Paper Citing NAMD - Abstract
Vashisth, Harish; Maragliano, Luca; Abrams, Cameron F.
"DFG-Flip" in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop
BIOPHYSICAL JOURNAL, 102:1979-1987, APR 18 2012
We have characterized a large-scale inactive-to-active conformational change in the activation-loop of the insulin receptor kinase domain at the atomistic level via untargeted temperature-accelerated molecular dynamics (TAMD) and free-energy calculations using the string method. TAMD simulations consistently show folding of the A-loop into a helical conformation followed by unfolding to an active conformation, causing the highly conserved DFG-motif (Asp(1150), Phe(1151), and Gly(1152)) to switch from the inactive "D-out/F-in" to the nucleotide-binding-competent "D-in/F-out" conformation. The minimum free-energy path computed from the string method preserves these helical intermediates along the inactive-to-active path, and the thermodynamic free-energy differences are consistent with previous work on various other kinases. The mechanisms revealed by TAMD also suggest that the regulatory spine can be dynamically assembled/disassembled either by DFG-flip or by movement of the alpha C-helix. Together, these findings both broaden our understanding of kinase activation and point to intermediates as specific therapeutic targets.
