Mechanosensing in Notch Figure 7. Structural properties of the HD domain with and without the LNR modules in atomistic simulations. a) The backbone RMSD as a function of the simulation time. Except for the full NRR, only 50-point running averages are plotted for clarity. b) The number of residues in a or b secondary structures as a function of time. c) The average structure of the HD domain calculated from the last 16 ns of the GBSW simulation of the full NRR (green). The X-ray structure (PDB: 3eto) is shown for comparison, where the HD domain is drawn in purple and the LNR modules in light gray. The backbone RMSD between the average and X-ray structures is 2.1 A˚ for the HD domain. d) The average structure of the HD domain computed from the last 16 ns of the GBSW simulation of the HD domain alone. The backbone RMSD from the X-ray structure is 2.4 A˚ . doi:10.1371/journal.pone.0022837.g007 Notch activation [21] proposes that the mechanical force exerted by ligand endocytosis is instrumental in relieving the auto- inhibited conformation and exposing the S2 site for cleavage [21]. However, direct biochemical or computational data supporting this model are missing. The current study explores for the first time the effects of mechanical force on the folding and unfolding mechanism of the human Notch1 NRR using computational approaches. Our topology-based coarse-grained modeling demonstrates that external force leads to sequential disengagement of the LNR modules from the HD domain. All these domains remain stably folded during this early stage of force induced-unfolding. Most Figure 8. Residue-residue map of correlated motions for the HD domain with and without the LNR modules. The maps were computed as the Ca-Ca covariance matrices, extracted from the last 16 ns of the 20-ns equilibrium GBSW simulations. The dashed boxes mark regions that illustrate weaker coupling of strand b5 to the rest of the HD domain. Approximate spans of the secondary structure elements are also marked. See the Fig. 2 caption for the residue ID mapping. doi:10.1371/journal.pone.0022837.g008 PLoS ONE | www.plosone.org 7 July 2011 | Volume 6 | Issue 7 | e22837