Research Summary

Membrane proteins represent ~60% of medical drug targets and encompass 1/5th of the human proteome; yet these proteins are vastly under-represented in structure and interaction databases. This discrepancy is due to biochemical and biophysical studies requiring proteins in a water-soluble state, while membrane proteins are naturally sequestered in a hydrophobic lipid environment. In order to render membrane proteins into a soluble state, that is amenable for their study, researchers generally use detergents to extract and purify these proteins. However, these surfactants have many undesired effects on protein structure, function and downstream analysis. Work from our group and others has focused on developing nanotechnology-based reconstitution systems to try replacing the natural lipid bilayer while maintaining water-solubility. These membrane mimetics, either protein-based scaffolds or synthetic polymers, have been around for a decade, yet their utilities did not reach the expected potential due to the optimization and adaptation required for each membrane protein system. Recently, our laboratory developed a “one-size-fits-all” formulation known as the Peptidisc— the Peptidisc is made by multiple copies of an amphipathic peptide that spontaneously associate around transmembrane domains of proteins upon removal of detergent. The peptide number adapts spontaneously to fit the size and shape of the protein, allowing for minimal reconstitution optimization.  The end result is a membrane protein that is stable, free of detergent effects, and soluble in aqueous solution. The Peptidisc is a new tool that we hope will allow more researchers, including those who are not expert biochemists, to study membrane proteins. This will yield a better understanding of the structure and function of the cellular membrane as it interacts with the environment. Since the approach is both simple and easy to apply, more membrane proteins may now be included in high-throughput searches for potential new drugs that may help treat various medical conditions.

Technologies & Methods
Bio

BSc, University of Marseilles, France, (1990)
PhD, University of Marseilles, France (1994)
Postdoc Fellow, Dartmouth Medical School, USA (1998)
Principal Investigator, CNRS-U of Paris-Sud, France (2004)

Publications

Young J, Duong F. (2019). Investigating the stability of the SecA–SecYEG complex during protein translocation across the bacterial membrane. JBC 10.1074/jbc.RA118.006447.

Carlson M, Young J, Zhao Z, Fabre L, Jun D, Li J, Li J, Dhupar H, Wason I, Mills A, Beatty T, Klassen J, Rouiller I, Duong F. (2018) The Peptidisc, a simple method for stabilizing membrane proteins in detergent-free solution. eLife 2018;7:e34085.

Bao H, Dalal K, Cytrynbaum E, Duong F. (2015). Sequential action of MalE and maltose allows coupling ATP Hydrolysis to translocation in the MalFGK2 transporter. J Biol Chem. jbc.M115.671826.

Duong F (2014). Capturing the bacterial holo-complex. Proc Natl Acad Sci U S A. 111:4739-40. 41.

Bao H, Duong F (2014). Nucleotide-free MalK drives the transition of the maltose transporter to the inward-facing conformation. J Biol Chem. 289:9844-51.

Mills A, Le HT, Coulton JW, Duong F (2014). Evaluating the FhuA interactions in a detergent-free nanodisc environment. Biochim Biophys Acta. 1838:364-71.

Bao H, Duong F (2013). Phosphatidylglycerol directs binding and inhibitory action of EIIAGlc on the maltose transporter. J Biol Chem. 288:23666-74.

Bao H, Dalal K, Wang V, Rouiller I, Duong F (2013). The maltose ABC transporter: action of membrane lipids on the transporter stability, coupling and ATPase activity. BBA Biomembranes. 1828:1723-1730.

Akopian D, Dalal K, Shen K, Duong F, Shan S-o (2013). SecYEG activates GTPases to drive the completion of cotranslational protein targeting. J Cell Biol. 200:397-405.

Bao H, Duong F (2013) ATP alone triggers the outward-facing conformation of the maltose ABC transporter. J Biol Chem. 288:3439-48.

Bao H, Duong F, Chan CS (2012). A step-by-step method for the reconstitution of an ABC transporter into nanodisc lipid particles. J Vis Exp, e3910. *corresponding author.

Bao H, Duong F (2012). Discovery of an auto-regulation mechanism for the maltose ABC transporter MalFGK2. PloS ONE 7:e34836. Important new findings for an otherwise well known transporter .

Dalal K, Chan CS, Sligar SG, Duong F (2012). Two copies of the SecY channel and acidic lipids are necessary to activate the SecA translocation ATPase. Proc Natl Acad Sci U S A 109:4104-4109. This work is a succesful the application of the nanodiscs to isolate and study membrane protein oligomers.

Fonseca BD, Diering GH, Bidinosti MA, Dalal K, Alain T, Balgi AD, Forestieri R, Nodwell M, Rajadurai CV, Gunaratnam C, Tee AR, Duong F, Andersen RJ, Orlowski J, Numata M, Sonenberg N, Roberge M (2012). Structure-activity analysis of niclosamide reveals potential role for cytoplasmic pH in control of mammalian target of rapamycin complex 1 (mTORC1) signaling. J Biol Chem 287:17530-45.

Zhang XX, Chan CS, Bao H, Fang Y, Foster LJ, Duong F (2012). Nanodiscs and SILAC-based mass spectrometry to identify a membrane protein interactome. J Proteome Res 11:1454-1459.

Dalal K, Duong F (2011). The SecY complex: conducting the orchestra of protein translocation. Trends in Cell Biology 21:506-514. Review.

Gold VA, Robson A, Bao H, Romantsov T, Duong F, Collinson I (2010). The action of cardiolipin on the bacterial translocon. Proc Natl Acad Sci U S A 107:10044-10049.

Dalal K, Bao H, Duong F (2010). Modulation of the SecY channel permeability by pore mutations and trivalent cations. Channels 4:83-96.

Dalal K, Duong F (2009). Reconstitution of the SecY complex in Nanodiscs. In Protein Secretion. Ed. E. Economou, Methods in Molecular Biology 619:145-156.

Dalal K, Duong F (2009). The SecY complex forms a channel capable of ionic discrimination. The EMBO Rep 10:762-768.

Dalal K, Nguyen N, Alami M, Tan J, Moraes TF, Lee WC, Maurus R, Sligar SS, Brayer GD, Duong F (2009). Binding, structure and activity of Syd, a SecY interacting protein. J Biol Chem 284:7897-7902. The details of the work were highlighted by the editor of Nature Structural & Molecular Biology 16, pp106 (2009).

Duong F (2007). “ Cell biology: Fraternal twins ” Nature News & Views, 446:741-743. Commentary.

Gold V, Duong F, Collinson I (2007). The bacterial protein translocation reaction. Mol Membr Biol 24:387-394. Review.

Alami M, Dalal K, Lelj-Garolla B, Sligar S and Duong F (2007). Nanodiscs unravel the stoichiometry of the interaction between the SecYEG channel and its cytosolic partner SecA. EMBO J 26:1995-2004. The principal discovery was highlighted by the editor of Science 316, pp174 (2007).

Maillard A, Lalani S, Silva F, Belin D, Duong F (2007). Deregulation of the SecYEG translocation channel upon removal of the plug domain. J Biol Chem 282:1281-1287.

Tam P, Maillard A, Chan K, Duong F (2005). Investigating the SecY-plug movement at the SecYEG translocation channel. EMBO J 24:3380-3388.

 

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