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      Retracted Article: Polymer nanodiscs and macro-nanodiscs of a varying lipid composition

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          Abstract

          Enhancing the utility of polymer lipid nanodiscs in structural biology applications.

          Abstract

          Polymer lipid nanodiscs have enabled some exciting structural biology and nanobiotechnology applications. The use of a small molecular weight polymer (SMA-EA) has been demonstrated to dramatically increase the size of nanodiscs (up to ∼60 nm diameter). Here, we report the first demonstration of the formation of macro-nanodiscs for a variety of lipids, and solid-state NMR experiments utilizing their magnetic-alignment properties.

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          Nanodiscs for structural and functional studies of membrane proteins.

          Ilia G Denisov, Stephen Sligar (2016)
          Membrane proteins have long presented a challenge to biochemical and functional studies. In the absence of a bilayer environment, individual proteins and critical macromolecular complexes may be insoluble and may display altered or absent activities. Nanodisc technology provides important advantages for the isolation, purification, structural resolution and functional characterization of membrane proteins. In addition, the ability to precisely control the nanodisc composition provides a nanoscale membrane surface for investigating molecular recognition events.
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            Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins.

            Franz Hagn, Manuel Etzkorn, Thomas Raschle … (2013)
            Structural studies of membrane proteins are still hampered by difficulties of finding appropriate membrane-mimicking media that maintain protein structure and function. Phospholipid nanodiscs seem promising to overcome the intrinsic problems of detergent-containing environments. While nanodiscs can offer a near-native environment, the large particle size complicates their routine use in the structural analysis of membrane proteins by solution NMR. Here, we introduce nanodiscs assembled from shorter ApoA-I protein variants that are of markedly smaller diameter and show that the resulting discs provide critical improvements for the structure determination of membrane proteins by NMR. Using the bacterial outer-membrane protein OmpX as an example, we demonstrate that the combination of small nanodisc size, high deuteration levels of protein and lipids, and the use of advanced non-uniform NMR sampling methods enable the NMR resonance assignment as well as the high-resolution structure determination of polytopic membrane proteins in a detergent-free, near-native lipid bilayer setting. By applying this method to bacteriorhodopsin, we show that our smaller nanodiscs can also be beneficial for the structural characterization of the important class of seven-transmembrane helical proteins. Our set of engineered nanodiscs of subsequently smaller diameters can be used to screen for optimal NMR spectral quality for small to medium-sized membrane proteins while still providing a functional environment. In addition to their key improvements for de novo structure determination, due to their smaller size these nanodiscs enable the investigation of interactions between membrane proteins and their (soluble) partner proteins, unbiased by the presence of detergents that might disrupt biologically relevant interactions.
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              A method for detergent-free isolation of membrane proteins in their local lipid environment

              Sarah Lee, Tim J Knowles, Vincent Postis … (2016)
              Despite the great importance of membrane proteins, structural and functional studies of these proteins present major challenges. A significant hurdle is the extraction of the functional protein from its natural lipid membrane. Traditionally achieved with detergents, purification procedures can be costly and time consuming. A critical flaw with detergent approaches is the removal of the protein from the native lipid environment required to maintain functionally stable protein. This protocol describes the preparation of styrene maleic acid (SMA) co-polymer to extract membrane proteins from prokaryotic and eukaryotic expression systems. Successful isolation of membrane proteins into SMA lipid particles (SMALPs) allows the proteins to remain with native lipid, surrounded by SMA. We detail procedures for obtaining 25 g of SMA (4 d); explain the preparation of protein-containing SMALPs using membranes isolated from Escherichia coli (2 d) and control protein-free SMALPS using E. coli polar lipid extract (1-2 h); investigate SMALP protein purity by SDS-PAGE analysis and estimate protein concentration (4 h); and detail biophysical methods such as circular dichroism (CD) spectroscopy and sedimentation velocity analytical ultracentrifugation (svAUC) to undertake initial structural studies to characterize SMALPs (∼2 d). Together, these methods provide a practical tool kit for those wanting to use SMALPs to study membrane proteins.
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                Author and article information

                Journal
                Journal ID (publisher-id): CHCOFS
                Title: Chemical Communications
                Abbreviated Title: Chem. Commun.
                Publisher: Royal Society of Chemistry (RSC)
                ISSN (Print): 1359-7345
                ISSN (Electronic): 1364-548X
                Publication date Created: September 28 2017
                Publication date (Electronic): 2017
                Volume: 53
                Issue: 78
                Pages: 10824-10826
                Affiliations
                [1 ]Biophysics Program and Department of Chemistry
                [2 ]The University of Michigan
                [3 ]Ann Arbor
                [4 ]USA
                Article
                DOI: 10.1039/C7CC06409H
                PMC ID: 5621649
                PubMed ID: 28926036
                SO-VID: 1095afee-871a-4a2e-aed8-76a878205402
                Copyright © © 2017
                License:

                http://rsc.li/journals-terms-of-use

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