NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significance of the Mg2+ Ion

• Published in: International journal of molecular sciences Vol. 24; no. 15; p. 12101
• Main Authors: Gadanecz, Márton, Fazekas, Zsolt, Pálfy, Gyula, Karancsiné Menyhárd, Dóra, Perczel, András
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 28.07.2023; MDPI
• Subjects: Automation; Binding sites; KRAS; Libraries; ligand binding; molecular dynamics simulation; Mutation; NMR; NMR spectroscopy; Nuclear magnetic resonance; protein dynamics; protein structure determination; Proteins; Protocol; Signal transduction; Software; Spectrum analysis
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms241512101

In this work, catalytically significant states of the oncogenic G12C variant of KRAS, those of Mg2+-free and Mg2+-bound GDP-loaded forms, have been determined using CS-Rosetta software and NMR-data-driven molecular dynamics simulations. There are several Mg2+-bound G12C KRAS/GDP structures deposited in the Protein Data Bank (PDB), so this system was used as a reference, while the structure of the Mg2+-free but GDP-bound state of the RAS cycle has not been determined previously. Due to the high flexibility of the Switch-I and Switch-II regions, which also happen to be the catalytically most significant segments, only chemical shift information could be collected for the most important regions of both systems. CS-Rosetta was used to derive an “NMR ensemble” based on the measured chemical shifts, which, however, did not contain the nonprotein components of the complex. We developed a torsional restraint set for backbone torsions based on the CS-Rosetta ensembles for MD simulations, overriding the force-field-based parametrization in the presence of the reinserted cofactors. This protocol (csdMD) resulted in complete models for both systems that also retained the structural features and heterogeneity defined by the measured chemical shifts and allowed a detailed comparison of the Mg2+-bound and Mg2+-free states of G12C KRAS/GDP.