Travel light: Essential packing for membrane proteins with an active lifestyle

Johansen, Nicolai Tidemand; Tidemand, Frederik Grønbæk; Pedersen, Martin Cramer; Arleth, Lise

doi:10.1016/j.biochi.2022.07.014

Cited by 9 publications

(3 citation statements)

References 211 publications

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“…During a standard membrane protein purification, lipids are typically removed from membrane proteins prior to structural studies (Supplemental Figure 1). Detergents are the most commonly used (Supplemental Figure 1B), but they are a poor mimic for the lipid bilayer environment and can cause structural changes or even denaturation of membrane proteins (Johansen et al, 2023). Lipids can be reintroduced in the form of mixed micelles, liposomes, or synthetic nanodiscs (Supplemental Figure 1C-E), but extraction from the native membrane with detergent is still a prerequisite step (Johansen et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

“…Detergents are the most commonly used (Supplemental Figure 1B), but they are a poor mimic for the lipid bilayer environment and can cause structural changes or even denaturation of membrane proteins (Johansen et al, 2023). Lipids can be reintroduced in the form of mixed micelles, liposomes, or synthetic nanodiscs (Supplemental Figure 1C-E), but extraction from the native membrane with detergent is still a prerequisite step (Johansen et al, 2023). A more recent approach is to use polymers to extract membrane proteins out of a lipid bilayer (Ratkeviciute et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Polymer-extracted structure of the mechanosensitive channel MscS reveals the role of protein-lipid interactions in the gating cycle

Moller,

Britt,

Zhou

et al. 2024

Preprint

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Membrane protein structure determination is not only technically challenging but is further complicated by the removal or displacement of lipids, which can result in non-native conformations or a strong preference for certain states at the exclusion of others. This is especially applicable to mechanosensitive channels (MSCs) that evolved to gate in response to subtle changes in membrane tension, such as MscS, a model bacterial system for MSC gating with homologs found across all phyla of walled organisms. MscS is highly adaptive, it readily opens under super-threshold tension but under lower tensions it inactivates and can only recover when tension is released. Functional data strongly suggests a restructuring of the protein-lipid boundary during the slow inactivation and recovery processes. Existing cryo-EM structures fall into two categories depending on the method of solubilization: (1) non-conductive (lipid reconstituted or mixed micelles) characterized by kinked pore-lining helices and splayed lipidfacing helices, or (2) semi-open (pure detergent or short-chain lipids). These structures do not explain the full functional gating cycle consisting of three well defined states: open, closed, and inactivated. Here, we present a 3 Angstrom MscS structure in native nanodiscs generated with Glyco DIBMA polymer solubilization which eliminates the lipid removal step common to all previous structures. Besides the protein in the splayed conformation, we observe well resolved densities that represent phospholipids intercalating between the lipid-facing and pore-lining helices in preferred orientations. The structure illustrates the lipid-based mechanism for the uncoupling of the tension sensing helical pairs from the gate and prompts critical questions on whether the two distinct tension driven opening-closing and inactivation-recovery pathways are separated by the kinetic principle and what types of forces drive the recovery back to a more compact closed state.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Polymer-extracted structure of the mechanosensitive channel MscS reveals the role of protein-lipid interactions in the gating cycle

Moller,

Britt,

Zhou

et al. 2024

Preprint

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“…For this purpose, Glyco-DIBMALPs were produced with two different phospholipids, either 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine (POPC) or 1,2-dimyristoyl- sn -glycero-3-phosphocholine (DMPC). POPC and DMPC have been widely used for the production of various kinds of nanodiscs , and are also among the lipids commonly used for the production of biological membrane models . Both phospholipids were used alone or in mixture with 10–30 mol % cholesterol.…”

Section: Introductionmentioning

confidence: 99%

Effect of Cholesterol on the Structure and Composition of Glyco-DIBMA Lipid Particles

et al. 2023

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Different amphiphilic co-polymers have been introduced to produce polymer–lipid particles with nanodisc structure composed of an inner lipid bilayer and polymer chains self-assembled as an outer belt. These particles can be used to stabilize membrane proteins in solution and enable their characterization by means of biophysical methods, including small-angle X-ray scattering (SAXS). Some of these co-polymers have also been used to directly extract membrane proteins together with their associated lipids from native membranes. Styrene/maleic acid and diisobutylene/maleic acid are among the most commonly used co-polymers for producing polymer–lipid particles, named SMALPs and DIBMALPs, respectively. Recently, a new co-polymer, named Glyco-DIBMA, was produced by partial amidation of DIBMA with the amino sugar N-methyl-d-glucosamine. Polymer–lipid particles produced with Glyco-DIBMA, named Glyco-DIBMALPs, exhibit improved structural properties and stability compared to those of SMALPs and DIBMALPs while retaining the capability of directly extracting membrane proteins from native membranes. Here, we characterize the structure and lipid composition of Glyco-DIBMALPs produced with either 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Glyco-DIBMALPs were also prepared with mixtures of either POPC or DMPC and cholesterol at different mole fractions. We estimated the lipid content in the Glyco-DIBMALPs and determined the particle structure and morphology by SAXS. We show that the Glyco-DIBMALPs are nanodisc-like particles whose size and shape depend on the polymer/lipid ratio. This is relevant for designing nanodisc particles with a tunable diameter according to the size of the membrane protein to be incorporated. We also report that the addition of >20 mol % cholesterol strongly perturbed the formation of Glyco-DIBMALPs. Altogether, we describe a detailed characterization of the Glyco-DIBMALPs, which provides relevant inputs for future application of these particles in the biophysical investigation of membrane proteins.

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Rationalizing the Optimization of Detergents for Membrane Protein Purification

Urner

Junge

Fiorentino

et al. 2023

Chemistry A European J

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Membrane protein purification by means of detergents is key to isolating membrane‐bound therapeutic targets. The role of the detergent structure in this process, however, is not well understood. Detergents are optimized empirically, leading to failed preparations, and thereby raising costs. Here we evaluate the utility of the hydrophilic‐lipophilic balance (HLB) concept, which was introduced by Griffin in 1949, for guiding the optimization of the hydrophobic tail in first‐generation, dendritic oligoglycerol detergents ([G1] OGDs). Our findings deliver qualitative HLB guidelines for rationalizing the optimization of detergents. Moreover, [G1] OGDs exhibit strongly delipidating properties, regardless of the structure of the hydrophobic tail, which delivers a methodological enabling step for investigating binding strengths of endogenous lipids and their role for membrane protein oligomerization. Our findings will facilitate the analysis of challenging drug targets in the future.

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Travel light: Essential packing for membrane proteins with an active lifestyle

Cited by 9 publications

References 211 publications

Polymer-extracted structure of the mechanosensitive channel MscS reveals the role of protein-lipid interactions in the gating cycle

Polymer-extracted structure of the mechanosensitive channel MscS reveals the role of protein-lipid interactions in the gating cycle

Effect of Cholesterol on the Structure and Composition of Glyco-DIBMA Lipid Particles

Rationalizing the Optimization of Detergents for Membrane Protein Purification

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