File S1 - The Effect of Tensile Stress on the Conformational Free Energy Landscape of Disulfide Bonds

Combined Supporting Information file. Figure S1. Macrocycle with the photoswitch, stiff stilbene, in its trans conformation leading to a strained disulfide bond. Figure S2. (a) Probability distribution function obtained from analyzing the X–ray crystal structures of disulfides in the Protein Data Bank (101087 observations) shown by contour lines with superimposed scatter plot of the conformational states of disulfide bonds in TDi proteins (40 observations) in blue circles, DO proteins (27 observations) as green diamonds and interchain Ig proteins (69 observations) as red squares. (b) Same as panel a but superimposing the scatter plot (circles) of the conformational states of disulfide bonds in intrachain Ig proteins (927 observations) showing the preference of closed/closed conformations, i.e. / 180°/180°. (c) Configuration of a representative interstrand disulfide bond (CYS A 132 – CYS A 192) in intact IgG1 monoclonal antibody (PDB ID 1IGY), which shows a closed/closed conformation that is typical to the preferred ones in panel b. The bridge is strained as a result of being suspended between the two strands shown in tube representation resulting into / 165°/178°. Figure S3. Probability distribution functions obtained from metadynamics simulations for DEDS at zero force and 0.3 nN in panels a and b, respectively. Figure S4. Probability distribution functions obtained from metadynamics simulations for cystine at zero force and 0.3 nN in panels a and b, respectively. Figure S5. Probability distribution functions obtained from metadynamics simulations for DEDS and cystine at 0.1 nN force in panels a and b, respectively. Figure S6. Total open character according to the and dihedral angles (see text) for the model polypeptide, cystine and DEDS as a function of constant external force. The inset shows the closed–closed (the right picture, and in the range 18050°) and the open–open conformation (the left picture, and all other values for the dihedral apart from 18050°) in these dihedrals. These data have been extracted from 150, 300, 1300 ns of zero force and force–clamp MD simulations performed on DEDS, cystine, and the model polypeptide, respectively. Figure S7. Mechanical coordinate, , for the model polypeptide, cystine and DEDS as a function of constant external force. Figure S8. Central disulfide dihedral angle C–S–S–C, , for the model polypeptide, cystine and DEDS as a function of constant external force; the inset visualizes the respective torsional degree of freedom. Note that this behavior, which is very similar for all three systems, is similar to the one found earlier for a cystine molecule. (PDF)