BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 180 219 39 43.16 0.67 2 181 184 3 152.37 0.02 3 181 185 4 138.80 1.30 4 181 216 35 44.27 0.84 5 181 217 36 44.26 0.84 6 182 185 3 146.08 1.80 7 182 186 4 132.38 1.91 8 183 186 3 152.12 0.10 9 183 187 4 132.38 1.91 10 183 216 33 50.55 2.10 11 184 187 3 150.94 1.49 12 184 188 4 143.53 3.67 13 184 207 23 76.59 1.22 14 184 216 32 54.56 0.09 15 185 188 3 154.73 1.41 16 185 189 4 269.68 0.16 17 185 224 39 44.20 0.94 18 185 227 42 43.82 0.83 19 185 228 43 43.81 0.83 20 187 207 20 111.77 2.05 21 187 216 29 65.38 1.02 22 188 207 19 139.94 0.71 23 188 224 36 46.49 0.09 24 189 228 39 43.84 0.83 25 189 231 42 42.58 1.29 26 192 228 36 46.38 0.16 27 192 235 43 37.22 0.72 28 192 239 47 30.12 0.21 29 193 235 42 36.30 1.19 30 193 238 45 31.60 0.59 31 193 239 46 29.93 0.29 32 194 239 45 30.14 0.22 33 195 239 44 30.48 0.06 34 197 239 42 31.12 0.26 35 197 240 43 31.11 0.26 36 200 224 24 57.24 1.43 37 200 225 25 54.51 0.07 38 202 206 4 276.93 4.42 39 203 206 3 147.91 0.79 40 203 207 4 145.91 1.81 41 204 207 3 153.19 1.25 42 204 208 4 146.53 1.53 43 204 218 14 71.27 0.22 44 204 219 15 69.79 0.25 45 204 221 17 57.25 1.41 46 204 224 20 54.66 0.11 47 205 208 3 149.84 0.12 48 205 209 4 149.83 0.13 49 206 209 3 150.26 0.34 50 206 210 4 145.93 1.82 51 207 210 3 148.56 0.54 52 207 211 4 145.22 1.57 53 207 216 9 104.58 1.65 54 207 218 11 76.27 0.34 55 208 211 3 151.22 1.43 56 208 212 4 148.62 0.12 57 208 218 10 79.92 2.16 58 209 212 3 148.62 0.14 59 209 213 4 149.34 0.49 60 210 213 3 149.97 0.18 61 210 214 4 148.22 0.33 62 210 216 6 129.75 5.13 63 211 214 3 148.08 0.40 64 211 215 4 141.27 0.79 65 211 216 5 103.46 1.09 66 211 218 7 90.00 1.34 67 212 215 3 133.59 2.96 68 219 223 4 143.53 0.11 69 220 223 3 151.41 0.07 70 220 224 4 146.18 0.65 71 221 224 3 147.88 1.50 72 221 225 4 146.95 0.89 73 222 225 3 160.28 1.73 74 222 226 4 151.15 0.95 75 223 226 3 153.34 0.15 76 223 227 4 151.15 0.95 77 224 227 3 159.16 0.54 78 224 228 4 152.70 0.17 79 225 228 3 152.70 0.17 80 225 229 4 152.69 0.17 81 226 229 3 158.43 1.70 82 226 230 4 152.69 0.17 83 227 230 3 156.96 0.96 84 227 231 4 154.00 2.81 85 228 231 3 157.33 1.15 86 228 235 7 130.50 0.54 87 231 235 4 146.81 0.03 88 232 235 3 154.17 3.22 89 232 236 4 154.38 3.12 90 233 236 3 155.82 0.59 91 233 237 4 150.00 0.01 92 234 237 3 151.78 0.91 93 234 238 4 149.46 0.83 94 235 238 3 152.40 0.65 95 235 239 4 153.22 0.24 96 236 239 3 160.39 0.35 97 236 240 4 153.22 0.23 98 237 240 3 155.00 0.66 99 237 241 4 135.83 1.50 100 238 241 3 150.30 1.23