<i>Ab initio</i> determination of the shape of membrane proteins in a nanodisc

Orioli, Simone; Hansen, Carl G. Henning; Arleth, Lise

doi:10.1107/s2059798320015405

Cited by 8 publications

(6 citation statements)

References 79 publications

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“…S10 to 16) because the membrane is fluid at room temperature and large compared to the protein. Similar behavior has been proposed based on results from small-angle scattering and cryo-TEM (42,43). In particular, we provide support that the roughly triangular features discernible in many frames (Fig.…”

Section: Resultssupporting

confidence: 89%

Electron videography of a lipid–protein tango

Smith,

Carnevale,

Das

et al. 2024

Sci. Adv.

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Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for “electron videography”—combining liquid phase electron microscopy with molecular modeling—with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid–protein interactions. Our results suggest that lipid–protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.

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Section: Resultssupporting

confidence: 89%

Electron videography of a lipid–protein tango

Smith,

Carnevale,

Das

et al. 2024

Sci. Adv.

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“…Although the prevailing concept suggests that the MPs are predominantly localized in the central region of the nanodisc surrounded by the lipid molecules, this depiction may inaccurately imply that the protein is passively floating in the lipid environment. On the contrary, our collective observations revealed a more dynamic behavior, supporting previous observations of an entropic-driven migration of MP toward the nanodisc edge (López et al 2019;Orioli et al 2021).…”

Section: Membrane Proteins Have a Spatial Preference Toward The Edge ...supporting

confidence: 91%

“…Our analysis focused on the structural heterogeneity in nanodiscs, which revealed that nanodiscs possess structural fluidity and that MPs move laterally within the nanodiscs. This behavior has been observed previously in silico (López et al 2019;Orioli et al 2021). Kern et al also experimentally observed interactions between SARS-CoV-2 ORF3a and MSP in the nanodisc environment (Kern et al 2021).…”

Section: Introductionsupporting

confidence: 82%

“…Their analysis showed that the MP moved toward the edge of the nanodisc, where it was stabilized. Other studies showed this movement is entropy-driven (Orioli et al 2021). To further investigate the general spatial preference of MPs within the nanodisc shells, we revisited nine datasets of various MPs reconstituted in nanodiscs from EMPIAR (Table S1).…”

Section: Membrane Proteins Have a Spatial Preference Toward The Edge ...mentioning

confidence: 99%

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Unraveling membrane protein localization and stabilization in nanodiscs

Kim

Koh

Roh

2023

Preprint

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Nanodiscs are nanoscale structures consisting of a lipid bilayer surrounded by membrane scaffold proteins (MSPs). They are widely used in the study of membrane proteins (MPs) because they provide a stable lipid environment. However, the precise mechanism governing MP behavior within the nanodisc remains elusive. Here, we examined the cryo-EM structures of various MPs reconstituted in nanodiscs from an electron microscopy database (EMPIAR). By analyzing the heterogeneity and interactions in the nanodiscs, we found that MPs within nanodiscs display a distinct spatial preference toward the edges of the nanodisc shells. Furthermore, we observed that MPs can establish direct, amphipathic interactions with the MSPs, promoting protein stability. These interactions may induce a rearrangement of the MSP-MSP interactions, leading to the formation of MP-MSP interactions Collectively, our study provides structural and biophysical insights into how nanodiscs contribute to MP structural behavior and stability.

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“…MPBuilder constructs atomistic models of membrane-mimicking systems and covers the cases of MSP or Salipro nanodiscs as well as detergent belts and bicelles; however, it also needs an atomic model of a membrane protein as the input data. The third approach is realized in the Marbles program [ 156 ]; it predicts the shape of membrane proteins embedded into nanodiscs using a hybrid approach that accounts for nanodiscs’ contribution to the SAXS intensity through a semianalytical model, while the embedded membrane protein is treated as a set of beads, similarly to as in well-known ab initio methods. Today, Marbles is the only approach for ab initio shape determination of MPs reconstituted in nanodiscs, and it combines shape determination with a search for the position of the protein in the nanodisc.…”

Section: Applications Of Lipodiscs In Structural Biologymentioning

confidence: 99%

Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review

et al. 2022

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Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.

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Ab initio determination of the shape of membrane proteins in a nanodisc

Cited by 8 publications

References 79 publications

Electron videography of a lipid–protein tango

Electron videography of a lipid–protein tango

Unraveling membrane protein localization and stabilization in nanodiscs

Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review

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