Membrane tubule formation by banana-shaped proteins with or without transient network structure

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Noguchi, Hiroshi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; CYTOSKELETON PROTEIN; FNBP1 PROTEIN, HUMAN; MICROTUBULE ASSOCIATED PROTEIN; MINOR HISTOCOMPATIBILITY ANTIGEN; PACSIN2 PROTEIN, HUMAN; PSTPIP1 PROTEIN, HUMAN; SIGNAL TRANSDUCING ADAPTOR PROTEIN; TRIP10 PROTEIN, HUMAN;

BIOLOGICAL MODEL; CELL MEMBRANE; CHEMISTRY; HUMAN; MEMBRANE FLUIDITY; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN DOMAIN;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; CARRIER PROTEINS; CELL MEMBRANE; CYTOSKELETAL PROTEINS; HUMANS; MEMBRANE FLUIDITY; MICROTUBULE-ASSOCIATED PROTEINS; MINOR HISTOCOMPATIBILITY ANTIGENS; MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS;

EID: 84958576255     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep20935     Document Type: Article

References (45)

1. Itoh, T. & De Camilli, P. BAR, F-BAR (EFC) and ENTH/ANTH domains in the regulation of membrane-cytosol interfaces and membrane curvature. Biochim. Biophys. Acta 1761, 897-912 (2006).
2. Masuda, M. & Mochizuki, N. Structural characteristics of BAR domain superfamily to sculpt the membrane. Semin. Cell Dev. Biol. 21, 391-398 (2010).
3. Mim, C. & Unger, M. V. Membrane curvature and its generation by BAR proteins. Trends Biochem. Sci. 37, 526-533 (2012).
4. Zimmerberg, J. & Kozlov, M. M. How proteins produce cellular membrane curvature. Nat. Rev. Mol. Cell Biol. 7, 9-19 (2006).
5. Baumgart, T., Capraro, B. R., Zhu, C. & Das, S. L. Thermodynamics and Mechanics of Membrane Curvature Generation and Sensing by Proteins and Lipids. Annu. Rev. Phys. Chem. 62, 483-507 (2010).
6. Johannes, L., Wunder, C. & Bassereau, P. Bending "On the Rocks"-A Cocktail of Biophysical Modules to Build Endocytic Pathways. Cold Spring Harbor Perspect. Biol. 6, a016741 (2014).
7. Suarez, A. et al. T. Bin/Amphiphysin/Rvs (BAR) family members bend membranes in cells. Sci. Rep. 4, 4693 (2014).
8. 2-rich membranes by an inverse BAR domain-like mechanism. J. Cell Biol. 176, 953-964 (2007).
9. Frost, A. et al. Structural basis of membrane invagination by F-BAR domains. Cell 132, 807-817 (2008).
10. Wang, Q. et al. Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin. Proc. Natl. Acad. Sci. USA 106, 12700-12705 (2009).
11. Sorre, B. et al. Nature of curvature coupling of amphiphysin with membranes depends on its bound density. Proc. Natl. Acad. Sci. USA 109, 173-178 (2012).
12. Zhu, C., Das, S. L. & Baumgart, T. Nonlinear Sorting, Curvature Generation, and Crowding of Endophilin N-BAR on Tubular Membranes. Biophys. J. 102, 1837-1845 (2012).
13. Tanaka-Takiguchi, Y. et al. Physicochemical Analysis from Real-Time Imaging of Liposome Tubulation Reveals the Characteristics of Individual F-BAR Domain Proteins. Langmuir 29, 328-336 (2013).
14. Ramesh, P. et al. FBAR Syndapin 1 recognizes and stabilizes highly curved tubular membranes in a concentration dependent manner. Sci. Rep. 3, 1565 (2013).
15. Shi, Z. & Baumbart, T. Membrane tension and peripheral protein density mediate membrane shape transitions. Nature Comm. 6, 5974 (2015).
16. Phillips, R., Ursell, T., Wiggins, P. & Sens, P. Emerging roles for lipids in shaping membrane-protein function. Nature 459, 379-385 (2009).
17. Reynwar, B. J. et al. Aggregation and vesiculation of membrane proteins by curvature-mediated interactions. Nature 447, 461-464 (2007).
18. Atilgan, E. & Sun, S. X. Shape transitions in lipid membranes and protein mediated vesicle fusion and fission. J. Chem. Phys. 126, 095102 (2007).
19. de Meyer, F. J., Venturoli, M. & Smit, B. Molecular simulations of lipid-mediated protein-protein interactions. Biophys. J. 95, 1851-1865 (2008).
20. Auth, T. & Gompper, G. Budding and vesiculation induced by conical membrane inclusions. Phys. Rev. E 80, 031901 (2009).
21. Šarić, A. & Cacciuto, A. Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles. Phys. Rev. Lett. 108, 118101 (2012).
22. Aimon, S. et al. Membrane Shape Modulates Transmembrane Protein Distribution. Dev. Cell 28, 212-218 (2014).
23. Lipowsky, R. Spontaneous tubulation of membranes and vesicles reveals membrane tension generated by spontaneous curvature. Faraday Discuss. 161, 305-331 (2013).
24. Canham, P. B. The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell. J. Theor. Biol. 26, 61-81 (1970).
25. Helfrich, W. Elastic properties of lipid bilayers: theory and possible experiments. Z. Naturforsch 28c, 693-703 (1973).
26. Fournier, J. B. Nontopological saddle-splay and curvature instabilities from anisotropic membrane inclusions. Phys. Rev. Lett. 76, 4436-4439 (1996).
27. Kabaso, D. et al. Attachment of Rod-Like (BAR) Proteins and Membrane Shape. Mini Rev. Med. Chem. 11, 272-282 (2011).
28. Iglič, A. et al. Curvature-induced accumulation of anisotropic membrane components and raft formation in cylindrical membrane protrusions. J. Theor. Biol. 240, 368-373 (2006).
29. Dommersnes, P. G. & Fournier, J. B. N-body study of anisotropic membrane inclusions: Membrane mediated interactions and ordered aggregation. Eur. Phys. J. B 12, 9-12 (1999).
30. Dommersnes, P. G. & Fournier, J. B. The many-body problem for anisotropic membrane inclusions and the self-assembly of "saddle" defects into an "egg carton". Biophys. J. 83, 2898-2905 (2002).
31. Arkhipov, A., Yin, Y. & Schulten, K. Four-scale description of membrane sculpting by BAR domains. Biophys. J. 95, 2806-2821 (2008).
32. Yu, H. & Schulten, K. Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations. PLoS Comput. Biol. 9, e1002892 (2013).
33. Simunovic, M., Srivastava, A. & Voth, G. A. Linear aggregation of proteins on the membrane as a prelude to membrane remodeling. Proc. Natl. Acad. Sci. USA 110, 20396-20401 (2013).
34. Simunovic, M. & Voth, G. A. Membrane tension controls the assembly of curvature-generating proteins. Nature Comm. 6, 7219 (2015).
35. Ramakrishnan, N., Ipsen, J. H. & Kumar, S. P. B. Role of disclinatons in determining the morphology of deformable fluid interfaces. Soft Matter 8, 3058-3061 (2012).
36. Ramakrishnan, N., Kumar, S. P. B. & Ipsen, J. H. Membrane-mediated aggregation of curvature-inducing nematogens and membrane tubulation. Biophys. J. 104, 1018-1028 (2013).
37. Ayton, G. S. et al. New Insights into BAR Domain-Induced Membrane Remodeling. Biophys. J. 97, 1616-1625 (2009).
38. Noguchi, H. Two-or three-step assembly of banana-shaped proteins coupled with shape transformation of lipid membranes. EPL 108, 48001 (2014).
39. Noguchi, H. Membrane simulation models from nanometer to micrometer scale. J. Phys. Soc. Jpn. 78, 041007 (2009).
40. Noguchi, H. & Gompper, G. Meshless membrane model based on the moving least-squares method. Phys. Rev. E 73, 021903 (2006).
41. Shiba, H. & Noguchi, H. Estimation of the bending rigidity and spontaneous curvature of fluid membranes in simulations. Phys. Rev. E 84, 031926 (2011).
42. Noguchi, H. Formation of polyhedral vesicles and polygonal membrane tubes induced by banana-shaped proteins. J. Chem. Phys. 143, 243109 (2015).
43. Saleem, M. et al. A balance between membrane elasticity and polymerization energy sets the shape of spherical clathrin coats. Nature Comm. 6, 6249 (2015).
44. Laporte, D., Coffman, V. C., Lee, I. J. & Wu, J. Q. Assembly and architecture of precursor nodes during fission yeast cytokinesis. J. Cell Biol. 192, 1005-1012 (2011).
45. Noguchi, H. Solvent-free coarse-grained lipid model for large-scale simulations. J. Chem. Phys. 134, 055101 (2011).