Micelles, Bicelles, and Nanodiscs: Comparing the Impact of Membrane Mimetics on Membrane Protein Backbone Dynamics

Frey, Lukas; Lakomek, Nils‐Alexander; Riek, Roland; Bibow, Stefan

doi:10.1002/anie.201608246

Cited by 93 publications

(114 citation statements)

References 42 publications

Supporting

Mentioning

109

Contrasting

Order By: Relevance

“…Hence, our experiments are carried out at pH 9.5. Whereas recent studies suggest that properties of membrane proteins measured in vitro using micellar systems, such as DPC, can represent their native behavior (33–36), whether our results from such a simplified system at non-native pH can be extrapolated to conditions in vivo is unclear.…”

Section: Resultsmentioning

confidence: 78%

Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein

Iyer

Zadafiya

Vetal

et al. 2017

Journal of Biological Chemistry

101

View full text Add to dashboard Cite

The free energy of water-to-interface amino acid partitioning is a major contributing factor in membrane protein folding and stability. The interface residues at the C terminus of transmembrane β-barrels form the β-signal motif required for assisted β-barrel assembly in vivo but are believed to be less important for β-barrel assembly in vitro. Here, we experimentally measured the thermodynamic contribution of all 20 amino acids at the β-signal motif to the unassisted folding of the model β-barrel protein PagP. We obtained the partitioning free energy for all 20 amino acids at the lipid-facing interface (ΔΔG0w,i(φ)) and the protein-facing interface (ΔΔG0w,i(π)) residues and found that hydrophobic amino acids are most favorably transferred to the lipid-facing interface, whereas charged and polar groups display the highest partitioning energy. Furthermore, the change in non-polar surface area correlated directly with the partitioning free energy for the lipid-facing residue and inversely with the protein-facing residue. We also demonstrate that the interface residues of the β-signal motif are vital for in vitro barrel assembly, because they exhibit a side chain–specific energetic contribution determined by the change in nonpolar accessible surface. We further establish that folding cooperativity and hydrophobic collapse are balanced at the membrane interface for optimal stability of the PagP β-barrel scaffold. We conclude that the PagP C-terminal β-signal motif influences the folding cooperativity and stability of the folded β-barrel and that the thermodynamic contributions of the lipid- and protein-facing residues in the transmembrane protein β-signal motif depend on the nature of the amino acid side chain.

show abstract

Section: Resultsmentioning

confidence: 78%

Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein

Iyer

Zadafiya

Vetal

et al. 2017

Journal of Biological Chemistry

101

View full text Add to dashboard Cite

show abstract

“…It is also true that the functional activity of membrane proteins is sometimes compromised in part by their reduced internal flexibility within detergent micelles, which is another reason for the appearance of some unitary conductance outliers. 13 …”

Section: Discussionmentioning

confidence: 99%

Interrogating Detergent Desolvation of Nanopore-Forming Proteins by Fluorescence Polarization Spectroscopy

et al. 2017

View full text Add to dashboard Cite

Understanding how membrane proteins interact with detergents is of fundamental and practical significance in structural and chemical biology as well as in nanobiotechnology. Current methods for inspecting protein-detergent complex (PDC) interfaces require high concentrations of protein and are of low throughput. Here, we describe a scalable, spectroscopic approach that uses nanomolar protein concentrations in native solutions. This approach, which is based on steady-state fluorescence polarization (FP) spectroscopy, kinetically resolves the dissociation of detergents from membrane proteins and protein unfolding. For satisfactorily solubilizing detergents, at concentrations much greater than the critical micelle concentration (CMC), the fluorescence anisotropy was independent of detergent concentration. In contrast, at detergent concentrations comparable with or below the CMC, the anisotropy readout underwent a time-dependent decrease, showing a specific and sensitive protein unfolding signature. Functionally reconstituted membrane proteins into a bilayer membrane confirmed predictions made by these FP-based determinations with respect to varying refolding conditions. From a practical point of view, this 96-well analytical approach will facilitate a massively parallel assessment of the PDC interfacial interactions under a fairly broad range of micellar and environmental conditions. We expect that these studies will potentially accelerate research in membrane proteins pertaining to their extraction, solubilization, stabilization, and crystallization, as well as reconstitution into bilayer membranes.

show abstract

“…These processes are regulated by various proteins, and invariably involve integral membrane proteins that span the lipid bilayer as beta barrels in mitochondria and prokaryotes, or as alpha helices in both eukaryotes and prokaryotes. Since the lipid bilayer may be necessary for maintaining membrane protein structure and function, it is crucial to develop methods for the study of membrane proteins in such near‐native environments . A key advantage of magic‐angle spinning (MAS) NMR in this context, is the ability to study membrane proteins prepared in planar lipid bilayers at atomic resolution for investigation of structure and dynamics .…”

Section: Figurementioning

confidence: 99%

Probing Membrane Protein Insertion into Lipid Bilayers by Solid‐State NMR

et al. 2018

View full text Add to dashboard Cite

Determination of the environment surrounding a protein is often key to understanding its function and can also be used to infer the structural properties of the protein. By using proton‐detected solid‐state NMR, we show that reduced spin diffusion within the protein under conditions of fast magic‐angle spinning, high magnetic field, and sample deuteration allows the efficient measurement of site‐specific exposure to mobile water and lipids. We demonstrate this site specificity on two membrane proteins, the human voltage dependent anion channel, and the alkane transporter AlkL from Pseudomonas putida. Transfer from lipids is observed selectively in the membrane spanning region, and an average lipid‐protein transfer rate of 6 s−1 was determined for residues protected from exchange. Transfer within the protein, as tracked in the 15N‐1H 2D plane, was estimated from initial rates and found to be in a similar range of about 8 to 15 s−1 for several resolved residues, explaining the site specificity.

show abstract

Micelles, Bicelles, and Nanodiscs: Comparing the Impact of Membrane Mimetics on Membrane Protein Backbone Dynamics

Cited by 93 publications

References 42 publications

Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein

Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein

Interrogating Detergent Desolvation of Nanopore-Forming Proteins by Fluorescence Polarization Spectroscopy

Probing Membrane Protein Insertion into Lipid Bilayers by Solid‐State NMR

Contact Info

Product

Resources

About