title: Membrane sculpting by F-BAR domains studied by molecular dynamics simulations.
abstract: Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called scaffolding mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domains 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy.
authors: Beckman Institute, University of Illinois, Urbana, Illinois, United States of America.
authors: Hang
authors: H
authors: Yu
authors: Klaus
authors: K
authors: Schulten
mesh_terms: D002462:Cell Membrane / Q000378:metabolism*; D019281:Dimerization; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation
chemical_list: D008565:Membrane Proteins
references: Science. 2002 Aug 16;297(5584):1193-6
references: 12183633
references: Microbiol Mol Biol Rev. 2006 Mar;70(1):37-120
references: 16524918
references: EMBO J. 2006 Jun 21;25(12):2898-910
references: 16763559
references: Biophys J. 2010 Sep 22;99(6):1783-90
references: 20858422
references: Annu Rev Biochem. 2000;69:699-727
references: 10966473
references: Biophys J. 2000 Jul;79(1):426-33
references: 10866968
references: Dev Cell. 2005 Dec;9(6):791-804
references: 16326391
references: J Chem Phys. 2006 Nov 28;125(20):204905
references: 17144738
references: Mol Cell. 2012 Apr 27;46(2):226-37
references: 22445486
references: Structure. 2007 Jul;15(7):839-52
references: 17540576
references: J Phys Chem B. 2010 Oct 28;114(42):13585-92
references: 20882985
references: J Mol Biol. 2011 Jan 7;405(1):298-314
references: 21050858
references: Structure. 2006 Dec;14(12):1767-77
references: 17161367
references: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references: 8744570
references: Int J Biochem Mol Biol. 2012;3(2):198-208
references: 22773959
references: Curr Opin Cell Biol. 2004 Aug;16(4):379-91
references: 15261670
references: Science. 2008 Aug 8;321(5890):798-800
references: 18687954
references: Biophys J. 2008 Sep;95(5):2325-39
references: 18515373
references: J Biomech. 2010 May 28;43(8):1612-7
references: 20185134
references: BMC Bioinformatics. 2006 Aug 16;7:382
references: 16914055
references: Structure. 2009 Jun 10;17(6):882-92
references: 19523905
references: Cell. 2012 Mar 30;149(1):137-45
references: 22464326
references: J Mol Biol. 2005 Aug 19;351(3):653-61
references: 16023669
references: Curr Opin Cell Biol. 2003 Aug;15(4):372-81
references: 12892776
references: Science. 1999 Jul 9;285(5425):215-20
references: 10398591
references: Cell. 2010 Mar 5;140(5):601-5
references: 20211126
references: J Cell Biol. 2006 Jan 16;172(2):269-79
references: 16418535
references: Nat Cell Biol. 1999 May;1(1):33-9
references: 10559861
references: Biophys J. 2012 May 2;102(9):2130-9
references: 22824277
references: Biochim Biophys Acta. 2006 Aug;1761(8):838-49
references: 16945584
references: Nat Rev Mol Cell Biol. 2006 Jan;7(1):9-19
references: 16365634
references: Mol Pharmacol. 2011 Sep;80(3):434-45
references: 21693623
references: J Comput Chem. 2005 Dec;26(16):1781-802
references: 16222654
references: J Phys Chem B. 1998 Apr 30;102(18):3586-616
references: 24889800
references: Genes Cells. 2011 Aug;16(8):868-78
references: 21762413
references: Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12700-5
references: 19549836
references: Biophys J. 2005 Feb;88(2):880-902
references: 15542561
references: Science. 2004 Jan 23;303(5657):495-9
references: 14645856
references: Biochemistry. 2006 Oct 31;45(43):12917-28
references: 17059209
references: Biophys J. 2008 Aug;95(4):1866-76
references: 18469070
references: Structure. 2007 Jul;15(7):751-3
references: 17637334
references: Biophys J. 2008 Nov 1;95(9):4163-73
references: 18641080
references: Annu Rev Biophys Biomol Struct. 2005;34:119-51
references: 15869386
references: Biophys J. 2009 Nov 18;97(10):2746-53
references: 19917228
references: Biophys J. 2008 Sep 15;95(6):2822-36
references: 18515401
references: Z Naturforsch C. 1973 Nov-Dec;28(11):693-703
references: 4273690
references: Biophys J. 2009 Nov 18;97(10):2727-35
references: 19917226
references: Biophys J. 2008 Sep 15;95(6):2806-21
references: 18515394
references: J Biomech. 2007;40(11):2492-500
references: 17198707
references: Trends Biochem Sci. 2012 Dec;37(12):526-33
references: 23058040
references: Cell. 2007 May 18;129(4):761-72
references: 17512409
references: Biophys J. 2009 Sep 16;97(6):1626-35
references: 19751667
references: J Cell Biol. 2011 Nov 28;195(5):889-902
references: 22123866
references: Biophys J. 2011 Nov 2;101(9):2092-101
references: 22067146
references: Commun Integr Biol. 2010 Mar;3(2):116-21
references: 20585502
references: J Cell Biol. 2007 Mar 26;176(7):953-64
references: 17371834
references: Nat Rev Mol Cell Biol. 2008 Jul;9(7):543-56
references: 18496517
references: Cell. 2008 Mar 7;132(5):807-17
references: 18329367
references: J Am Chem Soc. 2009 Dec 16;131(49):17843-52
references: 19995075
references: Nature. 2010 Jan 28;463(7280):439-40
references: 20110984
references: EMBO Rep. 2004 Mar;5(3):250-5
references: 14993925
references: Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):173-8
references: 22184226
references: Cell. 2012 Mar 30;149(1):124-36
references: 22464325
references: J Chem Phys. 2007 Sep 28;127(12):125101
references: 17902937
references: Nature. 2007 May 24;447(7143):461-4
references: 17522680
references: J Membr Biol. 2011 Jan;239(1-2):85-93
references: 21161516
references: Nature. 2002 Sep 26;419(6905):361-6
references: 12353027
references: Nature. 2005 Dec 1;438(7068):590-6
references: 16319878
references: Cell Cycle. 2010 Oct 15;9(20):4091-7
references: 20948299
references: Nat Cell Biol. 2003 Feb;5(2):103-8
references: 12563275
references: EMBO J. 2005 Jan 26;24(2):240-50
references: 15635447
references: Biophys J. 2009 Oct 21;97(8):2267-76
references: 19843459
references: J Cell Biol. 2001 Oct 15;155(2):193-200
references: 11604418
references: Phys Chem Chem Phys. 2011 Jun 14;13(22):10430-6
references: 21503332
references: Nat Cell Biol. 2010 Sep;12(9):902-8
references: 20729836
references: Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15068-72
references: 17008407