ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages

Studies on the Bin-Amphiphysin-Rvs (BAR) domain have advanced a fundamental understanding of how proteins deform membrane. We previously showed that a BAR domain in tandem with a Pleckstrin Homology (PH domain) underlies the assembly of ACAP1 (Arfgap with Coil-coil, Ankryin repeat, and PH domain I) into an unusual lattice structure that also uncovers a new paradigm for how a BAR protein deforms membrane. Here, we initially pursued computation-based refinement of the ACAP1 lattice to identify its critical protein contacts. Simulation studies then revealed how ACAP1, which dimerizes into a symmetrical structure in solution, is recruited asymmetrically to the membrane through dynamic behavior. We also pursued electron microscopy (EM)-based structural studies, which shed further insight into the dynamic nature of the ACAP1 lattice assembly. As ACAP1 is an unconventional BAR protein, our findings broaden the understanding of the mechanistic spectrum by which proteins assemble into higher-ordered structures to achieve membrane deformation.

[1]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[2]  J. Gruschus,et al.  Dynamic interaction between Arf GAP and PH domains of ASAP1 in the regulation of GAP activity. , 2008, Cellular signalling.

[3]  Benjamin A. Himes,et al.  Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site , 2016, Nature Communications.

[4]  Ying-hua Jin,et al.  Dimerization Interface of 3-Hydroxyacyl-CoA Dehydrogenase Tunes the Formation of Its Catalytic Intermediate , 2014, PloS one.

[5]  L. Foroni,et al.  Acaps Are Arf6 Gtpase-Activating Proteins That Function in the Cell Periphery , 2000, The Journal of cell biology.

[6]  Klaus Schulten,et al.  Symmetry-restrained flexible fitting for symmetric EM maps. , 2011, Structure.

[7]  Klaus Schulten,et al.  Cryo–EM structure of the ribosome–SecYE complex in the membrane environment , 2011, Nature Structural &Molecular Biology.

[8]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[9]  Schuster,et al.  Separation of a mixture of independent signals using time delayed correlations. , 1994, Physical review letters.

[10]  Shaoyi Jiang,et al.  Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces. , 2010, The Journal of chemical physics.

[11]  G. Voth,et al.  Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling. , 2013, Biophysical journal.

[12]  G. Voth,et al.  How curvature-generating proteins build scaffolds on membrane nanotubes , 2016, Proceedings of the National Academy of Sciences.

[13]  Shaoyi Jiang,et al.  Orientation of Adsorbed Antibodies on Charged Surfaces by Computer Simulation Based on a United-Residue Model , 2003 .

[14]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[15]  Z. Rao,et al.  Structure of the APPL 1 BAR-PH domain and characterization of its interaction with Rab 5 , 2013 .

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

[17]  Ralf Langen,et al.  Mechanism of endophilin N‐BAR domain‐mediated membrane curvature , 2006, The EMBO journal.

[18]  B. L. de Groot,et al.  CHARMM36m: an improved force field for folded and intrinsically disordered proteins , 2016, Nature Methods.

[19]  Soichi Takeda,et al.  Endophilin BAR domain drives membrane curvature by two newly identified structure‐based mechanisms , 2006, The EMBO journal.

[20]  N. Mizuno,et al.  Structural insights into the cooperative remodeling of membranes by amphiphysin/BIN1 , 2015, Scientific Reports.

[21]  H. Yamada,et al.  Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis , 2018, eLife.

[22]  Leonardo G. Trabuco,et al.  Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. , 2008, Structure.

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

[24]  Toni Giorgino,et al.  Identification of slow molecular order parameters for Markov model construction. , 2013, The Journal of chemical physics.

[25]  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.

[26]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[27]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[28]  Klaus Schulten,et al.  Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations , 2013, PLoS Comput. Biol..

[29]  E. Boucrot,et al.  Membrane curvature at a glance , 2015, Journal of Cell Science.

[30]  Klaus Schulten,et al.  Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method. , 2012, Biopolymers.

[31]  Robert H. Insall,et al.  F-BAR domains: multifunctional regulators of membrane curvature , 2008, Journal of Cell Science.

[32]  Jun Ma,et al.  Mechanistic Insights into Regulated Cargo Binding by ACAP1 Protein* , 2012, The Journal of Biological Chemistry.

[33]  P. Peters,et al.  ACAP1 promotes endocytic recycling by recognizing recycling sorting signals. , 2004, Developmental cell.

[34]  Pekka Lappalainen,et al.  I-BAR domain proteins: linking actin and plasma membrane dynamics. , 2011, Current opinion in cell biology.

[35]  Michael M. Lacy,et al.  Single-molecule imaging of the BAR-domain protein Pil1p reveals filament-end dynamics , 2017, Molecular biology of the cell.

[36]  T. Kirchhausen,et al.  An ACAP1-containing clathrin coat complex for endocytic recycling , 2007, The Journal of cell biology.

[37]  Nevan J. Krogan,et al.  Eisosome proteins assemble into a membrane scaffold , 2011, The Journal of cell biology.

[38]  E. Egelman,et al.  A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature. , 2014, Developmental cell.

[39]  G. Voth,et al.  When Physics Takes Over: BAR Proteins and Membrane Curvature. , 2015, Trends in cell biology.

[40]  T. Baumgart,et al.  Thermodynamics and mechanics of membrane curvature generation and sensing by proteins and lipids. , 2011, Annual review of physical chemistry.

[41]  Adam Frost,et al.  Structural Basis of Membrane Bending by the N-BAR Protein Endophilin , 2012, Cell.

[42]  Klaus Schulten,et al.  Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography , 2013, PLoS pathogens.

[43]  Renmin Han,et al.  A novel fully automatic scheme for fiducial marker-based alignment in electron tomography. , 2015, Journal of structural biology.

[44]  S. Scheres,et al.  Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging , 2015, Structure.

[45]  J. Andrade,et al.  A BAR Domain in the N Terminus of the Arf GAP ASAP1 Affects Membrane Structure and Trafficking of Epidermal Growth Factor Receptor , 2006, Current Biology.

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

[47]  H. Noguchi.  Membrane tubule formation by banana-shaped proteins with or without transient network structure , 2015, Scientific Reports.

[48]  Rohit Mittal,et al.  Structure and analysis of FCHo2 F-BAR domain: a dimerizing and membrane recruitment module that effects membrane curvature. , 2007, Structure.

[49]  L. Tong,et al.  Crystal structures of the BAR-PH and PTB domains of human APPL1. , 2007, Structure.

[50]  Alexander D. MacKerell,et al.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. , 2012, Journal of chemical theory and computation.

[51]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[52]  Jia Chen,et al.  Breathing Easier , 1996, Environmental Health Perspectives.

[53]  B. Brooks,et al.  Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .

[54]  Harvey T. McMahon,et al.  Membrane curvature and mechanisms of dynamic cell membrane remodelling , 2005, Nature.

[55]  M. L. Karlsen,et al.  Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering. , 2015, Structure.