Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability
| Autor: | Anastasia Theodoropoulou, Camilo Velez-Vega, Ioannis Andreadelis, Zoe Cournia, Sofia Kiriakidi, José S. Duca, John I. Manchester, Christos Lamprakis, Stefan Doerr, Alexios Chatzigoulas |
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| Rok vydání: | 2021 |
| Předmět: |
Cell signaling
education.field_of_study Dimer Population Molecular Conformation GTPase Molecular Dynamics Simulation Lipids Surfaces Coatings and Films Proto-Oncogene Proteins p21(ras) Cell membrane chemistry.chemical_compound Molecular dynamics Membrane medicine.anatomical_structure chemistry Mole Materials Chemistry ras Proteins Biophysics medicine lipids (amino acids peptides and proteins) Physical and Theoretical Chemistry education Protein Binding |
| DOI: | 10.26434/chemrxiv-2021-4pdzb |
| Popis: | Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the properties of Ras in terms of dimerization/clustering on the cell membrane. To understand the effects of anionic lipids on key spatiotemporal properties of dimeric K-Ras4B, we perform all-atom molecular dynamics simulations of the dimer K-Ras4B in the presence and absence of Raf[RBD/CRD] effectors on two model anionic lipid membranes: one containing 78% mol DOPC, 20% mol DOPS, and 2% mol PIP2 and another one with enhanced concentration of anionic lipids containing 50% mol DOPC, 40% mol DOPS, and 10% mol PIP2. Analysis of our results unveils the orientational space of dimeric K-Ras4B and shows that the stability of the dimer is enhanced on the membrane containing a high concentration of anionic lipids in the absence of Raf effectors. This enhanced stability is also observed in the presence of Raf[RBD/CRD] effectors although it is not influenced by the concentration of anionic lipids in the membrane, but rather on the ability of Raf[CRD] to anchor to the membrane. We generate dominant K-Ras4B conformations by Markov state modeling and yield the population of states according to the K-Ras4B orientation on the membrane. For the membrane containing anionic lipids, we observe correlations between the diffusion of K-Ras4B and PIP2 and anchoring of anionic lipids to the Raf[CRD] domain. We conclude that the presence of effectors with the Raf[CRD] domain anchoring on the membrane as well as the membrane composition both influence the conformational stability of the K-Ras4B dimer, enabling the preservation of crucial interface interactions. |
| Databáze: | OpenAIRE |
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