1. A comprehensive analysis of RAS-effector interactions reveals interaction hotspots and new binding partners
- Author
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Christoph Wittich, Claus A. M. Seidel, Radovan Dvorsky, Soheila Rezaei Adariani, Farhad Bazgir, Ehsan Amin, Mohammad Reza Ahmadian, and Neda S. Kazemein Jasemi
- Subjects
0301 basic medicine ,RIT, RAS-like protein expressed in many tissues ,GTPase-activating protein ,HRAS, Harvey rat sarcoma ,GTPase ,RALA, RAS-like protein A ,RASD, dexamethasone-induced RAS-related ,Biochemistry ,protein interactions ,RA, RAS association domain ,RB, RAS-binding domain ,NORE-1 ,GAP, GTPase-activating protein ,ERK, extracellular signal-regulated kinase ,GTP, guanosine triphosphate ,GTPase, guanosine triphosphatase ,RASSF, RAS association domain family ,RAF, rapidly accelerated fibrosarcoma ,biology ,PLCε, phospholipase C epsilon ,RAS association domain ,HK1, hexokinase-1 ,RIN, RAS and RAB interactor ,CR domain, cysteine-rich domain ,RALA ,TIAM, T-lymphoma invasion and metastasis protein ,RERGL, RAS-related and estrogen-regulated growth inhibitor-like protein ,RHEB, RAS homologous enriched in brain ,RAP, RAS proximate ,Guanine nucleotide exchange factor ,PI3K, phosphoinositide 3-kinase ,RHEB ,Research Article ,effectors ,Protein Binding ,Signal Transduction ,SHANK, SH3 and multiple ankyrin repeat domain ,RHO, RAS homologous ,RGS, regulator of G protein signaling ,AF6, ALL1-fused gene from chromosome 6 ,Computational biology ,PDZGEF, PDZ-domain-containing guanine nucleotide exchange factor ,Protein–protein interaction ,GEF, guanine nucleotide exchange factor ,03 medical and health sciences ,Regulator of G protein signaling ,RRAS, RAS-related protein ,NKIRAS, NF-kappa-B inhibitor-interacting RAS-like protein ,NRAS, neuroblastoma RAS ,PKC, protein kinase C ,RAS, rat sarcoma ,RERG, RAS-related and estrogen-regulated growth inhibitor ,Humans ,Protein Interaction Domains and Motifs ,HRAS ,SIN1, stress-activated protein kinase-interacting protein 1 ,Molecular Biology ,RALGDS, RAL guanine nucleotide dissociation stimulator ,KRAS, Kristen rat sarcoma ,030102 biochemistry & molecular biology ,SARAH, Salvador–RASSF–Hippo domain ,Tumor Suppressor Proteins ,Computational Biology ,Cell Biology ,NORE1, novel RAS effector ,RAS-binding domain ,030104 developmental biology ,HEK293 Cells ,MBP, maltose binding protein ,RGL, RAL guanine nucleotide dissociation stimulator-like ,MEK, MAPK/ERK kinase ,biology.protein ,ras Proteins ,RASSF5 ,SNX17, sorting nexin-17 ,RASSF1 ,Apoptosis Regulatory Proteins ,RASSF ,MAPK, mitogen-activated protein kinase ,RAS - Abstract
RAS effectors specifically interact with GTP-bound RAS proteins to link extracellular signals to downstream signaling pathways. These interactions rely on two types of domains, called RAS-binding (RB) and RAS association (RA) domains, which share common structural characteristics. Although the molecular nature of RAS-effector interactions is well-studied for some proteins, most of the RA/RB-domain-containing proteins remain largely uncharacterized. Here, we searched through human proteome databases, extracting 41 RA domains in 39 proteins and 16 RB domains in 14 proteins, each of which can specifically select at least one of the 25 members in the RAS family. We next comprehensively investigated the sequence–structure–function relationship between different representatives of the RAS family, including HRAS, RRAS, RALA, RAP1B, RAP2A, RHEB1, and RIT1, with all members of RA domain family proteins (RASSFs) and the RB-domain-containing CRAF. The binding affinity for RAS-effector interactions, determined using fluorescence polarization, broadly ranged between high (0.3 μM) and very low (500 μM) affinities, raising interesting questions about the consequence of these variable binding affinities in the regulation of signaling events. Sequence and structural alignments pointed to two interaction hotspots in the RA/RB domains, consisting of an average of 19 RAS-binding residues. Moreover, we found novel interactions between RRAS1, RIT1, and RALA and RASSF7, RASSF9, and RASSF1, respectively, which were systematically explored in sequence–structure–property relationship analysis, and validated by mutational analysis. These data provide a set of distinct functional properties and putative biological roles that should now be investigated in the cellular context.
- Published
- 2021