1
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Oepen K, Mater V, Schneider D. Unfolding Individual Domains of BmrA, a Bacterial ABC Transporter Involved in Multidrug Resistance. Int J Mol Sci 2023; 24:ijms24065239. [PMID: 36982314 PMCID: PMC10049088 DOI: 10.3390/ijms24065239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
The folding and stability of proteins are often studied via unfolding (and refolding) a protein with urea. Yet, in the case of membrane integral protein domains, which are shielded by a membrane or a membrane mimetic, urea generally does not induce unfolding. However, the unfolding of α-helical membrane proteins may be induced by the addition of sodium dodecyl sulfate (SDS). When protein unfolding is followed via monitoring changes in Trp fluorescence characteristics, the contributions of individual Trp residues often cannot be disentangled, and, consequently, the folding and stability of the individual domains of a multi-domain membrane protein cannot be studied. In this study, the unfolding of the homodimeric bacterial ATP-binding cassette (ABC) transporter Bacillus multidrug resistance ATP (BmrA), which comprises a transmembrane domain and a cytosolic nucleotide-binding domain, was investigated. To study the stability of individual BmrA domains in the context of the full-length protein, the individual domains were silenced by mutating the existent Trps. The SDS-induced unfolding of the corresponding constructs was compared to the (un)folding characteristics of the wild-type (wt) protein and isolated domains. The full-length variants BmrAW413Y and BmrAW104YW164A were able to mirror the changes observed with the isolated domains; thus, these variants allowed for the study of the unfolding and thermodynamic stability of mutated domains in the context of full-length BmrA.
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Affiliation(s)
- Kristin Oepen
- Department of Chemistry-Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Veronika Mater
- Department of Chemistry-Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry-Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
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2
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Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022; 23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Protein folding is a fundamental process of life with important implications throughout biology. Indeed, tens of thousands of mutations have been associated with diseases, and most of these mutations are believed to affect protein folding rather than function. Correct folding is also a key element of design. These factors have motivated decades of research on protein folding. Unfortunately, knowledge of membrane protein folding lags that of soluble proteins. This gap is partly caused by the greater technical challenges associated with membrane protein studies, but also because of additional complexities. While soluble proteins fold in a homogenous water environment, membrane proteins fold in a setting that ranges from bulk water to highly charged to apolar. Thus, the forces that drive folding vary in different regions of the protein, and this complexity needs to be incorporated into our understanding of the folding process. Here, we review our understanding of membrane protein folding biophysics. Despite the greater challenge, better model systems and new experimental techniques are starting to unravel the forces and pathways in membrane protein folding.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - James U Bowie
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
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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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Corin K, Bowie JU. How bilayer properties influence membrane protein folding. Protein Sci 2020; 29:2348-2362. [PMID: 33058341 DOI: 10.1002/pro.3973] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/24/2023]
Abstract
The question of how proteins manage to organize into a unique three-dimensional structure has been a major field of study since the first protein structures were determined. For membrane proteins, the question is made more complex because, unlike water-soluble proteins, the solvent is not homogenous or even unique. Each cell and organelle has a distinct lipid composition that can change in response to environmental stimuli. Thus, the study of membrane protein folding requires not only understanding how the unfolded chain navigates its way to the folded state, but also how changes in bilayer properties can affect that search. Here we review what we know so far about the impact of lipid composition on bilayer physical properties and how those properties can affect folding. A better understanding of the lipid bilayer and its effects on membrane protein folding is not only important for a theoretical understanding of the folding process, but can also have a practical impact on our ability to work with and design membrane proteins.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, California, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, California, USA
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5
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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6
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Cai H, Yao H, Li T, Tang Y, Li D. High-level heterologous expression of the human transmembrane sterol Δ8,Δ7-isomerase in Pichia pastoris. Protein Expr Purif 2019; 164:105463. [DOI: 10.1016/j.pep.2019.105463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 07/30/2019] [Indexed: 01/11/2023]
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7
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Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D. Characterization of Denatured States and Reversible Unfolding of Sensory Rhodopsin II. J Mol Biol 2018; 430:4068-4086. [PMID: 30098339 DOI: 10.1016/j.jmb.2018.07.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/23/2018] [Indexed: 12/27/2022]
Abstract
Our understanding on the folding of membrane proteins lags behind that of soluble proteins due to challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding pathways, we have systematically investigated the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 ΧSDS), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal-binding pocket is disrupted, with transmembrane residues becoming more solvent exposed. Folding of pSRII from an SDS-denatured state harboring a covalently bound retinal chromophore shows deviations from an apparent two-state behavior. SDS denaturation to form the sensory opsin apo-protein is reversible. We report pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin.
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Affiliation(s)
- Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom
| | - James Mitchell
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Judith Klein-Seetharaman
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom.
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8
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Qazi SJS, Turner RJ. Influence of quaternary cation compound on the size of the Escherichia coli small multidrug resistance protein, EmrE. Biochem Biophys Rep 2018; 13:129-140. [PMID: 29552647 PMCID: PMC5852267 DOI: 10.1016/j.bbrep.2018.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 12/04/2017] [Accepted: 02/05/2018] [Indexed: 11/26/2022] Open
Abstract
EmrE is a member of the small multidrug resistance (SMR) protein family in Escherichia coli. It confers resistance to a wide variety of quaternary cation compounds (QCCs) as an efflux transporter driven by the transmembrane proton motive force. We have expressed hexahistidinyl (His6) – myc epitope tagged EmrE, extracted it from membrane preparations using the detergent n-dodecyl-β-D-maltopyranoside (DDM), and purified it using nickel-affinity chromatography. The size of the EmrE protein, in DDM environment, was then examined in the presence and absence of a range of structurally different QCC ligands that varied in their chemical structure, charge and shape. We used dynamic light scattering and showed that the size and oligomeric state distributions are dependent on the type of QCC. We also followed changes in the Trp fluorescence and determined apparent dissociation constants (Kd). Overall, our in vitro analyses of epitope tagged EmrE demonstrated subtle but significant differences in the size distributions with different QCC ligands bound. Chemical shape of ligand has significant affect on binding. Shape of the ligand affects the multimeric state of EmrE. Binding affinities strongly depend upon the ligand shape. EmrE shows high plasticity of structure to accommodate a wide range of ligands.
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Affiliation(s)
- S Junaid S Qazi
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Raymond J Turner
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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9
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Slipski CJ, Zhanel GG, Bay DC. Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae. J Membr Biol 2018; 251:15-33. [PMID: 29063140 PMCID: PMC5840245 DOI: 10.1007/s00232-017-9992-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/04/2017] [Indexed: 02/03/2023]
Abstract
Bacterial resistance to biocides used as antiseptics, dyes, and disinfectants is a growing concern in food preparation, agricultural, consumer manufacturing, and health care industries, particularly among Gram-negative Enterobacteriaceae, some of the most common community and healthcare-acquired bacterial pathogens. Biocide resistance is frequently associated with antimicrobial cross-resistance leading to reduced activity and efficacy of both antimicrobials and antiseptics. Multidrug resistant efflux pumps represent an important biocide resistance mechanism in Enterobacteriaceae. An assortment of structurally diverse efflux pumps frequently co-exist in these species and confer both unique and overlapping biocide and antimicrobial selectivity. TolC-dependent multicomponent systems that span both the plasma and outer membranes have been shown to confer clinically significant resistance to most antimicrobials including many biocides, however, a growing number of single component TolC-independent multidrug resistant efflux pumps are specifically associated with biocide resistance: small multidrug resistance (SMR), major facilitator superfamily (MFS), multidrug and toxin extruder (MATE), cation diffusion facilitator (CDF), and proteobacterial antimicrobial compound efflux (PACE) families. These efflux systems are a growing concern as they are rapidly spread between members of Enterobacteriaceae on conjugative plasmids and mobile genetic elements, emphasizing their importance to antimicrobial resistance. In this review, we will summarize the known biocide substrates of these efflux pumps, compare their structural relatedness, Enterobacteriaceae distribution, and significance. Knowledge gaps will be highlighted in an effort to unravel the role that these apparent "lone wolves" of the efflux-mediated resistome may offer.
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Affiliation(s)
- Carmine J Slipski
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - Denice C Bay
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
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10
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Lee S, Wang C, Liu H, Xiong J, Jiji R, Hong X, Yan X, Chen Z, Hammel M, Wang Y, Dai S, Wang J, Jiang C, Zhang G. Hydrogen bonds are a primary driving force for de novo protein folding. Acta Crystallogr D Struct Biol 2017; 73:955-969. [PMID: 29199976 PMCID: PMC5713874 DOI: 10.1107/s2059798317015303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/20/2017] [Indexed: 01/09/2023] Open
Abstract
The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1-153; AID153), an optimized in vitro folding procedure was derived to obtain large amounts of AID153, which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the protein after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis-to-trans proline isomerization, or vice versa, during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo. It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.
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Affiliation(s)
- Schuyler Lee
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Chao Wang
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
| | - Haolin Liu
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Jian Xiong
- Department of Chemistry, University of Missouri, Columbus, Mississippi, USA
| | - Renee Jiji
- Department of Chemistry, University of Missouri, Columbus, Mississippi, USA
| | - Xia Hong
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
| | - Xiaoxue Yan
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
| | - Zhangguo Chen
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Michal Hammel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yang Wang
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Shaodong Dai
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Jing Wang
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Chengyu Jiang
- Department of Biochemistry and Molecular Biology, Peking Union Medical College, Beijing 100005, People’s Republic of China
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
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11
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GPCR-styrene maleic acid lipid particles (GPCR-SMALPs): their nature and potential. Biochem Soc Trans 2016; 44:619-23. [PMID: 27068979 DOI: 10.1042/bst20150284] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/17/2022]
Abstract
G-protein-coupled receptors (GPCRs) form the largest class of membrane proteins and are an important target for therapeutic drugs. These receptors are highly dynamic proteins sampling a range of conformational states in order to fulfil their complex signalling roles. In order to fully understand GPCR signalling mechanisms it is necessary to extract the receptor protein out of the plasma membrane. Historically this has universally required detergents which inadvertently strip away the annulus of lipid in close association with the receptor and disrupt lateral pressure exerted by the bilayer. Detergent-solubilized GPCRs are very unstable which presents a serious hurdle to characterization by biophysical methods. A range of strategies have been developed to ameliorate the detrimental effect of removing the receptor from the membrane including amphipols and reconstitution into nanodics stabilized by membrane scaffolding proteins (MSPs) but they all require exposure to detergent. Poly(styrene-co-maleic acid) (SMA) incorporates into membranes and spontaneously forms nanoscale poly(styrene-co-maleic acid) lipid particles (SMALPs), effectively acting like a 'molecular pastry cutter' to 'solubilize' GPCRs in the complete absence of detergent at any stage and with preservation of the native annular lipid throughout the process. GPCR-SMALPs have similar pharmacological properties to membrane-bound receptor, exhibit enhanced stability compared with detergent-solubilized receptors and being non-proteinaceous in nature, are fully compatible with downstream biophysical analysis of the encapsulated GPCR.
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12
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Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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13
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Di Bartolo N, Compton ELR, Warne T, Edwards PC, Tate CG, Schertler GFX, Booth PJ. Complete Reversible Refolding of a G-Protein Coupled Receptor on a Solid Support. PLoS One 2016; 11:e0151582. [PMID: 26982879 PMCID: PMC4794186 DOI: 10.1371/journal.pone.0151582] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 03/01/2016] [Indexed: 12/22/2022] Open
Abstract
The factors defining the correct folding and stability of integral membrane proteins are poorly understood. Folding of only a few select membrane proteins has been scrutinised, leaving considerable deficiencies in knowledge for large protein families, such as G protein coupled receptors (GPCRs). Complete reversible folding, which is problematic for any membrane protein, has eluded this dominant receptor family. Moreover, attempts to recover receptors from denatured states are inefficient, yielding at best 40–70% functional protein. We present a method for the reversible unfolding of an archetypal family member, the β1-adrenergic receptor, and attain 100% recovery of the folded, functional state, in terms of ligand binding, compared to receptor which has not been subject to any unfolding and retains its original, folded structure. We exploit refolding on a solid support, which could avoid unwanted interactions and aggregation that occur in bulk solution. We determine the changes in structure and function upon unfolding and refolding. Additionally, we employ a method that is relatively new to membrane protein folding; pulse proteolysis. Complete refolding of β1-adrenergic receptor occurs in n-decyl-β-D-maltoside (DM) micelles from a urea-denatured state, as shown by regain of its original helical structure, ligand binding and protein fluorescence. The successful refolding strategy on a solid support offers a defined method for the controlled refolding and recovery of functional GPCRs and other membrane proteins that suffer from instability and irreversible denaturation once isolated from their native membranes.
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Affiliation(s)
- Natalie Di Bartolo
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Emma L. R. Compton
- Organisational and Staff Development Unit, University of Strathclyde, Glasgow, United Kingdom
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Patricia C. Edwards
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Paula J. Booth
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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14
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Zheng JS, He Y, Zuo C, Cai XY, Tang S, Wang ZA, Zhang LH, Tian CL, Liu L. Robust Chemical Synthesis of Membrane Proteins through a General Method of Removable Backbone Modification. J Am Chem Soc 2016; 138:3553-61. [PMID: 26943264 DOI: 10.1021/jacs.6b00515] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical protein synthesis can provide access to proteins with post-translational modifications or site-specific labelings. Although this technology is finding increasing applications in the studies of water-soluble globular proteins, chemical synthesis of membrane proteins remains elusive. In this report, a general and robust removable backbone modification (RBM) method is developed for the chemical synthesis of membrane proteins. This method uses an activated O-to-N acyl transfer auxiliary to install in the Fmoc solid-phase peptide synthesis process a RBM group with switchable reactivity toward trifluoroacetic acid. The method can be applied to versatile membrane proteins because the RBM group can be placed at any primary amino acid. With RBM, the membrane proteins and their segments behave almost as if they were water-soluble peptides and can be easily handled in the process of ligation, purification, and mass characterizations. After the full-length protein is assembled, the RBM group can be readily removed by trifluoroacetic acid. The efficiency and usefulness of the new method has been demonstrated by the successful synthesis of a two-transmembrane-domain protein (HCV p7 ion channel) with site-specific isotopic labeling and a four-transmembrane-domain protein (multidrug resistance transporter EmrE). This method enables practical synthesis of small- to medium-sized membrane proteins or membrane protein domains for biochemical and biophysical studies.
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Affiliation(s)
- Ji-Shen Zheng
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Yao He
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chao Zuo
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Xiao-Ying Cai
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Shan Tang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Zhipeng A Wang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Long-Hua Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
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15
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Wang L, Zhou H, Li Z, Lim TK, Lim XS, Lin Q. One-step extraction of functional recombinant aquaporin Z from inclusion bodies with optimal detergent. Protein Expr Purif 2015; 115:146-52. [DOI: 10.1016/j.pep.2015.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/11/2015] [Accepted: 08/13/2015] [Indexed: 10/23/2022]
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16
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Heydenreich FM, Vuckovic Z, Matkovic M, Veprintsev DB. Stabilization of G protein-coupled receptors by point mutations. Front Pharmacol 2015; 6:82. [PMID: 25941489 PMCID: PMC4403299 DOI: 10.3389/fphar.2015.00082] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/31/2015] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are flexible integral membrane proteins involved in transmembrane signaling. Their involvement in many physiological processes makes them interesting targets for drug development. Determination of the structure of these receptors will help to design more specific drugs, however, their structural characterization has so far been hampered by the low expression and their inherent instability in detergents which made protein engineering indispensable for structural and biophysical characterization. Several approaches to stabilize the receptors in a particular conformation have led to breakthroughs in GPCR structure determination. These include truncations of the flexible regions, stabilization by antibodies and nanobodies, fusion partners, high affinity and covalently bound ligands as well as conformational stabilization by mutagenesis. In this review we focus on stabilization of GPCRs by insertion of point mutations, which lead to increased conformational and thermal stability as well as improved expression levels. We summarize existing mutagenesis strategies with different coverage of GPCR sequence space and depth of information, design and transferability of mutations and the molecular basis for stabilization. We also discuss whether mutations alter the structure and pharmacological properties of GPCRs.
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Affiliation(s)
- Franziska M Heydenreich
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Milos Matkovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
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17
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G-protein coupled receptor solubilization and purification for biophysical analysis and functional studies, in the total absence of detergent. Biosci Rep 2015; 35:BSR20140171. [PMID: 25720391 PMCID: PMC4400634 DOI: 10.1042/bsr20140171] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
G-protein coupled receptors (GPCRs) constitute the largest class of membrane proteins and are a major drug target. A serious obstacle to studying GPCR structure/function characteristics is the requirement to extract the receptors from their native environment in the plasma membrane, coupled with the inherent instability of GPCRs in the detergents required for their solubilization. In the present study, we report the first solubilization and purification of a functional GPCR [human adenosine A2A receptor (A2AR)], in the total absence of detergent at any stage, by exploiting spontaneous encapsulation by styrene maleic acid (SMA) co-polymer direct from the membrane into a nanoscale SMA lipid particle (SMALP). Furthermore, the A2AR–SMALP, generated from yeast (Pichia pastoris) or mammalian cells, exhibited increased thermostability (∼5°C) compared with detergent [DDM (n-dodecyl-β-D-maltopyranoside)]-solubilized A2AR controls. The A2AR–SMALP was also stable when stored for prolonged periods at 4°C and was resistant to multiple freeze-thaw cycles, in marked contrast with the detergent-solubilized receptor. These properties establish the potential for using GPCR–SMALP in receptor-based drug discovery assays. Moreover, in contrast with nanodiscs stabilized by scaffold proteins, the non-proteinaceous nature of the SMA polymer allowed unobscured biophysical characterization of the embedded receptor. Consequently, CD spectroscopy was used to relate changes in secondary structure to loss of ligand binding ([3H]ZM241385) capability. SMALP-solubilization of GPCRs, retaining the annular lipid environment, will enable a wide range of therapeutic targets to be prepared in native-like state to aid drug discovery and understanding of GPCR molecular mechanisms. It is universally acknowledged that exposing cell-surface receptors to detergent is detrimental. We have used a polymer to extract the receptor and surrounding lipid as a nanoparticle that provides a novel solution compatible with purification and receptor-based drug discovery assays.
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18
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Qazi SJS, Chew R, Bay DC, Turner RJ. Structural and functional comparison of hexahistidine tagged and untagged forms of small multidrug resistance protein, EmrE. Biochem Biophys Rep 2015; 1:22-32. [PMID: 29124131 PMCID: PMC5668558 DOI: 10.1016/j.bbrep.2015.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 03/13/2015] [Accepted: 03/18/2015] [Indexed: 02/04/2023] Open
Abstract
EmrE is a member of the small multidrug resistance (SMR) protein family in Escherichia coli. EmrE confers resistance to a wide variety of quaternary cation compounds (QCCs) as an efflux transporter driven by proton motive force. The purification yield of most membrane proteins are challenging because of difficulties in over expressing, isolating and solubilizing them and the addition of an affinity tag often improves purification. The purpose of this study is to compare the structure and function of hexahistidinyl (His6) tagged (T-EmrE) and untagged (UT-EmrE) versions of EmrE. In vivo QCC resistance assays determined that T-EmrE demonstrated reduced resistance as compared to UT-EmrE. We isolated EmrE using the two different purification methods, an organic solvent extraction method used to isolate UT-EmrE and nickel affinity chromatography of T-EmrE. All proteins were solubilized in the same buffered n-dodecyl-β-d-maltopyranoside (DDM) detergent and their conformations were examined in the presence/absence of different QCCs. In vitro analysis of protein multimerization using SDS-Tricine PAGE and dynamic light scattering analysis revealed that both proteins predominated as monomers, but the formation of dimers was more constant and uniform in T-EmrE compared to UT-EmrE. The aromatic residue conformations of both proteins indicate that T-EmrE form is more aqueous exposed than UT-EmrE, but UT-EmrE appeared to have a more dynamic environment surrounding its aromatic residues. Using fluorescence to obtain QCC ligand-binding curves indicated that the two forms had differences in dissociation constants (Kd) and maximum specific one-site binding (Bmax) values for particular QCCs. In vitro analyses of both proteins demonstrated subtle but significant differences in multimerization and QCC binding. In vivo analysis indicates differences caused by the addition of the tag, we also observed differences in vitro that could be a result of the tag and/or the different purification methods. Untagged and tagged EmrE are compared in same detergent environment. Purification methods leads to differences in multimeric state distributions. Untagged EmrE has a less constrained structure compared to tagged EmrE. Presence of a tag alters substrate binding to EmrE.
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Affiliation(s)
- S Junaid S Qazi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Raymond Chew
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Denice C Bay
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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19
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Miller DM, Gulbis JM. Engineering protocells: prospects for self-assembly and nanoscale production-lines. Life (Basel) 2015; 5:1019-53. [PMID: 25815781 PMCID: PMC4500129 DOI: 10.3390/life5021019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell "machines" assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
| | - Jacqueline M Gulbis
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
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20
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Elani Y, Purushothaman S, Booth PJ, Seddon JM, Brooks NJ, Law RV, Ces O. Measurements of the effect of membrane asymmetry on the mechanical properties of lipid bilayers. Chem Commun (Camb) 2015; 51:6976-9. [PMID: 25797170 DOI: 10.1039/c5cc00712g] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We detail an approach for constructing asymmetric membranes and characterising their mechanical properties, leading to the first measurement of the effect of asymmetry on lipid bilayer mechanics. Our results demonstrate that asymmetry induces a significant increase in rigidity compared to symmetric membranes. Given that all biological membranes are asymmetric our findings have profound implications for the role of this phenomenon in biology.
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Affiliation(s)
- Yuval Elani
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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21
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Folding membrane proteins in vitro: A table and some comments. Arch Biochem Biophys 2014; 564:314-26. [DOI: 10.1016/j.abb.2014.06.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/17/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
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22
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Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
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23
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Dutta A, Altenbach C, Mangahas S, Yanamala N, Gardner E, Hubbell WL, Klein-Seetharaman J. Differential dynamics of extracellular and cytoplasmic domains in denatured States of rhodopsin. Biochemistry 2014; 53:7160-9. [PMID: 25268658 PMCID: PMC4245987 DOI: 10.1021/bi401557e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Rhodopsin
is a model system for understanding membrane protein
folding. Recently, conditions that allow maximally denaturing rhodopsin
without causing aggregation have been determined, opening the door
to the first structural characterization of denatured states of rhodopsin
by nuclear magnetic resonance (NMR) and electron paramagnetic resonance
(EPR) spectroscopy. One-dimensional 1H NMR spectra confirm
a progressive increase in flexibility of resonances in rhodopsin with
increasing denaturant concentrations. Two-dimensional 1H–15N HSQC spectra of [15N]-α-lysine-labeled
rhodopsin in which signals arise primarily from residues in the cytoplasmic
(CP) domain and of [15N]-α,ε-tryptophan-labeled
rhodopsin in which signals arise only from transmembrane (TM) and
extracellular (EC) residues indicate qualitatively that EC and CP
domains may be differentially affected by denaturation. To obtain
residue-specific information, particular residues in EC and CP domains
were investigated by site-directed spin labeling. EPR spectra of the
spin-labeled samples indicate that the EC residues retain more rigidity
in the denatured states than the CP residues. These results support
the notion of residual structure in denatured states of rhodopsin.
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Affiliation(s)
- Arpana Dutta
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
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24
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Schuldiner S. Competition as a way of life for H(+)-coupled antiporters. J Mol Biol 2014; 426:2539-46. [PMID: 24862284 DOI: 10.1016/j.jmb.2014.05.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/15/2014] [Accepted: 05/18/2014] [Indexed: 12/13/2022]
Abstract
Antiporters are ubiquitous membrane proteins that catalyze obligatory exchange between two or more substrates across a membrane in opposite directions. Some utilize proton electrochemical gradients generated by primary pumps by coupling the downhill movement of one or more protons to the movement of a substrate. Since the direction of the proton gradient usually favors proton movement toward the cytoplasm, their function results in removal of substrates other than protons from the cytoplasm, either into acidic intracellular compartments or out to the medium. H(+)-coupled antiporters play central roles in living organisms, for example, storage of neurotransmitter and other small molecules, resistance to antibiotics, homeostasis of ionic content and more. Biochemical and structural data support a general mechanism for H(+)-coupled antiporters whereby the substrate and the protons cannot bind simultaneously to the protein. In several cases, it was shown that the binding sites overlap, and therefore, there is a direct competition between the protons and the substrate. In others, the "competition" seems to be indirect and it is most likely achieved by allosteric mechanisms. The pKa of one or more carboxyls in the protein must be tuned appropriately in order to ensure the feasibility of such a mechanism. In this review, I discuss in detail the case of EmrE, a multidrug transporter from Escherichia coli and evaluate the information available for other H(+)-coupled antiporters.
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Affiliation(s)
- Shimon Schuldiner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
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25
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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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26
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EmrE dimerization depends on membrane environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1817-22. [PMID: 24680655 DOI: 10.1016/j.bbamem.2014.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 11/22/2022]
Abstract
The small multi-drug resistant (SMR) transporter EmrE functions as a homodimer. Although the small size of EmrE would seem to make it an ideal model system, it can also make it challenging to work with. As a result, a great deal of controversy has surrounded even such basic questions as the oligomeric state. Here we show that the purified protein is a homodimer in isotropic bicelles with a monomer-dimer equilibrium constant (KMD(2D)) of 0.002-0.009mol% for both the substrate-free and substrate-bound states. Thus, the dimer is stabilized in bicelles relative to detergent micelles where the KMD(2D) is only 0.8-0.95mol% (Butler et al. 2004). In dilauroylphosphatidylcholine (DLPC) liposomes KMD(2D) is 0.0005-0.0008mol% based on Förster resonance energy transfer (FRET) measurements, slightly tighter than bicelles. These results emphasize the importance of the lipid membrane in influencing dimer affinity.
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27
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Harris NJ, Findlay HE, Simms J, Liu X, Booth PJ. Relative domain folding and stability of a membrane transport protein. J Mol Biol 2014; 426:1812-25. [PMID: 24530957 DOI: 10.1016/j.jmb.2014.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
There is a limited understanding of the folding of multidomain membrane proteins. Lactose permease (LacY) of Escherichia coli is an archetypal member of the major facilitator superfamily of membrane transport proteins, which contain two domains of six transmembrane helices each. We exploit chemical denaturation to determine the unfolding free energy of LacY and employ Trp residues as site-specific thermodynamic probes. Single Trp LacY mutants are created with the individual Trps situated at mirror image positions on the two LacY domains. The changes in Trp fluorescence induced by urea denaturation are used to construct denaturation curves from which unfolding free energies can be determined. The majority of the single Trp tracers report the same stability and an unfolding free energy of approximately +2 kcal mol(-1). There is one exception; the fluorescence of W33 at the cytoplasmic end of helix I on the N domain is unaffected by urea. In contrast, the equivalent position on the first helix, VII, of the C-terminal domain exhibits wild-type stability, with the single Trp tracer at position 243 on helix VII reporting an unfolding free energy of +2 kcal mol(-1). This indicates that the region of the N domain of LacY at position 33 on helix I has enhanced stability to urea, when compared the corresponding location at the start of the C domain. We also find evidence for a potential network of stabilising interactions across the domain interface, which reduces accessibility to the hydrophilic substrate binding pocket between the two domains.
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Affiliation(s)
- Nicola J Harris
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - John Simms
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Xia Liu
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Paula J Booth
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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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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Kirsten ML, Baron RA, Seabra MC, Ces O. Rab1a and Rab5a preferentially bind to binary lipid compositions with higher stored curvature elastic energy. Mol Membr Biol 2013; 30:303-14. [PMID: 23815289 DOI: 10.3109/09687688.2013.818725] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rab proteins are a large family of GTP-binding proteins that regulate cellular membrane traffic and organelle identity. Rab proteins cycle between association with membranes and binding to RabGDI. Bound on membranes, each Rab has a very specific cellular location and it is this remarkable degree of specificity with which Rab GTPases recognize distinct subsets of intracellular membranes that forms the basis of their ability to act as key cellular regulators, determining the recruitment of downstream effectors to the correct membrane at the correct time. The molecular mechanisms controlling Rab localization remain poorly understood. Here, we present a fluorescence-based assay to investigate Rab GTPase membrane extraction and delivery by RabGDI. Using EGFP-Rab fusion proteins the amount of Rab:GDI complex obtained by GDI extraction of Rab proteins from HEK293 membranes could be determined, enabling control of complex concentration. Subsequent partitioning of the Rab GTPases into vesicles made up of artificial binary lipid mixtures showed for the first time, that the composition of the target membrane plays a key role in the localization of Rab proteins by sensing the stored curvature elastic energy in the membrane.
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Affiliation(s)
- Marie L Kirsten
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, UK
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30
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Ong YS, Lakatos A, Becker-Baldus J, Pos KM, Glaubitz C. Detecting substrates bound to the secondary multidrug efflux pump EmrE by DNP-enhanced solid-state NMR. J Am Chem Soc 2013; 135:15754-62. [PMID: 24047229 DOI: 10.1021/ja402605s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli EmrE, a homodimeric multidrug antiporter, has been suggested to offer a convenient paradigm for secondary transporters due to its small size. It contains four transmembrane helices and forms a functional dimer. We have probed the specific binding of substrates TPP(+) and MTP(+) to EmrE reconstituted into 1,2-dimyristoyl-sn-glycero-3-phosphocholine liposomes by (31)P MAS NMR. Our NMR data show that both substrates occupy the same binding pocket but also indicate some degree of heterogeneity of the bound ligand population, reflecting the promiscuous nature of ligand binding by multidrug efflux pumps. Direct interaction between (13)C-labeled TPP(+) and key residues within the EmrE dimer has been probed by through-space (13)C-(13)C correlation spectroscopy. This was made possible by the use of solid-state NMR enhanced by dynamic nuclear polarization (DNP) through which a 19-fold signal enhancement was achieved. Our data provide clear evidence for the long assumed direct interaction between substrates such as TPP(+) and the essential residue E14 in transmembrane helix 1. Our work also demonstrates the power of DNP-enhanced solid-state NMR at low temperatures for the study for secondary transporters, which are highly challenging for conventional NMR detection.
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Affiliation(s)
- Yean Sin Ong
- Institute of Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance and ‡Institute of Biochemistry, Goethe University Frankfurt , Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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31
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Visualizing a multidrug resistance protein, EmrE, with major bacterial lipids using Brewster angle microscopy. Chem Phys Lipids 2013; 167-168:33-42. [DOI: 10.1016/j.chemphyslip.2013.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/22/2012] [Accepted: 01/18/2013] [Indexed: 11/17/2022]
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32
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Bay DC, Turner RJ. Membrane composition influences the topology bias of bacterial integral membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:260-70. [PMID: 22982496 DOI: 10.1016/j.bbamem.2012.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/31/2012] [Accepted: 09/07/2012] [Indexed: 11/19/2022]
Abstract
Small multidrug resistance (SMR) protein family members confer bacterial resistance to toxic antiseptics and are believed to function as dual topology oligomers. If dual topology is essential for SMR activity, then the topology bias should change as bacterial membrane lipid compositions alter to maintain a "neutral" topology bias. To test this hypothesis, a bioinformatic analysis of bacterial SMR protein sequences was performed to determine a membrane protein topology based on charged amino acid residues within loops, and termini regions according to the positive inside rule. Three bacterial lipid membrane parameters were examined, providing the proportion of polar lipid head group charges at the membrane surface (PLH), the relative hydrophobic fatty acid length (FAL), and the proportion of fatty acid unsaturation (FAU). Our analysis indicates that individual SMR pairs, and to a lesser extent SMR singleton topology biases, are significantly correlated to increasing PLH, FAL and FAU differences validating the hypothesis. Correlations between the topology biases of SMR proteins identified in Gram+ compared to Gram- species and each lipid parameter demonstrated a linear inverse relationship.
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Affiliation(s)
- Denice C Bay
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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33
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Small multidrug resistance protein EmrE reduces host pH and osmotic tolerance to metabolic quaternary cation osmoprotectants. J Bacteriol 2012; 194:5941-8. [PMID: 22942246 DOI: 10.1128/jb.00666-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The small multidrug resistance (SMR) transporter protein EmrE in Escherichia coli is known to confer resistance to toxic antiseptics classified as quaternary cation compounds (QCCs). Naturally derived QCCs synthesized during metabolic activities often act as osmoprotectants, such as betaine and choline, and participate in osmotic homoestasis. The goal of this study was to determine if EmrE proteins transport biological QCC-based osmoprotectants. Plasmid-encoded copies of E. coli emrE and the inactive variant emrE-E14C (emrE with the E → C change at position 14) were expressed in various E. coli strains grown in either rich or minimal media at various pHs (5 to 9) and under hypersaline (0.5 to 1.0 M NaCl and KCl) conditions to identify changes in growth phenotypes induced by osmoprotectant transport. The results demonstrated that emrE expression reduced pH tolerance of E. coli strains at or above neutral pH and when grown in hypersaline media at or above NaCl or KCl concentrations of 0.75 M. Hypersaline growth conditions were used to screen QCC osmoprotectants betaine, choline, l-carnitine, l-lysine, l-proline, and l-arginine. The study identified that betaine and choline are natural QCC substrates of EmrE.
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34
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Booth PJ. A successful change of circumstance: a transition state for membrane protein folding. Curr Opin Struct Biol 2012; 22:469-75. [DOI: 10.1016/j.sbi.2012.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/09/2012] [Accepted: 03/14/2012] [Indexed: 01/02/2023]
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35
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Spectroscopic analysis of small multidrug resistance protein EmrE in the presence of various quaternary cation compounds. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1318-31. [PMID: 22326892 DOI: 10.1016/j.bbamem.2012.01.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 01/09/2012] [Accepted: 01/26/2012] [Indexed: 12/12/2022]
Abstract
Escherichia coli EmrE protein is the archetypical member of the small multidrug resistance protein family in bacteria and confers host resistance to a wide assortment of toxic quaternary cation compounds by secondary active efflux. This protein can form a variety of multimers under various membrane mimetic conditions, and the consensus of most biochemical and biophysical studies indicate that the active form is a dimer. The purpose of this study is to characterize the conformation of organically extracted detergent solubilized EmrE protein known to predominate as monomer yet demonstrates ligand binding ability. Active site EmrE-E14 replacements were also examined as functionally inactive controls for this study. EmrE was solubilized in detergents, sodium dodecyl sulfate (SDS) and dodecyl maltoside (DDM), and protein conformation was examined in the presence of four known quaternary cation compound (QCC) substrates, tetraphenyl phosphonium (TPP), methyl viologen, cetylpyridinium, and ethidium. SDS-Tricine PAGE analysis of both detergent solubilized proteins revealed that DDM-EmrE preparations enhanced the formation of dimer (and in some cases trimer) forms in the presence of all four QCC above 25 QCC:1 EmrE molar ratios. Examination of EmrE and its active site variant tertiary structures in DDM by circular dichroism spectropolarimetry, intrinsic Trp fluorescence quenching and second order derivative ultraviolet absorbance revealed that the variant fails to bind TPP but interacts with all other compounds. The results of this study show that monomeric detergent solubilized EmrE is capable of forming multimeric complexes that are enhanced by chemically diverse QCCs.
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36
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Mitchell DC. Progress in understanding the role of lipids in membrane protein folding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:951-6. [PMID: 22236837 DOI: 10.1016/j.bbamem.2011.12.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 12/23/2011] [Accepted: 12/23/2011] [Indexed: 10/14/2022]
Abstract
Detailed investigations of membrane protein folding present a number of serious technical challenges. Most studies addressing this subject have emphasized aspects of protein amino acid sequence and structure. While it is generally accepted that the interplay between proteins and lipids plays an important role in membrane protein folding, the role(s) played by membrane lipids in this process have only recently been explored in any detail. This review is intended to summarize recent studies in which particular lipids or membrane physical properties have been shown to play a role in the folding of intact, functionally competent integral membrane proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Drake C Mitchell
- Department of Physics, Portland State University, Portland, OR 97207, USA.
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37
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A novel method of AquaporinZ incorporation via binary-lipid Langmuir monolayers. Colloids Surf B Biointerfaces 2012; 89:283-8. [DOI: 10.1016/j.colsurfb.2011.09.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 09/03/2011] [Accepted: 09/04/2011] [Indexed: 11/24/2022]
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38
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Gröger T, Nathoo S, Ku T, Sikora C, Turner RJ, Prenner EJ. Real-time imaging of lipid domains and distinct coexisting membrane protein clusters. Chem Phys Lipids 2011; 165:216-24. [PMID: 22227110 DOI: 10.1016/j.chemphyslip.2011.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 12/15/2011] [Accepted: 12/19/2011] [Indexed: 12/20/2022]
Abstract
A detailed understanding of biomembrane architecture is still a challenging task. Many in vitro studies have shown lipid domains but much less information is known about the lateral organization of membrane proteins because their hydrophobic nature limits the use of many experimental methods. We examined lipid domain formation in biomimetic Escherichia coli membranes composed of phosphatidylethanolamine and phosphatidylglycerol in the absence and presence of 1% and 5% (mol/mol) membrane multidrug resistance protein, EmrE. Monolayer isotherms demonstrated protein insertion into the lipid monolayer. Subsequently, Brewster angle microscopy was applied to image domains in lipid matrices and lipid-protein mixtures. The images showed a concentration dependent impact of the protein on lipid domain size and shape and more interestingly distinct coexisting protein clusters. Whereas lipid domains varied in size (14-47μm), protein clusters exhibited a narrow size distribution (2.6-4.8μm) suggesting a non-random process of cluster formation. A 3-D display clearly indicates that these proteins clusters protrude from the membrane plane. These data demonstrate distinct co-existing lipid domains and membrane protein clusters as the monofilm is being compressed and illustrate the significant mutual impact of lipid-protein interactions on lateral membrane architecture.
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Affiliation(s)
- Thomas Gröger
- Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherbeg, Germany
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39
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Antiparallel EmrE exports drugs by exchanging between asymmetric structures. Nature 2011; 481:45-50. [PMID: 22178925 PMCID: PMC3253143 DOI: 10.1038/nature10703] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 11/07/2011] [Indexed: 11/14/2022]
Abstract
Small multidrug resistance (SMR) transporters provide an ideal system to study the minimal requirements for active transport. EmrE is an E. coli SMR transporter that exports a broad class of polyaromatic cation substrates, thus conferring resistance to drug compounds matching this chemical description. However, a great deal of controversy has surrounded the topology of the EmrE homodimer. Here we show that asymmetric antiparallel EmrE exchanges between inward- and outward-facing states that are identical except that they have opposite orientation in the membrane. We quantitatively measure the global conformational exchange between these two states for substrate-bound EmrE in bicelles using solution NMR dynamics experiments. FRET reveals that the monomers within each dimer are antiparallel, and paramagnetic relaxation enhancement NMR experiments demonstrate differential water accessibility of the two monomers within each dimer. Our experiments reveal a “dynamic symmetry” that reconciles the asymmetric EmrE structure with the functional symmetry of residues in the active site.
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40
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Henzler-Wildman K. Analyzing conformational changes in the transport cycle of EmrE. Curr Opin Struct Biol 2011; 22:38-43. [PMID: 22100111 DOI: 10.1016/j.sbi.2011.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 11/24/2022]
Abstract
The small multidrug resistance transporters represent a unique model system for studying the mechanism of secondary active transport and membrane protein evolution. However, this seemingly simple protein has been highly controversial. Recent studies have provided experimental evidence that EmrE exists as an asymmetric dimer that exchanges between identical inward-facing and outward-facing states. Re-examination of the published literature in light of these findings fills in many details of the microscopic steps in the transport cycle. Future work will need to examine how the symmetry observed in vitro affects EmrE function in the asymmetric environment of its native Escherichia coli membrane.
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Affiliation(s)
- Katherine Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics Washington University School of Medicine, St. Louis, MO 63110, United States.
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41
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Harris NJ, Booth PJ. Folding and stability of membrane transport proteins in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1055-66. [PMID: 22100867 DOI: 10.1016/j.bbamem.2011.11.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/26/2011] [Accepted: 11/03/2011] [Indexed: 10/15/2022]
Abstract
Transmembrane transporters are responsible for maintaining a correct internal cellular environment. The inherent flexibility of transporters together with their hydrophobic environment means that they are challenging to study in vitro, but recently significant progress been made. This review will focus on in vitro stability and folding studies of transmembrane alpha helical transporters, including reversible folding systems and thermal denaturation. The successful re-assembly of a small number of ATP binding cassette transporters is also described as this is a significant step forward in terms of understanding the folding and assembly of these more complex, multi-subunit proteins. The studies on transporters discussed here represent substantial advances for membrane protein studies as well as for research into protein folding. The work demonstrates that large flexible hydrophobic proteins are within reach of in vitro folding studies, thus holding promise for furthering knowledge on the structure, function and biogenesis of ubiquitous membrane transporter families. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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42
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Devaraneni PK, Devereaux JJ, Valiyaveetil FI. In vitro folding of KvAP, a voltage-gated K+ channel. Biochemistry 2011; 50:10442-50. [PMID: 22044112 DOI: 10.1021/bi2012965] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this contribution, we report in vitro folding of the archaebacterial voltage-gated K(+) channel, K(v)AP. We show that in vitro folding of the K(v)AP channel from the extensively unfolded state requires lipid vesicles and that the refolded channel is biochemically and functionally similar to the native channel. The in vitro folding process is slow at room temperature, and the folding yield depends on the composition of the lipid bilayer. The major factor influencing refolding is temperature, and almost quantitative refolding of the K(v)AP channel is observed at 80 °C. To differentiate between insertion into the bilayer and folding within the bilayer, we developed a cysteine protection assay. Using this assay, we demonstrate that insertion of the unfolded protein into the bilayer is relatively fast at room temperature and independent of lipid composition, suggesting that temperature and bilayer composition influence folding within the bilayer. Further, we demonstrate that in vitro folding provides an effective method for obtaining high yields of the native channel. Our studies suggest that the K(v)AP channel provides a good model system for investigating the folding of a multidomain integral membrane protein.
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Affiliation(s)
- Prasanna K Devaraneni
- The Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, Oregon 97239, United States
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43
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Surfactant-free purification of membrane proteins with intact native membrane environment. Biochem Soc Trans 2011; 39:813-8. [PMID: 21599653 DOI: 10.1042/bst0390813] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order to study the structure and function of a protein, it is generally required that the protein in question is purified away from all others. For soluble proteins, this process is greatly aided by the lack of any restriction on the free and independent diffusion of individual protein particles in three dimensions. This is not the case for membrane proteins, as the membrane itself forms a continuum that joins the proteins within the membrane with one another. It is therefore essential that the membrane is disrupted in order to allow separation and hence purification of membrane proteins. In the present review, we examine recent advances in the methods employed to separate membrane proteins before purification. These approaches move away from solubilization methods based on the use of small surfactants, which have been shown to suffer from significant practical problems. Instead, the present review focuses on methods that stem from the field of nanotechnology and use a range of reagents that fragment the membrane into nanometre-scale particles containing the protein complete with the local membrane environment. In particular, we examine a method employing the amphipathic polymer poly(styrene-co-maleic acid), which is able to reversibly encapsulate the membrane protein in a 10 nm disc-like structure ideally suited to purification and further biochemical study.
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44
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Popot JL, Althoff T, Bagnard D, Banères JL, Bazzacco P, Billon-Denis E, Catoire LJ, Champeil P, Charvolin D, Cocco MJ, Crémel G, Dahmane T, de la Maza LM, Ebel C, Gabel F, Giusti F, Gohon Y, Goormaghtigh E, Guittet E, Kleinschmidt JH, Kühlbrandt W, Le Bon C, Martinez KL, Picard M, Pucci B, Sachs JN, Tribet C, van Heijenoort C, Wien F, Zito F, Zoonens M. Amphipols from A to Z. Annu Rev Biophys 2011; 40:379-408. [PMID: 21545287 DOI: 10.1146/annurev-biophys-042910-155219] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep integral membrane proteins (MPs) water soluble. In this review, we discuss their structure and solution behavior; the way they associate with MPs; and the structure, dynamics, and solution properties of the resulting complexes. All MPs tested to date form water-soluble complexes with APols, and their biochemical stability is in general greatly improved compared with MPs in detergent solutions. The functionality and ligand-binding properties of APol-trapped MPs are reviewed, and the mechanisms by which APols stabilize MPs are discussed. Applications of APols include MP folding and cell-free synthesis, structural studies by NMR, electron microscopy and X-ray diffraction, APol-mediated immobilization of MPs onto solid supports, proteomics, delivery of MPs to preexisting membranes, and vaccine formulation.
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Affiliation(s)
- J-L Popot
- Institut de Biologie Physico-Chimique, CNRS/Université Paris-7 UMR 7099, Paris, France.
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45
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Modulation of substrate efflux in bacterial small multidrug resistance proteins by mutations at the dimer interface. J Bacteriol 2011; 193:5929-35. [PMID: 21890698 DOI: 10.1128/jb.05846-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria evade the effects of cytotoxic compounds through the efflux activity of membrane-bound transporters such as the small multidrug resistance (SMR) proteins. Consisting typically of ca. 110 residues with four transmembrane (TM) α-helices, crystallographic studies have shown that TM helix 1 (TM1) through TM helix 3 (TM3) of each monomer create a substrate binding "pocket" within the membrane bilayer, while a TM4-TM4 interaction accounts for the primary dimer formation. Previous work from our lab has characterized a highly conserved small-residue heptad motif in the Halobacterium salinarum transporter Hsmr as (90)GLXLIXXGV(98) that lies along the TM4-TM4 dimer interface of SMR proteins as required for function. Focusing on conserved positions 91, 93, 94, and 98, we substituted the naturally occurring Hsmr residue for Ala, Phe, Ile, Leu, Met, and Val at each position in the Hsmr TM4-TM4 interface. Large-residue replacements were studied for their ability to dimerize on SDS-polyacrylamide gels, to bind the cytotoxic compound ethidium bromide, and to confer resistance by efflux. Although the relative activity of mutants did not correlate with dimer strength for all mutants, all functional mutants lay within 10% of dimerization relative to the wild type (WT), suggesting that the optimal dimer strength at TM4 is required for proper efflux. Furthermore, nonfunctional substitutions at the center of the dimerization interface that do not alter dimer strength suggest a dynamic TM4-TM4 "pivot point" that responds to the efflux requirements of different substrates. This functionally critical region represents a potential target for inhibiting the ability of bacteria to evade the effects of cytotoxic compounds.
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46
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Sanchez KM, Kang G, Wu B, Kim JE. Tryptophan-lipid interactions in membrane protein folding probed by ultraviolet resonance Raman and fluorescence spectroscopy. Biophys J 2011; 100:2121-30. [PMID: 21539779 DOI: 10.1016/j.bpj.2011.03.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/02/2011] [Accepted: 03/14/2011] [Indexed: 01/24/2023] Open
Abstract
Aromatic amino acids of membrane proteins are enriched at the lipid-water interface. The role of tryptophan on the folding and stability of an integral membrane protein is investigated with ultraviolet resonance Raman and fluorescence spectroscopy. We investigate a model system, the β-barrel outer membrane protein A (OmpA), and focus on interfacial tryptophan residues oriented toward the lipid bilayer (trp-7, trp-170, or trp-15) or the interior of the β-barrel pore (trp-102). OmpA mutants with a single tryptophan residue at a nonnative position 170 (Trp-170) or a native position 7 (Trp-7) exhibit the greatest stability, with Gibbs free energies of unfolding in the absence of denaturant of 9.4 and 6.7 kcal/mol, respectively. These mutants are more stable than the tryptophan-free OmpA mutant, which exhibits a free energy of unfolding of 2.6 kcal/mol. Ultraviolet resonance Raman spectra of Trp-170 and Trp-7 reveal evolution of a hydrogen bond in a nonpolar environment during the folding reaction, evidenced by systematic shifts in hydrophobicity and hydrogen bond markers. These observations suggest that the hydrogen bond acceptor is the lipid acyl carbonyl group, and this interaction contributes significantly to membrane protein stabilization. Other spectral changes are observed for a tryptophan residue at position 15, and these modifications are attributed to development of a tryptophan-lipid cation-π interaction that is more stabilizing than an intraprotein hydrogen bond by ∼2 kcal/mol. As expected, there is no evidence for lipid-protein interactions for the tryptophan residue oriented toward the interior of the β-barrel pore. These results highlight the significance of lipid-protein interactions, and indicate that the bilayer provides more than a hydrophobic environment for membrane protein folding. Instead, a paradigm of lipid-assisted membrane protein folding and stabilization must be adopted.
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Affiliation(s)
- Katheryn M Sanchez
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
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47
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Bay DC, Turner RJ. Spectroscopic analysis of the intrinsic chromophores within small multidrug resistance protein SugE. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2233-44. [PMID: 21600871 DOI: 10.1016/j.bbamem.2011.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/03/2011] [Accepted: 05/04/2011] [Indexed: 11/16/2022]
Abstract
Small multidrug resistance (SMR) protein family member, SugE, is an integral inner membrane protein that confers host resistance to antiseptic quaternary cation compounds (QCC). SugE studies generally focus on its resistance to limited substrates in comparison to SMR protein EmrE. This study examines the conformational characteristics of SugE protein in two detergents, sodium dodecyl sulphate (SDS) and dodecyl maltoside (DDM), commonly used to study SMR proteins. The influence of cetylpyridinium (CTP) and cetrimide (CET) using SugE aromatic residues (4W, 2Y, 1F) as intrinsic spectroscopic probes was also determined. Organically extracted detergent solubilized Escherichia coli SugE protein was examined by SDS-Tricine PAGE and various spectroscopic techniques. SDS-Tricine PAGE analysis of SugE in either detergent demonstrates the protein predominates as a monomer but also dimerizes in SDS. Far-UV region circular dichroism (CD) analysis determined that the overall α-helix content SugE in SDS and DDM was almost identical and unaltered by QCC. Near-UV region CD, fluorescence, and second-derivative ultraviolet absorption (SDUV) indicated that only DDM-SugE promoted hydrophobic environments for its Trp and Tyr residues that were perturbed by QCC addition. This study identified that only the tertiary structure of SugE protein in DDM is altered by QCC.
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Affiliation(s)
- Denice C Bay
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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48
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Banères JL, Popot JL, Mouillac B. New advances in production and functional folding of G-protein-coupled receptors. Trends Biotechnol 2011; 29:314-22. [PMID: 21497924 DOI: 10.1016/j.tibtech.2011.03.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/25/2011] [Accepted: 03/02/2011] [Indexed: 12/17/2022]
Abstract
G-protein-coupled receptors (GPCRs), the largest family of integral membrane proteins, participate in the regulation of many physiological functions and are the targets of approximately 30% of currently marketed drugs. However, knowledge of the structural and molecular bases of GPCR functions remains limited owing to difficulties related to their overexpression, purification and stabilization. The development of new strategies aimed at obtaining large amounts of functional GPCRs is therefore crucial. Here, we review the most recent advances in the production and functional folding of GPCRs from Escherichia coli inclusion bodies. Major breakthroughs open exciting perspectives for structural and dynamic investigations of GPCRs. In particular, combining targeting to bacterial inclusion bodies with amphipol-assisted folding is emerging as a highly powerful strategy.
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Affiliation(s)
- Jean-Louis Banères
- CNRS, UMR-5247, Institut des Biomolécules Max Mousseron, Faculté de Pharmacie, 15 avenue Charles Flahault, F-34000 Montpellier, France
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49
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Unfolding free energy of a two-domain transmembrane sugar transport protein. Proc Natl Acad Sci U S A 2010; 107:18451-6. [PMID: 20937906 DOI: 10.1073/pnas.1005729107] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding how an amino acid sequence folds into a functional, three-dimensional structure has proved to be a formidable challenge in biological research, especially for transmembrane proteins with multiple alpha helical domains. Mechanistic folding studies on helical membrane proteins have been limited to unusually stable, single domain proteins such as bacteriorhodopsin. Here, we extend such work to flexible, multidomain proteins and one of the most widespread membrane transporter families, the major facilitator superfamily, thus showing that more complex membrane proteins can be successfully refolded to recover native substrate binding. We determine the unfolding free energy of the two-domain, Escherichia coli galactose transporter, GalP; a bacterial homologue of human glucose transporters. GalP is reversibly unfolded by urea. Urea causes loss of substrate binding and a significant reduction in alpha helical content. Full recovery of helical structure and substrate binding occurs in dodecylmaltoside micelles, and the unfolding free energy can be determined. A linear dependence of this free energy on urea concentration allows the free energy of unfolding in the absence of urea to be determined as +2.5 kcal·mol(-1). Urea has often been found to be a poor denaturant for transmembrane helical structures. We attribute the denaturation of GalP helices by urea to the dynamic nature of the transporter structure allowing denaturant access via the substrate binding pocket, as well as to helical structure that extends beyond the membrane. This study gives insight into the final, critical folding step involving recovery of ligand binding for a multidomain membrane transporter.
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50
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Dutta A, Tirupula KC, Alexiev U, Klein-Seetharaman J. Characterization of membrane protein non-native states. 1. Extent of unfolding and aggregation of rhodopsin in the presence of chemical denaturants. Biochemistry 2010; 49:6317-28. [PMID: 20575534 DOI: 10.1021/bi100338e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Little is known about the general folding mechanisms of helical membrane proteins. Unfolded, i.e., non-native states, in particular, have not yet been characterized in detail. Here, we establish conditions under which denatured states of the mammalian membrane protein rhodopsin, a prototypic G protein coupled receptor with primary function in vision, can be studied. We investigated the effects of the chemical denaturants sodium dodecyl sulfate (SDS), urea, guanidine hydrochloride (GuHCl), and trifluoroacetic acid (TFA) on rhodopsin's secondary structure and propensity for aggregation. Ellipticity at 222 nm decreases in the presence of maximum concentrations of denaturants in the order TFA > GuHCl > urea > SDS + urea > SDS. Interpretation of these changes in ellipticity in terms of helix loss is challenged because the addition of some denaturants leads to aggregation. Through a combination of SDS-PAGE, dependence of ellipticity on protein concentration, and 1D (1)H NMR we show that aggregates form in the presence of GuHCl, TFA, and urea but not in any concentration of SDS, added over a range of 0.05%-30%. Mixed denaturant conditions consisting of 3% SDS and 8 M urea, added in this order, also did not result in aggregation. We conclude that SDS is able to prevent the exposure of large hydrophobic regions present in membrane proteins which otherwise leads to aggregation. Thus, 30% SDS and 3% SDS + 8 M urea are the denaturing conditions of choice to study maximally unfolded rhodopsin without aggregation.
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Affiliation(s)
- Arpana Dutta
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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