussion of the nonspecific effects of membrane components on TMD stability.
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Affiliation(s)
- Arianna Rath
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
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38
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Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney LJ, Liang J. Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. J Mol Biol 2012; 419:89-101. [PMID: 22391420 DOI: 10.1016/j.jmb.2012.02.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 02/24/2012] [Accepted: 02/25/2012] [Indexed: 12/14/2022]
Abstract
Biogenesis of β-barrel membrane proteins is a complex, multistep, and as yet incompletely characterized process. The bacterial porin family is perhaps the best-studied protein family among β-barrel membrane proteins that allows diffusion of small solutes across the bacterial outer membrane. In this study, we have identified residues that contribute significantly to the protein-protein interaction (PPI) interface between the chains of outer membrane protein F (OmpF), a trimeric porin, using an empirical energy function in conjunction with an evolutionary analysis. By replacing these residues through site-directed mutagenesis either with energetically favorable residues or substitutions that do not occur in natural bacterial outer membrane proteins, we succeeded in engineering OmpF mutants with dimeric and monomeric oligomerization states instead of a trimeric oligomerization state. Moreover, our results suggest that the oligomerization of OmpF proceeds through a series of interactions involving two distinct regions of the extensive PPI interface: two monomers interact to form a dimer through the PPI interface near G19. This dimer then interacts with another monomer through the PPI interface near G135 to form a trimer. We have found that perturbing the PPI interface near G19 results in the formation of the monomeric OmpF only. Thermal denaturation of the designed dimeric OmpF mutant suggests that oligomer dissociation can be separated from the process of protein unfolding. Furthermore, the conserved site near G57 and G59 is important for the PPI interface and might provide the essential scaffold for PPIs.
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Affiliation(s)
- Hammad Naveed
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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39
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Kaufman SB, González-Flecha FL, González-Lebrero RM. Opposing Effects of Na+ and K+ on the Thermal Stability of Na+,K+-ATPase. J Phys Chem B 2012; 116:3421-9. [DOI: 10.1021/jp2124108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sergio B. Kaufman
- Instituto
de Química y Fisicoquímica
Biológicas and Departamento de Química Biológica,
Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - F. Luis González-Flecha
- Instituto
de Química y Fisicoquímica
Biológicas and Departamento de Química Biológica,
Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rodolfo M. González-Lebrero
- Instituto
de Química y Fisicoquímica
Biológicas and Departamento de Química Biológica,
Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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40
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Naveed H, Xu Y, Jackups R, Liang J. Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins. J Am Chem Soc 2012; 134:1775-81. [PMID: 22148174 DOI: 10.1021/ja209895m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
β-Barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. They are important for pore formation, membrane anchoring, and enzyme activity. These proteins are also often responsible for bacterial virulence. Due to difficulties in experimental structure determination, they are sparsely represented in the protein structure databank. We have developed a computational method for predicting structures of the transmembrane (TM) domains of β-barrel membrane proteins. Based on physical principles, our method can predict structures of the TM domain of β-barrel membrane proteins of novel topology, including those from eukaryotic mitochondria. Our method is based on a model of physical interactions, a discrete conformational state space, an empirical potential function, as well as a model to account for interstrand loop entropy. We are able to construct three-dimensional atomic structure of the TM domains from sequences for a set of 23 nonhomologous proteins (resolution 1.8-3.0 Å). The median rmsd of TM domains containing 75-222 residues between predicted and measured structures is 3.9 Å for main chain atoms. In addition, stability determinants and protein-protein interaction sites can be predicted. Such predictions on eukaryotic mitochondria outer membrane protein Tom40 and VDAC are confirmed by independent mutagenesis and chemical cross-linking studies. These results suggest that our model captures key components of the organization principles of β-barrel membrane protein assembly.
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Affiliation(s)
- Hammad Naveed
- Department of Bioengineering, University of Illinois at Chicago, 835 South Wolcott Avenue, Chicago, Illinois 60607, USA
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41
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Schlebach JP, Cao Z, Bowie JU, Park C. Revisiting the folding kinetics of bacteriorhodopsin. Protein Sci 2011; 21:97-106. [PMID: 22095725 DOI: 10.1002/pro.766] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/05/2011] [Accepted: 11/07/2011] [Indexed: 01/09/2023]
Abstract
The elucidation of the physical principles that govern the folding and stability of membrane proteins is one of the greatest challenges in protein science. Several insights into the folding of α-helical membrane proteins have come from the investigation of the conformational equilibrium of H. halobium bacteriorhodopsin (bR) in mixed micelles using SDS as a denaturant. In an effort to confirm that folded bR and SDS-denatured bR reach the same conformational equilibrium, we found that bR folding is significantly slower than has been previously known. Interrogation of the effect of the experimental variables on folding kinetics reveals that the rate of folding is dependent not only on the mole fraction of SDS but also on the molar concentrations of mixed micelle components, a variable that was not controlled in the previous study of bR folding kinetics. Moreover, when the molar concentrations of mixed micelle components are fixed at the concentrations commonly employed for bR equilibrium studies, conformational relaxation in the transition zone is slower than hydrolysis of the retinal Schiff base. As a result, the conformational equilibrium between folded bR and SDS-denatured bR cannot be achieved under the conventional condition. Our finding suggests that the molar concentrations of mixed micelle components are important experimental variables in the investigation of the kinetics and thermodynamics of bR folding and should be accounted for to ensure the accurate assessment of the conformational equilibrium of bR without the interference of retinal hydrolysis.
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Affiliation(s)
- Jonathan P Schlebach
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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42
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Dewald AH, Hodges JC, Columbus L. Physical determinants of β-barrel membrane protein folding in lipid vesicles. Biophys J 2011; 100:2131-40. [PMID: 21539780 DOI: 10.1016/j.bpj.2011.03.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/25/2011] [Accepted: 03/14/2011] [Indexed: 10/18/2022] Open
Abstract
The spontaneous folding of two Neisseria outer membrane proteins, opacity-associated (Opa)(60) and Opa(50) into lipid vesicles was investigated by systematically varying bulk and membrane properties. Centrifugal fractionation coupled with sodium dodecyl sulfate polyacrylamide gel electrophoresis mobility assays enabled the discrimination of aggregate, unfolded membrane-associated, and folded membrane-inserted protein states as well as the influence of pH, ionic strength, membrane surface potential, lipid saturation, and urea on each. Protein aggregation was reduced with increasing lipid chain length, basic pH, low salt, the incorporation of negatively charged guest lipids, or by the addition of urea to the folding reaction. Insertion from the membrane-associated form was improved in shorter chain lipids, with more basic pH and low ionic strength; it is hindered by unsaturated or ether-linked lipids. The isolation of the physical determinants of insertion suggests that the membrane surface and dipole potentials are driving forces for outer membrane protein insertion and folding into lipid bilayers.
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Affiliation(s)
- Alison H Dewald
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
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43
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Lu W, Zhong M, Wei Y. Folding of AcrB Subunit Precedes Trimerization. J Mol Biol 2011; 411:264-74. [DOI: 10.1016/j.jmb.2011.05.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/20/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
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44
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Senes A. Computational design of membrane proteins. Curr Opin Struct Biol 2011; 21:460-6. [PMID: 21763125 DOI: 10.1016/j.sbi.2011.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 06/06/2011] [Accepted: 06/15/2011] [Indexed: 11/28/2022]
Abstract
This article reviews the recent successes of computational protein design techniques applied to integral membrane proteins. This emerging area is still handicapped by significant difficulties in the experimental characterization of the stability and structure of the designed proteins. Nevertheless, by focusing on oligomeric complexes of single-span transmembrane (TM) peptides with detectable activity, the computational design of membrane proteins has already produced very exciting results. The 'take-home message' is that optimization of van der Waals packing and hydrogen bonding (both 'canonical' and weak Cα-H⋯O bonds) can produce functional structures of remarkable stability and specificity in the membrane.
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Affiliation(s)
- Alessandro Senes
- University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Dr., Madison, WI 53706, USA.
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45
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High-throughput selection of transmembrane sequences that enhance receptor tyrosine kinase activation. J Mol Biol 2011; 412:43-54. [PMID: 21767549 DOI: 10.1016/j.jmb.2011.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/01/2011] [Accepted: 07/05/2011] [Indexed: 12/21/2022]
Abstract
Dimerization is a critical requirement for the activation of the intracellular kinase domains of receptor tyrosine kinases (RTKs). The single transmembrane (TM) helices of RTKs contribute to dimerization, but the details are not well understood. Work with TM helices in various model systems has revealed a small number of specific dimerization sequence motifs, and it has been suggested that RTK dimerization is modulated by such motifs. Yet questions remain about the universality of these sequence motifs for RTK dimerization and about how TM domain dimerization in model systems relates to RTK activation in mammalian membranes. To investigate these questions, we designed a 3888-member combinatorial peptide library based on the TM domain of Neu (ErbB2) as a model RTK. The library contains many closely related, Neu-like sequences, including thousands of sequences with known dimerization motifs. We used an SDS-PAGE-based screen to select peptides that dimerize better than the native Neu sequence, and we assayed the activation of chimeric Neu receptors in mammalian cells with TM sequences selected in the screen. Despite the very high abundance of known dimerization motifs in the library, only a very few dimerizing sequences were identified by SDS-PAGE. About half of those sequences activated the Neu kinase significantly more than did the wild-type TM sequence. This work furthers our knowledge about the requirements for membrane protein interactions and the requirements for RTK activation in cells.
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46
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Hong H, Bowie JU. Dramatic destabilization of transmembrane helix interactions by features of natural membrane environments. J Am Chem Soc 2011; 133:11389-98. [PMID: 21682279 DOI: 10.1021/ja204524c] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins have evolved to fold and function in a lipid bilayer, so it is generally assumed that their stability should be optimized in a natural membrane environment. Yet optimal stability is not always in accord with optimization of function, so evolutionary pressure, occurring in a complex membrane environment, may favor marginal stability. Here, we find that the transmembrane helix dimer, glycophorin A (GpATM), is actually much less stable in the heterogeneous environment of a natural membrane than it is in model membranes and even common detergents. The primary destabilizing factors are electrostatic interactions between charged lipids and charged GpATM side chains, and nonspecific competition from other membrane proteins. These effects overwhelm stabilizing contributions from lateral packing pressure and excluded volume. Our work illustrates how evolution can employ membrane composition to modulate protein stability.
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Affiliation(s)
- Heedeok Hong
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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47
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Otzen D. Protein–surfactant interactions: A tale of many states. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:562-91. [DOI: 10.1016/j.bbapap.2011.03.003] [Citation(s) in RCA: 362] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/23/2011] [Accepted: 03/04/2011] [Indexed: 10/18/2022]
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48
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Pace CJ, Huang Q, Wang F, Palla KS, Fuller AA, Gao J. A FlAsH-Tetracysteine Assay for Quantifying the Association and Orientation of Transmembrane α-Helices. Chembiochem 2011; 12:1018-22. [DOI: 10.1002/cbic.201000736] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Indexed: 11/08/2022]
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49
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Schick S, Chen L, Li E, Lin J, Köper I, Hristova K. Assembly of the m2 tetramer is strongly modulated by lipid chain length. Biophys J 2011; 99:1810-7. [PMID: 20858425 DOI: 10.1016/j.bpj.2010.07.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/13/2010] [Accepted: 07/19/2010] [Indexed: 12/17/2022] Open
Abstract
The influenza virus matrix protein 2 (M2) assembles into a tetramer in the host membrane during viral uncoating and maturation. It has been used as a model system to understand the relative contributions of protein-lipid and protein-protein interactions to membrane protein structure and association. Here we investigate the effect of lipid chain length on the association of the M2 transmembrane domain into tetramers using Förster resonance energy transfer. We observe that the interactions between the M2 helices are much stronger in 1,2-dilauroyl-sn-glycero-3-phosphocholine than in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers. Thus, lipid chain length and bilayer thickness not only modulate peptide interactions, but could also be a major determinant of the association of transmembrane helices into functional membrane protein oligomers.
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Affiliation(s)
- Sandra Schick
- Department of Materials Science and Engineering, The Johns Hopkins University, Baltimore, Maryland, USA
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50
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Schlebach JP, Kim MS, Joh NH, Bowie JU, Park C. Probing membrane protein unfolding with pulse proteolysis. J Mol Biol 2010; 406:545-51. [PMID: 21192947 DOI: 10.1016/j.jmb.2010.12.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 12/06/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
Abstract
Technical challenges have greatly impeded the investigation of membrane protein folding and unfolding. To develop a new tool that facilitates the study of membrane proteins, we tested pulse proteolysis as a probe for membrane protein unfolding. Pulse proteolysis is a method to monitor protein folding and unfolding, which exploits the significant difference in proteolytic susceptibility between folded and unfolded proteins. This method requires only a small amount of protein and, in many cases, may be used with unpurified proteins in cell lysates. To evaluate the effectiveness of pulse proteolysis as a probe for membrane protein unfolding, we chose Halobacterium halobium bacteriorhodopsin (bR) as a model system. The denaturation of bR in SDS has been investigated extensively by monitoring the change in the absorbance at 560 nm (A(560)). In this work, we demonstrate that denaturation of bR by SDS results in a significant increase in its susceptibility to proteolysis by subtilisin. When pulse proteolysis was applied to bR incubated in varying concentrations of SDS, the remaining intact protein determined by electrophoresis shows a cooperative transition. The midpoint of the cooperative transition (C(m)) shows excellent agreement with that determined by A(560). The C(m) values determined by pulse proteolysis for M56A and Y57A bRs are also consistent with the measurements made by A(560). Our results suggest that pulse proteolysis is a quantitative tool to probe membrane protein unfolding. Combining pulse proteolysis with Western blotting may allow the investigation of membrane protein unfolding in situ without overexpression or purification.
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Affiliation(s)
- Jonathan P Schlebach
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907-2091, USA
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