Molecular simulations find stable structures in fragments of protein G

We perform all-atom computer simulations on nearly one hundred 6-, 8-, 10-, and 12-mer peptide fragments of protein G, and look for stable states. We simulated by replica-exchange molecular dynamics using Amber7 with the parm96 force-field and a GB/SA (generalized-Born/solvent accessible) implicit solvent model. We find that useful diagnostics for identifying stable converged structures are the conformational entropy and free energy of each state. A large gap in the ground-state free-energy, and a low entropy indicate convergence to a single preferred peptide conformation. We find that a non-negligible fraction of such structures have some native-like character. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.