A Model of a MAPK•Substrate Complex in an Active Conformation: A Computational and Experimental Approach

Sunbae Lee is with UT Austin; Mangalika Warthaka is with UT Austin; Tamer S. Kaoud is with UT Austin; Kevin N. Dalby is with UT Austin; Chunli Yan is with UT Austin; Pengyu Ren is with UT Austin; Andrea Piserchio is with the City College of New York; Ranajeet Ghose is with the City College of New York.The mechanisms by which MAP kinases recognize and phosphorylate substrates are not completely understood. Efforts to understand the mechanisms have been compromised by the lack of MAPK-substrate structures. While MAPK-substrate docking is well established as a viable mechanism for bringing MAPKs and substrates into close proximity the molecular details of how such docking promotes phosphorylation is an unresolved issue. In the present study computer modeling approaches, with restraints derived from experimentally known interactions, were used to predict how the N-terminus of Ets-1 associates with ERK2. Interestingly, the N-terminus does not contain a consensus-docking site ((R/K)2-3-X2-6-ΦA-X-ΦB, where Φ is aliphatic hydrophobic) for ERK2. The modeling predicts that the N-terminus of Ets-1 makes important contributions to the stabilization of the complex, but remains largely disordered. The computer-generated model was used to guide mutagenesis experiments, which support the notion that Leu-11 and possibly Ile-13 and Ile-14 of Ets-1 1-138 (Ets) make contributions through binding to the hydrophobic groove of the ERK2 D-recruiting site (DRS). Based on the modeling, a consensus-docking site was introduced through the introduction of an arginine at residue 7, to give the consensus 7RK-X2-ΦA-X-ΦB13. This results in a 2-fold increase in kcat/Kmfor the phosphorylation of Ets by ERK2. Similarly, the substitution of the N-terminus for two different consensus docking sites derived from Elk-1 and MKK1 also improves kcat/Km by two-fold compared to Ets. Disruption of the N-terminal docking through deletion of residues 1-23 ofEts results in a 14-fold decrease in kcat/Km, with little apparent change in kcat. A peptide that binds to the DRS of ERK2 affects Km, but not kcat. Our kinetic analysis suggests that the unstructured N-terminus provides 10-fold uniform stabilization of the ground state ERK2•Ets•MgATP complex and intermediates of the enzymatic reaction.Financial support was from grants from the National Institute of General Medical Sciences to KND (R01GM059802) 2) to PR (R01 GM079686) and to RG (R01 GM084278). The Welch Foundation also supported KND (F-1390). Computing resources were provided by TeraGrid (MCB100057). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biomedical Engineerin