scholarly journals Fake It ‘Till You Make It—The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics

2020 ◽  
Vol 22 (1) ◽  
pp. 50
Author(s):  
Johannes Thoma ◽  
Björn M. Burmann
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Cubic Phase ◽  
Advantages And Disadvantages ◽  
Membrane Mimetic ◽  
Lipid Environment ◽  
Protein Biophysics ◽  
And Function ◽  
Biological Methods

Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.

scholarly journals Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers

2011 ◽  
Vol 137 (2) ◽  
pp. 217-223 ◽  
Author(s):  
Sourabh Banerjee ◽  
Crina M. Nimigean
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayer ◽  
Lipid Bilayers ◽  
Single Molecule ◽  
Lipid Membranes ◽  
Single Channel ◽  
Black Lipid Membranes ◽  
Potassium Channel Kcsa ◽  
Lipid Environment ◽  
Biochemical Preparation

Discoidal lipoproteins are a novel class of nanoparticles for studying membrane proteins (MPs) in a soluble, native lipid environment, using assays that have not been traditionally applied to transmembrane proteins. Here, we report the successful delivery of an ion channel from these particles, called nanoscale apolipoprotein-bound bilayers (NABBs), to a distinct, continuous lipid bilayer that will allow both ensemble assays, made possible by the soluble NABB platform, and single-molecule assays, to be performed from the same biochemical preparation. We optimized the incorporation and verified the homogeneity of NABBs containing a prototypical potassium channel, KcsA. We also evaluated the transfer of KcsA from the NABBs to lipid bilayers using single-channel electrophysiology and found that the functional properties of the channel remained intact. NABBs containing KcsA were stable, homogeneous, and able to spontaneously deliver the channel to black lipid membranes without measurably affecting the electrical properties of the bilayer. Our results are the first to demonstrate the transfer of a MP from NABBs to a different lipid bilayer without involving vesicle fusion.

scholarly journals Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers

Membranes ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 857
Author(s):  
Md. Sirajul Islam ◽  
James P. Gaston ◽  
Matthew A. B. Baker
Keyword(s):  
Ion Channels ◽  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Protein Composition ◽  
Cellular Processes ◽  
Model Lipid Membranes ◽  
Wide Range ◽  
Lipid Environment

Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.

scholarly journals Methods for the solubilisation of membrane proteins: the micelle-aneous world of membrane protein solubilisation

2021 ◽  
Author(s):  
Giedre Ratkeviciute ◽  
Benjamin F. Cooper ◽  
Timothy J. Knowles
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Stability ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Modus Operandi ◽  
Membrane Mimetic ◽  
Aqueous Environments ◽  
Recent Developments

The solubilisation of membrane proteins (MPs) necessitates the overlap of two contradictory events; the extraction of MPs from their native lipid membranes and their subsequent stabilisation in aqueous environments. Whilst the current myriad of membrane mimetic systems provide a range of modus operandi, there are no golden rules for selecting the optimal pipeline for solubilisation of a specific MP hence a miscellaneous approach must be employed balancing both solubilisation efficiency and protein stability. In recent years, numerous diverse lipid membrane mimetic systems have been developed, expanding the pool of available solubilisation strategies. This review provides an overview of recent developments in the membrane mimetic field, with particular emphasis placed upon detergents, polymer-based nanodiscs and amphipols, highlighting the latest reagents to enter the toolbox of MP research.

scholarly journals Towards a native environment: structure and function of membrane proteins in lipid bilayers by NMR

2021 ◽  
Author(s):  
Kai Xue ◽  
Kumar Tekwani Movellan ◽  
Xizhou Cecily Zhang ◽  
Eszter E. Najbauer ◽  
Marcel C. Forster ◽  
...  
Keyword(s):  
Solid State ◽  
Membrane Proteins ◽  
Small Molecules ◽  
Lipid Bilayers ◽  
Biological Samples ◽  
Solid State Nmr ◽  
Structure And Function ◽  
Versatile Technique ◽  
And Function

Solid-state NMR (ssNMR) is a versatile technique that can be used for the characterization of various materials, ranging from small molecules to biological samples, including membrane proteins, as reviewed here.

scholarly journals Mass spectrometry of membrane protein complexes

2019 ◽  
Vol 400 (7) ◽  
pp. 813-829 ◽  
Author(s):  
Julian Bender ◽  
Carla Schmidt
Keyword(s):  
Mass Spectrometry ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Membrane Protein Complexes ◽  
Hydrophobic Nature ◽  
Alternative Approaches ◽  
Lipid Environment ◽  
And Function

Abstract Membrane proteins are key players in the cell. Due to their hydrophobic nature they require solubilising agents such as detergents or membrane mimetics during purification and, consequently, are challenging targets in structural biology. In addition, their natural lipid environment is crucial for their structure and function further hampering their analysis. Alternative approaches are therefore required when the analysis by conventional techniques proves difficult. In this review, we highlight the broad application of mass spectrometry (MS) for the characterisation of membrane proteins and their interactions with lipids. We show that MS unambiguously identifies the protein and lipid components of membrane protein complexes, unravels their three-dimensional arrangements and further provides clues of protein-lipid interactions.

scholarly journals State-dependent mapping of GlyR-cholesterol interactions by coupling crosslinking with mass spectrometry

2020 ◽  
Author(s):  
Nicholas A. Ferraro ◽  
Michael Cascio
Keyword(s):  
Mass Spectrometry ◽  
Lipid Bilayers ◽  
Glycine Receptor ◽  
Transmembrane Helix ◽  
Covalent Attachment ◽  
Channel Dynamics ◽  
State Dependent ◽  
Extracellular Region ◽  
Lipid Environment ◽  
And Function

AbstractPentameric ligand-gated ion channel (pLGIC) allostery is dependent on dynamic associations with its diverse environment. The cellular membrane’s lipid composition influences channel function with cholesterol being a key regulator of channel activity. Human α1 glycine receptor (GlyR) was purified from baculovirus infected insect cells and reconstituted in unilamellar vesicles at physiological cholesterol:lipid ratios with aliquots of azi-cholesterol, a photoactivatable non-specific crosslinker. The receptor in vesicles was then enriched in either a resting, open, or desensitized state prior to photocrosslinking. Following photoactivation, crosslinked cholesterol-GlyR was trypsinized and sites of direct covalent attachment to peptides were identified by targeted MS/MS. Dozens of state-dependent crosslinks were identified and differential patterns of cholesterol-GlyR crosslinks were observed in the extracellular region nearing the lipid bilayer, in the M4 transmembrane helix, and in the large intracellular M3-M4 loop. Unique crosslinks in comparative studies identify changes in lipid accessibility or modulation of hydrophobic cavities in GlyR as a function of receptor allostery. Most notably, the outward twisting of M4 and differential crosslinking within the M3-M4 loop provide new insight into allosteric repositioning of GlyR. More generally, this study provides an accurate and sensitive approach to mapping the protein-lipid interactions to discern state-dependent structural movements of membrane proteins embedded in lipid-bilayers.SignificanceIon channels are highly allosteric molecular machines whose structure and function are sensitive to lipids and ligands. While the structures of many pLGICs are known, these are often truncated forms of the receptor in a membrane-mimetic environment locked in ligand-bound conformational states that may not accurately reflect the conformation and dynamics of the receptor in a native lipid environment. Crosslinking coupled with mass spectrometry (CX-MS) has the capability of interrogating the structure of full-length receptors in a lipid environment. In this study, CX-MS was used to identify state-dependent cholesterol-GlyR interactions to identify differential cholesterol accessibility as a function of channel dynamics upon gating and desensitization.

scholarly journals Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Dianfan Li ◽  
Martin Caffrey
Keyword(s):  
Membrane Proteins ◽  
Diacylglycerol Kinase ◽  
Phase Method ◽  
Cubic Phase ◽  
X Ray ◽  
Nanoporous Membrane ◽  
Membrane Mimetic ◽  
Test Protein ◽  
Bicontinuous Cubic

Abstract Membrane proteins play vital roles in the life of the cell and are important therapeutic targets. Producing them in large quantities, pure and fully functional is a major challenge. Many promising projects end when intractable aggregates or precipitates form. Here we show how such unfolded aggregates can be solubilized and the solution mixed with lipid to spontaneously self-assemble a bicontinuous cubic mesophase into the bilayer of which the protein, in a confined, chaperonin-like environment, reconstitutes with 100% efficiency. The test protein, diacylglycerol kinase, reconstituted in the bilayer of the mesophase, was then crystallized in situ by the in meso or lipid cubic phase method providing an X-ray structure to a resolution of 2.55 Å. This highly efficient, inexpensive, simple and rapid approach should find application wherever properly folded, membrane reconstituted and functional proteins are required where the starting material is a denatured aggregate.

scholarly journals Investigating the Lipid Selectivity of the Ammonium Transporter AmtB in Heterogeneous Nanodiscs

2021 ◽  
Author(s):  
James E. Keener ◽  
Michael T Marty
Keyword(s):  
Lipid Bilayers ◽  
Tight Binding ◽  
Native Mass Spectrometry ◽  
Ammonium Transporter ◽  
Lipid Interactions ◽  
Head Groups ◽  
Bound Lipids ◽  
Lipid Environment ◽  
And Function ◽  
Triton X

The structure and function of membrane proteins can be significantly impacted by the surrounding lipid environment, but membrane protein-lipid interactions in lipid bilayers are often difficult to study due to their transient and polydisperse nature. Here, we used two native mass spectrometry (MS) approaches to investigate how the Escherichia coli ammonium transporter (AmtB) selectively remodels its local lipid environment in heterogeneous lipoprotein nanodiscs. First, we used gas-phase ejection to isolate AmtB with bound lipids from heterogeneous nanodiscs with different combinations of lipids. Second, we used solution-phase detergent flash extraction as an orthogonal approach to study AmtB remodeling with native MS. Flash extraction of AmtB showed that Triton X-100 retains lipid selectivity, but C8E4 distorts preferential lipid interactions. Both approaches reveal that AmtB has a few tight binding sites for PC, is selective for binding PG over-all, and is nonselective for PE, providing a detailed picture of how AmtB binds different lipid head groups in the context of mixed lipid bilayers.

scholarly journals Occupancy distributions of membrane proteins in heterogeneous liposome populations

2019 ◽  
Author(s):  
Lucy Cliff ◽  
Rahul Chadda ◽  
Janice L. Robertson
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Single Molecule ◽  
Skewed Distribution ◽  
Liposome Size ◽  
Protein Incorporation ◽  
Size Heterogeneity ◽  
The Right ◽  
And Function

AbstractMeasurements of membrane protein structure and function often rely on reconstituting the protein into lipid bilayers through the formation of liposomes. Many measurements conducted in proteoliposomes, e.g. transport rates, single-molecule dynamics, monomer-oligomer equilibrium, require some understanding of the occupancy statistics of the liposome population for correct interpretation of the results. In homogenous liposomes, this is easy to calculate as the act of protein incorporation can be described by the Poisson distribution. However, in reality, liposomes are heterogeneous, which alters the statistics of occupancy in several ways. Here, we determine the liposome occupancy distribution for membrane protein reconstitution while taking into account liposome size heterogeneity. We calculate the protein occupancy for a homogenous population of liposomes with radius r = 200 nm, representing an idealization of vesicles extruded through 400 nm pores and compare it to the right-skewed distribution of 400 nm 2:1 POPE:POPG vesicles. As is the case for E. coli polar lipids, this synthetic composition yields a sub-population of small liposomes, ∼25 nm in radius with a long tail of larger vesicles. Previously published microscopy data of the co-localization of the CLC-ec1 Cl-/H+ transporter with liposomes, and vesicle occupancy measurements using functional transport assays, shows agreement with the heterogeneous 2:1 POPE:POPG population. Next, distributions of 100 nm and 30 nm extruded 2:1 POPE:POPG liposomes are measured by cryo-electron microscopy, demonstrating that extrusion through smaller pores does not shift the peak, but reduces polydispersity arising from large liposomes. Single-molecule photobleaching analysis of CLC-ec1-Cy5 shows the 30 nm extruded population increases the ‘Poisson-dilution’ range, reducing the probability of vesicles with more than one protein at higher protein/lipid densities. These results demonstrate that the occupancy distributions of membrane proteins into vesicles can be accurately predicted in heterogeneous populations with experimental knowledge of the liposome size distribution.

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