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 3 79 76 21.29 0.43 2 3 80 77 21.14 0.35 3 3 135 132 25.48 1.06 4 4 7 3 500.49 3.23 5 5 8 3 480.06 2.89 6 5 9 4 487.25 3.40 7 5 132 127 26.23 0.71 8 5 135 130 27.20 0.25 9 6 9 3 496.90 1.44 10 6 10 4 476.63 1.92 11 6 79 73 27.29 0.19 12 6 80 74 27.29 0.19 13 7 10 3 478.00 2.60 14 7 11 4 477.54 3.27 15 8 11 3 486.87 1.35 16 8 12 4 483.55 0.30 17 8 128 120 46.54 1.15 18 8 129 121 46.52 1.16 19 8 132 124 46.52 1.15 20 9 12 3 487.19 1.47 21 9 13 4 483.60 0.33 22 9 76 67 46.53 1.15 23 9 79 70 46.56 1.16 24 9 132 123 46.54 1.15 25 9 133 124 46.52 1.16 26 9 136 127 46.52 1.16 27 10 13 3 485.23 0.48 28 10 14 4 485.22 0.48 29 10 76 66 46.60 1.15 30 10 79 69 46.62 1.14 31 10 80 70 47.95 0.48 32 11 14 3 499.05 0.91 33 11 15 4 494.15 2.86 34 12 15 3 513.24 1.97 35 12 16 4 494.15 2.86 36 12 121 109 53.62 0.07 37 12 129 117 52.67 0.28 38 12 133 121 51.25 0.43 39 13 16 3 491.98 3.95 40 13 17 4 485.03 0.57 41 13 69 56 53.58 0.07 42 13 72 59 53.47 0.12 43 13 73 60 53.47 0.12 44 13 76 63 51.28 0.44 45 13 117 104 53.58 0.08 46 13 133 120 53.30 0.01 47 14 17 3 487.75 1.72 48 14 18 4 487.72 1.91 49 15 18 3 504.74 2.29 50 15 121 106 58.18 2.14 51 16 19 3 495.86 2.16 52 16 20 4 486.19 2.67 53 16 23 7 322.76 3.60 54 16 69 53 59.50 2.86 55 16 116 100 53.70 0.10 56 16 117 101 53.70 0.10 57 17 20 3 495.86 2.16 58 19 22 3 496.40 2.44 59 19 23 4 484.07 1.01 60 20 23 3 491.72 0.10 61 20 24 4 478.64 3.72 62 20 66 46 87.48 2.72 63 20 69 49 84.85 1.45 64 21 24 3 484.08 1.01 65 21 25 4 482.97 1.54 66 21 62 41 94.95 0.67 67 21 65 44 94.92 0.68 68 21 66 45 93.75 0.10 69 22 25 3 484.57 0.74 70 22 26 4 481.63 0.83 71 23 26 3 483.84 0.36 72 23 27 4 481.54 0.79 73 23 69 46 96.88 1.53 74 23 116 93 101.37 0.49 75 23 120 97 112.09 1.60 76 24 27 3 489.96 2.10 77 24 28 4 481.53 0.79 78 24 65 41 100.01 1.83 79 24 69 45 96.91 1.51 80 25 28 3 491.01 4.50 81 25 29 4 476.36 1.79 82 25 56 31 114.29 2.49 83 25 65 40 111.65 2.88 84 26 29 3 483.88 0.94 85 26 30 4 476.94 1.44 86 26 115 89 113.73 2.35 87 26 116 90 113.65 2.35 88 27 30 3 494.56 3.62 89 27 31 4 479.67 3.83 90 27 72 45 113.77 2.29 91 27 112 85 113.65 2.38 92 27 113 86 113.62 2.35 93 27 116 89 113.73 2.35 94 28 31 3 479.67 3.83 95 28 32 4 479.70 3.81 96 28 61 33 114.31 2.50 97 28 64 36 114.30 2.50 98 28 65 37 114.25 2.46 99 28 68 40 114.11 2.41 100 29 32 3 502.37 0.28 101 29 33 4 477.04 2.46 102 30 33 3 486.01 0.66 103 30 34 4 473.28 0.58 104 30 112 82 113.93 2.48 105 30 115 85 114.14 2.47 106 31 34 3 488.19 1.74 107 31 35 4 473.27 0.58 108 31 38 7 398.17 3.43 109 31 108 77 113.92 2.47 110 31 109 78 113.92 2.48 111 31 112 81 114.00 2.48 112 32 35 3 479.57 2.56 113 32 36 4 441.45 11.08 114 32 38 6 404.77 0.12 115 32 39 7 336.47 21.15 116 32 42 10 344.23 5.28 117 32 52 20 114.99 2.69 118 32 55 23 114.99 2.69 119 32 61 29 114.64 2.52 120 34 108 74 114.02 2.48 121 34 112 78 114.23 2.48 122 35 38 3 507.06 1.55 123 35 108 73 114.08 2.50 124 36 39 3 505.17 2.03 125 36 40 4 507.29 2.03 126 37 40 3 518.90 1.39 127 38 41 3 506.24 1.51 128 38 42 4 504.50 2.38 129 38 105 67 113.71 2.42 130 39 42 3 508.30 3.60 131 39 49 10 129.49 3.23 132 39 50 11 129.53 3.22 133 39 51 12 129.46 3.23 134 39 52 13 129.18 3.14 135 39 55 16 129.02 3.39 136 40 43 3 514.40 0.55 137 40 48 8 173.05 24.95 138 41 101 60 112.06 1.86 139 42 49 7 251.28 8.67 140 42 61 19 128.61 3.35 141 42 64 22 128.38 3.23 142 43 47 4 410.69 9.51 143 43 48 5 310.82 21.11 144 44 47 3 495.82 1.32 145 44 49 5 438.58 8.89 146 44 58 14 129.72 3.24 147 44 60 16 129.63 3.27 148 44 61 17 129.65 3.27 149 44 64 20 129.61 3.28 150 45 60 15 129.72 3.25 151 49 54 5 453.36 8.29 152 49 55 6 328.78 13.02 153 49 58 9 281.79 2.44 154 49 61 12 255.18 3.08 155 50 54 4 485.61 1.41 156 51 54 3 491.92 2.42 157 51 55 4 491.92 2.42 158 52 55 3 496.45 0.15 159 52 56 4 493.24 1.76 160 53 56 3 496.45 0.15 161 53 57 4 486.63 0.23 162 54 57 3 492.28 1.94 163 54 58 4 482.93 2.07 164 55 58 3 489.23 1.54 165 55 61 6 434.45 4.18 166 56 61 5 462.54 2.59 167 56 62 6 401.29 12.40 168 56 65 9 399.17 13.46 169 58 61 3 478.12 4.29 170 58 62 4 466.36 0.72 171 59 62 3 482.09 2.31 172 59 63 4 472.62 2.40 173 60 63 3 487.58 5.06 174 60 64 4 477.91 0.23 175 61 64 3 485.12 3.83 176 61 65 4 485.12 3.83 177 62 65 3 485.12 3.83 178 62 66 4 485.76 3.50 179 63 66 3 485.76 3.50 180 63 67 4 485.76 3.50 181 64 67 3 479.63 0.43 182 64 68 4 478.57 0.09 183 65 68 3 480.95 0.84 184 65 69 4 479.19 0.41 185 66 69 3 486.44 3.21 186 66 70 4 479.22 0.41 187 67 70 3 481.29 0.62 188 67 71 4 479.23 0.41 189 68 71 3 481.48 0.71 190 68 72 4 475.23 2.42 191 69 72 3 483.65 0.55 192 69 73 4 474.06 2.96 193 69 116 47 167.09 2.13 194 70 73 3 486.25 0.85 195 70 74 4 474.03 2.94 196 71 74 3 486.25 0.85 197 71 75 4 479.04 0.36 198 71 88 17 150.75 2.31 199 71 89 18 142.74 6.01 200 71 92 21 140.32 7.21 201 72 75 3 478.30 0.01 202 72 76 4 478.29 0.01 203 72 113 41 167.03 2.15 204 72 133 61 173.78 1.22 205 73 76 3 478.29 0.01 206 73 77 4 478.29 0.01 207 74 77 3 478.42 0.06 208 74 78 4 476.75 0.78 209 74 85 11 195.26 16.11 210 75 78 3 475.16 1.69 211 75 79 4 454.50 0.57 212 75 82 7 275.09 5.55 213 75 85 10 206.68 15.61 214 75 136 61 173.76 1.21 215 75 140 65 166.78 2.09 216 76 79 3 454.52 0.58 217 76 133 57 186.77 2.38 218 76 136 60 178.97 1.38 219 78 81 3 488.26 0.96 220 78 82 4 390.58 2.11 221 78 84 6 280.12 3.43 222 78 85 7 275.06 5.54 223 79 136 57 196.65 0.81 224 81 84 3 505.70 0.18 225 82 85 3 495.62 1.88 226 82 86 4 477.72 0.63 227 82 136 54 216.91 3.79 228 82 139 57 213.37 3.44 229 82 140 58 212.34 3.94 230 83 86 3 475.24 1.22 231 85 88 3 478.63 0.21 232 85 89 4 471.17 2.21 233 86 89 3 482.31 1.57 234 86 90 4 472.29 1.66 235 87 90 3 485.19 3.73 236 87 91 4 474.25 0.67 237 87 146 59 229.18 8.80 238 88 91 3 491.39 1.65 239 88 92 4 475.38 1.22 240 89 92 3 475.44 1.20 241 89 93 4 475.43 1.20 242 89 140 51 229.71 8.69 243 89 143 54 229.66 8.68 244 89 144 55 229.65 8.69 245 90 93 3 478.45 0.93 246 90 94 4 471.34 2.44 247 90 143 53 229.69 8.69 248 90 144 54 229.66 8.69 249 90 146 56 229.52 8.73 250 91 94 3 485.85 4.82 251 91 95 4 471.46 2.40 252 92 95 3 481.21 2.42 253 92 96 4 473.68 1.34 254 92 144 52 229.69 8.69 255 93 96 3 479.35 0.85 256 93 97 4 473.13 1.61 257 93 144 51 229.70 8.69 258 93 148 55 229.49 8.75 259 94 97 3 494.15 0.25 260 94 98 4 472.31 2.02 261 94 147 53 229.49 8.75 262 95 98 3 481.53 2.58 263 95 99 4 480.69 6.99 264 96 99 3 489.34 4.31 265 96 100 4 480.67 7.00 266 96 101 5 431.77 8.03 267 96 144 48 229.90 8.75 268 96 148 52 229.68 8.71 269 97 100 3 489.34 4.31 270 97 101 4 452.67 2.31 271 97 147 50 229.74 8.70 272 97 148 51 229.67 8.71 273 101 148 47 230.03 8.75 274 102 105 3 496.31 2.59 275 102 148 46 230.04 8.75 276 103 106 3 503.63 1.07 277 103 145 42 230.19 8.73 278 103 148 45 230.06 8.76 279 104 107 3 510.60 1.53 280 105 108 3 499.38 3.21 281 105 109 4 481.01 3.00 282 106 109 3 491.25 1.55 283 106 110 4 481.00 2.99 284 106 137 31 232.06 8.54 285 106 141 35 230.94 8.68 286 106 144 38 231.01 8.70 287 106 148 42 230.72 8.64 288 107 110 3 482.14 1.59 289 107 111 4 475.48 0.24 290 108 111 3 485.24 4.70 291 108 112 4 464.66 2.42 292 109 112 3 485.25 4.70 293 109 113 4 466.39 4.33 294 109 137 28 232.24 8.50 295 110 113 3 483.63 0.78 296 110 114 4 474.84 2.67 297 110 137 27 232.23 8.50 298 111 114 3 483.00 1.42 299 111 115 4 474.84 2.67 300 112 115 3 491.38 2.77 301 112 116 4 474.82 2.67 302 113 116 3 490.98 2.96 303 113 117 4 474.31 2.81 304 113 133 20 233.72 8.40 305 113 137 24 233.10 8.68 306 114 117 3 479.62 0.16 307 114 118 4 476.19 1.88 308 114 125 11 246.66 2.61 309 114 130 16 233.77 8.41 310 114 133 19 233.72 8.40 311 114 134 20 233.71 8.40 312 115 118 3 479.47 0.24 313 115 119 4 471.38 4.28 314 116 119 3 489.08 3.06 315 116 120 4 473.81 3.07 316 117 120 3 492.34 1.43 317 117 121 4 469.42 3.33 318 117 125 8 246.69 2.62 319 117 133 16 233.77 8.42 320 118 121 3 493.25 1.73 321 118 122 4 450.61 6.08 322 118 125 7 246.59 2.58 323 121 124 3 484.12 2.64 324 121 125 4 403.38 12.36 325 122 125 3 492.49 0.50 326 123 126 3 512.73 1.07 327 125 129 4 453.29 4.72 328 125 130 5 453.29 4.72 329 125 133 8 418.62 7.91 330 126 129 3 481.94 2.37 331 126 130 4 481.95 2.37 332 127 130 3 483.46 3.06 333 127 131 4 483.46 3.06 334 128 131 3 485.69 2.91 335 128 132 4 483.45 3.07 336 129 132 3 487.43 3.27 337 129 133 4 483.45 3.07 338 130 133 3 489.71 2.12 339 130 134 4 483.45 3.08 340 131 134 3 496.65 1.34 341 131 135 4 487.48 1.03 342 132 135 3 489.42 1.99 343 132 136 4 480.43 3.58 344 133 136 3 487.48 1.02 345 133 137 4 478.18 4.71 346 134 137 3 484.26 3.30 347 134 138 4 478.18 4.71 348 135 138 3 482.32 2.64 349 135 139 4 478.20 4.70 350 136 139 3 482.62 2.49 351 136 140 4 479.63 5.44 352 137 140 3 484.07 3.22 353 137 141 4 462.12 0.58 354 138 141 3 484.07 3.21 355 138 142 4 463.63 1.07 356 139 142 3 488.09 1.22 357 139 143 4 471.13 2.67 358 140 143 3 490.38 2.39 359 140 144 4 481.04 2.29 360 141 144 3 490.38 2.39 361 141 145 4 471.12 2.64 362 142 145 3 490.38 2.39 363 142 146 4 482.03 2.73 364 143 146 3 500.97 1.74 365 144 148 4 511.16 0.40 366 145 148 3 507.65 0.74