M. Cebecauer, M. Spitaler, A. Serge, and A. I. Magee, Signalling complexes and clusters: functional advantages and methodological hurdles, Journal of Cell Science, vol.123, pp.309-320, 2010.
DOI : 10.1242/jcs.061739
URL : https://hal.archives-ouvertes.fr/hal-00502965

M. A. Lemmon and J. Schlessinger, Cell Signaling by Receptor Tyrosine Kinases, Cell, vol.141, pp.1117-1134, 2010.

M. E. Call and K. W. Wucherpfennig, Common themes in the assembly and architecture of activating immune receptors, Nature Reviews Immunology, vol.7, pp.841-850, 2007.

I. D. Campbell and M. J. Humphries, Integrin Structure, Activation, and Interactions. Cold Spring Harbor Perspectives in Biology 3, 2011.
DOI : 10.1101/cshperspect.a004994
URL : http://cshperspectives.cshlp.org/content/3/3/a004994.full.pdf

M. Audet and M. Bouvier, Restructuring G-Protein-Coupled Receptor Activation, Cell, vol.151, pp.14-23, 2012.

A. J. Beevers and A. M. Dixon, Helical membrane peptides to modulate cell function, Chem Soc Rev, vol.39, pp.2146-2157, 2010.
DOI : 10.1039/b912944h

N. Bordag and S. Keller, Alpha-helical transmembrane peptides: a ''divide and conquer'' approach to membrane proteins, Chem Phys Lipids, vol.163, pp.1-26, 2010.
DOI : 10.1016/j.chemphyslip.2009.07.009

F. Cymer, A. Veerappan, and D. Schneider, Transmembrane helix-helix interactions are modulated by the sequence context and by lipid bilayer properties, Biochim Biophys Acta, vol.1818, pp.963-973, 2011.
DOI : 10.1016/j.bbamem.2011.07.035
URL : https://doi.org/10.1016/j.bbamem.2011.07.035

A. Fink, N. Sal-man, D. Gerber, and Y. Shai, Transmembrane domains interactions within the membrane milieu: Principles, advances and challenges, Biochim Biophys Acta, vol.1818, pp.974-983, 2011.
DOI : 10.1016/j.bbamem.2011.11.029
URL : https://doi.org/10.1016/j.bbamem.2011.11.029

P. Hubert, P. Sawma, J. P. Duneau, J. Khao, and J. Henin, Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye?, Cell Adh Migr, vol.4, pp.313-324, 2010.
DOI : 10.4161/cam.4.2.12430
URL : http://www.tandfonline.com/doi/pdf/10.4161/cam.4.2.12430?needAccess=true

E. Li, W. C. Wimley, and K. Hristova, Transmembrane helix dimerization: beyond the search for sequence motifs, Biochim Biophys Acta, vol.1818, pp.183-193, 2012.
DOI : 10.1016/j.bbamem.2011.08.031
URL : https://doi.org/10.1016/j.bbamem.2011.08.031

E. E. Matthews, M. Zoonens, and D. M. Engelman, Dynamic helix interactions in transmembrane signaling, Cell, vol.127, pp.447-450, 2006.

M. A. Lemmon, J. M. Flanagan, J. F. Hunt, B. D. Adair, and B. J. Bormann, Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices, J Biol Chem, vol.267, pp.7683-7689, 1992.

K. R. Mackenzie, Folding and stability of alpha-helical integral membrane proteins, Chem Rev, vol.106, pp.1931-1977, 2006.

K. R. Mackenzie and D. M. Engelman, Structure-based prediction of the stability of transmembrane helix-helix interactions: the sequence dependence of glycophorin A dimerization, Proc Natl Acad Sci U S A, vol.95, pp.3583-3590, 1998.

K. R. Mackenzie, J. H. Prestegard, and D. M. Engelman, A transmembrane helix dimer: structure and implications, NRP1 and PLXA1 Transmembrane Domains Recognition PLOS ONE |, vol.276, pp.131-133, 1997.

D. T. Moore, B. W. Berger, and W. F. Degrado, Protein-protein interactions in the membrane: sequence, structural, and biological motifs, Structure, vol.16, pp.991-1001, 2008.

W. P. Russ and D. M. Engelman, The GxxxG motif: a framework for transmembrane helix-helix association, J Mol Biol, vol.296, pp.911-919, 2000.

A. Arkhipov, Y. B. Shan, R. Das, N. F. Endres, and M. P. Eastwood, Architecture and Membrane Interactions of the EGF Receptor, Cell, vol.152, pp.557-569, 2013.

N. F. Endres, R. Das, A. W. Smith, A. Arkhipov, and E. Kovacs, Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor, Cell, vol.152, pp.543-556, 2013.

L. Roth, E. Koncina, S. Satkauskas, G. Cremel, and D. Aunis, The many faces of semaphorins: from development to pathology, Cell Mol Life Sci, vol.66, pp.649-666, 2009.

G. Neufeld and O. Kessler, The semaphorins: versatile regulators of tumour progression and tumour angiogenesis, Nat Rev Cancer, vol.8, pp.632-645, 2008.

G. Neufeld, A. D. Sabag, N. Rabinovicz, and O. Kessler, Semaphorins in angiogenesis and tumor progression, Cold Spring Harb Perspect Med, vol.2, p.6718, 2012.

S. Soker, S. Takashima, H. Q. Miao, G. Neufeld, and M. Klagsbrun, Neuropilin-1 is expressed by endothelial and tumor cells as an isoform-specific receptor for vascular endothelial growth factor, Cell, vol.92, pp.735-745, 1998.

H. Chen, A. Chedotal, Z. He, C. S. Goodman, and M. Tessier-lavigne, Neuropilin-2, a novel member of the neuropilin family, is a high affinity receptor for the semaphorins Sema E and Sema IV but not Sema III, Neuron, vol.19, pp.547-559, 1997.

T. Takahashi, F. Nakamura, J. Z. Kalb, R. G. Strittmatter, and S. M. , Semaphorins A and E act as antagonists of neuropilin-1 and agonists of neuropilin-2 receptors, Nat Neurosci, vol.1, pp.487-493, 1998.

L. Feiner, A. M. Koppel, H. Kobayashi, and J. A. Raper, Secreted chick semaphorins bind recombinant neuropilin with similar affinities but bind different subsets of neurons in situ, Neuron, vol.19, pp.539-545, 1997.

A. L. Kolodkin, D. V. Levengood, E. G. Rowe, Y. T. Tai, and R. J. Giger, Neuropilin is a semaphorin III receptor, Cell, vol.90, pp.753-762, 1997.

F. Nakamura, M. Tanaka, T. Takahashi, R. G. Kalb, and S. M. Strittmatter, Neuropilin-1 extracellular domains mediate semaphorin D/III-induced growth cone collapse, Neuron, vol.21, pp.1093-1100, 1998.

A. Sharma, J. Verhaagen, and A. R. Harvey, Receptor complexes for each of the Class 3 Semaphorins, Front Cell Neurosci, vol.6, p.28, 2012.

B. Rohm, A. Ottemeyer, M. Lohrum, and A. W. Puschel, Plexin/neuropilin complexes mediate repulsion by the axonal guidance signal semaphorin 3A, Mech Dev, vol.93, pp.95-104, 2000.

T. Takahashi, A. Fournier, F. Nakamura, L. H. Wang, and Y. Murakami, Plexin-neuropilin-1 complexes form functional semaphorin-3A receptors, Cell, vol.99, pp.59-69, 1999.
DOI : 10.1016/s0092-8674(00)80062-8
URL : https://doi.org/10.1016/s0092-8674(00)80062-8

L. Tamagnone, S. Artigiani, H. Chen, Z. He, and G. I. Ming, Plexins are a large family of receptors for transmembrane, secreted, and GPI-anchored semaphorins in vertebrates, Cell, vol.99, pp.71-80, 1999.

A. Antipenko, J. P. Himanen, K. Van-leyen, V. Nardi-dei, and J. Lesniak, Structure of the semaphorin-3A receptor binding module, Neuron, vol.39, pp.589-598, 2003.
DOI : 10.1016/s0896-6273(03)00502-6
URL : https://doi.org/10.1016/s0896-6273(03)00502-6

C. A. Love, K. Harlos, N. Mavaddat, S. J. Davis, and D. I. Stuart, The ligandbinding face of the semaphorins revealed by the high-resolution crystal structure of SEMA4D, Nat Struct Biol, vol.10, pp.843-848, 2003.

B. J. Janssen, R. A. Robinson, F. Perez-branguli, C. H. Bell, and K. J. Mitchell, Structural basis of semaphorin-plexin signalling, Nature, vol.467, pp.1118-1122, 2010.
DOI : 10.1038/nature09468
URL : http://europepmc.org/articles/pmc3587840?pdf=render

A. Klostermann, M. Lohrum, R. H. Adams, and A. W. Puschel, The chemorepulsive activity of the axonal guidance signal semaphorin D requires dimerization, J Biol Chem, vol.273, pp.7326-7331, 1998.

H. Liu, Z. S. Juo, A. H. Shim, P. J. Focia, and X. Chen, Structural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1, Cell, vol.142, pp.749-761, 2010.
DOI : 10.1016/j.cell.2010.07.040
URL : https://doi.org/10.1016/j.cell.2010.07.040

T. Nogi, N. Yasui, E. Mihara, Y. Matsunaga, and M. Noda, Structural basis for semaphorin signalling through the plexin receptor, Nature, vol.467, pp.1123-1127, 2010.
DOI : 10.1038/nature09473

Y. Tong, P. Chugha, P. K. Hota, R. S. Alviani, and M. Li, Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain, J Biol Chem, vol.282, pp.37215-37224, 2007.

I. Oinuma, H. Katoh, and M. Negishi, Molecular dissection of the semaphorin 4D receptor plexin-B1-stimulated R-Ras GTPase-activating protein activity and neurite remodeling in hippocampal neurons, J Neurosci, vol.24, pp.11473-11480, 2004.

T. Takahashi and S. M. Strittmatter, Plexina1 autoinhibition by the plexin sema domain, Neuron, vol.29, pp.429-439, 2001.
DOI : 10.1016/s0896-6273(01)00216-1
URL : https://doi.org/10.1016/s0896-6273(01)00216-1

B. J. Janssen, T. Malinauskas, G. A. Weir, M. Z. Cader, and C. Siebold, Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex, Nat Struct Mol Biol, vol.19, pp.1293-1299, 2012.
DOI : 10.1038/nsmb.2416
URL : http://europepmc.org/articles/pmc3590443?pdf=render

L. Tamagnone and P. M. Comoglio, Signalling by semaphorin receptors: cell guidance and beyond, Trends Cell Biol, vol.10, pp.377-383, 2000.
DOI : 10.1016/s0962-8924(00)01816-x

L. Roth, C. Nasarre, S. Dirrig-grosch, D. Aunis, and G. Cremel, Transmembrane domain interactions control biological functions of neuropilin, 2008.
DOI : 10.1091/mbc.e07-06-0625
URL : http://www.molbiolcell.org/content/19/2/646.full.pdf

, Mol Biol Cell, vol.19, pp.646-654

C. Nasarre, M. Roth, L. Jacob, L. Roth, and E. Koncina, Peptide-based interference of the transmembrane domain of neuropilin-1 inhibits glioma growth in vivo, Oncogene, vol.29, pp.2381-2392, 2010.

B. Chaudhary, Y. S. Khaled, B. J. Ammori, and E. Elkord, Neuropilin 1: function and therapeutic potential in cancer, Cancer Immunol Immunother, 2013.

S. J. Marrink, A. H. De-vries, and A. E. Mark, Coarse grained model for semiquantitative lipid simulations, vol.108, pp.750-760, 2004.

S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. De-vries, The MARTINI force field: coarse grained model for biomolecular simulations, J Phys Chem B, vol.111, pp.7812-7824, 2007.

L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, and D. P. Tieleman, The MARTINI coarse grained forcefield: extension to proteins, J Chem Theory and Comput, vol.4, pp.819-834, 2008.

B. A. Hall, A. P. Chetwynd, and M. S. Sansom, Exploring peptide-membrane interactions with coarse-grained MD simulations, Biophys J, vol.100, pp.1940-1948, 2011.
DOI : 10.1016/j.bpj.2011.02.041
URL : https://doi.org/10.1016/j.bpj.2011.02.041

J. Henin, A. Pohorille, and C. Chipot, Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A, J Am Chem Soc, vol.127, pp.8478-8484, 2005.

L. Janosi, A. Prakash, and M. Doxastakis, Lipid-modulated sequence-specific association of glycophorin A in membranes, Biophys J, vol.99, pp.284-292, 2010.

D. Sengupta and S. J. Marrink, Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes, Phys Chem Chem Phys, vol.12, pp.12987-12996, 2010.

E. Psachoulia, P. W. Fowler, P. J. Bond, and M. S. Sansom, Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization, Biochemistry, vol.47, pp.10503-10512, 2008.

P. J. Bond and M. S. Sansom, Insertion and assembly of membrane proteins via simulation, J Am Chem Soc, vol.128, pp.2697-2704, 2006.
DOI : 10.1021/ja0569104
URL : http://europepmc.org/articles/pmc4618310?pdf=render

J. Domanski, S. J. Marrink, and L. V. Schafer, Transmembrane helices can induce domain formation in crowded model membranes, Biochim Biophys Acta, vol.1818, pp.984-994, 2012.

E. Psachoulia, D. P. Marshall, and M. S. Sansom, Molecular dynamics simulations of the dimerization of transmembrane alpha-helices, Acc Chem Res, vol.43, pp.388-396, 2010.

L. V. Schafer, D. H. Jong, A. Holt, A. J. Rzepiela, and A. H. De-vries, Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes, Proc Natl Acad Sci U S A, vol.108, pp.1343-1348, 2011.

X. Periole, A. M. Knepp, T. P. Sakmar, S. J. Marrink, and T. Huber, Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers, Journal of the American Chemical Society, vol.134, pp.10959-10965, 2012.

A. K. Doura, F. J. Kobus, L. Dubrovsky, E. Hibbard, and K. G. Fleming, Sequence context modulates the stability of a GxxxG-mediated transmembrane helix-helix dimer, J Mol Biol, vol.341, pp.991-998, 2004.

F. Cymer and D. Schneider, Transmembrane helix-helix interactions involved in ErbB receptor signaling, Cell Adh Migr, vol.4, pp.299-312, 2010.
DOI : 10.4161/cam.4.2.11191
URL : http://www.tandfonline.com/doi/pdf/10.4161/cam.4.2.11191?needAccess=true

C. Escher, F. Cymer, and D. Schneider, Two GxxxG-like motifs facilitate promiscuous interactions of the human ErbB transmembrane domains, J Mol Biol, vol.389, pp.10-16, 2009.
DOI : 10.1016/j.jmb.2009.04.002

S. J. Fleishman, J. Schlessinger, and N. Ben-tal, A putative molecular-activation switch in the transmembrane domain of erbB2, Proc Natl Acad Sci, vol.99, pp.15937-15940, 2002.

J. M. Mendrola, M. B. Berger, M. C. King, and M. A. Lemmon, The single transmembrane domains of ErbB receptors self-associate in cell membranes, J Biol Chem, vol.277, pp.4704-4712, 2002.

K. S. Mineev, E. V. Bocharov, Y. E. Pustovalova, O. V. Bocharova, and V. V. Chupin, Spatial structure of the transmembrane domain heterodimer of ErbB1 and ErbB2 receptor tyrosine kinases, J Mol Biol, vol.400, pp.231-243, 2010.

X. Periole and S. J. Marrink, The Martini coarse-grained force field, Methods Mol Biol, vol.924, pp.533-565, 2013.
DOI : 10.1007/978-1-62703-017-5_20

Z. Ic, How neuropilin-1 regulates receptor tyrosine kinase signalling: the knowns and known unknowns, Biochemical Society Transactions, vol.39, pp.1583-1591, 2011.

H. Yin, J. S. Slusky, B. W. Berger, R. S. Walters, and G. Vilaire, Computational design of peptides that target transmembrane helices, Science, vol.315, pp.1817-1822, 2007.
DOI : 10.1126/science.1136782

A. Battesti and E. Bouveret, The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli, Methods, vol.58, pp.325-334, 2012.
DOI : 10.1016/j.ymeth.2012.07.018
URL : https://hal.archives-ouvertes.fr/hal-01458246

B. Hess, C. Kutzner, D. Van-der-spoel, and E. Lindahl, Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, J Chem Theory Comp, vol.4, pp.435-447, 2008.
DOI : 10.1021/ct700301q

D. Van-der-spoel, B. Lindahl, G. Hess, G. Groenhof, and A. E. Mark, GROMACS: fast, flexible, and free, J Comput Chem, vol.26, pp.1701-1718, 2005.

W. Humphrey, A. Dalke, and K. Schulten, VMD-Visual Molecular Dynamics, J Molec Graphics, vol.14, pp.33-38, 1996.
DOI : 10.1016/0263-7855(96)00018-5

H. Berendsen, J. Postma, W. F. Van-gunsteren, A. Dinola, and J. R. Haak, Molecular dynamics with coupling to an external bath, J Chem Phys, vol.81, pp.3684-3690, 1984.
DOI : 10.1063/1.448118

D. A. Case, . Cheatham-te-3rd, T. Darden, H. Gohlke, and R. Luo, The Amber biomolecular simulation programs, J Comput Chem, vol.26, pp.1668-1688, 2005.
DOI : 10.1002/jcc.20290
URL : http://europepmc.org/articles/pmc1989667?pdf=render

J. W. Ponder and D. A. Case, Force fields for protein simulations, Adv Protein Chem, vol.66, pp.27-85, 2003.
DOI : 10.1016/s0065-3233(03)66002-x

S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method, J Comput Chem, vol.13, pp.1011-1021, 1992.
DOI : 10.1002/jcc.540130812