Parallel Computing and Protein Design

The possibility that the free energy landscape of proteins is multi-funnel shaped is tested by comparing the thermodynamic stability of non-native structures of four proteins with that of their corresponding native structures. Different cluster architectures were tried to maximize the speed of molecular dynamics simulations with AMBER. Intra- and inter-trajectory root mean square deviations between conformations sampled in the last 25 nanoseconds of 50 nanoseconds simulations indicate that the non-native structures are as thermodynamically stable as the respective native conformations. If confirmed by longer simulations, these results imply that, contrary to the thermodynamics hypothesis, the native structures are not the global free energy minimum of the protein amino acid sequences. The implication is that protein folding is a kinetic process, something that has important consequences in protocols for protein folding and protein design.