GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation
Oncogenic Ras proteins are known to present multiple conformational states, as reported by the great variety of crystallographic structures. The GTP-bound states are grouped into two main states: the “inactive” state 1 and the “active” state 2. Recent reports on H-Ras have shown that state 2 exhibit...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-01-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/25/3/1430 |
| _version_ | 1797318740748009472 |
|---|---|
| author | Alexandra Farcas Lorant Janosi |
| author_facet | Alexandra Farcas Lorant Janosi |
| author_sort | Alexandra Farcas |
| collection | DOAJ |
| description | Oncogenic Ras proteins are known to present multiple conformational states, as reported by the great variety of crystallographic structures. The GTP-bound states are grouped into two main states: the “inactive” state 1 and the “active” state 2. Recent reports on H-Ras have shown that state 2 exhibits two substates, directly related to the orientation of Tyr32: toward the GTP-bound pocket and outwards. In this paper, we show that N-Ras exhibits another substate of state 2, related to a third orientation of Tyr32, toward Ala18 and parallel to the GTP-bound pocket. We also show that this substate is highly sampled in the G12V mutation of N-Ras and barely present in its wild-type form, and that the G12V mutation prohibits the sampling of the GTPase-activating protein (GAP) binding substate, rendering this mutation oncogenic. Furthermore, using molecular dynamics simulations, we explore the importance of the membrane on N-Ras’ conformational state dynamics and its strong influence on Ras protein stability. Moreover, the membrane has a significant influence on the conformational (sub)states sampling of Ras. This, in turn, is of crucial importance in the activation/deactivation cycle of Ras, due to the binding of guanine nucleotide exchange factor proteins (GEFs)/GTPase-activating proteins (GAPs). |
| first_indexed | 2024-03-08T03:56:44Z |
| format | Article |
| id | doaj.art-79c43de3669447a4b32ced18ee2c61ee |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T03:56:44Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-79c43de3669447a4b32ced18ee2c61ee2024-02-09T15:13:13ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-01-01253143010.3390/ijms25031430GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point MutationAlexandra Farcas0Lorant Janosi1Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat Street, 400293 Cluj-Napoca, RomaniaDepartment of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat Street, 400293 Cluj-Napoca, RomaniaOncogenic Ras proteins are known to present multiple conformational states, as reported by the great variety of crystallographic structures. The GTP-bound states are grouped into two main states: the “inactive” state 1 and the “active” state 2. Recent reports on H-Ras have shown that state 2 exhibits two substates, directly related to the orientation of Tyr32: toward the GTP-bound pocket and outwards. In this paper, we show that N-Ras exhibits another substate of state 2, related to a third orientation of Tyr32, toward Ala18 and parallel to the GTP-bound pocket. We also show that this substate is highly sampled in the G12V mutation of N-Ras and barely present in its wild-type form, and that the G12V mutation prohibits the sampling of the GTPase-activating protein (GAP) binding substate, rendering this mutation oncogenic. Furthermore, using molecular dynamics simulations, we explore the importance of the membrane on N-Ras’ conformational state dynamics and its strong influence on Ras protein stability. Moreover, the membrane has a significant influence on the conformational (sub)states sampling of Ras. This, in turn, is of crucial importance in the activation/deactivation cycle of Ras, due to the binding of guanine nucleotide exchange factor proteins (GEFs)/GTPase-activating proteins (GAPs).https://www.mdpi.com/1422-0067/25/3/1430molecular dynamicsRas proteinN-RasRas statesplasma membranelipid bilayer |
| spellingShingle | Alexandra Farcas Lorant Janosi GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation International Journal of Molecular Sciences molecular dynamics Ras protein N-Ras Ras states plasma membrane lipid bilayer |
| title | GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation |
| title_full | GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation |
| title_fullStr | GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation |
| title_full_unstemmed | GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation |
| title_short | GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation |
| title_sort | gtp bound n ras conformational states and substates are modulated by membrane and point mutation |
| topic | molecular dynamics Ras protein N-Ras Ras states plasma membrane lipid bilayer |
| url | https://www.mdpi.com/1422-0067/25/3/1430 |
| work_keys_str_mv | AT alexandrafarcas gtpboundnrasconformationalstatesandsubstatesaremodulatedbymembraneandpointmutation AT lorantjanosi gtpboundnrasconformationalstatesandsubstatesaremodulatedbymembraneandpointmutation |