CHARACTERIZATION OF THE TRANSITION-STATE OF PROTEIN UNFOLDING BY USE OF MOLECULAR-DYNAMICS - CHYMOTRYPSIN INHIBITOR-2

Temperature-induced unfolding of chymotrypsin inhibitor 2 in water was investigated by molecular dynamics simulations. The major transition state of unfolding was identified on the basis of structural and confo rmational changes in the protein during the unfolding reaction. The na tive tertiary contacts in the hydrophobic core were considerably disru pted in the transition state, whereas the secondary structure was part ially intact. The extent of structural change of the protein around a particular residue was represented quantitatively by the ratio of the number of contacts the residue makes in the transition state relative to the native state, (Phi)MD, which allows quantitative comparison wit h the experimentally determined F-Phi values. For the region of the un folding trajectory that is identified as the transition state, the (Ph i)MD and F-Phi values are in good agreement, suggesting that the trans ition state identified in the unfolding simulation corresponds to that probed with protein engineering methods. Although speculative, the tr ansition state identified in the simulation is consistent with availab le experimental data and provides an in-depth view of what the transit ion state of unfolding may look like.