Year 2019, Volume 31 , Issue 1, Pages 90 - 99 2019-03-31

Elucidating Structural Details of Ras-Effector Interactions
Ras-Efektör Etkileşimlerinin Yapısal Detaylarının Açığa Çıkarılması

Serena MURATCIOĞLU [1] , Saliha Ece ACUNER ÖZBABACAN [2]


Small membrane-associated Ras proteins mediate a wide range of cellular functions, such as cell proliferation, migration, survival, and differentiation; through binding and activating numerous effectors. Constitutively active mutant Ras proteins are detected in various types of human cancer and Ras community seeks approaches other than small-molecule Ras inhibitors; such as targeting the protein-protein interactions in the downstream Ras effector pathways and preventing its membrane localization. Although the most studied effectors of Ras, i.e. Raf, PI3K and RalGDS, bind Ras through the same site, they elicit opposing signaling pathways and thus, the temporal and spatial decision of the cell among them is critical. Elucidating the structural details of Ras/effector interactions can help us understand the cell decision and target the protein-protein interactions precisely. However, only a few crystal structures of Ras in complex with an effector are deposited in PDB. Here, the 3D structures of Ras/effector complexes were modeled with the PRISM algorithm and important binding sites as well as hot spot residues on Ras were identified. The effectors were also classified according to the binding regions on Ras, to determine the competitive pathways and the binding regions other than the “effector lobe”. The modeled complexes reveal important information about the interfaces between Ras and its partners with the potential of guiding drug design studies to block oncogenic Ras signaling.

Hücre zarıyla ilintili küçük Ras proteinleri pek çok efektöre bağlanıp onları aktif hale getirerek hücre çoğalması, göçü, hayatta kalma ve farklılaşması gibi çeşitli hücresel işlevleri kontrol ederler. Ras üzerindeki mutasyonlar, yapısal olarak aktif proteine sebebiyet verir ve insandaki birçok kanser tipinde tespit edilmişlerdir ve Ras topluluğu Ras’ı hedef alan küçük moleküllü inhibitörler tasarlamak yerine Ras’ın efektör yolaklarındaki protein-protein etkileşimlerini hedef alarak Ras’ın zar üzerindeki lokalizasyonunu engellemeyi amaçlamaktadır. Ras’ın en çok çalışılan efektörleri, Raf, PI3K ve RalGDS, Ras’a aynı yüzeyden bağlanmasına rağmen karşıt sinyal yolaklarını ortaya çıkarırlar ve dolayısıyla hücrenin bu yolaklar arasındaki zamansal ve mekansal kararları kritik öneme sahiptir. Ras/efektör etkileşimlerinin yapısal detaylarını açığa çıkarmak, hücrenin karar mekanizmasını anlamamıza ve protein-protein etkileşimlerini hassas olarak hedeflememize yardımcı olabilir. Bununla birlikte, sadece birkaç Ras/efektör kompleksinin kristal yapısı PDB'de bulunmaktadır. Bu çalışmada, Ras/efektör komplekslerinin 3 boyutlu yapıları PRISM algoritması ile modellenmiştir ve Ras üzerindeki sıcak nokta kalıntılarının yanı sıra önemli bağlanma bölgeleri belirlenmiştir. Efektörler ayrıca, rekabetçi yolları ve "efektör lobu" dışındaki bağlayıcı bölgeleri belirlemek için Ras'daki bağlayıcı bölgelere göre sınıflandırılmıştır. Modellenen kompleksler, Ras ve ortakları arasındaki arayüzeyler hakkında onkojenik Ras sinyal iletimini bloke etmek için ilaç tasarım çalışmalarına rehberlik etme potansiyeli olan önemli bilgiler ortaya koymaktadır.

  • [1] Campbell, S. L., Khosravi-Far, R., Rossman, K. L., Clark, G. J., & Der, C. J. (1998). Increasing complexity of Ras signaling. Oncogene, 17(11 Reviews), 1395-1413.
  • [2] Reuther, G. W., & Der, C. J. (2000). The Ras branch of small GTPases: Ras family members don't fall far from the tree. Curr Opin Cell Biol, 12(2), 157-165.
  • [3] Cherfils, J., & Zeghouf, M. (2013). Regulation of small GTPases by GEFs, GAPs, and GDIs. Physiol Rev, 93(1), 269-309.
  • [4] Geyer, M., & Wittinghofer, A. (1997). GEFs, GAPs, GDIs and effectors: taking a closer (3D) look at the regulation of Ras-related GTP-binding proteins. Curr Opin Struct Biol, 7(6), 786-792.
  • [5] Sprang, S. R. (1997). G proteins, effectors and GAPs: structure and mechanism. Curr Opin Struct Biol, 7(6), 849-856.
  • [6] Reuther, G. W., & Der, C. J. (2000). The Ras branch of small GTPases: Ras family members don’t fall far from the tree. Current opinion in cell biology, 12(2), 157-165.
  • [7] Takai, Y., Sasaki, T., & Matozaki, T. (2001). Small GTP-binding proteins. Physiological reviews, 81(1), 153-208.
  • [8] Muegge, I., Schweins, T., Langen, R., & Warshel, A. (1996). Electrostatic control of GTP and GDP binding in the oncoprotein p21ras. Structure, 4(4), 475-489.
  • [9] Muratcioglu, S., Chavan, T. S., Freed, B. C., et al. (2015). GTP-Dependent K-Ras Dimerization. Structure, 23(7), 1325-1335.
  • [10] Lu, S., Jang, H., Muratcioglu, S., et al. (2016). Ras Conformational Ensembles, Allostery, and Signaling. Chem Rev, 116(11), 6607-6665.
  • [11] Gorfe, A. A., Grant, B. J., & McCammon, J. A. (2008). Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure, 16(6), 885-896.
  • [12] Buhrman, G., O'Connor, C., Zerbe, B., et al. (2011). Analysis of binding site hot spots on the surface of Ras GTPase. J Mol Biol, 413(4), 773-789.
  • [13] Buhrman, G., Holzapfel, G., Fetics, S., & Mattos, C. (2010). Allosteric modulation of Ras positions Q61 for a direct role in catalysis. Proc Natl Acad Sci U S A, 107(11), 4931-4936.
  • [14] Barbacid, M. (1987). ras genes. Annu Rev Biochem, 56, 779-827.
  • [15] Bos, J. L. (1989). ras oncogenes in human cancer: a review. Cancer Res, 49(17), 4682-4689.
  • [16] Rojas, A. M., Fuentes, G., Rausell, A., & Valencia, A. (2012). The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol, 196(2), 189-201.
  • [17] Forbes, S. A., Bindal, N., Bamford, S., et al. (2011). COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res, 39(Database issue), D945-950.
  • [18] Karnoub, A. E., & Weinberg, R. A. (2008). Ras oncogenes: split personalities. Nat Rev Mol Cell Biol, 9(7), 517-531.
  • [19] Cox, A. D., Fesik, S. W., Kimmelman, A. C., Luo, J., & Der, C. J. (2014). Drugging the undruggable RAS: Mission possible? Nat Rev Drug Discov, 13(11), 828-851.
  • [20] Maurer, T., Garrenton, L. S., Oh, A., et al. (2012). Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity. Proc Natl Acad Sci U S A, 109(14), 5299-5304.
  • [21] Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A., & Shokat, K. M. (2013). K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature, 503(7477), 548-551.
  • [22] Shima, F., Yoshikawa, Y., Ye, M., et al. (2013). In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction. Proc Natl Acad Sci U S A, 110(20), 8182-8187.
  • [23] Sun, Q., Burke, J. P., Phan, J., et al. (2012). Discovery of small molecules that bind to K-Ras and inhibit Sos-mediated activation. Angew Chem Int Ed Engl, 51(25), 6140-6143.
  • [24] Athuluri-Divakar, S. K., Vasquez-Del Carpio, R., Dutta, K., et al. (2016). A Small Molecule RAS-Mimetic Disrupts RAS Association with Effector Proteins to Block Signaling. Cell, 165(3), 643-655.
  • [25] Cruz-Migoni, A., Canning, P., Quevedo, C. E., et al. (2019). Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds. Proc Natl Acad Sci U S A.
  • [26] Engin, H. B., Carlin, D., Pratt, D., & Carter, H. (2017). Modeling of RAS complexes supports roles in cancer for less studied partners. BMC Biophys, 10(Suppl 1), 5.
  • [27] Wittinghofer, A., & Herrmann, C. (1995). Ras-effector interactions, the problem of specificity. FEBS Lett, 369(1), 52-56.
  • [28] Marshall, C. J. (1996). Ras effectors. Curr Opin Cell Biol, 8(2), 197-204.
  • [29] McCormick, F., & Wittinghofer, A. (1996). Interactions between Ras proteins and their effectors. Curr Opin Biotechnol, 7(4), 449-456.
  • [30] Koide, H., Satoh, T., Nakafuku, M., & Kaziro, Y. (1993). GTP-dependent association of Raf-1 with Ha-Ras: identification of Raf as a target downstream of Ras in mammalian cells. Proc Natl Acad Sci U S A, 90(18), 8683-8686.
  • [31] Spoerner, M., Herrmann, C., Vetter, I. R., Kalbitzer, H. R., & Wittinghofer, A. (2001). Dynamic properties of the Ras switch I region and its importance for binding to effectors. Proceedings of the National Academy of Sciences, 98(9), 4944-4949.
  • [32] Mott, H. R., & Owen, D. (2015). Structures of Ras superfamily effector complexes: What have we learnt in two decades? Crit Rev Biochem Mol Biol, 50(2), 85-133.
  • [33] Kolch, W. (2000). Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions. Biochem J, 351 Pt 2, 289-305.
  • [34] Pacold, M. E., Suire, S., Perisic, O., et al. (2000). Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase γ. Cell, 103(6), 931-944.
  • [35] Rodriguez-Viciana, P., & McCormick, F. (2005). RalGDS comes of age. Cancer Cell, 7(3), 205-206.
  • [36] Datta, S. R., Brunet, A., & Greenberg, M. E. (1999). Cellular survival: a play in three Akts. Genes & development, 13(22), 2905-2927.
  • [37] Khwaja, A., Rodriguez‐Viciana, P., Wennström, S., Warne, P. H., & Downward, J. (1997). Matrix adhesion and Ras transformation both activate a phosphoinositide 3‐OH kinase and protein kinase B/Akt cellular survival pathway. The EMBO journal, 16(10), 2783-2793.
  • [38] Feig, L. A., Urano, T., & Cantor, S. (1996). Evidence for a Ras/Ral signaling cascade. Trends in biochemical sciences, 21(11), 438-441.
  • [39] Hofer, F., Fields, S., Schneider, C., & Martin, G. S. (1994). Activated Ras interacts with the Ral guanine nucleotide dissociation stimulator. Proceedings of the National Academy of Sciences, 91(23), 11089-11093.
  • [40] Marais, R., Light, Y., Paterson, H., & Marshall, C. (1995). Ras recruits Raf‐1 to the plasma membrane for activation by tyrosine phosphorylation. The EMBO journal, 14(13), 3136-3145.
  • [41] Yordy, J. S., & Muise-Helmericks, R. C. (2000). Signal transduction and the Ets family of transcription factors. Oncogene, 19(55), 6503.
  • [42] Vojtek, A. B., Hollenberg, S. M., & Cooper, J. A. (1993). Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell, 74(1), 205-214.
  • [43] Chuang, E., Barnard, D., Hettich, L., Zhang, X. F., Avruch, J., & Marshall, M. S. (1994). Critical binding and regulatory interactions between Ras and Raf occur through a small, stable N-terminal domain of Raf and specific Ras effector residues. Mol Cell Biol, 14(8), 5318-5325.
  • [44] Ghosh, S., & Bell, R. M. (1994). Identification of discrete segments of human Raf-1 kinase critical for high affinity binding to Ha-Ras. J Biol Chem, 269(49), 30785-30788.
  • [45] Gohlke, H., Kiel, C., & Case, D. A. (2003). Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol, 330(4), 891-913.
  • [46] Krygowska, A. A., & Castellano, E. (2018). PI3K: a crucial piece in the RAS signaling puzzle. Cold Spring Harbor perspectives in medicine, 8(6), a031450.
  • [47] Fetics, S. K., Guterres, H., Kearney, B. M., et al. (2015). Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. Structure, 23(3), 505-516.
  • [48] Aytuna, A. S., Gursoy, A., & Keskin, O. (2005). Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics, 21(12), 2850-2855.
  • [49] Ogmen, U., Keskin, O., Aytuna, A. S., Nussinov, R., & Gursoy, A. (2005). PRISM: protein interactions by structural matching. Nucleic Acids Res, 33(Web Server issue), W331-336.
  • [50] Tuncbag, N., Gursoy, A., Nussinov, R., & Keskin, O. (2011). Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc, 6(9), 1341-1354.
  • [51] Tuncbag, N., Keskin, O., Nussinov, R., & Gursoy, A. (2012). Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins, 80(4), 1239-1249.
  • [52] Mashiach, E., Nussinov, R., & Wolfson, H. J. (2010). FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins, 78(6), 1503-1519.
  • [53] Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40.
  • [54] Cukuroglu, E., Gursoy, A., & Keskin, O. (2012). HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res, 40(Database issue), D829-833.
  • [55] Feig, L. A., & Buchsbaum, R. J. (2002). Cell signaling: life or death decisions of ras proteins. Curr Biol, 12(7), R259-261.
  • [56] Mitin, N., Konieczny, S. F., & Taparowsky, E. J. (2006). RAS and the RAIN/RasIP1 effector. Methods Enzymol, 407, 322-335.
  • [57] Choy, E., Chiu, V. K., Silletti, J., et al. (1999). Endomembrane trafficking of ras: the CAAX motif targets proteins to the ER and Golgi. Cell, 98(1), 69-80.
  • [58] Liedtke, M., Ayton, P. M., Somervaille, T. C., Smith, K. S., & Cleary, M. L. (2010). Self-association mediated by the Ras association 1 domain of AF6 activates the oncogenic potential of MLL-AF6. Blood, 116(1), 63-70.
  • [59] Smith, M. J., Ottoni, E., Ishiyama, N., et al. (2017). Evolution of AF6-RAS association and its implications in mixed-lineage leukemia. Nat Commun, 8(1), 1099.
Primary Language en
Subjects Science, Engineering, Basic Sciences
Journal Section Research Articles
Authors

Orcid: 0000-0002-5983-294X
Author: Serena MURATCIOĞLU
Institution: University of California Berkeley
Country: United States


Orcid: 0000-0003-0336-0645
Author: Saliha Ece ACUNER ÖZBABACAN (Primary Author)
Institution: ISTANBUL MEDENIYET UNIVERSITY
Country: Turkey


Dates

Publication Date : March 31, 2019

Bibtex @research article { jeps528662, journal = {International Journal of Advances in Engineering and Pure Sciences}, issn = {}, eissn = {2636-8277}, address = {fbedergi@marmara.edu.tr}, publisher = {Marmara University}, year = {2019}, volume = {31}, pages = {90 - 99}, doi = {10.7240/jeps.528662}, title = {Elucidating Structural Details of Ras-Effector Interactions}, key = {cite}, author = {MURATCIOĞLU, Serena and ACUNER ÖZBABACAN, Saliha Ece} }
APA MURATCIOĞLU, S , ACUNER ÖZBABACAN, S . (2019). Elucidating Structural Details of Ras-Effector Interactions. International Journal of Advances in Engineering and Pure Sciences , 31 (1) , 90-99 . DOI: 10.7240/jeps.528662
MLA MURATCIOĞLU, S , ACUNER ÖZBABACAN, S . "Elucidating Structural Details of Ras-Effector Interactions". International Journal of Advances in Engineering and Pure Sciences 31 (2019 ): 90-99 <https://dergipark.org.tr/en/pub/jeps/issue/43950/528662>
Chicago MURATCIOĞLU, S , ACUNER ÖZBABACAN, S . "Elucidating Structural Details of Ras-Effector Interactions". International Journal of Advances in Engineering and Pure Sciences 31 (2019 ): 90-99
RIS TY - JOUR T1 - Elucidating Structural Details of Ras-Effector Interactions AU - Serena MURATCIOĞLU , Saliha Ece ACUNER ÖZBABACAN Y1 - 2019 PY - 2019 N1 - doi: 10.7240/jeps.528662 DO - 10.7240/jeps.528662 T2 - International Journal of Advances in Engineering and Pure Sciences JF - Journal JO - JOR SP - 90 EP - 99 VL - 31 IS - 1 SN - -2636-8277 M3 - doi: 10.7240/jeps.528662 UR - https://doi.org/10.7240/jeps.528662 Y2 - 2019 ER -
EndNote %0 International Journal of Advances in Engineering and Pure Sciences Elucidating Structural Details of Ras-Effector Interactions %A Serena MURATCIOĞLU , Saliha Ece ACUNER ÖZBABACAN %T Elucidating Structural Details of Ras-Effector Interactions %D 2019 %J International Journal of Advances in Engineering and Pure Sciences %P -2636-8277 %V 31 %N 1 %R doi: 10.7240/jeps.528662 %U 10.7240/jeps.528662
ISNAD MURATCIOĞLU, Serena , ACUNER ÖZBABACAN, Saliha Ece . "Elucidating Structural Details of Ras-Effector Interactions". International Journal of Advances in Engineering and Pure Sciences 31 / 1 (March 2019): 90-99 . https://doi.org/10.7240/jeps.528662
AMA MURATCIOĞLU S , ACUNER ÖZBABACAN S . Elucidating Structural Details of Ras-Effector Interactions. JEPS. 2019; 31(1): 90-99.
Vancouver MURATCIOĞLU S , ACUNER ÖZBABACAN S . Elucidating Structural Details of Ras-Effector Interactions. International Journal of Advances in Engineering and Pure Sciences. 2019; 31(1): 99-90.