GTP-Dependent K-Ras Dimerization.

Ras proteins recruit and activate effectors, including Raf, that transmit receptor-initiated signals. Monomeric Ras can bind Raf; however, activation of Raf requires its dimerization. It has been suspected that dimeric Ras may promote dimerization and activation of Raf. Here, we show that the GTP-bound catalytic domain of K-Ras4B, a highly oncogenic splice variant of the K-Ras isoform, forms stable homodimers. We observe two major dimer interfaces. The first, highly populated β-sheet dimer interface is at the Switch I and effector binding regions, overlapping the binding surfaces of Raf, PI3K, RalGDS, and additional effectors. This interface has to be inhibitory to such effectors. The second, helical interface also overlaps the binding sites of some effectors. This interface may promote activation of Raf. Our data reveal how Ras self-association can regulate effector binding and activity, and suggest that disruption of the helical dimer interface by drugs may abate Raf signaling in cancer.

[1]  R. Klein,et al.  Structurally encoded intraclass differences in EphA clusters drive distinct cell responses , 2013, Nature Structural &Molecular Biology.

[2]  H. Wolfson,et al.  A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.

[3]  R. Nussinov,et al.  Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region* , 2015, The Journal of Biological Chemistry.

[4]  R. Nussinov,et al.  The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation? , 2014, Physical chemistry chemical physics : PCCP.

[5]  M. Rodnina,et al.  Thermodynamics of the GTP-GDP-operated Conformational Switch of Selenocysteine-specific Translation Factor SelB* , 2012, The Journal of Biological Chemistry.

[6]  R. Nussinov,et al.  Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM , 2011, Nature Protocols.

[7]  Ozlem Keskin,et al.  Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces , 2005, Bioinform..

[8]  Joseph Avruch,et al.  A dimeric 14-3-3 protein is an essential cofactor for Raf kinase activity , 1998, Nature.

[9]  M. Therrien,et al.  Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization , 2013, Nature chemical biology.

[10]  R. Nussinov,et al.  Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. , 2012, Journal of proteome research.

[11]  R. Nussinov,et al.  Principles of protein-protein interactions: what are the preferred ways for proteins to interact? , 2008, Chemical reviews.

[12]  Ozlem Keskin,et al.  Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. , 2012, Journal of structural biology.

[13]  H. Wolfson,et al.  Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. , 1996, Critical reviews in biochemistry and molecular biology.

[14]  Wan-Chen Lin,et al.  H-Ras forms dimers on membrane surfaces via a protein–protein interface , 2014, Proceedings of the National Academy of Sciences.

[15]  Herbert Waldmann,et al.  N-Ras forms dimers at POPC membranes. , 2012, Biophysical journal.

[16]  Ozlem Keskin,et al.  PRISM: protein interactions by structural matching , 2005, Nucleic Acids Res..

[17]  Joe W. Gray,et al.  Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling , 2013, Proceedings of the National Academy of Sciences.

[18]  A. Gorfe,et al.  Ras membrane orientation and nanodomain localization generate isoform diversity , 2010, Proceedings of the National Academy of Sciences.

[19]  Julian Downward,et al.  RAS Interaction with PI3K: More Than Just Another Effector Pathway. , 2011, Genes & cancer.

[20]  W. Kolch Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions. , 2000, The Biochemical journal.

[21]  R. Nussinov,et al.  Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. , 2015, Structure.

[22]  Dieter Braun,et al.  Molecular interaction studies using microscale thermophoresis. , 2011, Assay and drug development technologies.

[23]  K. Inouye,et al.  Formation of the Ras Dimer Is Essential for Raf-1 Activation* , 2000, The Journal of Biological Chemistry.

[24]  D. Mittar,et al.  Nitric oxide activates Rap1 and Ral in a Ras-independent manner. , 2004, Biochemical and biophysical research communications.

[25]  V. Gaponenko,et al.  Expression, purification, and characterization of soluble K-Ras4B for structural analysis. , 2010, Protein expression and purification.

[26]  V. Gaponenko,et al.  Application of Reductive 13C-Methylation of Lysines to Enhance the Sensitivity of Conventional NMR Methods , 2013, Molecules.

[27]  Ruth Nussinov,et al.  The spatial structure of cell signaling systems , 2013, Physical biology.

[28]  Ozlem Keskin,et al.  Fast and accurate modeling of protein–protein interactions by combining template‐interface‐based docking with flexible refinement , 2012, Proteins.

[29]  H. Wolfson,et al.  FiberDock: Flexible induced‐fit backbone refinement in molecular docking , 2010, Proteins.

[30]  Robert A. Weinberg,et al.  Ras oncogenes: split personalities , 2008, Nature Reviews Molecular Cell Biology.

[31]  Ozlem Keskin,et al.  HotPoint: hot spot prediction server for protein interfaces , 2010, Nucleic Acids Res..

[32]  Alma L. Burlingame,et al.  A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK , 2011, Nature.

[33]  F. Sarkar,et al.  A molecular rheostat at the interface of cancer and diabetes. , 2013, Biochimica et biophysica acta.

[34]  S. Gabriel,et al.  Discovery and saturation analysis of cancer genes across 21 tumor types , 2014, Nature.

[35]  C. Der,et al.  Signaling Interplay in Ras Superfamily Function , 2005, Current Biology.

[36]  B. Spencer‐Dene,et al.  Requirement for Interaction of PI3-Kinase p110α with RAS in Lung Tumor Maintenance , 2013, Cancer cell.

[37]  Robert G Parton,et al.  H-ras, K-ras, and inner plasma membrane raft proteins operate in nanoclusters with differential dependence on the actin cytoskeleton , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  C. Marshall,et al.  A polybasic domain or palmitoylation is required in addition to the CAAX motif to localize p21 ras to the plasma membrane , 1990, Cell.

[39]  D. Morrison,et al.  The importance of Raf dimerization in cell signaling , 2013, Small GTPases.

[40]  Channing J Der,et al.  Renewing the conspiracy theory debate: does Raf function alone to mediate Ras oncogenesis? , 2004, Trends in cell biology.

[41]  D. Esposito,et al.  Dragging ras back in the ring. , 2014, Cancer cell.

[42]  Eugenio Santos,et al.  Dimerization Opens New Avenues into Ras Signaling Research , 2014, Science Signaling.

[43]  Marc Therrien,et al.  A dimerization-dependent mechanism drives RAF catalytic activation , 2009, Nature.

[44]  G. Montelione,et al.  (19)F NMR reveals multiple conformations at the dimer interface of the nonstructural protein 1 effector domain from influenza A virus. , 2014, Structure.

[45]  David S. Goodsell,et al.  The RCSB Protein Data Bank: views of structural biology for basic and applied research and education , 2014, Nucleic Acids Res..

[46]  Hans Robert Kalbitzer,et al.  Conformational States of Human Rat Sarcoma (Ras) Protein Complexed with Its Natural Ligand GTP and Their Role for Effector Interaction and GTP Hydrolysis* , 2010, The Journal of Biological Chemistry.

[47]  A. Kusumi,et al.  Raf Inhibitors Target Ras Spatiotemporal Dynamics , 2012, Current Biology.

[48]  P. W. Janes,et al.  Architecture of Eph receptor clusters , 2010, Proceedings of the National Academy of Sciences.

[49]  Adam Srebniak,et al.  Protein interface classification by evolutionary analysis , 2012, BMC Bioinformatics.

[50]  Carla Mattos,et al.  A comprehensive survey of Ras mutations in cancer. , 2012, Cancer research.

[51]  Helen Thompson,et al.  US National Cancer Institute's new Ras project targets an old foe , 2013, Nature Medicine.

[52]  Ruth Nussinov,et al.  A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery. , 2013, Biochimica et biophysica acta.