Abstract
Ras dimers have been proposed as building blocks for initiating the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) cellular signaling pathway. To better examine the structure of possible dimer interfaces, the dynamics of Ras dimerization, and its potential signaling consequences, we performed molecular dynamics simulations totaling 1 ms of sampling, using an all-atom model of two full-length, farnesylated, guanosine triphosphate (GTP)-bound, wild-type KRas4b proteins diffusing on 29%POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine)-mixed POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Our simulations unveil an ensemble of thermodynamically weak KRas dimers spanning multiple conformations. The most stable conformations, having the largest interface areas, involve helix α2 and a hypervariable region (HVR). Among the dimer conformations, we found that the HVR of each KRas has frequent interactions with various parts of the dimer, thus potentially mediating the dimerization. Some dimer configurations have one KRas G-domain elevated above the lipid bilayer surface by residing on top of the other G-domain, thus likely contributing to the recruitment of cytosolic Raf kinases in the context of a stably formed multi-protein complex. We identified a variant of the α4-α5 KRas-dimer interface that is similar to the interfaces obtained with fluorescence resonance energy transfer (FRET) data of HRas on lipid bilayers. Interestingly, we found two arginine fingers, R68 and R149, that directly interact with the beta-phosphate of the GTP bound in KRas, in a manner similar to what is observed in a crystal structure of GAP-HRas complex, which can facilitate the GTP hydrolysis via the arginine finger of GTPase-activating protein (GAP).
| Original language | English |
|---|---|
| Pages (from-to) | 3730-3744 |
| Number of pages | 15 |
| Journal | Biophysical Journal |
| Volume | 121 |
| Issue number | 19 |
| DOIs | |
| State | Published - Oct 4 2022 |
Funding
V.A.N. was a director’s postdoctoral fellow at Los Alamos National Laboratory ( LANL ) and his work was fully supported by this fellowship ( 20170692PRD4 ), 2018–2021. V.A.N. acknowledges the Center for Nonlinear Studies for support, and Drs. Sumantra Sarkar and Chris Neale for their comments and suggestions on the manuscript. A.E.G. was partially supported by LDRD funds (projects XWJX and XX01 ). A.E.G. acknowledges discussions with the DOE/NCI Pilot 2 and Uncertainty Quantification teams. Computational resources were provided by the LANL Institutional Computing Program, which is supported by the US DOE National Nuclear Security Administration (NNSA) under contract no. DE-AC52-06NA25396 . V.A.N. was a director's postdoctoral fellow at Los Alamos National Laboratory (LANL) and his work was fully supported by this fellowship (20170692PRD4), 2018–2021. V.A.N. acknowledges the Center for Nonlinear Studies for support, and Drs. Sumantra Sarkar and Chris Neale for their comments and suggestions on the manuscript. A.E.G. was partially supported by LDRD funds (projects XWJX and XX01). A.E.G. acknowledges discussions with the DOE/NCI Pilot 2 and Uncertainty Quantification teams. Computational resources were provided by the LANL Institutional Computing Program, which is supported by the US DOE National Nuclear Security Administration (NNSA) under contract no. DE-AC52-06NA25396.