1
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Xiao P, Drewniak P, Dingwell DA, Brown LS, Ladizhansky V. Probing the energy barriers and stages of membrane protein unfolding using solid-state NMR spectroscopy. SCIENCE ADVANCES 2024; 10:eadm7907. [PMID: 38758787 DOI: 10.1126/sciadv.adm7907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially challenging for membrane proteins that reside in the complex environment of a lipid bilayer. Here, we obtain an atomic-level picture of the thermally induced unfolding of a membrane-embedded α-helical protein, human aquaporin 1, using solid-state nuclear magnetic resonance spectroscopy. Our data reveal the hierarchical two-step pathway that begins with unfolding of a structured extracellular loop and proceeds to an intermediate state with a native-like helical packing. In the second step, the transmembrane domain unravels as a single unit, resulting in a heterogeneous misfolded state with high helical content but with nonnative helical packing. Our results show the importance of loops for the kinetic stabilization of the whole membrane protein structure and support the three-stage membrane protein folding model.
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Affiliation(s)
- Peng Xiao
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Philip Drewniak
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Dylan Archer Dingwell
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
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2
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Yang H, Zhou D, Zhou Z, Duan M, Yu H. Mechanistic Insight into the Mechanical Unfolding of the Integral Membrane Diacylglycerol Kinase. JACS AU 2024; 4:1422-1435. [PMID: 38665647 PMCID: PMC11040704 DOI: 10.1021/jacsau.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/28/2024]
Abstract
The essential forces stabilizing membrane proteins and governing their folding and unfolding are difficult to decipher. Single-molecule atomic force spectroscopy mechanically unfolds individual membrane proteins and quantifies their dynamics and energetics. However, it remains challenging to structurally assign unfolding intermediates precisely and to deduce dominant interactions between specific residues that facilitate either the localized stabilization of these intermediates or the global assembly of membrane proteins. Here, we performed force spectroscopy experiments and multiscale molecular dynamics simulations to study the unfolding pathway of diacylglycerol kinase (DGK), a small trimeric multispan transmembrane enzyme. The remarkable agreement between experiments and simulations allowed precise structural assignment and interaction analysis of unfolding intermediates, bypassing existing limitations on structural mapping, and thus provided mechanistic explanations for the formation of these states. DGK unfolding was found to proceed with structural segments varying in size that do not correlate with its secondary structure. We identified intermolecular side-chain packing interactions as one of the major contributions to the stability of unfolding intermediates. Mutagenesis creating packing defects induced a dramatic decrease in the mechano-stability of corresponding intermediates and also in the thermo-stability of DGK trimer, in good agreement with predictions from simulations. Hence, the molecular determinants of the mechano- and thermo-stability of a membrane protein can be identified at residue resolution. The accurate structural assignment established and microscopic mechanism revealed in this work may substantially expand the scope of single-molecule studies of membrane proteins.
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Affiliation(s)
- Huiying Yang
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Daihong Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Zhangyi Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Mojie Duan
- Innovation
Academy for Precision Measurement Science and Technology, Chinese
Academy of Sciences, Wuhan 430071, China
| | - Hao Yu
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
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3
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Wu C, Liu Y, Hu Y, Ding M, Cui X, Liu Y, Liu P, Zhang H, Yang Y, Zhang H. An Investigation into the Performance and Mechanisms of Soymilk-Sized Handmade Xuan Paper at Different Concentrations of Soymilk. Molecules 2023; 28:6791. [PMID: 37836634 PMCID: PMC10574515 DOI: 10.3390/molecules28196791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Invaluable paper relics that embody a rich traditional culture have suffered damage, requiring urgent restoration. In this context, the utilization of soymilk as a sizing agent holds great significance and reverence. This study investigates the use of soymilk as a sizing agent for Xuan paper and evaluates its effects on various properties and the long-term behavior of the paper. The findings reveal that the application of soymilk as a sizing agent for Xuan paper imparts distinct properties, including hydrophobicity, improved mechanical properties, and unique chromaticity. These characteristics-arising from the papillae on the surface of the Xuan paper, the protein folding of the soy protein, and hydrogen-bonding interactions between the soy protein and paper fibers-play a crucial role in shaping the paper's unique attributes. From a physicochemical perspective, the aging process leads to multiple changes in paper properties. These changes include acidification, which refers to a decrease in pH, as well as a decline in mechanical strength, an increase in chromaticity, and a decrease in the degree of polymerization (DP) of the paper. The Ekenstam equation is employed to predict the lifespan of the paper, showing longer lifespans for Sheng Xuan paper and a negative correlation between soymilk concentration and lifespan in soymilk-sized paper. Our work provides valuable insights for the preservation and maintenance of paper, highlighting the potential benefits and challenges of using soymilk for surface sizing.
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Affiliation(s)
- Chunfang Wu
- Institute for Preservation and Conservation of Chinese Ancient Books, Fudan University, Shanghai 200433, China; (C.W.)
| | - Yangyang Liu
- School of Creative Art and Fashion Design, Huzhou Vocational and Technical College, Huzhou 313000, China
| | - Yanxiao Hu
- Institute for Preservation and Conservation of Chinese Ancient Books, Fudan University, Shanghai 200433, China; (C.W.)
| | - Ming Ding
- Behavioral and Cognitive Neuroscience Center, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiang Cui
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yixin Liu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Peng Liu
- Institute for Preservation and Conservation of Chinese Ancient Books, Fudan University, Shanghai 200433, China; (C.W.)
| | - Hongbin Zhang
- Institute for Preservation and Conservation of Chinese Ancient Books, Fudan University, Shanghai 200433, China; (C.W.)
| | - Yuliang Yang
- Institute for Preservation and Conservation of Chinese Ancient Books, Fudan University, Shanghai 200433, China; (C.W.)
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Hongdong Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
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4
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Müller W, Beales PA, Muniz AR, Jeuken LJC. Unraveling the Phase Behavior, Mechanical Stability, and Protein Reconstitution Properties of Polymer-Lipid Hybrid Vesicles. Biomacromolecules 2023; 24:4156-4169. [PMID: 37539954 PMCID: PMC10498451 DOI: 10.1021/acs.biomac.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/20/2023] [Indexed: 08/05/2023]
Abstract
Hybrid vesicles consisting of natural phospholipids and synthetic amphiphilic copolymers have shown remarkable material properties and potential for biotechnology, combining the robustness of polymers with the biocompatibility of phospholipid membranes. To predict and optimize the mixing behavior of lipids and copolymers, as well as understand the interaction between the hybrid membrane and macromolecules like membrane proteins, a comprehensive understanding at the molecular level is essential. This can be achieved by a combination of molecular dynamics simulations and experiments. Here, simulations of POPC and PBD22-b-PEO14 hybrid membranes are shown, uncovering different copolymer configurations depending on the polymer-to-lipid ratio. High polymer concentrations created thicker membranes with an extended polymer conformation, while high lipid content led to the collapse of the polymer chain. High concentrations of polymer were further correlated with a decreased area compression modulus and altered lateral pressure profiles, hypothesized to result in the experimentally observed improvement in membrane protein reconstitution and resistance toward destabilization by detergents. Finally, simulations of a WALP peptide embedded in the bilayer showed that only membranes with up to 50% polymer content favored a transmembrane configuration. These simulations correlate with previous and new experimental results and provide a deeper understanding of the properties of lipid-copolymer hybrid membranes.
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Affiliation(s)
- Wagner
A. Müller
- Department
of Chemical Engineering, Universidade Federal
do Rio Grande do Sul, Porto
Alegre 90035-003, Brazil
| | - Paul A. Beales
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - André R. Muniz
- Department
of Chemical Engineering, Universidade Federal
do Rio Grande do Sul, Porto
Alegre 90035-003, Brazil
| | - Lars J. C. Jeuken
- Leiden
Institute of Chemistry, University Leiden, PO Box 9502, 2300RA Leiden, The
Netherlands
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5
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Mohri M, Moghadam A, Burketova L, Ryšánek P. Genome-wide identification of the opsin protein in Leptosphaeria maculans and comparison with other fungi (pathogens of Brassica napus). Front Microbiol 2023; 14:1193892. [PMID: 37692395 PMCID: PMC10485269 DOI: 10.3389/fmicb.2023.1193892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/28/2023] [Indexed: 09/12/2023] Open
Abstract
The largest family of transmembrane receptors are G-protein-coupled receptors (GPCRs). These receptors respond to perceived environmental signals and infect their host plants. Family A of the GPCR includes opsin. However, there is little known about the roles of GPCRs in phytopathogenic fungi. We studied opsin in Leptosphaeria maculans, an important pathogen of oilseed rape (Brassica napus) that causes blackleg disease, and compared it with six other fungal pathogens of oilseed rape. A phylogenetic tree analysis of 31 isoforms of the opsin protein showed six major groups and six subgroups. All three opsin isoforms of L. maculans are grouped in the same clade in the phylogenetic tree. Physicochemical analysis revealed that all studied opsin proteins are stable and hydrophobic. Subcellular localization revealed that most isoforms were localized in the endoplasmic reticulum membrane except for several isoforms in Verticillium species, which were localized in the mitochondrial membrane. Most isoforms comprise two conserved domains. One conserved motif was observed across all isoforms, consisting of the BACTERIAL_OPSIN_1 domain, which has been hypothesized to have an identical sensory function. Most studied isoforms showed seven transmembrane helices, except for one isoform of V. longisporum and four isoforms of Fusarium oxysporum. Tertiary structure prediction displayed a conformational change in four isoforms of F. oxysporum that presumed differences in binding to other proteins and sensing signals, thereby resulting in various pathogenicity strategies. Protein-protein interactions and binding site analyses demonstrated a variety of numbers of ligands and pockets across all isoforms, ranging between 0 and 13 ligands and 4 and 10 pockets. According to the phylogenetic analysis in this study and considerable physiochemically and structurally differences of opsin proteins among all studied fungi hypothesized that this protein acts in the pathogenicity, growth, sporulation, and mating of these fungi differently.
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Affiliation(s)
- Marzieh Mohri
- Department of Plant Protection, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Lenka Burketova
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Pavel Ryšánek
- Department of Plant Protection, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences, Prague, Czechia
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6
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Zhao Y, Yang J, Liu M, Zhao J. Switchable Double Inversion of Chirality in a Helical Polyelectrolyte. ACS Macro Lett 2023:667-672. [PMID: 37156738 DOI: 10.1021/acsmacrolett.3c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Switchable inversion of chirality between opposite handedness by varying pH is discovered for a histidine pendant polymer, polymethyl (4-vinylbenzoyl) histidinate (PBHis), as demonstrated by the circular dichroism as well as the changes of hydrodynamic radius measured by fluorescence correlation spectroscopy at the single molecular level. The polyelectrolyte is found to take an M-helicity below pH 8.0 and change into P-helicity above pH 8.0. Such helicity further inverses into M-chirality above pH 10.6. All these helical structures with opposite handedness can be switched using pH variations. The mechanism of such a unique phenomenon is attributed to the protonation and deprotonation of the imidazole group and the hydroxide-ion-mediated hydrogen bonding, which determine the mutual orientation between the adjacent side groups under the hydrogen bonds and π-π stacking and therefore the handedness of the helical structure.
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Affiliation(s)
- Yang Zhao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Yang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghua Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Zhao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Weissig V. From Olive Oil Emulsions to COVID-19 Vaccines: Liposomes Came First. Methods Mol Biol 2023; 2622:1-19. [PMID: 36781746 DOI: 10.1007/978-1-0716-2954-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
It has been a long journey from Pliny the Elder (23-79 AD) to the FDA approval of the first injectable nanomedicine in 1997. A journey powered by intellectual curiosity, which began with sprinkling olive oil on seawater and culminated in playing around with smears of egg lecithin on microscopic slides. This brief review highlights how a few pairs of gifted hands attached to highly motivated brains have turned a curious discovery made under a microscopic lens into novel nanotherapeutics including liposome-based anti-cancer drugs and potent liposomal vaccines given to millions.
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Affiliation(s)
- Volkmar Weissig
- Midwestern University College of Pharmacy Glendale, Department of Pharmaceutical Sciences, Glendale, AZ, USA.
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8
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Oram BK, Sarkar S, Monu, Bandyopadhyay B. A comparative study of the potential energy surfaces of (CO)2, CO-CS and (CS)2. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Nwamba OC. Membranes as the third genetic code. Mol Biol Rep 2020; 47:4093-4097. [PMID: 32279211 DOI: 10.1007/s11033-020-05437-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
Biological membranes and their compositions influence cellular function, age and disease states of organisms. They achieve this by effecting the outcome of bound enzymes/proteins and carbohydrate moieties. While the membrane-bound carbohydrates give rise to antigenicity, membranes impact the eventual outcome of protein structures that would function even outside their enclosure. This is achieved by membrane modulation of translational and post-translational protein folding. Thus, the eventual 3D structures and functions of proteins might not be solely dependent on their primary amino acid sequences and surrounding environments. The 3D protein structures would also depend on enclosing membrane properties such as fluidity, other intrinsic and extrinsic proteins and carbohydrate functionalities. Also, membranes moderate DNA activities with consequences on gene activation-inactivation mechanisms. Consequently, membranes are almost indispensable to the functioning of other cell compositions and serve to modulate these other components. Besides, membrane lipid compositions are also moderated by nutrition and diets and the converse is true. Thus, it could be argued that membranes are the third genetic codes. Suggestively, membranes are at the center of the interplay between nature and nurture in health and disease states.
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10
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Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
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11
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Solid-state NMR spectroscopy based atomistic view of a membrane protein unfolding pathway. Nat Commun 2019; 10:3867. [PMID: 31455771 PMCID: PMC6711998 DOI: 10.1038/s41467-019-11849-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/06/2019] [Indexed: 01/17/2023] Open
Abstract
Membrane protein folding, structure, and function strongly depend on a cell membrane environment, yet detailed characterization of folding within a lipid bilayer is challenging. Studies of reversible unfolding yield valuable information on the energetics of folding and on the hierarchy of interactions contributing to protein stability. Here, we devise a methodology that combines hydrogen-deuterium (H/D) exchange and solid-state NMR (SSNMR) to follow membrane protein unfolding in lipid membranes at atomic resolution through detecting changes in the protein water-accessible surface, and concurrently monitoring the reversibility of unfolding. We obtain atomistic description of the reversible part of a thermally induced unfolding pathway of a seven-helical photoreceptor. The pathway is visualized through SSNMR-detected snapshots of H/D exchange patterns as a function of temperature, revealing the unfolding intermediate and its stabilizing factors. Our approach is transferable to other membrane proteins, and opens additional ways to characterize their unfolding and stabilizing interactions with atomic resolution.
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12
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Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane. Biophys J 2019; 116:1692-1700. [PMID: 31000156 DOI: 10.1016/j.bpj.2019.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/08/2023] Open
Abstract
Transmembrane peptides contain polar residues in the interior of the membrane, which may alter the electrostatic environment and favor hydration in the otherwise nonpolar environment of the membrane core. Here, we demonstrate a general, nonperturbative strategy to probe hydration of the peptide backbone at specific depths within the bilayer using a combination of site-specific isotope labels, ultrafast two-dimensional infrared spectroscopy, and spectral modeling based on molecular dynamics simulations. Our results show that the amphiphilic pH-low insertion peptide supports a highly heterogeneous environment, with significant backbone hydration of nonpolar residues neighboring charged residues. For example, a leucine residue located as far as 1 nm into the hydrophobic bulk reports hydrogen-bonded populations as high as ∼20%. These findings indicate that the polar nature of these residues may facilitate the transport of water molecules into the hydrophobic core of the membrane.
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13
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Frotscher E, Krainer G, Hartmann A, Schlierf M, Keller S. Conformational Dynamics Govern the Free-Energy Landscape of a Membrane-Interacting Protein. ACS OMEGA 2018; 3:12026-12032. [PMID: 31459283 PMCID: PMC6690567 DOI: 10.1021/acsomega.8b01609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 05/08/2023]
Abstract
The equilibrium stabilities and the folding rates of membrane-bound proteins are determined by hydrophobic and polar intermolecular contacts with their environment as well as by intramolecular packing and conformational dynamics. The contributions of these factors, however, remain elusive and might vary considerably among proteins. Mistic from Bacillus subtilis is a particularly intriguing example of an α-helical protein that associates with membranes in spite of its unusual hydrophilicity. In micelles, Mistic is stabilized by hydrophobic and polar interactions with detergents, but it is unclear whether and how these intermolecular contacts are coupled to structural and dynamic adaptations of the protein itself. Here, we investigated the packing and the conformational dynamics of Mistic as functions of detergent headgroup chemistry and chain length, employing single-molecule Förster resonance energy transfer spectroscopy and time-resolved intrinsic tryptophan fluorescence spectroscopy. Surprisingly, in nonionic detergents, more effective hydrophobic burial and, thus, greater protein stability with increasing hydrophobic micellar thickness were accompanied by a gradual loosening of the helical bundle. By contrast, Mistic was found to assume a stable, compact fold in zwitterionic detergents that allowed faster dynamics on the nanosecond timescale. Thus, intramolecular packing per se is insufficient for conferring high protein stability; instead, enhanced nanosecond dynamics and, consequently, greater conformational entropy in the compact folded state account for Mistic's high equilibrium stability and fast folding rates in zwitterionic micelles even at the expense of less effective hydrophobic burial.
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Affiliation(s)
- Erik Frotscher
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Georg Krainer
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Andreas Hartmann
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Michael Schlierf
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
- E-mail: (M.S.)
| | - Sandro Keller
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- E-mail: (S.K.)
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14
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Krainer G, Hartmann A, Anandamurugan A, Gracia P, Keller S, Schlierf M. Ultrafast Protein Folding in Membrane-Mimetic Environments. J Mol Biol 2018; 430:554-564. [DOI: 10.1016/j.jmb.2017.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/12/2017] [Accepted: 10/27/2017] [Indexed: 01/06/2023]
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15
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Beaven AH, Sodt AJ, Pastor RW, Koeppe RE, Andersen OS, Im W. Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. J Chem Theory Comput 2017; 13:5054-5064. [PMID: 28870079 DOI: 10.1021/acs.jctc.7b00400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Previous experiments have shown that the lifetime of a gramicidin A dimer channel (which forms from two nonconducting monomers) in a lipid bilayer is modulated by mutations of the tryptophan (Trp) residues at the bilayer-water interface. We explore this further using extensive molecular dynamics simulations of various gA dimer and monomer mutants at the Trp positions in phosphatidylcholine bilayers with different tail lengths. gA interactions with the surrounding bilayer are strongly modulated by mutating these Trp residues. There are three principal effects: eliminating residue hydrogen bonding ability (i.e., reducing the channel-monolayer coupling strength) reduces the extent of the bilayer deformation caused by the assembled dimeric channel; a residue's size and geometry affects its orientation, leading to different hydrogen bonding partners; and increasing a residue's hydrophobicity increases the depth of gA monomer insertion relative to the bilayer center, thereby increasing the lipid bending frustration.
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Affiliation(s)
- Andrew H Beaven
- Department of Chemistry, The University of Kansas , Lawrence, Kansas 66045, United States
| | | | | | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College , New York, New York 10065, United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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16
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Briant K, Johnson N, Swanton E. Transmembrane domain quality control systems operate at the endoplasmic reticulum and Golgi apparatus. PLoS One 2017; 12:e0173924. [PMID: 28384259 PMCID: PMC5383021 DOI: 10.1371/journal.pone.0173924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 02/28/2017] [Indexed: 01/14/2023] Open
Abstract
Multiple protein quality control systems operate to ensure that misfolded proteins are efficiently cleared from the cell. While quality control systems that assess the folding status of soluble domains have been extensively studied, transmembrane domain (TMD) quality control mechanisms are poorly understood. Here, we have used chimeras based on the type I plasma membrane protein CD8 in which the endogenous TMD was substituted with transmembrane sequences derived from different polytopic membrane proteins as a mode to investigate the quality control of unassembled TMDs along the secretory pathway. We find that the three TMDs examined prevent trafficking of CD8 to the cell surface via potentially distinct mechanisms. CD8 containing two distinct non-native transmembrane sequences escape the ER and are subsequently retrieved from the Golgi, possibly via Rer1, leading to ER localisation at steady state. A third chimera, containing an altered transmembrane domain, was predominantly localised to the Golgi at steady state, indicating the existence of an additional quality control checkpoint that identifies non-native transmembrane domains that have escaped ER retention and retrieval. Preliminary experiments indicate that protein retained by quality control mechanisms at the Golgi are targeted to lysosomes for degradation.
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Affiliation(s)
- Kit Briant
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas Johnson
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Eileithyia Swanton
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- * E-mail:
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17
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Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Structure 2017; 25:384-392. [DOI: 10.1016/j.str.2016.12.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/20/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022]
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18
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Abstract
It has been a long journey from Pliny the Elder (23-79 AD) to the FDA approval of the first injectable Nanomedicine in 1997. It has been a journey powered by intellectual curiosity, which began with sprinkling olive oil on seawater and culminated in playing around with smears of egg lecithin on microscopic slides. This brief review highlights how a few pairs of gifted hands attached to highly motivated brains have launched Liposome Technology.
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Affiliation(s)
- Volkmar Weissig
- Department of Pharmaceutical Sciences, Midwestern University College of Pharmacy Glendale, 19555 North 59th Ave., Glendale, AZ, 85308, USA.
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Contreras-García J, Boto RA, Izquierdo-Ruiz F, Reva I, Woller T, Alonso M. A benchmark for the non-covalent interaction (NCI) index or… is it really all in the geometry? Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1977-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Lazarova T, Mlynarczyk K, Querol E, Tenchov B, Filipek S, Padrós E. Identification of Specific Effect of Chloride on the Spectral Properties and Structural Stability of Multiple Extracellular Glutamic Acid Mutants of Bacteriorhodopsin. PLoS One 2016; 11:e0162952. [PMID: 27657718 PMCID: PMC5033488 DOI: 10.1371/journal.pone.0162952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/31/2016] [Indexed: 11/18/2022] Open
Abstract
In the present work we combine spectroscopic, DSC and computational approaches to examine the multiple extracellular Glu mutants E204Q/E194Q, E204Q/E194Q/E9Q and E204Q/E194Q/E9Q/E74Q of bacteriorhodopsin by varying solvent ionic strength and composition. Absorption spectroscopy data reveal that the absorption maxima of multiple EC Glu mutants can be tuned by the chloride concentration in the solution. Visible Circular dichroism spectra imply that the specific binding of Cl- can modulate weakened exciton chromophore coupling and reestablish wild type-like bilobe spectral features of the mutants. The DSC data display reappearance of the reversible thermal transition, higher Tm of denaturation and an increase in the enthalpy of unfolding of the mutants in 1 M KCl solutions. Molecular dynamics simulations indicate high affinity binding of Cl- to Arg82 and to Gln204 and Gln194 residues in the mutants. Analysis of the experimental data suggests that simultaneous elimination of the negatively charged side chain of Glu194 and Glu204 is the major cause for mutants' alterations. Specific Cl- binding efficiently coordinates distorted hydrogen bonding interactions of the EC region and reconstitutes the conformation and structure stability of mutated bR in WT-like fashion.
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Affiliation(s)
- Tzvetana Lazarova
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail: (TL); (EP)
| | - Krzysztof Mlynarczyk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Enric Querol
- Institut de Biomedicina i Biotecnologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Boris Tenchov
- Department of Medical Physics and Biophysics, Faculty of Medicine, Medical University – Sofia, Sofia, Bulgaria
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Esteve Padrós
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail: (TL); (EP)
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21
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Urano R, Okamoto Y. Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin. J Chem Phys 2016; 143:235101. [PMID: 26696075 DOI: 10.1063/1.4935964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank's data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.
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Affiliation(s)
- Ryo Urano
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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22
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Baumann A, Kerruth S, Fitter J, Büldt G, Heberle J, Schlesinger R, Ataka K. In-Situ Observation of Membrane Protein Folding during Cell-Free Expression. PLoS One 2016; 11:e0151051. [PMID: 26978519 PMCID: PMC4792443 DOI: 10.1371/journal.pone.0151051] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/23/2016] [Indexed: 12/31/2022] Open
Abstract
Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando) at molecular resolution.
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Affiliation(s)
- Axel Baumann
- Forschungszentrum Jülich, Institute of Complex Systems, Molecular Biophysics (ICS-5), 52425 Jülich, Germany
| | - Silke Kerruth
- Freie Universität Berlin, Department of Physics, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Fitter
- Forschungszentrum Jülich, Institute of Complex Systems, Molecular Biophysics (ICS-5), 52425 Jülich, Germany
- Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
| | - Georg Büldt
- Forschungszentrum Jülich, Institute of Complex Systems, Molecular Biophysics (ICS-5), 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, Laboratory for Advanced Studies of Membrane Proteins, 141700 Dolgoprudniy, Russia
| | - Joachim Heberle
- Freie Universität Berlin, Department of Physics, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Ramona Schlesinger
- Freie Universität Berlin, Department of Physics, Genetic Biophysics, Arnimallee 14, 14195 Berlin, Germany
- * E-mail: (KA); (RS)
| | - Kenichi Ataka
- Freie Universität Berlin, Department of Physics, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
- * E-mail: (KA); (RS)
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Gimpl K, Klement J, Keller S. Characterising protein/detergent complexes by triple-detection size-exclusion chromatography. Biol Proced Online 2016; 18:4. [PMID: 26880869 PMCID: PMC4753644 DOI: 10.1186/s12575-015-0031-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/29/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In vitro investigations of membrane proteins usually depend on detergents for protein solubilisation and stabilisation. The amount of detergent bound to a membrane protein is relevant to successful experiment design and data analysis but is often unknown. Triple-detection size-exclusion chromatography enables simultaneous separation of protein/detergent complexes and protein-free detergent micelles and determination of their molar masses in a straightforward and absolute manner. Size-exclusion chromatography is used to separate different species, while ultraviolet absorbance, static light scattering, and refractive index measurements allow molar mass determination of protein and detergent components. RESULTS We refined standard experimental and data-analysis procedures for challenging membrane-protein samples that elude routine approaches. The general procedures including preparatory steps, measurements, and data analysis for the characterisation of both routine and complex samples in difficult solvents such as concentrated denaturant solutions are demonstrated. The applicability of the protocol but also its limitations and possible solutions are discussed, and an extensive troubleshooting section is provided. CONCLUSIONS We established and validated a protocol for triple-detection size-exclusion chromatography that enables the inexperienced user to perform and analyse measurements of well-behaved protein/detergent complexes. More experienced users are provided with an example of a more sophisticated analysis procedure allowing mass determination under challenging separation conditions.
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Affiliation(s)
- Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Jessica Klement
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
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24
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A Complete NCI Perspective: From New Bonds to Reactivity. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2016. [DOI: 10.1007/978-3-319-29022-5_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Shiu YJ, Hayashi M, Shih O, Su C, Tsai MY, Yeh YQ, Su CJ, Huang YS, Lin SH, Jeng US. Intrinsic coordination for revealing local structural changes in protein folding–unfolding. Phys Chem Chem Phys 2016; 18:3179-87. [DOI: 10.1039/c5cp06309d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The local dislocations may be tracked relatively easily with respect to the internal rigid rod.
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Affiliation(s)
- Ying-Jen Shiu
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
| | - Michitoshi Hayashi
- Center for Condensed Matter Sciences
- National Taiwan University
- Taipei 106
- Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Charlene Su
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
- Taiwan
| | - Min-Yeh Tsai
- Department of Applied Chemistry
- National Chiao Tung University
- Hsinchu 300
- Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Yu-Shan Huang
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
| | - Sheng-Hsien Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
- Taiwan
- Department of Applied Chemistry
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center
- Hsinchu 30076
- Taiwan
- Department of Chemical Engineering
- National Tsing Hua University
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26
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Hartmann A, Krainer G, Keller S, Schlierf M. Quantification of Millisecond Protein-Folding Dynamics in Membrane-Mimetic Environments by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Anal Chem 2015; 87:11224-32. [PMID: 26457727 DOI: 10.1021/acs.analchem.5b03207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An increasing number of membrane proteins in different membrane-mimetic systems have become accessible to reversible unfolding experiments monitored by well-established ensemble techniques. However, only little information is available about kinetic processes during membrane-protein folding, mainly because of experimental challenges and a lack of methods suitable for observing highly dynamic membrane proteins. Here, we present single-molecule Förster resonance energy transfer (smFRET) confocal spectroscopy as a powerful tool in kinetic studies of membrane-protein folding in membrane-mimetic environments. We have developed a rigorous workflow demonstrating how to identify and quantify such dynamic processes using a set of qualitative, semiquantitative, and quantitative analytical tools. Using this workflow, we analyzed urea-induced folding and unfolding experiments on the α-helical membrane protein Mistic in the presence of the zwitterionic detergent n-dodecylphosphocholine (DPC). We identified two-state interconversion dynamics on the millisecond time scale of a protein folding into and out of detergent micelles. Our results demonstrate that smFRET is a promising tool for probing the chemical physics of membrane-protein structure and dynamics in the complex and anisotropic environment of a hydrophilic/hydrophobic interface, providing insights into protein interconversion dynamics without the need and challenges of synchronization.
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Affiliation(s)
- Andreas Hartmann
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstr. 18, 01307 Dresden, Germany
| | - Georg Krainer
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstr. 18, 01307 Dresden, Germany.,Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Michael Schlierf
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstr. 18, 01307 Dresden, Germany
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27
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Briant K, Koay YH, Otsuka Y, Swanton E. ERAD of proteins containing aberrant transmembrane domains requires ubiquitylation of cytoplasmic lysine residues. J Cell Sci 2015; 128:4112-25. [PMID: 26446255 PMCID: PMC4712780 DOI: 10.1242/jcs.171215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 09/28/2015] [Indexed: 11/29/2022] Open
Abstract
Clearance of misfolded proteins from the endoplasmic reticulum (ER) is mediated by the ubiquitin-proteasome system in a process known as ER-associated degradation (ERAD). The mechanisms through which proteins containing aberrant transmembrane domains are degraded by ERAD are poorly understood. To address this question, we generated model ERAD substrates based on CD8 with either a non-native transmembrane domain but a folded ER luminal domain (CD8TMD*), or the native transmembrane domain but a misfolded luminal domain (CD8LUM*). Although both chimeras were degraded by ERAD, we found that the location of the folding defect determined the initial site of ubiquitylation. Ubiquitylation of cytoplasmic lysine residues was required for the extraction of CD8TMD* from the ER membrane during ERAD, whereas CD8LUM* continued to be degraded in the absence of cytoplasmic lysine residues. Cytoplasmic lysine residues were also required for degradation of an additional ERAD substrate containing an unassembled transmembrane domain and when a non-native transmembrane domain was introduced into CD8LUM*. Our results suggest that proteins with defective transmembrane domains are removed from the ER through a specific ERAD mechanism that depends upon ubiquitylation of cytoplasmic lysine residues. Summary: Proteins containing defective transmembrane domains are removed from the endoplasmic reticulum through a specific mechanism that depends upon the ubiquitylation of cytoplasmic lysine residues.
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Affiliation(s)
- Kit Briant
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yee-Hui Koay
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yuka Otsuka
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Eileithyia Swanton
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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28
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Madhusudan Makwana K, Mahalakshmi R. Implications of aromatic-aromatic interactions: From protein structures to peptide models. Protein Sci 2015; 24:1920-33. [PMID: 26402741 DOI: 10.1002/pro.2814] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022]
Abstract
With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
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29
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Martinez-Gil L, Mingarro I. Viroporins, Examples of the Two-Stage Membrane Protein Folding Model. Viruses 2015; 7:3462-82. [PMID: 26131957 PMCID: PMC4517110 DOI: 10.3390/v7072781] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/21/2022] Open
Abstract
Viroporins are small, α-helical, hydrophobic virus encoded proteins, engineered to form homo-oligomeric hydrophilic pores in the host membrane. Viroporins participate in multiple steps of the viral life cycle, from entry to budding. As any other membrane protein, viroporins have to find the way to bury their hydrophobic regions into the lipid bilayer. Once within the membrane, the hydrophobic helices of viroporins interact with each other to form higher ordered structures required to correctly perform their porating activities. This two-step process resembles the two-stage model proposed for membrane protein folding by Engelman and Poppot. In this review we use the membrane protein folding model as a leading thread to analyze the mechanism and forces behind the membrane insertion and folding of viroporins. We start by describing the transmembrane segment architecture of viroporins, including the number and sequence characteristics of their membrane-spanning domains. Next, we connect the differences found among viroporin families to their viral genome organization, and finalize focusing on the pathways used by viroporins in their way to the membrane and on the transmembrane helix-helix interactions required to achieve proper folding and assembly.
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Affiliation(s)
- Luis Martinez-Gil
- Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Spain.
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Spain.
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30
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Nadeau VG, Gao A, Deber CM. Design and characterization of a membrane protein unfolding platform in lipid bilayers. PLoS One 2015; 10:e0120253. [PMID: 25799099 PMCID: PMC4370600 DOI: 10.1371/journal.pone.0120253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/20/2015] [Indexed: 11/29/2022] Open
Abstract
Accurate measurement of membrane protein stability—and particularly how it may vary as a result of disease-phenotypic mutations—ideally requires a denaturant that can unfold a membrane-embedded structure while leaving the solubilizing environment unaffected. The steric trap method fulfills this requirement by using monovalent streptavidin (mSA) molecules to unfold membrane proteins engineered with two spatially close biotin tags. Here we adapted this method to an 87-residue helix-loop-helix (hairpin) construct derived from helices 3 and 4 in the transmembrane domain of the human cystic fibrosis transmembrane conductance regulator (CFTR), wherein helix-helix tertiary interactions are anticipated to confer a portion of construct stability. The wild type CFTR TM3/4 hairpin construct was modified with two accessible biotin tags for mSA-induced unfolding, along with two helix-terminal pyrene labels to monitor loss of inter-helical contacts by pyrene excimer fluorescence. A series of eight constructs with biotin tags at varying distances from the helix-terminal pyrene labels were expressed, purified and labeled appropriately; all constructs exhibited largely helical circular dichroism spectra. We found that addition of mSA to an optimized construct in lipid vesicles led to a complete and reversible loss in pyrene excimer fluorescence and mSA binding, and hence hairpin unfolding—results further supported by SDS-PAGE visualization of mSA bound and unbound species. While some dimeric/oligomeric populations persist that may affect quantitation of the unfolding step, our characterization of the design yields a promising prototype of a future platform for the systematic study of membrane protein folding in a lipid bilayer environment.
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Affiliation(s)
- Vincent G. Nadeau
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Anqi Gao
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- * E-mail:
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31
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Frotscher E, Danielczak B, Vargas C, Meister A, Durand G, Keller S. Ein fluoriertes Detergens für Membranprotein-Anwendungen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Frotscher E, Danielczak B, Vargas C, Meister A, Durand G, Keller S. A Fluorinated Detergent for Membrane-Protein Applications. Angew Chem Int Ed Engl 2015; 54:5069-73. [DOI: 10.1002/anie.201412359] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 01/22/2015] [Indexed: 11/06/2022]
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33
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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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34
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Baturin S, Galka JJ, Piyadasa H, Gajjeraman S, O'Neil JD. The effects of a protein osmolyte on the stability of the integral membrane protein glycerol facilitator. Biochem Cell Biol 2014; 92:564-75. [PMID: 25387032 DOI: 10.1139/bcb-2014-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Osmolytes are naturally occurring molecules used by a wide variety of organisms to stabilize proteins under extreme conditions of temperature, salinity, hydrostatic pressure, denaturant concentration, and desiccation. The effects of the osmolyte trimethylamine N-oxide (TMAO) as well as the influence of detergent head group and acyl chain length on the stability of the Escherichia coli integral membrane protein glycerol facilitator (GF) tetramer to thermal and chemical denaturation by sodium dodecyl sulphate (SDS) are reported. TMAO promotes the association of the normally tetrameric α-helical protein into higher order oligomers in dodecyl-maltoside (DDM), but not in tetradecyl-maltoside (TDM), lyso-lauroylphosphatidyl choline (LLPC), or lyso-myristoylphosphatidyl choline (LMPC), as determined by dynamic light scattering (DLS); an octameric complex is particularly stable as indicated by SDS polyacrylamide gel electrophoresis. TMAO increases the heat stability of the GF tetramer an average of 10 °C in the 4 detergents and also protects the protein from denaturation by SDS. However, it did not promote re-association to the tetramer when added to SDS-dissociated protein. TMAO also promotes the formation of rod-like detergent micelles, and DLS was found to be useful for monitoring the structure of the protein and the redistribution of detergent during thermal dissociation of the protein. The protein is more thermally stable in detergents with the phosphatidylcholine head group (LLPC and LMPC) than in the maltoside detergents. The implications of the results for osmolyte mechanism, membrane protein stability, and protein-protein interactions are discussed.
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Affiliation(s)
- Simon Baturin
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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35
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Broecker J, Fiedler S, Gimpl K, Keller S. Polar Interactions Trump Hydrophobicity in Stabilizing the Self-Inserting Membrane Protein Mistic. J Am Chem Soc 2014; 136:13761-8. [DOI: 10.1021/ja5064795] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jana Broecker
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
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36
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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37
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Abstract
All life on earth can be naturally classified into cellular life forms and virus-like selfish elements, the latter being fully dependent on the former for their reproduction. Cells are reproducers that not only replicate their genome but also reproduce the cellular organization that depends on semipermeable, energy-transforming membranes and cannot be recovered from the genome alone, under the famous dictum of Rudolf Virchow, Omnis cellula e cellula. In contrast, simple selfish elements are replicators that can complete their life cycles within the host cell starting from genomic RNA or DNA alone. The origin of the cellular organization is the central and perhaps the hardest problem of evolutionary biology. I argue that the origin of cells can be understood only in conjunction with the origin and evolution of selfish genetic elements. A scenario of precellular evolution is presented that involves cohesion of the genomes of the emerging cellular life forms from primordial pools of small genetic elements that eventually segregated into hosts and parasites. I further present a model of the coevolution of primordial membranes and membrane proteins, discuss protocellular and non-cellular models of early evolution, and examine the habitats on the primordial earth that could have been conducive to precellular evolution and the origin of cells.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD, 20894, USA,
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38
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Bermejo IL, Arnulphi C, Ibáñez de Opakua A, Alonso-Mariño M, Goñi FM, Viguera AR. Membrane partitioning of the pore-forming domain of colicin A. Role of the hydrophobic helical hairpin. Biophys J 2014; 105:1432-43. [PMID: 24047995 DOI: 10.1016/j.bpj.2013.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022] Open
Abstract
The colicins are bacteriocins that target Escherichia coli and kill bacterial cells through different mechanisms. Colicin A forms ion channels in the inner membranes of nonimmune bacteria. This activity resides exclusively in its C-terminal fragment (residues 387-592). The soluble free form of this domain is a 10 α-helix bundle. The hydrophobic helical hairpin, H8-H9, is buried inside the structure and shielded by eight amphipathic surface helices. The interaction of the C-terminal colicin A domain and several chimeric variants with lipidic vesicles was examined here by isothermal titration calorimetry. In the mutant constructions, natural sequences of the hydrophobic helices H8 and H9 were either removed or substituted by polyalanine or polyleucine. All the constructions fully associated with DOPG liposomes including the mutant that lacked helices H8 and H9, indicating that amphipathic rather than hydrophobic helices were the major determinants of the exothermic binding reactions. Alanine is not specially favored in the lipid-bound form; the chimeric construct with polyalanine produced lower enthalpy gain. On the other hand, the large negative heat capacities associated with partitioning, a characteristic feature of the hydrophobic effect, were found to be dependent on the sequence hydrophobicity of helices H8 and H9.
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Affiliation(s)
- Ivan L Bermejo
- Unidad de Biofísica (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain
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39
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Rakowska PD, Lamarre B, Ryadnov MG. Probing label-free intracellular quantification of free peptide by MALDI-ToF mass spectrometry. Methods 2014; 68:331-7. [PMID: 24657280 DOI: 10.1016/j.ymeth.2014.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 02/27/2014] [Accepted: 03/03/2014] [Indexed: 12/15/2022] Open
Abstract
Cell-penetrating peptides are promising reagents for gene and drug delivery. They can efficiently traverse the plasma membrane and deliver various cargo materials ranging from genes to nanoparticles. The functional efficiency of cargo often depends on the completeness of intracellular peptide uptake, which can be measured, but its quantification remains largely inconclusive. Existing approaches rely on the use of radioactive and fluorescent labels or tags which allow colorimetric, fluorescent or spectrometric detection, but lack the ability to detect free peptide. Herein we describe a generic label- and tag-free method to measure the concentration of internalised peptide by matrix-assisted laser desorption/ionisation time of flight mass spectrometry. Quantification is preceded by two-dimensional chromatography and is performed at benign temperatures for the lysates of human dermal fibroblasts transfected with cell penetrating peptides in free form. Isotopically labelled peptides of the same structure are used as internal standards to enable accurate determination of concentration of the recovered free peptide. The method offers a minimalistic approach for intracellular quantification, which can be used as a correlative measure for fluorescence-based imaging methods.
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Affiliation(s)
| | - Baptiste Lamarre
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; School of Physics and Astronomy, University of Edinburgh, EH9 3JZ, UK.
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40
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Andrés J, Berski S, Contreras-García J, González-Navarrete P. Following the Molecular Mechanism for the NH3 + LiH → LiNH2 + H2 Chemical Reaction: A Study Based on the Joint Use of the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interaction (NCI) Index. J Phys Chem A 2014; 118:1663-72. [DOI: 10.1021/jp4111376] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Andrés
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Slawomir Berski
- Faculty
of Chemistry, University of Wroclaw, 14 F. Joliot-Curie, 50-383 Wroclaw, Poland
| | - Julia Contreras-García
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC Univ Paris 06, UMR 7616, F-75005 Paris, France
- CNRS, UMR 7616, LCT, F-75005 Paris, France
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41
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Jahnke N, Krylova OO, Hoomann T, Vargas C, Fiedler S, Pohl P, Keller S. Real-time monitoring of membrane-protein reconstitution by isothermal titration calorimetry. Anal Chem 2013; 86:920-7. [PMID: 24354292 PMCID: PMC3886389 DOI: 10.1021/ac403723t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
Phase diagrams offer a wealth of
thermodynamic information on aqueous
mixtures of bilayer-forming lipids and micelle-forming detergents,
providing a straightforward means of monitoring and adjusting the
supramolecular state of such systems. However, equilibrium phase diagrams
are of very limited use for the reconstitution of membrane proteins
because of the occurrence of irreversible, unproductive processes
such as aggregation and precipitation that compete with productive
reconstitution. Here, we exemplify this by dissecting the effects
of the K+ channel KcsA on the process of bilayer self-assembly
in a mixture of Escherichia coli polar lipid extract
and the nonionic detergent octyl-β-d-glucopyranoside.
Even at starting concentrations in the low micromolar range, KcsA
has a tremendous impact on the supramolecular organization of the
system, shifting the critical lipid/detergent ratios at the onset
and completion of vesicle formation by more than 2-fold. Thus, equilibrium
phase diagrams obtained for protein-free lipid/detergent mixtures
would be misleading when used to guide the reconstitution process.
To address this issue, we demonstrate that, even under such nonequilibrium
conditions, high-sensitivity isothermal titration calorimetry can
be exploited to monitor the progress of membrane-protein reconstitution
in real time, in a noninvasive manner, and at high resolution to yield
functional proteoliposomes with a narrow size distribution for further
downstream applications.
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Affiliation(s)
- Nadin Jahnke
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
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42
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Jacso T, Bardiaux B, Broecker J, Fiedler S, Baerwinkel T, Mainz A, Fink U, Vargas C, Oschkinat H, Keller S, Reif B. The Mechanism of Denaturation and the Unfolded State of the α-Helical Membrane-Associated Protein Mistic. J Am Chem Soc 2013; 135:18884-91. [DOI: 10.1021/ja408644f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tomas Jacso
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Benjamin Bardiaux
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Jana Broecker
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Tom Baerwinkel
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Andi Mainz
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Uwe Fink
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Carolyn Vargas
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Sandro Keller
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Bernd Reif
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
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43
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Kedrov A, Sustarsic M, de Keyzer J, Caumanns JJ, Wu ZC, Driessen AJ. Elucidating the Native Architecture of the YidC: Ribosome Complex. J Mol Biol 2013; 425:4112-24. [DOI: 10.1016/j.jmb.2013.07.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/24/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
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44
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Huysmans GHM, Guilvout I, Pugsley AP. Sequential steps in the assembly of the multimeric outer membrane secretin PulD. J Biol Chem 2013; 288:30700-30707. [PMID: 24019525 DOI: 10.1074/jbc.m113.489112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Investigations into protein folding are largely dominated by studies on monomeric proteins. However, the transmembrane domain of an important group of membrane proteins is only formed upon multimerization. Here, we use in vitro translation-coupled folding and insertion into artificial liposomes to investigate kinetic steps in the assembly of one such protein, the outer membrane secretin PulD of the bacterial type II secretion system. Analysis of the folding kinetics, measured by the acquisition of distinct determinants of the native state, provides unprecedented evidence for a sequential multistep process initiated by membrane-driven oligomerization. The effects of varying the lipid composition of the liposomes indicate that PulD first forms a "prepore" structure that attains the native state via a conformational switch.
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Affiliation(s)
- Gerard H M Huysmans
- From the Molecular Genetics Unit, Departments of Microbiology and Structural Biology and Chemistry, and CNRS ERL3526, Institut Pasteur, rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Ingrid Guilvout
- From the Molecular Genetics Unit, Departments of Microbiology and Structural Biology and Chemistry, and CNRS ERL3526, Institut Pasteur, rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Anthony P Pugsley
- From the Molecular Genetics Unit, Departments of Microbiology and Structural Biology and Chemistry, and CNRS ERL3526, Institut Pasteur, rue du Dr. Roux, 75724 Paris Cedex 15, France.
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45
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Broecker J, Keller S. Impact of urea on detergent micelle properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8502-8510. [PMID: 23745835 DOI: 10.1021/la4013747] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Co-solvents, such as urea, can entail drastic changes in the micellization behavior of detergents. We present a systematic quantification of the impact of urea on the critical micellar concentration, the micellization thermodynamics, and the micelle size in three homologous series of commonly used non-ionic alkyl detergents. To this end, we performed demicellization experiments by isothermal titration calorimetry and hydrodynamic size measurements by dynamic light scattering on alkyl maltopyranosides, cyclohexyl alkyl maltopyranosides, and alkyl glucopyranosides at urea concentrations of 0-8 M. For all detergents studied, we found that the critical micellar concentration increases exponentially because the absolute Gibbs free energy of micellization decreases linearly over the entire urea concentration range, as does the micelle size. In contrast, the enthalpic and entropic contributions to micellization reveal more complex, nonlinear dependences on urea concentration. Both free energy and size changes are more pronounced for long-chain detergents, which bury more apolar surface area upon micelle formation. The Gibbs free energy increments per methylene group within each detergent series depend on urea concentration in a linear fashion, although they result from the entropic term for alkyl maltosides but are of enthalpic origin for cyclohexyl alkyl maltosides. We compare our results to transfer free energies of amino acid side chains, relate them to protein-folding data, and discuss how urea-induced changes in detergent micelle properties affect in vitro investigations on membrane proteins.
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Affiliation(s)
- Jana Broecker
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
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46
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Pogozheva ID, Tristram-Nagle S, Mosberg HI, Lomize AL. Structural adaptations of proteins to different biological membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2592-608. [PMID: 23811361 DOI: 10.1016/j.bbamem.2013.06.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/04/2013] [Accepted: 06/19/2013] [Indexed: 02/06/2023]
Abstract
To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds.
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Affiliation(s)
- Irina D Pogozheva
- College of Pharmacy, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.
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47
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Riley KE, Hobza P. On the importance and origin of aromatic interactions in chemistry and biodisciplines. Acc Chem Res 2013; 46:927-36. [PMID: 22872015 DOI: 10.1021/ar300083h] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic systems contain both σ- and π-electrons, which in turn constitute σ- and π-molecular orbitals (MOs). In discussing the properties of these systems, researchers typically refer to the highest occupied and lowest unoccupied MOs, which are π MOs. The characteristic properties of aromatic systems, such as their low ionization potentials and electron affinities, high polarizabilities and stabilities, and small band gaps (in spectroscopy called the N → V1 space), can easily be explained based on their electronic structure. These one-electron properties point to characteristic features of how aromatic systems interact with each other. Unlike hydrogen bonding systems, which primarily interact through electrostatic forces, complexes containing aromatic systems, especially aromatic stacked pairs, are predominantly stabilized by dispersion attraction. The stabilization energy in the benzene dimer is rather small (~2.5 kcal/mol) but strengthens with heteroatom substitution. The stacked interaction of aromatic nucleic acid bases is greater than 10 kcal/mol, and for the most stable stacked pair, guanine and cytosine, it reaches approximately 17 kcal/mol. Although these values do not equal the planar H-bonded interactions of these bases (~29 kcal/mol), stacking in DNA is more frequent than H-bonding and, unlike H-bonding, is not significantly weakened when passing from the gas phase to a water environment. Consequently, the stacking of aromatic systems represents the leading stabilization energy contribution in biomacromolecules and in related nanosystems. Therefore stacking (dispersion) interactions predominantly determine the double helical structure of DNA, which underlies its storage and transfer of genetic information. Similarly, dispersion is the dominant contributor to attractive interactions involving aromatic amino acids within the hydrophobic core of a protein, which is critical for folding. Therefore, understanding the nature of aromatic interactions, which depend greatly on quantum mechanical (QM) calculations, is of key importance in biomolecular science. This Account shows that accurate binding energies for aromatic complexes should be based on computations made at the (estimated) CCSD(T)/complete basis set limit (CBS) level of theory. This method is the least computationally intensive one that can give accurate stabilization energies for all common classes of noncovalent interactions (aromatic-aromatic, H-bonding, ionic, halogen bonding, charge-transfer, etc.). These results allow for direct comparison of binding energies between different interaction types. Conclusions based on lower-level QM calculations should be considered with care.
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Affiliation(s)
- Kevin E. Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 771 46 Olomouc, Czech Republic
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48
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Gromiha MM, Ou YY. Bioinformatics approaches for functional annotation of membrane proteins. Brief Bioinform 2013; 15:155-68. [DOI: 10.1093/bib/bbt015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Fiedler S, Cole L, Keller S. Automated Circular Dichroism Spectroscopy for Medium-Throughput Analysis of Protein Conformation. Anal Chem 2013; 85:1868-72. [DOI: 10.1021/ac303244g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sebastian Fiedler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str.
13, 67663 Kaiserslautern, Germany
| | - Lindsay Cole
- Applied Photophysics Ltd., 21 Mole Business Park, Leatherhead, Surrey KT22
7BA, Leatherhead, United Kingdom
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str.
13, 67663 Kaiserslautern, Germany
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50
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Lipid-protein nanodiscs promote in vitro folding of transmembrane domains of multi-helical and multimeric membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:776-84. [PMID: 23159810 DOI: 10.1016/j.bbamem.2012.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 11/04/2012] [Accepted: 11/06/2012] [Indexed: 12/12/2022]
Abstract
Production of helical integral membrane proteins (IMPs) in a folded state is a necessary prerequisite for their functional and structural studies. In many cases large-scale expression of IMPs in cell-based and cell-free systems results in misfolded proteins, which should be refolded in vitro. Here using examples of the bacteriorhodopsin ESR from Exiguobacterium sibiricum and full-length homotetrameric K(+) channel KcsA from Streptomyces lividans we found that the efficient in vitro folding of the transmembrane domains of the polytopic and multimeric IMPs could be achieved during the protein encapsulation into the reconstructed high-density lipoprotein particles, also known as lipid-protein nanodiscs. In this case the self-assembly of the IMP/nanodisc complexes from a mixture containing apolipoprotein, lipids and the partially denatured protein solubilized in a harsh detergent induces the folding of the transmembrane domains. The obtained folding yields showed significant dependence on the properties of lipids used for nanodisc formation. The largest recovery of the spectroscopically active ESR (~60%) from the sodium dodecyl sulfate (SDS) was achieved in the nanodiscs containing anionic saturated lipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPG) and was approximately twice lower in the zwitterionic DMPC lipid. The reassembly of tetrameric KcsA from the acid-dissociated monomer solubilized in SDS was the most efficient (~80%) in the nanodiscs containing zwitterionic unsaturated lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The charged and saturated lipids provided lower tetramer quantities, and the lowest yield (<20%) was observed in DMPC. The overall yield of the ESR and KcsA folding was mainly restricted by the efficiency of the protein encapsulation into the nanodiscs.
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