Investigation of the interactions between the EphB2 receptor and SNEW peptide variants

References

• Beauchamp A, Debinski W. 2012. Ephs and ephrins in cancer: Ephrin-A1 signalling. Semin Cell Dev Biol 23:109–115
   PubMed Web of Science ®Google Scholar
• Bochenek ML, Dickinson S, Astin JW, Adams RH, Nobes CD. 2010. Ephrin-B2 regulates endothelial cell morphology and motility independently of Eph-receptor binding. J Cell Sci 123:1235–1246
   Web of Science ®Google Scholar
• Bowden TA, Aricescu AR, Nettleship JE, Siebold C, Rahman-Huq N, Owens RJ, Stuart DI, Jones EY. 2009. Structural plasticity of eph receptor A4 facilitates cross-class ephrin signaling. Structure 17:1386–1397
   Google Scholar
• Boyd AW, Bartlett PF, Lackmann M. 2014. Therapeutic targeting of EPH receptors and their ligands, Nature reviews. Drug Discov 13:39–62
   Google Scholar
• Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217
   Web of Science ®Google Scholar
• Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, et al. 2005. The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688
   PubMed Web of Science ®Google Scholar
• Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H, et al. 2007. Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J Biol Chem 282:36505–36513
   PubMed Web of Science ®Google Scholar
• Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, et al. 1996. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol 117, pg 5179, 1995). J Am Chem Soc 118:2309–2309
   Web of Science ®Google Scholar
• Dahmann C, Oates AC, Brand M. 2011. Boundary formation and maintenance in tissue development. Nat Rev Genet 12:43–55
   PubMed Web of Science ®Google Scholar
• Dai D, Huang Q, Nussinov R, Ma B. 2014. Promiscuous and specific recognition among ephrins and Eph receptors. Biochim Biophys Acta 1844:1729–1740
   Google Scholar
• Darden T, York D, Pedersen L. 1993. Particle Mesh Ewald – An N. Log (N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092
   Web of Science ®Google Scholar
• Dravis C, Yokoyama N, Chumley MJ, Cowan CA, Silvany RE, Shay J, Baker LA, Henkemeyer M. 2004. Bidirectional signaling mediated by ephrin-B2 and EphB2 controls urorectal development. Dev Biol 271:272–290
   PubMedGoogle Scholar
• Falivelli G, Lisabeth EM, Rubio de la Torre E, Perez-Tenorio G, Tosato G, Salvucci O, Pasquale EB. 2013. Attenuation of eph receptor kinase activation in cancer cells by coexpressed ephrin ligands. PloS One 8:e81445
   PubMedGoogle Scholar
• Feller SE, Zhang YH, Pastor RW, Brooks BR. 1995. Constant-pressure molecular-dynamics simulation – The Langevin Piston Method. J Chem Phys 103:4613–4621
   Web of Science ®Google Scholar
• Frisen J, Holmberg J, Barbacid M. 1999. Ephrins and their Eph receptors: Multi talented directors of embryonic development. EMBO J 18:5159–5165
   PubMed Web of Science ®Google Scholar
• Egea J, Klein R. 2007. Bidirectional Eph-ephrin signaling during axon guidance. Trends Cell Biol 17:230–238
   PubMed Web of Science ®Google Scholar
• Genander M, Frisen J. 2010. Ephrins and Eph receptors in stem cells and cancer. Curr Opin Cell Biol 22:611–616
   PubMed Web of Science ®Google Scholar
• Genander M, Halford MM, Xu NJ, Eriksson M, Yu Z, Qiu Z, Martling A, et al. 2009. Dissociation of EphB2 signaling pathways mediating progenitor cell proliferation and tumor suppression. Cell 139:679–692
   PubMed Web of Science ®Google Scholar
• Goparaju C, Donington JS, Hsu T, Harrington R, Hirsch N, Pass HI. 2013. Overexpression of EPH receptor B2 in malignant mesothelioma correlates with oncogenic behavior. J Thoracic Oncol: Off Publ Int Assoc Study Lung Cancer 8:1203–1211
   Google Scholar
• Janes PW, Griesshaber B, Atapattu L, Nievergall E, Hii LL, Mensinga A, Chheang C, et al. 2011. Eph receptor function is modulated by heterooligomerization of A and B type Eph receptors. J Cell Biol 195:1033–1045
   Google Scholar
• Jorgensen C, Sherman A, Chen GI, Pasculescu A, Poliakov A, Hsiung M, Larsen B, et al. 2009. Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326:1502–1509
   PubMed Web of Science ®Google Scholar
• Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, et al. 1999. NAMD2: Greater scalability for parallel molecular dynamics. J Comput Phys 151:283–312
   Web of Science ®Google Scholar
• Kandouz M. 2012. The Eph/Ephrin family in cancer metastasis: Communication at the service of invasion. Cancer Metast Rev 31:353–373
   Google Scholar
• Koolpe M, Burgess R, Dail M, Pasquale EB. 2005. EphB receptor-binding peptides identified by phage display enable design of an antagonist with ephrin-like affinity. J Biol Chem 280:17301–17311
   PubMed Web of Science ®Google Scholar
• Koolpe M, Dail M, Pasquale EB. 2002. An ephrin mimetic peptide that selectively targets the EphA2 receptor. J Biol Chem 277:46974–46979
   PubMed Web of Science ®Google Scholar
• Lackmann M, Boyd AW. 2008. Eph, a protein family coming of age: More confusion, insight, or complexity? Sci Signal 1:re2
   PubMed Web of Science ®Google Scholar
• Lamberto I, Qin H, Noberini R, Premkumar L, Bourgin C, Riedl SJ, Song J, Pasquale EB. 2012. Distinctive binding of three antagonistic peptides to the ephrin-binding pocket of the EphA4 receptor. Biochem J 445:47–56
   Google Scholar
• Ma B, Nussinov R. 2014. Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Curr Pharm Des 20:1293–1301
   Google Scholar
• MacKerell AD, Bashford D, Bellott M, Dunbrack Jr RL, Evanseck JD, Field MJ, Fischer S, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616
   PubMed Web of Science ®Google Scholar
• Martyna GJ, Tobias DJ, Klein ML. 1994. Constant-pressure molecular-dynamics algorithms. J Chem Phys 101:4177–4189
   Web of Science ®Google Scholar
• Murai KK, Nguyen LN, Koolpe M, McLennan R, Krull CE, Pasquale EB. 2003. Targeting the EphA4 receptor in the nervous system with biologically active peptides. Mol Cell Neurosci 24:1000–1011
   Google Scholar
• Nakada M, Niska JA, Tran NL, McDonough WS, Berens ME. 2005. EphB2/R-Ras signaling regulates glioma cell adhesion, growth, and invasion. Am J Pathol 167:565–576
   PubMed Web of Science ®Google Scholar
• Noberini R, Lamberto I, Pasquale EB. 2012. Targeting Eph receptors with peptides and small molecules: Progress and challenges. Semin Cell Dev Biol 23:51–57
   Google Scholar
• Noberini R, Mitra S, Salvucci O, Valencia F, Duggineni S, Prigozhina N, Wei K, et al. 2011. PEGylation potentiates the effectiveness of an antagonistic peptide that targets the EphB4 receptor with nanomolar affinity. PloS One 6:e28611
   Google Scholar
• Noberini R, Pasquale EB. 2009. Proliferation and tumor suppression: Not mutually exclusive for Eph receptors. Cancer Cell 16:452–454
   Google Scholar
• Nussinov R, Ma B. 2012. Protein dynamics and conformational selection in bidirectional signal transduction. BMC Biol 10:2
   PubMed Web of Science ®Google Scholar
• Oba SM, Wang YJ, Song JP, Li ZY, Kobayashi K, Tsugane S, Hamada GS, et al. 2001. Genomic structure and loss of heterozygosity of EPHB2 in colorectal cancer. Cancer Lett 164:97–104
   PubMedGoogle Scholar
• Pasquale EB. 2010. Eph receptors and ephrins in cancer: Bidirectional signalling and beyond, Nature reviews. Cancer 10:165–180
   Google Scholar
• Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, et al. 2005. Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802
   PubMed Web of Science ®Google Scholar
• Pitulescu ME, Adams RH. 2010. Eph/ephrin molecules – A hub for signaling and endocytosis. Genes Dev 24:2480–2492
   PubMed Web of Science ®Google Scholar
• Qin H, Lim L, Song J. 2012. Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations. BMC Biophys 5:2
   Google Scholar
• Risley M, Garrod D, Henkemeyer M, McLean W. 2009. EphB2 and EphB3 forward signalling are required for palate development. Mech Dev 126:230–239
   Google Scholar
• Ryckaert JP, Ciccotti G, Berendsen HJC. 1977. Numerical-integration of Cartesian equations of motion of a system with constraints – Molecular-dynamics of N-alkanes. J Comput Phys 23:327–341
   Web of Science ®Google Scholar
• Salvucci O, de la Luz Sierra M, Martina JA, McCormick PJ, Tosato G. 2006. EphB2 and EphB4 receptors forward signaling promotes SDF-1-induced endothelial cell chemotaxis and branching remodeling. Blood 108:2914–2922
   Google Scholar
• Salvucci O, Tosato G. 2012. Essential roles of EphB receptors and EphrinB ligands in endothelial cell function and angiogenesis. Adv Cancer Res 114:21–57
   PubMed Web of Science ®Google Scholar
• Singh A, Winterbottom E, Daar IO. 2012. Eph/ephrin signaling in cell–cell and cell–substrate adhesion. Front Biosci (Landmark Ed) 17:473–497
   Google Scholar
• Surawska H, Ma PC, Salgia R. 2004. The role of ephrins and Eph receptors in cancer. Cytokine Growth Factor Rev 15:419–433
   PubMed Web of Science ®Google Scholar
• Pasquale EB. 2008. Eph-ephrin bidirectional signaling in physiology and disease. Cell 133:38–52
   PubMed Web of Science ®Google Scholar
• Pretze M, Kuchar M, Bergmann R, Steinbach J, Pietzsch J, Mamat C. 2013. An efficient bioorthogonal strategy using CuAAC click chemistry for radiofluorinations of SNEW peptides and the role of copper depletion. Chem Med Chem 8:935–945
   Google Scholar
• Tong J, Elowe S, Nash P, Pawson T. 2003. Manipulation of EphB2 regulatory motifs and SH2 binding sites switches MAPK signaling and biological activity. J Biol Chem 278:6111–6119
   PubMed Web of Science ®Google Scholar
• Warner N, Wybenga-Groot LE, Pawson T. 2008. Analysis of EphA4 receptor tyrosine kinase substrate specificity using peptide-based arrays. FEBS J 275:2561–2573
   Google Scholar
• Wiesner S, Wybenga-Groot LE, Warner N, Lin H, Pawson T, Forman-Kay JD, Sicheri F. 2006. A change in conformational dynamics underlies the activation of Eph receptor tyrosine kinases. EMBO J 25:4686–4696
   PubMed Web of Science ®Google Scholar
• Wu Q, Suo Z, Kristensen GB, Baekelandt M, Nesland JM. 2006. The prognostic impact of EphB2/B4 expression on patients with advanced ovarian carcinoma. Gynecol Oncol 102:15–21
   Google Scholar