Sequence of events in folding mechanism: Beyond the Go model

Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same way so that the folding features of a protein are determined only by the geometry of its native conformation. We present an extended version of a C-alpha-based Go model where different residues interact with different energies. The model is used to calculate the thermodynamics of three small proteins (Protein G, Src-SH3, and CI2) and the effect of mutations (Delta Delta G(U-N), Delta Delta G(double dagger-N), Delta Delta G(double dagger-U), and phi-values) on the wild-type sequence. The model allows us to investigate some of the most controversial areas in protein folding, such as its earliest stages and the nature of the unfolded state, subjects that have lately received particular attention.