Millisecond molecular dynamics simulations of KRas-dimer formation and interfaces

Area of Science:

• Molecular Biology
• Biophysics
• Cellular Signaling

Background:

• Ras dimers are proposed initiators of the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) pathway.
• Understanding Ras dimer structure and dynamics is key to deciphering upstream signaling events.

Purpose of the Study:

• To investigate the structural dynamics of KRas4b dimerization on a lipid membrane.
• To explore the potential signaling consequences of KRas4b dimer formation.

Main Methods:

• Performed 1 ms all-atom molecular dynamics simulations of two full-length, farnesylated, GTP-bound KRas4b proteins.
• Simulations utilized a mixed 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane model.

Main Results:

• Unveiled an ensemble of thermodynamically weak KRas dimers with diverse conformations.
• Identified stable dimer conformations involving helix α2 and the hypervariable region (HVR), with HVR mediating interactions.
• Observed dimer configurations positioning one KRas G-domain above another, potentially aiding Raf kinase recruitment.
• Found an α4-α5 KRas dimer interface variant similar to HRas FRET data.
• Discovered arginine fingers (R68, R149) interacting with GTP, mimicking GAP-HRas complex interactions and potentially facilitating GTP hydrolysis.

Conclusions:

• KRas4b forms multiple weak dimer conformations on membranes, with specific interfaces involving helix α2 and HVR.
• The HVR plays a significant role in mediating KRas dimerization.
• Observed dimer structures suggest mechanisms for recruiting downstream signaling partners like Raf kinases.
• Identified GTP-binding site interactions that may influence GTP hydrolysis, akin to GAP regulation.