Brenner, Robert J.Landgraf, Alexander D.Bum-Erdene, KhuchtumurGonzalez-Gutierrez, GiovanniMeroueh, Samy O.2024-06-112024-06-112023Brenner RJ, Landgraf AD, Bum-Erdene K, Gonzalez-Gutierrez G, Meroueh SO. Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling. Biochemistry. 2023;62(22):3206-3213. doi:10.1021/acs.biochem.3c00378https://hdl.handle.net/1805/41405KRAS GTPases harbor oncogenic mutations in more than 25% of human tumors. KRAS is considered to be largely undruggable due to the lack of a suitable small-molecule binding site. Here, we report a unique crystal structure of His-tagged KRASG12D that reveals a remarkable conformational change. The Switch I loop of one His-KRASG12D structure extends into the Switch I/II pocket of another His-KRASG12D in an adjacent unit cell to create an elaborate interface that is reminiscent of high-affinity protein-protein complexes. We explore the contributions of amino acids at this interface using alanine-scanning studies with alchemical free energy perturbation calculations based on explicit-solvent molecular dynamics simulations. Several interface amino acids were found to be hot spots as they contributed more than 1.5 kcal/mol to the protein-protein interaction. Computational analysis of the complex revealed the presence of two large binding pockets that possess physicochemical features typically found in pockets considered druggable. Small-molecule binding to these pockets may stabilize this autoinhibited structure of KRAS if it exists in cells to provide a new strategy to inhibit RAS signaling.en-USPublisher PolicyAmino acidsMolecular dynamics simulationMutationProtein bindingSignal transductionArticle