Structural Basis of Membrane Bending by the N-BAR Protein Endophilin

Functioning as key players in cellular regulation of membrane curvature, BAR domain proteins bend bilayers and recruit interaction partners through poorly understood mechanisms. Using electron cryomicroscopy, we present reconstructions of full-length endophilin and its N-terminal N-BAR domain in their membrane-bound state. Endophilin lattices expose large areas of membrane surface and are held together by promiscuous interactions between endophilin's amphipathic N-terminal helices. Coarse-grained molecular dynamics simulations reveal that endophilin lattices are highly dynamic and that the N-terminal helices are required for formation of a stable and regular scaffold. Furthermore, endophilin accommodates different curvatures through a quantized addition or removal of endophilin dimers, which in some cases causes dimerization of endophilin's SH3 domains, suggesting that the spatial presentation of SH3 domains, rather than affinity, governs the recruitment of downstream interaction partners.

[1]  P. De Camilli,et al.  Generation of high curvature membranes mediated by direct endophilin bilayer interactions , 2001, The Journal of cell biology.

[2]  B. Różycki,et al.  Membrane Budding , 2010, Cell.

[3]  I. Haworth,et al.  Roles of Amphipathic Helices and the Bin/Amphiphysin/Rvs (BAR) Domain of Endophilin in Membrane Curvature Generation* , 2010, The Journal of Biological Chemistry.

[4]  Frank Noé,et al.  Crystal structure of nucleotide-free dynamin , 2011, Nature.

[5]  Gregory A. Voth,et al.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.

[6]  B. Peter,et al.  BAR Domains as Sensors of Membrane Curvature: The Amphiphysin BAR Structure , 2004, Science.

[7]  Edward H Egelman,et al.  Single-particle reconstruction from EM images of helical filaments. , 2007, Current opinion in structural biology.

[8]  John C Dawson,et al.  Bar domain proteins: a role in tubulation, scission and actin assembly in clathrin-mediated endocytosis. , 2006, Trends in cell biology.

[9]  Jim Pfaendtner,et al.  A systematic methodology for defining coarse-grained sites in large biomolecules. , 2008, Biophysical journal.

[10]  H. McMahon,et al.  Bar Domains and Membrane Curvature: Bringing Your Curves to the Bar , 2022 .

[11]  Winfried Weissenhorn,et al.  Crystal structure of the endophilin-A1 BAR domain. , 2005, Journal of molecular biology.

[12]  Markus R Wenk,et al.  Amphiphysin 2 (Bin1) and T-Tubule Biogenesis in Muscle , 2002, Science.

[13]  A. Steven,et al.  Multiple Modes of Endophilin-mediated Conversion of Lipid Vesicles into Coated Tubes , 2010, The Journal of Biological Chemistry.

[14]  Essi V. Koskela,et al.  Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures , 2011, Nature Structural &Molecular Biology.

[15]  Pietro De Camilli,et al.  Functional partnership between amphiphysin and dynamin in clathrin-mediated endocytosis , 1999, Nature Cell Biology.

[16]  Anchi Cheng,et al.  Automated molecular microscopy: the new Leginon system. , 2005, Journal of structural biology.

[17]  A Leith,et al.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. , 1996, Journal of structural biology.

[18]  Gregory A Voth,et al.  Water under the BAR. , 2010, Biophysical journal.

[19]  P. Bassereau,et al.  Membrane curvature controls dynamin polymerization , 2010, Proceedings of the National Academy of Sciences.

[20]  P. De Camilli,et al.  Coordinated actions of actin and BAR proteins upstream of dynamin at endocytic clathrin-coated pits. , 2009, Developmental cell.

[21]  S. Schmid,et al.  A Pseudoatomic Model of the Dynamin Polymer Identifies a Hydrolysis-Dependent Powerstroke , 2011, Cell.

[22]  S. Nosé.  A unified formulation of the constant temperature molecular dynamics methods , 1984 .

[23]  Gregory A. Voth,et al.  The Multiscale Coarse‐Graining Method , 2012 .

[24]  Adam Frost,et al.  Structural Basis of Membrane Invagination by F-BAR Domains , 2008, Cell.

[25]  K. Kaibuchi,et al.  Rho mediates endocytosis of epidermal growth factor receptor through phosphorylation of endophilin A1 by Rho‐kinase , 2005, Genes to cells : devoted to molecular & cellular mechanisms.

[26]  F. L. Szeto,et al.  Kinetics of Src Homology 3 Domain Association with the Proline-rich Domain of Dynamins , 2005, Journal of Biological Chemistry.

[27]  L. Lagnado,et al.  Endophilin Drives the Fast Mode of Vesicle Retrieval in a Ribbon Synapse , 2011, The Journal of Neuroscience.

[28]  B. Berne.  Modification of the overlap potential to mimic a linear site-site potential , 1981 .

[29]  G. Voth,et al.  Hybrid coarse-graining approach for lipid bilayers at large length and time scales. , 2009, The journal of physical chemistry. B.

[30]  R. Chan,et al.  Synaptojanin 1-mediated PI(4,5)P2 hydrolysis is modulated by membrane curvature and facilitates membrane fission. , 2011, Developmental cell.

[31]  Sumio Sugano,et al.  Curved EFC/F-BAR-Domain Dimers Are Joined End to End into a Filament for Membrane Invagination in Endocytosis , 2007, Cell.

[32]  N. Grigorieff,et al.  Ab initio resolution measurement for single particle structures. , 2007, Journal of structural biology.

[33]  P. McPherson,et al.  SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination. , 2009, Molecular cell.

[34]  Gregory A Voth,et al.  A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.

[35]  Gregory A Voth,et al.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. , 2008, The Journal of chemical physics.

[36]  J M Carazo,et al.  XMIPP: a new generation of an open-source image processing package for electron microscopy. , 2004, Journal of structural biology.

[37]  Gregory A Voth,et al.  Reconstructing protein remodeled membranes in molecular detail from mesoscopic models. , 2011, Physical chemistry chemical physics : PCCP.

[38]  Clinton S Potter,et al.  ACE: automated CTF estimation. , 2005, Ultramicroscopy.

[39]  G. Voth,et al.  Mechanism of membrane curvature sensing by amphipathic helix containing proteins. , 2011, Biophysical journal.

[40]  O. Shupliakov,et al.  An endophilin–dynamin complex promotes budding of clathrin-coated vesicles during synaptic vesicle recycling , 2011, Journal of Cell Science.

[41]  Gregory A Voth,et al.  Membrane binding by the endophilin N-BAR domain. , 2009, Biophysical journal.

[42]  F. Polleux,et al.  The F-BAR Domain of srGAP2 Induces Membrane Protrusions Required for Neuronal Migration and Morphogenesis , 2009, Cell.

[43]  P. De Camilli,et al.  The SH3p4/Sh3p8/SH3p13 protein family: binding partners for synaptojanin and dynamin via a Grb2-like Src homology 3 domain. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[45]  S. Mayor,et al.  Induced Domain Formation in Endocytic Invagination, Lipid Sorting, and Scission , 2010, Cell.

[46]  M. Kozlov,et al.  Protein-lipid interplay in fusion and fission of biological membranes. , 2003, Annual review of biochemistry.

[47]  A. Mittermaier,et al.  Binding mechanism of an SH3 domain studied by NMR and ITC. , 2009, Journal of the American Chemical Society.

[48]  P. Camilli,et al.  The BAR Domain Superfamily: Membrane-Molding Macromolecules , 2009, Cell.

[49]  G. Voth,et al.  Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. , 2010, Faraday discussions.

[50]  Alan L. Munn,et al.  The BAR Domain Proteins: Molding Membranes in Fission, Fusion, and Phagy , 2006, Microbiology and Molecular Biology Reviews.