Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding
A) Probability of each α and β secondary structural element normalized to the native protein structure as a function of amino acid residues is calculated. Comparison of I1 and I2 with N (native) reveals multiple conformational changes of β-sheets and α-helices as marked above in blue and green respectively. The secondary structures were assigned with DSSP. Error bars denote the standard deviation calculated from three simulations. B) The top panel shows the time occurrence of α-helix (magenta) to β-sheet (green) transition observed in α4 helix in one of the representative trajectory. In addition, α4 hydrogen bonds (in blue) and dihedral angle of His118 belonging to α4 (below) as a function of time are displayed, to indicate rearrangement of local bonding patterns.