Replica-exchange molecular dynamics simulations for a small-sized protein folding with implicit solvent

The free energy landscape of a small-sized designed protein, constructed by 28 amino acid residues, was studied with a replica-exchange molecular dynamics simulation. Solvation was taken into account by using implicit Generalized Born/surface area model. In the simulation, it is found that there is an energy local and global minimum on the free energy surface at 274 K. The sampled structure of the global minimum was very similar to the native structure, but the beta-sheet was not formed. In the sampled structure of the local minimum, only a native-like alpha-helix was formed, but the beta-sheet region of the native structure was fully destroyed. The remarkable difference between the structure of the global and local minimum was hydrophobic packing (alpha-helix/beta-sheet packing), which caused an energy barrier between the global and local minimum on the free energy landscape. (C) 2003 Elsevier B.V. All rights reserved.