1
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Jayasekera HS, Mohona FA, Ewbank M, Marty MT. Simultaneous Native Mass Spectrometry Analysis of Single and Double Mutants To Probe Lipid Binding to Membrane Proteins. Anal Chem 2024; 96:10426-10433. [PMID: 38859611 PMCID: PMC11215972 DOI: 10.1021/acs.analchem.4c01704] [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] [Indexed: 06/12/2024]
Abstract
Lipids are critical modulators of membrane protein structure and function. However, it is challenging to investigate the thermodynamics of protein-lipid interactions because lipids can simultaneously bind membrane proteins at different sites with different specificities. Here, we developed a native mass spectrometry (MS) approach using single and double mutants to measure the relative energetic contributions of specific residues on Aquaporin Z (AqpZ) toward cardiolipin (CL) binding. We first mutated potential lipid-binding residues on AqpZ, and mixed mutant and wild-type proteins together with CL. By using native MS to simultaneously resolve lipid binding to the mutant and wild-type proteins in a single spectrum, we directly determined the relative affinities of CL binding, thereby revealing the relative Gibbs free energy change for lipid binding caused by the mutation. Comparing different mutants revealed that W14 contributes to the tightest CL binding site, with R224 contributing to a lower affinity site. Using double mutant cycling, we investigated the synergy between W14 and R224 sites on CL binding. Overall, this novel native MS approach provides unique insights into the binding of lipids to specific sites on membrane proteins.
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Affiliation(s)
- Hiruni S. Jayasekera
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Farhana Afrin Mohona
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Megan Ewbank
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Michael T. Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
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2
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Ashrafuzzaman M, Koeppe RE, Andersen OS. Intrinsic Lipid Curvature and Bilayer Elasticity as Regulators of Channel Function: A Comparative Single-Molecule Study. Int J Mol Sci 2024; 25:2758. [PMID: 38474005 PMCID: PMC10931550 DOI: 10.3390/ijms25052758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Perturbations in bilayer material properties (thickness, lipid intrinsic curvature and elastic moduli) modulate the free energy difference between different membrane protein conformations, thereby leading to changes in the conformational preferences of bilayer-spanning proteins. To further explore the relative importance of curvature and elasticity in determining the changes in bilayer properties that underlie the modulation of channel function, we investigated how the micelle-forming amphiphiles Triton X-100, reduced Triton X-100 and the HII lipid phase promoter capsaicin modulate the function of alamethicin and gramicidin channels. Whether the amphiphile-induced changes in intrinsic curvature were negative or positive, amphiphile addition increased gramicidin channel appearance rates and lifetimes and stabilized the higher conductance states in alamethicin channels. When the intrinsic curvature was modulated by altering phospholipid head group interactions, however, maneuvers that promote a negative-going curvature stabilized the higher conductance states in alamethicin channels but destabilized gramicidin channels. Using gramicidin channels of different lengths to probe for changes in bilayer elasticity, we found that amphiphile adsorption increases bilayer elasticity, whereas altering head group interactions does not. We draw the following conclusions: first, confirming previous studies, both alamethicin and gramicidin channels are modulated by changes in lipid bilayer material properties, the changes occurring in parallel yet differing dependent on the property that is being changed; second, isolated, negative-going changes in curvature stabilize the higher current levels in alamethicin channels and destabilize gramicidin channels; third, increases in bilayer elasticity stabilize the higher current levels in alamethicin channels and stabilize gramicidin channels; and fourth, the energetic consequences of changes in elasticity tend to dominate over changes in curvature.
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Affiliation(s)
- Mohammad Ashrafuzzaman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
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3
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Lenaz G, Nesci S, Genova ML. Understanding differential aspects of microdiffusion (channeling) in the Coenzyme Q and Cytochrome c regions of the mitochondrial respiratory system. Mitochondrion 2024; 74:101822. [PMID: 38040170 DOI: 10.1016/j.mito.2023.11.005] [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: 08/04/2023] [Revised: 11/18/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Over the past decades, models of the organization of mitochondrial respiratory system have been controversial. The goal of this perspective is to assess this "conflict of models" by focusing on specific kinetic evidence in the two distinct segments of Coenzyme Q- and Cytochrome c-mediated electron transfer. Respiratory supercomplexes provide kinetic advantage by allowing a restricted diffusion of Coenzyme Q and Cytochrome c, and short-range interaction with their partner enzymes. In particular, electron transfer from NADH is compartmentalized by channeling of Coenzyme Q within supercomplexes, whereas succinate oxidation proceeds separately using the free Coenzyme Q pool. Previous evidence favoring Coenzyme Q random diffusion in the NADH-dependent electron transfer is due to downstream flux interference and misinterpretation of results. Indeed, electron transfer by complexes III and IV via Cytochrome c is less strictly dependent on substrate channeling in mammalian mitochondria. We briefly describe these differences and their physiological implications.
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Affiliation(s)
- Giorgio Lenaz
- University of Bologna, Via Zamboni 33, 40126 Bologna, Italy.
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Maria Luisa Genova
- Department of Biomedical and Neuromotor Sciences, O.U. Biochemistry, University of Bologna, Via Irnerio 48, 40126 Bologna, BO, Italy.
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4
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Jayasekera HS, Mohona FA, Ewbank M, Marty MT. SIMULTANEOUS NATIVE MASS SPECTROMETRY ANALYSIS OF SINGLE AND DOUBLE MUTANTS TO PROBE LIPID BINDING TO MEMBRANE PROTEINS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558516. [PMID: 37781586 PMCID: PMC10541089 DOI: 10.1101/2023.09.19.558516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Lipids are critical modulators of membrane protein structure and function. However, it is challenging to investigate the thermodynamics of protein-lipid interactions because lipids can simultaneously bind membrane proteins at different sites with different specificities. Here, we developed a native mass spectrometry (MS) approach using single and double mutants to measure the relative energetic contributions of specific residues on Aquaporin Z (AqpZ) toward cardiolipin (CL) binding. We first mutated potential lipid-binding residues on AqpZ, and mixed mutant and wild-type proteins together with CL. By using native MS to simultaneously resolve lipid binding to the mutant and wild-type proteins in a single spectrum, we directly determined the relative affinities of CL binding, thereby revealing the relative Gibbs free energy change for lipid binding caused by the mutation. Comparing different mutants revealed that the W14 contributes to the tightest CL binding site, with R224 contributing to a lower affinity site. Using double mutant cycling, we investigated the synergy between W14 and R224 sites on CL binding. Overall, this novel native MS approach provides unique insights into lipid binding to specific sites on membrane proteins.
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Affiliation(s)
- Hiruni S. Jayasekera
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Farhana Afrin Mohona
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Megan Ewbank
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Michael T. Marty
- [a] Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
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5
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Moritz MNO, Dores-Silva PR, Coto ALS, Selistre-de-Araújo HS, Leitão A, Cauvi DM, De Maio A, Carra S, Borges JC. Human HSP70-escort protein 1 (hHep1) interacts with negatively charged lipid bilayers and cell membranes. Cell Stress Chaperones 2023; 28:1001-1012. [PMID: 38001371 PMCID: PMC10746634 DOI: 10.1007/s12192-023-01394-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Human Hsp70-escort protein 1 (hHep1) is a cochaperone that assists in the function and stability of mitochondrial HSPA9. Similar to HSPA9, hHep1 is located outside the mitochondria and can interact with liposomes. In this study, we further investigated the structural and thermodynamic behavior of interactions between hHep1 and negatively charged liposomes, as well as interactions with cellular membranes. Our results showed that hHep1 interacts peripherally with liposomes formed by phosphatidylserine and cardiolipin and remains partially structured, exhibiting similar affinities for both. In addition, after being added to the cell membrane, recombinant hHep1 was incorporated by cells in a dose-dependent manner. Interestingly, the association of HSPA9 with hHep1 improved the incorporation of these proteins into the lipid bilayer. These results demonstrated that hHep1 can interact with lipids also present in the plasma membrane, indicating roles for this cochaperone outside of mitochondria.
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Affiliation(s)
- Milene N O Moritz
- São Carlos Institute of Chemistry, University of São Paulo - USP, P.O. Box 780, São Carlos, SP, 13560-970, Brazil
| | - Paulo R Dores-Silva
- São Carlos Institute of Chemistry, University of São Paulo - USP, P.O. Box 780, São Carlos, SP, 13560-970, Brazil
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Amanda L S Coto
- São Carlos Institute of Chemistry, University of São Paulo - USP, P.O. Box 780, São Carlos, SP, 13560-970, Brazil
| | | | - Andrei Leitão
- São Carlos Institute of Chemistry, University of São Paulo - USP, P.O. Box 780, São Carlos, SP, 13560-970, Brazil
| | - David M Cauvi
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Antonio De Maio
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Serena Carra
- Centre for Neuroscience and Nanotechnology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Júlio Cesar Borges
- São Carlos Institute of Chemistry, University of São Paulo - USP, P.O. Box 780, São Carlos, SP, 13560-970, Brazil.
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6
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Marlow B, Kuenze G, Meiler J, Koehler Leman J. Docking cholesterol to integral membrane proteins with Rosetta. PLoS Comput Biol 2023; 19:e1010947. [PMID: 36972273 PMCID: PMC10042369 DOI: 10.1371/journal.pcbi.1010947] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 03/29/2023] Open
Abstract
Lipid molecules such as cholesterol interact with the surface of integral membrane proteins (IMP) in a mode different from drug-like molecules in a protein binding pocket. These differences are due to the lipid molecule's shape, the membrane's hydrophobic environment, and the lipid's orientation in the membrane. We can use the recent increase in experimental structures in complex with cholesterol to understand protein-cholesterol interactions. We developed the RosettaCholesterol protocol consisting of (1) a prediction phase using an energy grid to sample and score native-like binding poses and (2) a specificity filter to calculate the likelihood that a cholesterol interaction site may be specific. We used a multi-pronged benchmark (self-dock, flip-dock, cross-dock, and global-dock) of protein-cholesterol complexes to validate our method. RosettaCholesterol improved sampling and scoring of native poses over the standard RosettaLigand baseline method in 91% of cases and performs better regardless of benchmark complexity. On the β2AR, our method found one likely-specific site, which is described in the literature. The RosettaCholesterol protocol quantifies cholesterol binding site specificity. Our approach provides a starting point for high-throughput modeling and prediction of cholesterol binding sites for further experimental validation.
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Affiliation(s)
- Brennica Marlow
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, United States of America
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7
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Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023; 21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Membrane proteins mediate a wide spectrum of biological processes, such as signal transduction and cell communication. Due to the arduous and costly nature inherent to the experimental process, membrane proteins have long been devoid of well-resolved atomic-level tertiary structures and, consequently, the understanding of their functional roles underlying a multitude of life activities has been hampered. Currently, computational tools dedicated to furthering the structure-function understanding are primarily focused on utilizing intelligent algorithms to address a variety of site-wise prediction problems (e.g., topology and interaction sites), but are scattered across different computing sources. Moreover, the recent advent of deep learning techniques has immensely expedited the development of computational tools for membrane protein-related prediction problems. Given the growing number of applications optimized particularly by manifold deep neural networks, we herein provide a review on the current status of computational strategies mainly in membrane protein type classification, topology identification, interaction site detection, and pathogenic effect prediction. Meanwhile, we provide an overview of how the entire prediction process proceeds, including database collection, data pre-processing, feature extraction, and method selection. This review is expected to be useful for developing more extendable computational tools specific to membrane proteins.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Headington, Oxford OX3 7LD, UK
| | - Arulsamy Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Kai Hu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India,Corresponding authors.
| | - Yuan Zhang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China,Corresponding authors.
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8
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Blackholly LR, Harris NJ, Findlay HE, Booth PJ. Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein. Front Mol Biosci 2022; 9:795212. [PMID: 35187078 PMCID: PMC8847741 DOI: 10.3389/fmolb.2022.795212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/23/2023] Open
Abstract
The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. In contrast, most mechanistic folding studies address refolding of full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. We summarise the benefits of this approach and show how it can be successfully extended to a membrane protein with a complex topology. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. Unlike major facilitator superfamily transporters, where changes in lipids can optimise the amount of correctly inserted protein, LeuT insertion yields are much less dependent on the lipid composition. The presence of a bacterial translocon either in native membrane extracts or in reconstituted membranes also has little influence on the yield of LeuT incorporated into the lipid membrane, except at high reconstitution concentrations. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family. This work provides a method in which to probe the formation of a protein as the polypeptide chain is being synthesised on a ribosome and inserting into lipids. We show that in comparison with the simpler major facilitator transporter structures, LeuT inserts less efficiently into membranes when synthesised cell-free, suggesting that more of the protein aggregates, likely as a result of the challenging formation of the knotted topology in the membrane.
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Affiliation(s)
| | | | | | - Paula J. Booth
- Department of Chemistry, King’s College London, London, United Kingdom
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9
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Harris NJ, Reading E, Booth PJ. Cell-Free Synthesis Strategies to Probe Co-translational Folding of Proteins Within Lipid Membranes. Methods Mol Biol 2022; 2433:273-292. [PMID: 34985751 DOI: 10.1007/978-1-0716-1998-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In order to comprehend the molecular basis of transmembrane protein biogenesis, methods are required that are capable of investigating the co-translational folding of these hydrophobic proteins. Equally, in artificial cell studies, controllable methods are desirable for in situ synthesis of membrane proteins that then direct reactions in the synthetic cell membrane. Here we describe a method that exploits cell-free expression systems and tunable membrane mimetics to facilitate co-translational studies. Alteration of the lipid bilayer composition improves the efficiency of the folding system. The approach also enables membrane transport proteins to be made and inserted into artificial cell platforms such as droplet interface bilayers. Importantly, this gives a new facet to the droplet networks by enabling specific transport of molecules across the synthetic bilayer against a concentration gradient. This method also includes a protocol to pause and restart translation of membrane proteins at specified positions during their co-translational folding. This stop-start strategy provides an avenue to investigate whether the proteins fold in sequence order, or if the correct fold of N-terminal regions is reliant on the synthesis of downstream residues.
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Affiliation(s)
| | - Eamonn Reading
- Department of Chemistry, King's College London, London, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, London, UK.
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10
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Weigle AT, Carr M, Shukla D. Impact of Increased Membrane Realism on Conformational Sampling of Proteins. J Chem Theory Comput 2021; 17:5342-5357. [PMID: 34339605 DOI: 10.1021/acs.jctc.1c00276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The realism and accuracy of lipid bilayer simulations through molecular dynamics (MD) are heavily dependent on the lipid composition. While the field is pushing toward implementing more heterogeneous and realistic membrane compositions, a lack of high-resolution lipidomic data prevents some membrane protein systems from being modeled with the highest level of realism. Given the additional diversity of real-world cellular membranes and protein-lipid interactions, it is still not fully understood how altering membrane complexity affects modeled membrane protein functions or if it matters over long-timescale simulations. This is especially true for organisms whose membrane environments have little to no computational study, such as the plant plasma membrane. Tackling these issues in tandem, a generalized, realistic, and asymmetric plant plasma membrane with more than 10 different lipid species is constructed herein. Classical MD simulations of pure membrane constructs were performed to evaluate how altering the compositional complexity of the membrane impacted the plant membrane properties. The apo form of a plant sugar transporter, OsSWEET2b, was inserted into membrane models where lipid diversity was calculated in either a size-dependent or size-independent manner. An adaptive sampling simulation regime validated by Markov-state models was performed to capture the gating dynamics of OsSWEET2b in each of these membrane constructs. In comparison to previous OsSWEET2b simulations performed in a pure POPC bilayer, we confirm that simulations performed within a native-like membrane composition alter the stabilization of apo OsSWEET2b conformational states by ∼1 kcal/mol. The free-energy barriers of intermediate conformational states decrease when realistic membrane complexity is simplified, albeit roughly within sampling error, suggesting that protein-specific responses to membranes differ due to altered packing caused by compositional fluctuations. This work serves as a case study where a more realistic bilayer composition makes unbiased conformational sampling easier to achieve than with simplified bilayers.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Matthew Carr
- Independent Software Development Provider310 East Marlette Avenue, Phoenix, Arizona 85012, United States
| | - Diwakar Shukla
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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11
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Chen P, Vorobyov I, Roux B, Allen TW. Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness. J Phys Chem B 2021; 125:1020-1035. [PMID: 33493394 DOI: 10.1021/acs.jpcb.0c08613] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Different mechanisms have been proposed to explain the permeation of charged compounds through lipid membranes. Overall, it is expected that an ion-induced defect permeation mechanism, where substantial membrane deformations accompany ion movement, should be dominant in thin membranes but that a solubility-diffusion mechanism, where ions partition into the membrane core with large associated dehydration energy costs, becomes dominant in thicker membranes. However, while this physical picture is intuitively reasonable, capturing the interconversion between these two permeation mechanisms in molecular dynamics (MD) simulations based on atomic models is challenging. In particular, simulations relying on nonpolarizable force fields are artificially unfavorable to the solubility-diffusion mechanism, as induced polarization of the nonpolar hydrocarbon is ignored, causing overestimated free energy costs for charged molecules to enter into this region of the membrane. In this study, all-atom MD simulations based on nonpolarizable and polarizable force fields are used to quantitatively characterize the permeation process for the arginine side chain analog methyl-guanidinium through bilayer membranes of mono-unsaturated phosphatidylcholine lipids with and without cholesterol, resulting in thicknesses spanning from ∼24 to ∼42 Å. With simulations based on a nonpolarizable force field, ion translocation can take place solely through an ion-induced defect mechanism, with free energy barriers increasing linearly from 14 to 40 kcal/mol, depending on the thickness. However, with simulations based on a polarizable force field, ion translocation is predominantly dominated by an ion-induced defect mechanism in thin membranes, which progressively converts to a solubility-diffusion mechanism as the membranes get thicker. The transition between the two mechanisms occurs at a thickness of ∼29 Å, with lipid tails of 22 or more carbon atoms. This situation appears to represent the upper limit for ion-induced defect permeation within the current polarizable models. Beyond this thickness, it becomes energetically preferable for the ion to dehydrate and partition into the membrane core-a phenomenon that cannot be captured using the nonpolarizable models. Induced electronic polarizability therefore leads not just to a shift in permeation energetics but to an interconversion between two strikingly different physical mechanisms. The result highlights the importance of induced polarizability in modeling lipid membranes.
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Affiliation(s)
- Peiran Chen
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology, Department of Pharmacology, University of California, Davis, California 95616, United States
| | - Benoît Roux
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Toby W Allen
- School of Science, RMIT University, Melbourne 3001, Australia
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12
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Kim GC, Cheon DH, Lee Y. Challenge to overcome current limitations of cell-penetrating peptides. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140604. [PMID: 33453413 DOI: 10.1016/j.bbapap.2021.140604] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
The penetration of biological membranes is a prime obstacle for the delivery of pharmaceutical drugs. Cell-penetrating peptide (CPP) is an efficient vehicle that can deliver various cargos across the biological membranes. Since the discovery, CPPs have been rigorously studied to unveil the underlying penetrating mechanism as well as to exploit CPPs for various biomedical applications. This review will focus on the various strategies to overcome current limitations regarding stability, selectivity, and efficacy of CPPs.
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Affiliation(s)
- Gyu Chan Kim
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Dae Hee Cheon
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yan Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea.
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13
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Harris NJ, Pellowe GA, Booth PJ. Cell-free expression tools to study co-translational folding of alpha helical membrane transporters. Sci Rep 2020; 10:9125. [PMID: 32499529 PMCID: PMC7272624 DOI: 10.1038/s41598-020-66097-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 11/28/2022] Open
Abstract
Most helical membrane proteins fold co-translationally during unidirectional polypeptide elongation by the ribosome. Studies thus far, however, have largely focussed on refolding full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation offers opportunities to remedy this deficit in folding studies and has previously been used for membrane proteins. We exploit this cell-free approach to develop tools to probe co-translational folding. We show that two transporters from the ubiquitous Major Facilitator Superfamily can successfully insert into a synthetic bilayer without the need for translocon insertase apparatus that is essential in vivo. We also assess the cooperativity of domain insertion, by expressing the individual transporter domains cell-free. Furthermore, we manipulate the cell-free reaction to pause and re-start protein synthesis at specific points in the protein sequence. We find that full-length protein can still be made when stalling after the first N terminal helix has inserted into the bilayer. However, stalling after the first three helices have exited the ribosome cannot be successfully recovered. These three helices cannot insert stably when ribosome-bound during co-translational folding, as they require insertion of downstream helices.
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Affiliation(s)
- Nicola J Harris
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A Pellowe
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Paula J Booth
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
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14
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Sarkar P, Chattopadhyay A. Cholesterol interaction motifs in G protein-coupled receptors: Slippery hot spots? WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1481. [PMID: 32032482 DOI: 10.1002/wsbm.1481] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/28/2019] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
Abstract
G protein-coupled receptors (GPCRs) are cell membrane associated signaling hubs that orchestrate a multitude of cellular functions upon binding to a diverse variety of extracellular ligands. Since GPCRs are integral membrane proteins with seven-transmembrane domain architecture, their function, organization and dynamics are intimately regulated by membrane lipids, such as cholesterol. Cholesterol is an extensively studied lipids in terms of its effects on GPCR structure and function. One of the possible mechanisms underlying modulation of GPCR function by cholesterol is via specific interaction of GPCRs with membrane cholesterol. These interactions of GPCRs with membrane cholesterol are often attributed to structural features of GPCRs that could facilitate their preferential association with cholesterol. In this backdrop, cholesterol interaction motifs represent putative interaction sites on GPCRs that could facilitate cholesterol-sensitive function of these receptors. In this review, we provide an overview of cholesterol interaction motifs found in GPCRs, which have been identified through a combination of crystallography, bioinformatics analysis, and functional studies. In addition, we will highlight, using specific examples, why mere presence of a cholesterol interaction motif at a given site may not directly implicate its role in interaction with membrane cholesterol. We therefore believe that experimental approaches, followed by functional analysis of cholesterol sensitivity of GPCRs, would provide a better understanding of the role played by these motifs in cholesterol-sensitive function. We envision that a comprehensive knowledge of cholesterol interaction sites in GPCRs would allow us to develop a better understanding of GPCR structure-function paradigm, and could be useful in future therapeutics. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods.
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Affiliation(s)
- Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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15
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Bteich M, Poulin P, Haddad S. The potential protein-mediated hepatic uptake: discussion on the molecular interactions between albumin and the hepatocyte cell surface and their implications for the in vitro-to-in vivo extrapolations of hepatic clearance of drugs. Expert Opin Drug Metab Toxicol 2019; 15:633-658. [DOI: 10.1080/17425255.2019.1640679] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Michel Bteich
- Department of Environmental and Occupational Health, School of Public Health, Université de Montréal, Montreal, Quebec, Canada
| | - Patrick Poulin
- Department of Environmental and Occupational Health, School of Public Health, Université de Montréal, Montreal, Quebec, Canada
- Consultant Patrick Poulin Inc., Québec city, Canada
| | - Sami Haddad
- Department of Environmental and Occupational Health, School of Public Health, Université de Montréal, Montreal, Quebec, Canada
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16
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Abstract
Cell nutrition, detoxification, signalling, homeostasis and response to drugs, processes related to cell growth, differentiation and survival are all mediated by plasma membrane (PM) proteins called transporters. Despite their distinct fine structures, mechanism of function, energetic requirements, kinetics and substrate specificities, all transporters are characterized by a main hydrophobic body embedded in the PM as a series of tightly packed, often intertwined, α-helices that traverse the lipid bilayer in a zigzag mode, connected with intracellular or extracellular loops and hydrophilic N- and C-termini. Whereas longstanding genetic, biochemical and biophysical evidence suggests that specific transmembrane segments, and also their connecting loops, are responsible for substrate recognition and transport dynamics, emerging evidence also reveals the functional importance of transporter N- and C-termini, in respect to transport catalysis, substrate specificity, subcellular expression, stability and signalling. This review highlights selected prototypic examples of transporters in which their termini play important roles in their functioning.
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Affiliation(s)
- Emmanuel Mikros
- Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, 15771 Athens, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
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17
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Rasmussen T, Rasmussen A, Yang L, Kaul C, Black S, Galbiati H, Conway SJ, Miller S, Blount P, Booth IR. Interaction of the Mechanosensitive Channel, MscS, with the Membrane Bilayer through Lipid Intercalation into Grooves and Pockets. J Mol Biol 2019; 431:3339-3352. [PMID: 31173776 DOI: 10.1016/j.jmb.2019.05.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 10/26/2022]
Abstract
All membrane proteins have dynamic and intimate relationships with the lipids of the bilayer that may determine their activity. Mechanosensitive channels sense tension through their interaction with the lipids of the membrane. We have proposed a mechanism for the bacterial channel of small conductance, MscS, that envisages variable occupancy of pockets in the channel by lipid chains. Here, we analyze protein-lipid interactions for MscS by quenching of tryptophan fluorescence with brominated lipids. By this strategy, we define the limits of the bilayer for TM1, which is the most lipid exposed helix of this protein. In addition, we show that residues deep in the pockets, created by the oligomeric assembly, interact with lipid chains. On the cytoplasmic side, lipids penetrate as far as the pore-lining helices and lipid molecules can align along TM3b perpendicular to lipids in the bilayer. Cardiolipin, free fatty acids, and branched lipids can access the pockets where the latter have a distinct effect on function. Cholesterol is excluded from the pockets. We demonstrate that introduction of hydrophilic residues into TM3b severely impairs channel function and that even "conservative" hydrophobic substitutions can modulate the stability of the open pore. The data provide important insights into the interactions between phospholipids and MscS and are discussed in the light of recent developments in the study of Piezo1 and TrpV4.
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Affiliation(s)
- Tim Rasmussen
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Akiko Rasmussen
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Limin Yang
- Department of Physiology, U.T. Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9040, USA.
| | - Corinna Kaul
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Susan Black
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Heloisa Galbiati
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
| | - Samantha Miller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Paul Blount
- Department of Physiology, U.T. Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9040, USA.
| | - Ian Rylance Booth
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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18
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Stability of the two-dimensional lattice of bacteriorhodopsin reconstituted in partially fluorinated phosphatidylcholine bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:631-642. [DOI: 10.1016/j.bbamem.2018.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/27/2018] [Accepted: 12/20/2018] [Indexed: 11/21/2022]
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19
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Vázquez L, Corzo-Martínez M, Arranz-Martínez P, Barroso E, Reglero G, Torres C. Bioactive Lipids. BIOACTIVE MOLECULES IN FOOD 2019. [DOI: 10.1007/978-3-319-78030-6_58] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Transporter oligomerisation: roles in structure and function. Biochem Soc Trans 2018; 47:433-440. [PMID: 30578344 PMCID: PMC6393857 DOI: 10.1042/bst20180316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/18/2018] [Accepted: 11/15/2018] [Indexed: 01/27/2023]
Abstract
Oligomerisation is a key feature of integral membrane transporters with roles in structure, function and stability. In this review, we cover some very recent advances in our understanding of how oligomerisation affects these key transporter features, with emphasis on a few groups of transporters, including the nucleobase ascorbate transporters, neurotransmitter sodium symporters and major facilitator superfamily members.
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21
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Membrane protein nanoparticles: the shape of things to come. Biochem Soc Trans 2018; 46:1495-1504. [PMID: 30464048 PMCID: PMC6299238 DOI: 10.1042/bst20180139] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/23/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
The use of styrene–maleic acid (SMA) for the purification of a wide range of membrane proteins (MPs) from both prokaryotic and eukaryotic sources has begun to make an impact in the field of MP biology. This method is growing in popularity as a means to purify and thoroughly investigate the structure and function of MPs and biological membranes. The amphiphilic SMA copolymer can effectively extract MPs directly from a native lipid bilayer to form discs ∼10 nm in diameter. The resulting lipid particles, or styrene–maleic acid lipid particles (SMALPs), contain SMA, protein and membrane lipid. MPs purified in SMALPs are able to retain their native structure and, in many cases, functional activity, and growing evidence suggests that MPs purified using SMA have enhanced thermal stability compared with detergent-purified proteins. The SMALP method is versatile and is compatible with a wide range of cell types across taxonomic domains. It can readily be adapted to replace detergent in many protein purification methods, often with only minor changes made to the existing protocol. Moreover, biophysical analysis and structural determination may now be a possibility for many large, unstable MPs. Here, we review recent advances in the area of SMALP purification and how it is affecting the field of MP biology, critically assess recent progress made with this method, address some of the associated technical challenges which may remain unresolved and discuss opportunities for exploiting SMALPs to expand our understanding of structural and functional properties of MPs.
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22
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Abstract
Vascular endothelial cells (ECs) maintain circulatory system homeostasis by changing their functions in response to changes in hemodynamic forces, including shear stress and stretching. However, it is unclear how ECs sense changes in shear stress and stretching and transduce these changes into intracellular biochemical signals. The plasma membranes of ECs have recently been shown to respond to shear stress and stretching differently by rapidly changing their lipid order, fluidity, and cholesterol content. Such changes in the membranes' physical properties trigger the activation of membrane receptors and cell responses specific to each type of force. Artificial lipid-bilayer membranes show similar changes in lipid order in response to shear stress and stretching, indicating that they are physical phenomena rather than biological reactions. These findings suggest that the plasma membranes of ECs act as mechanosensors; in response to mechanical forces, they first alter their physical properties, modifying the conformation and function of membrane proteins, which then activates downstream signaling pathways. This new appreciation of plasma membranes as mechanosensors could help to explain the distinctive features of mechanotransduction in ECs involving shear stress and stretching, which activate a variety of membrane proteins and multiple signal transduction pathways almost simultaneously.
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Affiliation(s)
- Kimiko Yamamoto
- Laboratory of System Physiology, Department of Biomedical Engineering, Graduate School of Medicine, The University of Tokyo
| | - Joji Ando
- Laboratory of Biomedical Engineering, School of Medicine, Dokkyo Medical University
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23
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Wang L, Biswas KH, Yoon BK, Kawakami LM, Park S, Groves JT, Li L, Huang W, Cho NJ. Membrane Reconstitution of Monoamine Oxidase Enzymes on Supported Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10764-10773. [PMID: 30049212 DOI: 10.1021/acs.langmuir.8b01348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Monoamine oxidase A and B (MAO-A and B) are mitochondrial outer membrane enzymes that are implicated in a number of human diseases, and the pharmacological inhibition of these enzymes is a promising therapeutic strategy to alleviate disease symptoms. It has been suggested that optimal levels of enzymatic activity occur in the membrane-associated state, although details of the membrane association process remain to be understood. Herein, we have developed a supported lipid bilayer platform to study MAO-A and B binding and evaluate the effects of known pharmacological inhibitors on the membrane association process. By utilizing the quartz crystal microbalance-dissipation (QCM-D) technique, it was determined that both MAOs exhibit tight binding to negatively and positively charged bilayers with distinct concentration-dependent binding profiles while only transiently binding to neutral bilayers. Importantly, in the presence of known inhibitors, the MAOs showed increased binding to negatively charged bilayers, although there was no effect of inhibitor treatment on binding to positively charged bilayers. Taken together, our findings establish that the membrane association of MAOs is highly dependent on membrane surface charge, and we outline an experimental platform to support the in vitro reconstitution of monoamine oxidases on synthetic membranes, including the evaluation of pharmacological drug candidates.
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Affiliation(s)
- Liulin Wang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech) , Nanjing 211816 , China
- School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798 , Singapore
| | - Kabir H Biswas
- School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798 , Singapore
| | - Bo Kyeong Yoon
- School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798 , Singapore
| | - Lisa M Kawakami
- School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798 , Singapore
| | - Soohyun Park
- School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798 , Singapore
| | - Jay T Groves
- School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798 , Singapore
- Department of Chemistry , University of California, Berkeley , Berkeley , California 94720 , United States of America
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech) , Nanjing 211816 , China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech) , Nanjing 211816 , China
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798 , Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University , Singapore 637459 , Singapore
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24
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Lipids modulate the insertion and folding of the nascent chains of alpha helical membrane proteins. Biochem Soc Trans 2018; 46:1355-1366. [PMID: 30190329 DOI: 10.1042/bst20170424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
Membrane proteins must be inserted into a membrane and folded into their correct structure to function correctly. This insertion occurs during translation and synthesis by the ribosome for most α-helical membrane proteins. Precisely how this co-translational insertion and folding occurs, and the role played by the surrounding lipids, is still not understood. Most of the work on the influence of the lipid environment on folding and insertion has focussed on denatured, fully translated proteins, and thus does not replicate folding during unidirectional elongation of nascent chains that occurs in the cell. This review aims to highlight recent advances in elucidating lipid composition and bilayer properties optimal for insertion and folding of nascent chains in the membrane and in the assembly of oligomeric proteins.
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25
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Stroud Z, Hall SCL, Dafforn TR. Purification of membrane proteins free from conventional detergents: SMA, new polymers, new opportunities and new insights. Methods 2018; 147:106-117. [PMID: 29608964 DOI: 10.1016/j.ymeth.2018.03.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/19/2018] [Accepted: 03/26/2018] [Indexed: 11/17/2022] Open
Abstract
Membrane proteins remain a somewhat enigmatic group of biomolecules. On the one hand they mediate some of the most important processes in biology with molecular mechanisms that are often elegantly complex. On the other hand they are exceptionally challenging to produce, making studies of membrane protein structure and function among the most difficult projects undertaken by biochemists. The central issue with studies of a membrane protein has been the need to extract them from their native lipid environment before purification and production of a homogenous sample. Historical approaches have utilized detergent solubilisation but these often lead to a sample with low activity and stability. In the past 15 years a new approach that focuses on preserving the local lipid environment surrounding the membrane proteins has been developed. The latest, and perhaps most complete, incarnation of this method has been the use of polymers based on styrene maleic acid (SMA) to stabilise nanoscale discs of lipid that contain membrane proteins. In this review we examine the range of SMA-related polymers that have now been shown to have utility in the production of membrane proteins. We discuss the differences between the polymers and attempt to discover rules and trends that explain their behavior.
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Affiliation(s)
- Zoe Stroud
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Stephen C L Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
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26
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Bories F, Constantin D, Galatola P, Fournier JB. Coupling between Inclusions and Membranes at the Nanoscale. PHYSICAL REVIEW LETTERS 2018; 120:128104. [PMID: 29694104 DOI: 10.1103/physrevlett.120.128104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 06/08/2023]
Abstract
The activity of cell membrane inclusions (such as ion channels) is influenced by the host lipid membrane, to which they are elastically coupled. This coupling concerns the hydrophobic thickness of the bilayer (imposed by the length of the channel, as per the hydrophobic matching principle) but also its slope at the boundary of the inclusion. However, this parameter has never been measured so far. We combine small-angle x-ray scattering data and a complete elastic model to measure the slope for the model gramicidin channel and show that it is surprisingly steep in two membrane systems with very different elastic properties. This conclusion is confirmed and generalized by the comparison with recent results in the simulation literature and with conductivity measurements.
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Affiliation(s)
- Florent Bories
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université Paris 7 Diderot, 75205 Paris Cedex 13, France
| | - Doru Constantin
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Paolo Galatola
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université Paris 7 Diderot, 75205 Paris Cedex 13, France
| | - Jean-Baptiste Fournier
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université Paris 7 Diderot, 75205 Paris Cedex 13, France
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27
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Schulze Greiving VC, de Boer HL, Bomer JG, van den Berg A, Le Gac S. Integrated microfluidic biosensing platform for simultaneous confocal microscopy and electrophysiological measurements on bilayer lipid membranes and ion channels. Electrophoresis 2017; 39:496-503. [PMID: 29193178 DOI: 10.1002/elps.201700346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/04/2017] [Accepted: 11/05/2017] [Indexed: 01/19/2023]
Abstract
Combining high-resolution imaging and electrophysiological recordings is key for various types of experimentation on lipid bilayers and ion channels. Here, we propose an integrated biosensing platform consisting of a microfluidic cartridge and a dedicated chip-holder to conduct such dual measurements on suspended lipid bilayers, in a user-friendly manner. To illustrate the potential of the integrated platform, we characterize lipid bilayers in terms of thickness and fluidity while simultaneously monitoring single ion channel currents. For that purpose, POPC lipid bilayers are supplemented with a fluorescently-tagged phospholipid (NBD-PE, 1% mol) for Fluorescence Recovery After Photobleaching (FRAP) measurements and a model ion channel (gramicidin, 1 nM). These combined measurements reveal that NBD-PE has no effect on the lipid bilayer thickness while gramicidin induces thinning of the membrane. Furthermore, the presence of gramicidin does not alter the lipid bilayer fluidity. Surprisingly, in lipid bilayers supplemented with both probes, a reduction in gramicidin open probability and lifetime is observed compared to lipid bilayers with gramicidin only, suggesting an influence of NBD-PE on the gramicidin ion function. Altogether, our proposed microfluidic biosensing platform in combination with the herein presented multi-parametric measurement scheme paves the way to explore the interdependent relationship between lipid bilayer properties and ion channel function.
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Affiliation(s)
- Verena C Schulze Greiving
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Hans L de Boer
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Johan G Bomer
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Albert van den Berg
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Séverine Le Gac
- BIOS, Lab on a chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
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28
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β 1-Integrin-Mediated Adhesion Is Lipid-Bilayer Dependent. Biophys J 2017; 113:1080-1092. [PMID: 28877491 DOI: 10.1016/j.bpj.2017.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/19/2017] [Accepted: 07/13/2017] [Indexed: 11/21/2022] Open
Abstract
Integrin-mediated adhesion is a central feature of cellular adhesion, locomotion, and endothelial cell mechanobiology. Although integrins are known to be transmembrane proteins, little is known about the role of membrane biophysics and dynamics in integrin adhesion. We treated human aortic endothelial cells with exogenous amphiphiles, shown previously in model membranes, and computationally, to affect bilayer thickness and lipid phase separation, and subsequently measured single-integrin-molecule adhesion kinetics using an optical trap, and diffusion using fluorescence correlation spectroscopy. Benzyl alcohol (BA) partitions to liquid-disordered (Ld) domains, thins them, and causes the greatest increase in hydrophobic mismatch between liquid-ordered (Lo) and Ld domains among the three amphiphiles, leading to domain separation. In human aortic endothelial cells, BA increased β1-integrin-Arg-Gly-Asp-peptide affinity by 18% with a transition from single to double valency, consistent with a doubling of the molecular brightness of mCherry-tagged β1-integrins measured using fluorescence correlation spectroscopy. Accordingly, BA caused an increase in the size of focal-adhesion-kinase/paxillin-positive peripheral adhesions and reduced migration speeds as measured using wound-healing assays. Vitamin E, which thickens Lo domains and disperses them by lowering edge energy on domain boundaries, left integrin affinity unchanged but reduced binding probability, leading to smaller focal adhesions and equivalent migration speed relative to untreated cells. Vitamin E reversed the BA-induced decrease in migration speed. Triton X-100 also thickens Lo domains, but partitions to both lipid phases and left unchanged binding kinetics, focal adhesion sizes, and migration speed. These results demonstrate that only the amphiphile that thinned Ld lipid domains increased β1-integrin-Arg-Gly-Asp-peptide affinity and valency, thus implicating Ld domains in modulation of integrin adhesion, nascent adhesion formation, and cell migration.
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29
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Grau B, Javanainen M, García-Murria MJ, Kulig W, Vattulainen I, Mingarro I, Martínez-Gil L. The role of hydrophobic matching on transmembrane helix packing in cells. Cell Stress 2017; 1:90-106. [PMID: 31225439 PMCID: PMC6551820 DOI: 10.15698/cst2017.11.111] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Folding and packing of membrane proteins are highly influenced by the lipidic component of the membrane. Here, we explore how the hydrophobic mismatch (the difference between the hydrophobic span of a transmembrane protein region and the hydrophobic thickness of the lipid membrane around the protein) influences transmembrane helix packing in a cellular environment. Using a ToxRED assay in Escherichia coli and a Bimolecular Fluorescent Complementation approach in human-derived cells complemented by atomistic molecular dynamics simulations we analyzed the dimerization of Glycophorin A derived transmembrane segments. We concluded that, biological membranes can accommodate transmembrane homo-dimers with a wide range of hydrophobic lengths. Hydrophobic mismatch and its effects on dimerization are found to be considerably weaker than those previously observed in model membranes, or under in vitro conditions, indicating that biological membranes (particularly eukaryotic membranes) can adapt to structural deformations through compensatory mechanisms that emerge from their complex structure and composition to alleviate membrane stress. Results based on atomistic simulations support this view, as they revealed that Glycophorin A dimers remain stable, despite of poor hydrophobic match, using mechanisms based on dimer tilting or local membrane thickness perturbations. Furthermore, hetero-dimers with large length disparity between their monomers are also tolerated in cells, and the conclusions that one can draw are essentially similar to those found with homo-dimers. However, large differences between transmembrane helices length hinder the monomer/dimer equilibrium, confirming that, the hydrophobic mismatch has, nonetheless, biologically relevant effects on helix packing in vivo.
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Affiliation(s)
- Brayan Grau
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
| | - Matti Javanainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland
| | - Maria Jesús García-Murria
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
| | - Waldemar Kulig
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland.,MEMPHYS - Centre for Biomembrane Physics
| | - Ismael Mingarro
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
| | - Luis Martínez-Gil
- Departamento de Bioquímica y Biología Molecular, ERI BioTecMed, Universitat de València, E-46100 Burjassot, Spain
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30
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Patrick JW, Gamez RC, Russell DH. The Influence of Lipid Bilayer Physicochemical Properties on Gramicidin A Conformer Preferences. Biophys J 2017; 110:1826-1835. [PMID: 27119642 DOI: 10.1016/j.bpj.2016.03.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/11/2016] [Accepted: 03/07/2016] [Indexed: 11/19/2022] Open
Abstract
The conformational preferences adopted by gramicidin A (GA) dimers inserted into phospholipid bilayers are reported as a function of the bilayer cholesterol content, temperature, and incubation time. Through use of vesicle capture-freeze drying methodology, GA dimers were captured in lipid bilayers and the conformational preferences of the complex were analyzed using ion mobility-mass spectrometry. Perturbations that affect the physicochemical interactions in the lipid bilayer such as cholesterol incorporation, temperature, and incubation time directly alter the conformer preferences of the complex. Regardless of bilayer cholesterol concentration, the antiparallel double helix (ADH) conformation was observed to be most abundant for GA dimers in bilayers composed of lipids with 12 to 22 carbon acyl chains. Incorporation of cholesterol into lipid bilayers yields increased bilayer thickness and rigidity, and an increased abundance of parallel double helix (PDH) and single-stranded head-to-head (SSHH) dimers were observed. Bilayers prepared using 1,2-dilauroyl-sn-glycero-3-phosphocholine, a lipid with 12 carbon acyl chains, yielded a nascent conformer that decreased in abundance as a function of bilayer cholesterol content. High resolution ion mobility-mass spectrometry data revealed two peaks in the ADH region suggesting that ADH populations are composed of two distinct conformers. The conformer preferences of GA dimers from 1,2-distearoyl-sn-glycero-3-phosphocholine bilayers were significantly different for samples incubated at 4°C vs. 60°C; increased cholesterol content yielded more PDH and SSHH at 60°C. The addition of cholesterol as well as incubating samples of 1,2-distearoyl-sn-glycero-3-phosphocholine at 60°C for 24-72 h yielded an increase in PDH and SSHH abundance.
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Affiliation(s)
- John W Patrick
- Department of Chemistry, Texas A&M University, College Station, Texas
| | - Roberto C Gamez
- Department of Chemistry, Texas A&M University, College Station, Texas
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas.
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31
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Peng B, Ding XY, Sun C, Yang YN, Gao YJ, Zhao X. The chain order of binary unsaturated lipid bilayers modulated by aromatic-residue-containing peptides: an ATR-FTIR spectroscopy study. RSC Adv 2017. [DOI: 10.1039/c7ra01145h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
It highlights the importance of aromatic residues in influencing peptide binding to the membrane, demonstrates that the stability of the membranes depends on the lipid composition and the sequence, structural context, and orientation of the peptides.
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Affiliation(s)
- Bo Peng
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Xiao-Yan Ding
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Chao Sun
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Ya-Nan Yang
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Yu-Jiao Gao
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
| | - Xin Zhao
- Shanghai Key Laboratory of Magnetic Resonance
- Department of Physics
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
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32
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Miller DM, Findlay HE, Ces O, Templer RH, Booth PJ. Light-activated control of protein channel assembly mediated by membrane mechanics. NANOTECHNOLOGY 2016; 27:494004. [PMID: 27831930 DOI: 10.1088/0957-4484/27/49/494004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photochemical processes provide versatile triggers of chemical reactions. Here, we use a photoactivated lipid switch to modulate the folding and assembly of a protein channel within a model biological membrane. In contrast to the information rich field of water-soluble protein folding, there is only a limited understanding of the assembly of proteins that are integral to biological membranes. It is however possible to exploit the foreboding hydrophobic lipid environment and control membrane protein folding via lipid bilayer mechanics. Mechanical properties such as lipid chain lateral pressure influence the insertion and folding of proteins in membranes, with different stages of folding having contrasting sensitivities to the bilayer properties. Studies to date have relied on altering bilayer properties through lipid compositional changes made at equilibrium, and thus can only be made before or after folding. We show that light-activation of photoisomerisable di-(5-[[4-(4-butylphenyl)azo]phenoxy]pentyl)phosphate (4-Azo-5P) lipids influences the folding and assembly of the pentameric bacterial mechanosensitive channel MscL. The use of a photochemical reaction enables the bilayer properties to be altered during folding, which is unprecedented. This mechanical manipulation during folding, allows for optimisation of different stages of the component insertion, folding and assembly steps within the same lipid system. The photochemical approach offers the potential to control channel assembly when generating synthetic devices that exploit the mechanosensitive protein as a nanovalve.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, The University of Melbourne, 3052, Australia
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33
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Duneau JP, Khao J, Sturgis JN. Lipid perturbation by membrane proteins and the lipophobic effect. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:126-134. [PMID: 27794424 DOI: 10.1016/j.bbamem.2016.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 11/26/2022]
Abstract
Understanding how membrane proteins interact with their environment is fundamental to the understanding of their structure, function and interactions. We have performed coarse-grained molecular dynamics simulations on a series of membrane proteins in a membrane environment to examine the perturbations of the lipids by the presence of protein. We analyze these perturbations in terms of elastic membrane deformations and local lipid protein interactions. However these two factors are insufficient to describe the variety of effects that we observe and the changes caused by membranes proteins to the structure and dynamics of their lipid environment. Other factors that change the conformation available to lipid molecules are evident and are able to modify lipid structure far from the protein surface, and thus mediate long-range interactions between membrane proteins. We suggest that these multiple modifications to lipid behavior are responsible, at the molecular level, for the lipophobic effect we have proposed to account for our observations of membrane protein organization.
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Affiliation(s)
- Jean-Pierre Duneau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
| | - Jonathan Khao
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France
| | - James N Sturgis
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
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34
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Uncovering the lipidic basis for the preparation of functional nicotinic acetylcholine receptor detergent complexes for structural studies. Sci Rep 2016; 6:32766. [PMID: 27641515 PMCID: PMC5027579 DOI: 10.1038/srep32766] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 08/15/2016] [Indexed: 01/10/2023] Open
Abstract
This study compares the lipid composition, including individual phospholipid molecular species of solubilized nAChR detergent complexes (nAChR-DCs) with those of the bulk lipids from their source, Torpedo californica (Tc) electric tissue. This lipidomic analysis revealed seventy-seven (77) phospholipid species in the Tc tissue. Analysis of affinity-purified nAChR-DCs prepared with C-12 to C-16 phospholipid analog detergents alkylphosphocholine (FC) and lysofoscholine (LFC) demonstrated that nAChR-DCs prepared with FC12, LFC14, and LFC16 contained >60 phospholipids/nAChR, which was more than twice of those prepared with FC14, FC16, and LFC12. Significantly, all the nAChR-DCs lacked ethanolamine and anionic phospholipids, contained only four cholesterol molecules, and a limited number of phospholipid molecular species per nAChR. Upon incorporation into oocytes, FC12 produce significant functionality, whereas LFC14 and LFC16 nAChR-DCs displayed an increased functionality as compared to the crude Tc membrane. All three nAChR-DCs displayed different degrees of alterations in macroscopic activation and desensitization kinetics.
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35
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Landreh M, Marty MT, Gault J, Robinson CV. A sliding selectivity scale for lipid binding to membrane proteins. Curr Opin Struct Biol 2016; 39:54-60. [PMID: 27155089 PMCID: PMC5287393 DOI: 10.1016/j.sbi.2016.04.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/11/2016] [Accepted: 04/20/2016] [Indexed: 01/24/2023]
Abstract
Biological membranes form barriers that are essential for cellular integrity and compartmentalisation. Proteins in the membrane have co-evolved with their hydrophobic lipid environment, which serves as a solvent for proteins with very diverse requirements. As a result, their interactions range from non-selective to highly discriminating. Mass spectrometry enables us to monitor how lipids interact with membrane proteins and assess their effects on structure and dynamics. Recent studies illustrate the ability to differentiate specific lipid binding, preferential interactions with lipid subsets, and nonselective annular contacts. Here, we consider the biological implications of different lipid-binding scenarios and propose that binding occurs on a sliding selectivity scale, in line with the view of biological membranes as facilitators of dynamic protein and lipid organization.
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Affiliation(s)
- Michael Landreh
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Michael T Marty
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Joseph Gault
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Carol V Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom.
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36
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Gault J, Donlan JAC, Liko I, Hopper JTS, Gupta K, Housden NG, Struwe WB, Marty MT, Mize T, Bechara C, Zhu Y, Wu B, Kleanthous C, Belov M, Damoc E, Makarov A, Robinson CV. High-resolution mass spectrometry of small molecules bound to membrane proteins. Nat Methods 2016; 13:333-6. [PMID: 26901650 PMCID: PMC4856209 DOI: 10.1038/nmeth.3771] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/13/2016] [Indexed: 12/24/2022]
Abstract
Small molecules are known to stabilize membrane proteins and to modulate their function and oligomeric state, but such interactions are often hard to precisely define. Here we develop and apply a high-resolution, Orbitrap mass spectrometry-based method for analyzing intact membrane protein-ligand complexes. Using this platform, we resolve the complexity of multiple binding events, quantify small molecule binding and reveal selectivity for endogenous lipids that differ only in acyl chain length.
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Affiliation(s)
- Joseph Gault
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Joseph A C Donlan
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Jonathan T S Hopper
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Kallol Gupta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | | | - Weston B Struwe
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Michael T Marty
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Todd Mize
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Cherine Bechara
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Ya Zhu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, China
| | | | | | | | | | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
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37
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Assessment of the functionality and stability of detergent purified nAChR from Torpedo using lipidic matrixes and macroscopic electrophysiology. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:47-56. [PMID: 26454038 DOI: 10.1016/j.bbamem.2015.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/17/2015] [Accepted: 10/01/2015] [Indexed: 11/21/2022]
Abstract
In our previous study we examined the functionality and stability of nicotinic acetylcholine receptor (nAChR)-detergent complexes (nAChR-DCs) from affinity-purified Torpedo californica (Tc) using fluorescence recovery after photobleaching (FRAP) in Lipidic Cubic Phase (LCP) and planar lipid bilayer (PLB) recordings for phospholipid and cholesterol like detergents. In the present study we enhanced the functional characterization of nAChR-DCs by recording macroscopic ion channel currents in Xenopus oocytes using the two electrode voltage clamp (TEVC). The use of TEVC allows for the recording of macroscopic currents elicited by agonist activation of nAChR-DCs that assemble in the oocyte plasma membrane. Furthermore, we examined the stability of nAChR-DCs, which is obligatory for the nAChR crystallization, using a 30 day FRAP assay in LCP for each detergent. The present results indicate a marked difference in the fractional fluorescence recovery (ΔFFR) within the same detergent family during the 30 day period assayed. Within the cholesterol analog family, sodium cholate and CHAPSO displayed a minimum ΔFFR and a mobile fraction (MF) over 80%. In contrast, CHAPS and BigCHAP showed a marked decay in both the mobile fraction and diffusion coefficient. nAChR-DCs containing phospholipid analog detergents with an alkylphosphocholine (FC) and lysofoscholine (LFC) of 16 carbon chains (FC-16, LFC-16) were more effective in maintaining a mobile fraction of over 80% compared to their counterparts with shorter acyl chain (C12, C14). The significant differences in macroscopic current amplitudes, activation and desensitization rates among the different nAChR-DCs evaluated in the present study allow to dissect which detergent preserves both, agonist activation and ion channel function. Functionality assays using TEVC demonstrated that LFC16, LFC14, and cholate were the most effective detergents in preserving macroscopic ion channel function, however, the nAChR-cholate complex display a significant delay in the ACh-induce channel activation. In summary, these results suggest that the physical properties of the lipid analog detergents (headgroup and acyl chain length) are the most effective in maintaining both the stability and functionality of the nAChR in the detergent solubilized complex.
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38
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Shaikh SR, Boyle S, Edidin M. A high fat diet containing saturated but not unsaturated fatty acids enhances T cell receptor clustering on the nanoscale. Prostaglandins Leukot Essent Fatty Acids 2015; 100:1-4. [PMID: 26143085 PMCID: PMC4554807 DOI: 10.1016/j.plefa.2015.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/07/2015] [Indexed: 01/16/2023]
Abstract
Cell culture studies show that the nanoscale lateral organization of surface receptors, their clustering or dispersion, can be altered by changing the lipid composition of the membrane bilayer. However, little is known about similar changes in vivo, which can be effected by changing dietary lipids. We describe the use of a newly developed method, k-space image correlation spectroscopy, kICS, for analysis of quantum dot fluorescence to show that a high fat diet can alter the nanometer-scale clustering of the murine T cell receptor, TCR, on the surface of naive CD4(+) T cells. We found that diets enriched primarily in saturated fatty acids increased TCR nanoscale clustering to a level usually seen only on activated cells. Diets enriched in monounsaturated or n-3 polyunsaturated fatty acids had no effect on TCR clustering. Also none of the high fat diets affected TCR clustering on the micrometer scale. Furthermore, the effect of the diets was similar in young and middle aged mice. Our data establish proof-of-principle that TCR nanoscale clustering is sensitive to the composition of dietary fat.
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MESH Headings
- Animals
- CD4-Positive T-Lymphocytes/metabolism
- Diet, High-Fat
- Fatty Acids/metabolism
- Fatty Acids, Monounsaturated/metabolism
- Fatty Acids, Omega-3/metabolism
- Mice
- Mice, Transgenic
- Protein Multimerization
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Spectrum Analysis/methods
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Affiliation(s)
- Saame Raza Shaikh
- Department of Biochemistry & Molecular Biology, East Carolina Diabetes & Obesity Institute, East Carolina University, 600 Moye Blvd, Greenville, NC 27834, USA.
| | - Sarah Boyle
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Michael Edidin
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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Rice AJ, Alvarez FJD, Davidson AL, Pinkett HW. Effects of lipid environment on the conformational changes of an ABC importer. Channels (Austin) 2015; 8:327-33. [PMID: 24852576 PMCID: PMC4203734 DOI: 10.4161/chan.29294] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In order to shuttle substrates across the lipid bilayer, membrane proteins undergo a series of conformation changes that are influenced by protein structure, ligands, and the lipid environment. To test the effect of lipid on conformation change of the ABC transporter MolBC, EPR studies were conducted in lipids and detergents of variable composition. In both a detergent and lipid environment, MolBC underwent the same general conformation changes as detected by site-directed EPR spectroscopy. However, differences in activity and the details of the EPR analysis indicate conformational rigidity that is dependent on the lipid environment. From these observations, we conclude that native-like lipid mixtures provide the transporter with greater activity and conformational flexibility as well as technical advantages such as reconstitution efficiency and protein stability.
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40
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Bechara C, Robinson CV. Different Modes of Lipid Binding to Membrane Proteins Probed by Mass Spectrometry. J Am Chem Soc 2015; 137:5240-7. [DOI: 10.1021/jacs.5b00420] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chérine Bechara
- Department of Chemistry,
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry,
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
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41
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Kalli AC, Sansom MSP, Reithmeier RAF. Molecular dynamics simulations of the bacterial UraA H+-uracil symporter in lipid bilayers reveal a closed state and a selective interaction with cardiolipin. PLoS Comput Biol 2015; 11:e1004123. [PMID: 25729859 PMCID: PMC4346270 DOI: 10.1371/journal.pcbi.1004123] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/09/2015] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli UraA H+-uracil symporter is a member of the nucleobase/ascorbate transporter (NAT) family of proteins, and is responsible for the proton-driven uptake of uracil. Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2-oleoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2-oleoyl-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmitoyl 2-oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2-oleoyl-diphosphatidylglycerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations. Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains. Anionic lipids, including POPG and especially CL, were found to associate with UraA, involving interactions between specific basic residues in loop regions and phosphate oxygens of the CL head group. In particular, three CL binding sites were identified on UraA: two in the inner leaflet and a single site in the outer leaflet. Mutation of basic residues in the binding sites resulted in the loss of CL binding in the simulations. CL may play a role as a “proton trap” that channels protons to and from this transporter within CL-enriched areas of the inner bacterial membrane. Symporters are proteins that are responsible for the co-transport of ions and small molecule solutes across cell membranes. UraA is an example of a symporter, and is responsible for the proton-driven uptake of uracil in bacteria like E. coli. Despite its importance as a member of a large family of nucleobase/ascorbate transporters (NAT) and the existence of structural and functional data, the mechanism by which UraA transports uracil across the bacterial membrane, and in particular the role of its diverse and complex lipid environment in the transport mechanism, remains elusive. In this study, we have used a multiscale computational methodology to examine the dynamics of UraA and to elucidate its interactions with lipids that resemble its native environment in the bacterial inner membrane. Our results demonstrate that negatively-charged lipids in the membrane (phosphatidylglycerol and cardiolipin) associate preferentially with UraA and may play a role in its function. Additionally, our simulations resulted in a closed state of UraA, a likely intermediate in the transport mechanism that may not be readily accessible by experimental methods.
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Affiliation(s)
- Antreas C. Kalli
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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42
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A subset of annular lipids is linked to the flippase activity of an ABC transporter. Nat Chem 2015; 7:255-62. [DOI: 10.1038/nchem.2172] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/19/2014] [Indexed: 12/18/2022]
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43
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Loll PJ. Membrane proteins, detergents and crystals: what is the state of the art? ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1576-83. [PMID: 25484203 DOI: 10.1107/s2053230x14025035] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022]
Abstract
At the time when the first membrane-protein crystal structure was determined, crystallization of these molecules was widely perceived as extremely arduous. Today, that perception has changed drastically, and the process is regarded as routine (or nearly so). On the occasion of the International Year of Crystallography 2014, this review presents a snapshot of the current state of the art, with an emphasis on the role of detergents in this process. A survey of membrane-protein crystal structures published since 2012 reveals that the direct crystallization of protein-detergent complexes remains the dominant methodology; in addition, lipidic mesophases have proven immensely useful, particularly in specific niches, and bicelles, while perhaps undervalued, have provided important contributions as well. Evolving trends include the addition of lipids to protein-detergent complexes and the gradual incorporation of new detergents into the standard repertoire. Stability has emerged as a critical parameter controlling how a membrane protein behaves in the presence of detergent, and efforts to enhance stability are discussed. Finally, although discovery-based screening approaches continue to dwarf mechanistic efforts to unravel crystallization, recent technical advances offer hope that future experiments might incorporate the rational manipulation of crystallization behaviors.
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Affiliation(s)
- Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
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44
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Identification and in silico analysis of helical lipid binding regions in proteins belonging to the amphitropic protein family. J Biosci 2014; 39:771-83. [DOI: 10.1007/s12038-014-9479-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Membrane-associated proteins and peptides. Methods Mol Biol 2014. [PMID: 25330961 DOI: 10.1007/978-1-4939-1465-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter discusses the practical aspects of setting up molecular dynamics simulations of membrane-associated proteins and peptides, and the analysis thereof. Topology files for selected lipids are provided and selected analysis tools presented. These include tools for the creation of lipid bilayers of mixed lipid content (DOPE) and easy extraction of lipid coordinates (g_zcoor, g_xycoor), the calculation of helical axes (g_helixaxis) and aromatic order parameters (g_arom), the determination of peptide- or protein-interacting lipids (g_under), and the investigation of lipid-specific interactions through the calculation of lipid-bridged residue-residue contacts (g_prolip).
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46
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Teng J, Loukin S, Anishkin A, Kung C. The force-from-lipid (FFL) principle of mechanosensitivity, at large and in elements. Pflugers Arch 2014; 467:27-37. [PMID: 24888690 DOI: 10.1007/s00424-014-1530-2] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 04/29/2014] [Accepted: 05/05/2014] [Indexed: 12/27/2022]
Abstract
Focus on touch and hearing distracts attention from numerous subconscious force sensors, such as the vital control of blood pressure and systemic osmolarity, and sensors in nonanimals. Multifarious manifestations should not obscure invariant and fundamental physicochemical principles. We advocate that force from lipid (FFL) is one such principle. It is based on the fact that the self-assembled bilayer necessitates inherent forces that are large and anisotropic, even at life's origin. Functional response of membrane proteins is governed by bilayer force changes. Added stress can redirect these forces, leading to geometric changes of embedded proteins such as ion channels. The FFL principle was first demonstrated when purified bacterial mechanosensitive channel of large conductance (MscL) remained mechanosensitive (MS) after reconstituting into bilayers. This key experiment has recently been unequivocally replicated with two vertebrate MS K2p channels. Even the canonical Kv and the Drosophila canonical transient receptor potentials (TRPCs) have now been shown to be MS in biophysical and in physiological contexts, supporting the universality of the FFL paradigm. We also review the deterministic role of mechanical force during stem cell differentiation as well as the cell-cell and cell-matrix tethers that provide force communications. In both the ear hair cell and the worm's touch neuron, deleting the cadherin or microtubule tethers reduces but does not eliminate MS channel activities. We found no evidence to distinguish whether these tethers directly pull on the channel protein or a surrounding lipid platform. Regardless of the implementation, pulling tether tenses up the bilayer. Membrane tenting is directly visible at the apexes of the stereocilia.
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Affiliation(s)
- Jinfeng Teng
- Laboratory of Molecular Biology, University of Wisconsin, Madison, WI, 53706, USA
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47
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Why are membrane targets discovered by phenotypic screens and genome sequencing in Mycobacterium tuberculosis? Tuberculosis (Edinb) 2013; 93:569-88. [DOI: 10.1016/j.tube.2013.09.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 12/11/2022]
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48
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Duneau JP, Sturgis JN. Lateral organization of biological membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:843-50. [DOI: 10.1007/s00249-013-0933-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/13/2013] [Accepted: 09/26/2013] [Indexed: 11/24/2022]
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49
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Maurya SR, Chaturvedi D, Mahalakshmi R. Modulating lipid dynamics and membrane fluidity to drive rapid folding of a transmembrane barrel. Sci Rep 2013; 3:1989. [PMID: 23771099 PMCID: PMC3683699 DOI: 10.1038/srep01989] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/08/2013] [Indexed: 11/09/2022] Open
Abstract
Lipid-protein interactions, critical for the folding, stability and function of membrane proteins, can be both of mechanical and chemical nature. Mechanical properties of lipid systems can be suitably influenced by physical factors so as to facilitate membrane protein folding. We demonstrate here that by modulating lipid dynamics transiently using heat, rapid folding of two 8-stranded transmembrane β-barrel proteins OmpX and OmpA1–171, in micelles and vesicles, can be achieved within seconds. Folding kinetics using this ‘heat shock’ method shows a dramatic ten to several hundred folds increase in refolding rate along with ~100% folding efficiency. We establish that OmpX thus folded is highly thermostable even in detergent micelles, and retains structural characteristics comparable to the protein in bilayers.
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Affiliation(s)
- Svetlana Rajkumar Maurya
- Department of Biological Sciences, Indian Institute of Science Education and Research, Govindpura, Bhopal, India
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50
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Lee S, Zheng H, Shi L, Jiang QX. Reconstitution of a Kv channel into lipid membranes for structural and functional studies. J Vis Exp 2013:e50436. [PMID: 23892292 DOI: 10.3791/50436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
To study the lipid-protein interaction in a reductionistic fashion, it is necessary to incorporate the membrane proteins into membranes of well-defined lipid composition. We are studying the lipid-dependent gating effects in a prototype voltage-gated potassium (Kv) channel, and have worked out detailed procedures to reconstitute the channels into different membrane systems. Our reconstitution procedures take consideration of both detergent-induced fusion of vesicles and the fusion of protein/detergent micelles with the lipid/detergent mixed micelles as well as the importance of reaching an equilibrium distribution of lipids among the protein/detergent/lipid and the detergent/lipid mixed micelles. Our data suggested that the insertion of the channels in the lipid vesicles is relatively random in orientations, and the reconstitution efficiency is so high that no detectable protein aggregates were seen in fractionation experiments. We have utilized the reconstituted channels to determine the conformational states of the channels in different lipids, record electrical activities of a small number of channels incorporated in planar lipid bilayers, screen for conformation-specific ligands from a phage-displayed peptide library, and support the growth of 2D crystals of the channels in membranes. The reconstitution procedures described here may be adapted for studying other membrane proteins in lipid bilayers, especially for the investigation of the lipid effects on the eukaryotic voltage-gated ion channels.
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Affiliation(s)
- Sungsoo Lee
- Department of Cell Biology, University of Texas Southwestern Medical Center at Dallas, USA
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