A protein engineering analysis of the transition state for protein folding: simulation in the lattice model

Background: Protein engineering has been used extensively to evaluate the properties of transition states in protein folding. Although the method has proved useful, its limitations and the details of interpretation of the obtained results remain largely unexplored.

Results: Lattice model simulations are used to test and verify the protein engineering analysis of the transition state in protein folding. It is shown that in some cases –  but not always –  this method is able to determine the transition state with reasonable accuracy. Limitations of protein engineering are revealed and analyzed. In particular, the change in non-native interactions as a result of mutations is shown to influence the results of the protein engineering analysis. Furthermore, the temperature dependencies of ϕ values (which are a measure of the participation of a residue in the transition state) and the character of the transition state ensemble are studied. It is shown that as a general trend ϕ values decrease when the temperature decreases, a finding consistent with recent experimental results. Our analysis suggests that this trend results primarily from the formation of some contacts (native and non-native) in the unfolded state at a lower temperature, when the barrier for folding is energetic.

Conclusions: Our analysis helps to interpret the results of protein engineering and allows observed ϕ values to be directly related to structural features of the unfolded state, the transition state and the native state.