Molecular Simulation Studies of the Insulin Receptor Family
Harish Vashisth
Advisor: Dr. Cameron Abrams
Molecular simulations of the ligands and receptors of the insulin family were
conducted. First, phenol dissociation mechanisms in the pharmaceutical storage form of
insulin, R6 insulin hexamer, are studied using random acceleration molecular dynamics
(RAMD) simulations. Three major escape pathways for phenols are observed. Several
residues that directly participate in escape events serve to resolve ambiguities from
previous NMR experiments. Potentials of mean force (PMFs) along the reaction
coordinate for each pathway are further resolved using steered molecular dynamics
(SMD) simulations. The results for binding free energy, ΔF, agree reasonably well within
the range of known experimental and previous simulation magnitudes of this quantity.
Structural analysis and energetic barriers for each pathway suggest a plausible
preferred mechanism of phenolic exchange that differs from previous mechanisms, but
is consistent with RAMD results. Several weakly-bound metastable states, supported by
experimental evidence, are also observed. These results give detailed insights into the
dissolution kinetics of insulin hexamers.
Next, the flexibility mechanisms of the ectodomains of the insulin receptor (IR)
and the type-1 insulin-like growth factor receptor (IGF1R) are studied. Both receptors
are served to display asymmetric mechanisms of flexibility due to interdomain and
intersubunit conformational fluctuations that do not alter their quaternary structures.
Subtle variations in intersubunit buried surface areas of both receptors are observed to
coincide well with these conformational fluctuations, resulting in one easily-accessible
ligand binding pocket with the other blocked. Further, Monte Carlo (MC) docking
simulations are used to construct all-atom structural models of the ligand/receptor
complexes which are consistent with a variety of known experimental data, and provide
detailed structural bases for ligand-recognition in the IR family.
Finally, a large-scale conformational change in the activation-loop (A-loop) of the
insulin receptor kinase domain (IRKD) is studied using temperature-accelerated
molecular dynamics (TAMD). The A-loop is observed to form a transient three-turn
helical conformation during TAMD, which facilitates the conserved DFG-motif (D1150,
F1151, and G1152) to switch from a “D-out/F-in” to “D-in/F-out” conformation, thereby
burying F1151 underneath αC-helix, and simultaneously presenting D1150 for ATP binding.
These transient helical conformations of the A-loop have been observed in the crystal
structures of related kinase families, and may be useful for the design of novel inhibitors
targeting IRKD.