KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation

The first step of RAF activation involves binding to active RAS, resulting in the recruitment of RAF to the plasma membrane. To understand the molecular details of RAS-RAF interaction, we present crystal structures of wild-type and oncogenic mutants of KRAS complexed with the RAS-binding domain (RBD) and the membrane-interacting cysteine-rich domain (CRD) from the N-terminal regulatory region of RAF1. Our structures reveal that RBD and CRD interact with each other to form one structural entity in which both RBD and CRD interact extensively with KRAS. Mutations at the KRAS-CRD interface result in a significant reduction in RAF1 activation despite only a modest decrease in binding affinity. Combining our structures and published data, we provide a model of RAS-RAF complexation at the membrane, and molecular insights into RAS-RAF interaction during the process of RAS-mediated RAF activation. The molecular details of the RAS-RAF interaction are still not fully understood. Here, the authors present crystal structures of wild-type and mutant KRAS in complex with the RAS-binding and membrane-interacting cysteine-rich domains of RAF1, and propose a model of the membrane-bound RAS-RAF complex.

[1]  M. Ikura,et al.  Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane , 2020, Proceedings of the National Academy of Sciences.

[2]  J. Hartley,et al.  The Frequency of Ras Mutations in Cancer , 2020, Cancer Research.

[3]  M. Holderfield,et al.  Homogeneous Dual-Parametric-Coupled Assay for Simultaneous Nucleotide Exchange and KRAS/RAF-RBD Interaction Monitoring , 2020, Analytical chemistry.

[4]  S. Malek,et al.  Negative regulation of RAF kinase activity by ATP is overcome by 14-3-3-induced dimerization , 2020, Nature Structural & Molecular Biology.

[5]  A. Garcia,et al.  The plasma membrane as a competitive inhibitor and positive allosteric modulator of KRas4B signaling , 2019, bioRxiv.

[6]  S. Ficarro,et al.  Architecture of autoinhibited and active BRAF/MEK1/14-3-3 complexes , 2019, Nature.

[7]  S. Subramaniam,et al.  Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases , 2019, Science.

[8]  P. Alexander,et al.  Structures of N-terminally processed KRAS provide insight into the role of N-acetylation , 2019, Scientific Reports.

[9]  D. Fletcher,et al.  Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane , 2018, The Journal of Biological Chemistry.

[10]  W. Jahnke,et al.  Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site. , 2018, Cell chemical biology.

[11]  F. McCormick,et al.  SHOC2–MRAS–PP1 complex positively regulates RAF activity and contributes to Noonan syndrome pathogenesis , 2018, Proceedings of the National Academy of Sciences.

[12]  Timothy Travers,et al.  Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain , 2018, Scientific Reports.

[13]  Ruth Nussinov,et al.  Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling. , 2018, Structure.

[14]  Mohammad Reza Ahmadian,et al.  The RAS-Effector Interface: Isoform-Specific Differences in the Effector Binding Regions , 2016, PloS one.

[15]  K. Shokat,et al.  Direct small-molecule inhibitors of KRAS: from structural insights to mechanism-based design , 2016, Nature Reviews Drug Discovery.

[16]  Priyanka Prakash,et al.  Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis. , 2016, Biophysical journal.

[17]  Mitsuhiko Ikura,et al.  Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site , 2015, Proceedings of the National Academy of Sciences.

[18]  M. Therrien,et al.  Regulation of RAF protein kinases in ERK signalling , 2015, Nature Reviews Molecular Cell Biology.

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

[20]  Ariana Peck,et al.  Structure of the BRAF-MEK complex reveals a kinase activity independent role for BRAF in MAPK signaling. , 2014, Cancer cell.

[21]  Xavier Robert,et al.  Deciphering key features in protein structures with the new ENDscript server , 2014, Nucleic Acids Res..

[22]  Piotr Sliz,et al.  Collaboration gets the most out of software , 2013, eLife.

[23]  Susan S. Taylor,et al.  Allosteric Activation of Functionally Asymmetric RAF Kinase Dimers , 2013, Cell.

[24]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[25]  M. Digilio,et al.  Germline BRAF mutations in Noonan, LEOPARD, and cardiofaciocutaneous syndromes: Molecular diversity and associated phenotypic spectrum , 2009, Human mutation.

[26]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[27]  W. Kolch,et al.  Regulation and Role of Raf-1/B-Raf Heterodimerization , 2006, Molecular and Cellular Biology.

[28]  R. Thapar,et al.  NMR characterization of full-length farnesylated and non-farnesylated H-Ras and its implications for Raf activation. , 2004, Journal of molecular biology.

[29]  Richard Marais,et al.  The RAF proteins take centre stage , 2004, Nature Reviews Molecular Cell Biology.

[30]  F. McCormick,et al.  Signaling Specificity by Ras Family GTPases Is Determined by the Full Spectrum of Effectors They Regulate , 2004, Molecular and Cellular Biology.

[31]  Péter Várnai,et al.  Structural determinants of Ras-Raf interaction analyzed in live cells. , 2002, Molecular biology of the cell.

[32]  U. Rapp,et al.  Active Ras induces heterodimerization of cRaf and BRaf. , 2001, Cancer research.

[33]  C. Der,et al.  Elucidation of Binding Determinants and Functional Consequences of Ras/Raf-Cysteine-rich Domain Interactions* , 2000, The Journal of Biological Chemistry.

[34]  T. Kataoka,et al.  The Strength of Interaction at the Raf Cysteine-Rich Domain Is a Critical Determinant of Response of Raf to Ras Family Small GTPases , 1999, Molecular and Cellular Biology.

[35]  R. Bell,et al.  Mutational analysis of Raf-1 cysteine rich domain: Requirement for a cluster of basic aminoacids for interaction with phosphatidylserine , 1999, Molecular and Cellular Biochemistry.

[36]  A. Wittinghofer,et al.  The RafC1 Cysteine-Rich Domain Contains Multiple Distinct Regulatory Epitopes Which Control Ras-Dependent Raf Activation , 1998, Molecular and Cellular Biology.

[37]  P. Graves,et al.  14-3-3 Proteins Are Required for Maintenance of Raf-1 Phosphorylation and Kinase Activity , 1998, Molecular and Cellular Biology.

[38]  R. Stephens,et al.  Autoregulation of the Raf-1 serine/threonine kinase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Sandrine Roy,et al.  Activity of Plasma Membrane-recruited Raf-1 Is Regulated by Ras via the Raf Zinc Finger* , 1997, The Journal of Biological Chemistry.

[40]  H. Mott,et al.  The solution structure of the Raf-1 cysteine-rich domain: a novel ras and phospholipid binding site. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Ralf Janknecht,et al.  Ras/Rap effector specificity determined by charge reversal , 1996, Nature Structural Biology.

[42]  A. Wittinghofer,et al.  Quantitative structure-activity analysis correlating Ras/Raf interaction in vitro to Raf activation in vivo , 1996, Nature Structural Biology.

[43]  M. White,et al.  Ras Interaction with Two Distinct Binding Domains in Raf-1 5 Be Required for Ras Transformation (*) , 1996, The Journal of Biological Chemistry.

[44]  S. Yokoyama,et al.  Cysteine-rich Region of Raf-1 Interacts with Activator Domain of Post-translationally Modified Ha-Ras (*) , 1995, The Journal of Biological Chemistry.

[45]  C. Der,et al.  Two Distinct Raf Domains Mediate Interaction with Ras (*) , 1995, The Journal of Biological Chemistry.

[46]  W. Xie,et al.  The cysteine-rich region of raf-1 kinase contains zinc, translocates to liposomes, and is adjacent to a segment that binds GTP-ras. , 1994, The Journal of biological chemistry.

[47]  D. Morrison,et al.  Ras-Mediated Activation of the Raf Family Kinases. , 2019, Cold Spring Harbor perspectives in medicine.

[48]  D. Esposito,et al.  Optimizing Expression and Solubility of Proteins in E. coli Using Modified Media and Induction Parameters. , 2017, Methods in molecular biology.

[49]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[50]  Dominic Esposito,et al.  Gateway cloning for protein expression. , 2009, Methods in molecular biology.

[51]  Vincent B. Chen,et al.  Acta Crystallographica Section D Biological , 2001 .