Dataset Information

Dynamic conformational equilibria in the active states of KRas and NRas

ABSTRACT: The design of potent RAS inhibitors benefits from a molecular understanding of the dynamics in KRAS and NRAS and their oncogenic mutants. Here we characterize switch-1 dynamics in GTP-state KRAS and NRAS by 31P NMR, by 15N relaxation dispersion NMR, hydrogen-deuterium exchange mass spectrometry (HDX-MS), and molecular dynamics simulations. In GMPPNP-bound KRAS and NRAS, we see the co-existence of two conformational states, corresponding to an “inactive” state-1 and an “active” state-2, as previously reported. The KRAS oncogenic mutations G12D, G12C and G12V only slightly affect this equilibrium towards the “inactive” state-1, with rank order wt < G12C < G12D < G12V. In contrast, the NRAS Q61R oncogenic mutation shifts the equilibrium fully towards the “active” state-2. Our molecular dynamics simulations explain this by the observation of a transient hydrogen bond between the Arg61 side chain and the Thr35 backbone carbonyl oxygen. NMR relaxation dispersion experiments with GTP-bound KRAS Q61R confirm a drastic decrease in the population of state-1, but still detect a small residual population (1.8%) of this conformer. HDX-MS indicates that higher populations of state-1 correspond to increased hydrogen-deuterium exchange rates in some regions and increased flexibility, whereas low state-1 populations are associated with KRAS rigidification. We elucidated the mechanism of action of a potent KRAS G12D inhibitor, MRTX1133. Binding of this inhibitor to the switch-2 pocket causes a complete shift of KRAS G12D towards the “inactive” conformation and prevents binding of effector RAS-binding domain (RBD), by signaling through an allosteric network.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Thomas Wales

LAB HEAD: Thomas E. Wales

PROVIDER: PXD054924 | Pride | 2025-05-07

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	1_WT_NRAS_GMPPNP_10m_04.raw.zip	Raw
	1_WT_NRAS_GMPPNP_10m_16.raw.zip	Raw
	1_WT_NRAS_GMPPNP_10m_20.raw.zip	Raw
	1_WT_NRAS_GMPPNP_10m_21.raw.zip	Raw
	1_WT_NRAS_GMPPNP_10s_02.raw.zip	Raw

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Dynamic conformational equilibria in the active states of KRAS and NRAS.

Rennella Enrico E Henry Chrystèle C Dickson Callum J CJ Georgescauld Florian F Wales Thomas E TE Erdmann Dirk D Cotesta Simona S Maira Michel M Sedrani Richard R Brachmann Saskia M SM Ostermann Nils N Engen John R JR Kay Lewis E LE Beyer Kim S KS Wilcken Rainer R Jahnke Wolfgang W

RSC chemical biology 20241125 1

The design of potent RAS inhibitors benefits from a molecular understanding of the dynamics in KRAS and NRAS and their oncogenic mutants. Here we characterize switch-1 dynamics in GTP-state KRAS and NRAS by <sup>31</sup>P NMR, by <sup>15</sup>N relaxation dispersion NMR, hydrogen-deuterium exchange mass spectrometry (HDX-MS), and molecular dynamics simulations. In GMPPNP-bound KRAS and NRAS, we see the co-existence of two conformational states, corresponding to an "inactive" state-1 and an "acti ...[more]

PMID: 39664928

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