Multiscale Coarse-Graining of the Protein Energy Landscape
Figure 2
Pairwise interaction potential between nonbonded backbone alpha carbons generated from atomistic force matching.
Unfolding (498 K) simulations of Trpzip (red), Leu15 (green) and Ala15 (blue) as well as 300 K MD of Ala15 (pink) yield attractive potentials that share a minimum at ∼0.6 nm. Inset (same xy scale): Correspondence in the interaction potentials between apolar sidechain sites for Trpzip (red) and a dipeptide solution of the 20 amino acids (black).