PXD054924-1

PXD054924 is an original dataset announced via ProteomeXchange.

Title	Dynamic conformational equilibria in the active states of KRas and NRas
Description	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.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_00:41:29.821.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thomas Wales
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-15 02:52:50	ID requested
⏵ 1	2025-05-07 00:41:30	announced

Rennella E, Henry C, Dickson CJ, Georgescauld F, Wales TE, Erdmann D, Cotesta S, Maira M, Sedrani R, Brachmann SM, Ostermann N, Engen JR, Kay LE, Beyer KS, Wilcken R, Jahnke W, Dynamic conformational equilibria in the active states of KRAS and NRAS. RSC Chem Biol, 6(1):106-118(2025) [pubmed]

10.1039/d4cb00233d;

submitter keyword: RAS inhibitors

NRAS

KRAS

HDX-MS

hydrogen/deuterium exchange mass spectrometry

oncogenic mutants

Thomas E. Wales
contact affiliation	Northeastern University
contact email	t.wales@northeastern.edu
lab head
Thomas Wales
contact affiliation	Northeastern University
contact email	t.wales@northeastern.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054924
     1. Label: PRIDE project
     2. Name: Dynamic conformational equilibria in the active states of KRas and NRas