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 m ethod has proved useful, its limitations and the details of interpreta tion of the obtained results remain largely unexplored, Results: Latti ce model simulations are used to test and verify the protein engineeri ng analysis of the transition state in protein folding. It is shown th at in some cases - but not always - this method is able to determine t he transition state with reasonable accuracy. Limitations of protein e ngineering are revealed and analyzed. In particular, the change in non -native interactions as a result of mutations is shown to influence th e results of the protein engineering analysis. Furthermore, the temper ature dependencies of phi values (which are a measure of the participa tion of a residue in the transition state) and the character of the tr ansition state ensemble are studied. It is shown that as a general tre nd phi values decrease when the temperature decreases, a finding consi stent with recent experimental results. Our analysis suggests that thi s 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 phi v alues to be directly related to structural features of the unfolded st ate, the transition state and the native state. (C) Current Biology Lt d ISSN 1359-0278.