Off-Lattice Models For Denaturation of Ubiquitin

The Ubiquitin protein for its simple topology and the large amount of experimental data is an ideal candidate to compare theoretical approaches. In this work we compare the Gō-model and the chemically based SHG model through molecular dynamic simulations. The Gō-model reproduces the folding and unfolding mechanism of the small protein Ubiquitin and the folding/unfolding pathways of the secondary structure in a cooperative and reversible process, while the SHG model predicts in the folding a collapse and a structural rearrangement and in the unfolding the presence of intermediate states. In this work the thermodynamics of mutant proteins to determine the properties of the chain was simulated. The helix α1 is the most stable part of the native structure for Gō-model. The results for SHG-model suggest that the optimized sequence 68- residues proposed by Sorenson and Head-Gordon (2000,2002) is not a good folder.