Paper Citing NAMD - Abstract
Ponmurugan, M.; Vemparala, Satyavani
Studies on structural and average unfolding behaviours of FNIII domain of Contactin-1 protein by molecular dynamics simulation
FRONTIERS IN LIFE SCIENCE, 6:33-45, JUN 1 2012
Steered molecular dynamics (SMD) simulations are routinely used for unraveling folded domains of proteins to reveal intermediate structures and to compute associated forces and free energies. Using the example of a neuronal adhesion protein, Contactin, we discuss the effect of pulling velocities on unfolding forces and suggest a work-velocity scaling relation, which may give an estimate of the non-equilibrium nature of SMD simulations performed in complex environments. Implications of the existence of such a scaling relation and validity of Jarzynski's equality in the context of fast unfolding velocities are also discussed. Multiple unfolding pathways and protein intermediates along these pathways have been identified.
