Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics

Molecular dynamics simulations were performed to unfold a homologous pair of thermophilic and mesophilic cold shock proteins at high temperatures. The two proteins differ in just 11 of 66 residues and have very similar structures with a closed five-stranded antiparallel beta-barrel. A long flexible loop connects the N-terminal side of the barrel, formed by three strands (beta 1-beta 3), with the C-terminal side, formed by two strands (beta 4-beta 5). The two proteins were found to follow the same unfolding pathway, but with the thermophilic protein showing much slower unfolding. Unfolding started with the melting of C-terminal strands, leading to exposure of the hydrophobic core. Subsequent melting of beta 3 and the beta-hairpin formed by the first two strands then resulted in unfolding of the whole protein. The slower unfolding of the thermophilic protein could be attributed to ion pair formation of Arg-3 with Glu-46, Glu-21, and the C-terminal. These ion pairs were also found to be important for the difference in folding stability between the pair of proteins. Thus electrostatic interactions appear to play similar roles in the difference in folding stability and kinetics between the pair of proteins.