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 5 8 3 551.43 1.35 2 5 9 4 551.43 1.34 3 6 9 3 555.46 3.31 4 6 10 4 547.85 0.45 5 6 159 153 22.35 0.56 6 7 10 3 548.82 0.55 7 7 11 4 541.56 1.20 8 8 11 3 542.87 1.85 9 8 12 4 541.39 1.11 10 9 12 3 551.17 1.72 11 9 13 4 545.67 1.02 12 9 152 143 32.69 1.51 13 9 159 150 29.64 0.09 14 10 13 3 549.92 1.30 15 10 14 4 541.48 1.17 16 10 156 146 34.68 0.51 17 11 14 3 547.70 3.77 18 11 15 4 541.41 1.21 19 12 15 3 561.63 1.74 20 12 16 4 534.69 0.31 21 12 152 140 39.66 0.67 22 13 16 3 555.98 4.57 23 13 17 4 540.09 2.40 24 13 27 14 153.96 6.44 25 13 153 140 39.92 0.80 26 13 156 143 39.92 0.80 27 14 17 3 554.52 4.82 28 14 18 4 537.83 3.53 29 15 18 3 542.81 1.21 30 15 19 4 537.82 3.54 31 15 148 133 59.66 0.77 32 16 19 3 541.88 1.68 33 16 20 4 542.07 1.58 34 16 27 11 288.31 58.98 35 16 45 29 146.27 2.56 36 16 49 33 146.19 2.60 37 16 148 132 59.66 0.77 38 16 153 137 59.55 0.75 39 17 21 4 529.48 0.73 40 17 22 5 459.24 1.19 41 17 23 6 459.24 1.20 42 17 24 7 409.62 1.67 43 17 27 10 286.56 59.85 44 18 21 3 515.26 0.86 45 19 66 47 146.47 2.54 46 19 148 129 61.17 0.38 47 20 55 35 146.05 2.49 48 20 59 39 146.31 2.55 49 20 66 46 146.42 2.56 50 20 145 125 69.25 0.15 51 21 52 31 146.51 2.54 52 21 66 45 146.51 2.54 53 22 26 4 513.96 2.58 54 22 27 5 495.19 4.40 55 22 49 27 146.56 2.52 56 22 52 30 146.56 2.52 57 23 26 3 532.71 6.79 58 23 27 4 521.34 2.52 59 24 27 3 532.19 2.90 60 24 28 4 513.07 2.13 61 25 29 4 527.07 2.43 62 26 29 3 548.50 1.38 63 26 30 4 533.78 0.92 64 26 89 63 150.88 1.55 65 27 30 3 549.22 1.03 66 27 31 4 543.46 3.91 67 27 45 18 152.49 1.18 68 27 153 126 60.55 0.69 69 28 31 3 545.72 4.49 70 28 32 4 544.64 3.32 71 28 157 129 60.20 0.75 72 29 32 3 553.47 0.61 73 29 33 4 543.62 3.82 74 30 33 3 552.66 3.97 75 30 34 4 546.26 0.77 76 30 45 15 152.65 1.21 77 30 48 18 152.47 1.16 78 30 91 61 152.43 1.18 79 31 34 3 546.82 0.49 80 31 35 4 551.34 1.77 81 31 41 10 153.15 1.11 82 31 45 14 152.62 1.23 83 31 154 123 60.79 0.67 84 31 157 126 60.55 0.70 85 32 35 3 561.13 3.25 86 32 36 4 563.59 1.64 87 32 41 9 153.18 1.10 88 33 36 3 565.44 1.10 89 33 48 15 152.83 1.12 90 33 91 58 152.55 1.14 91 34 37 3 565.44 1.10 92 34 41 7 153.62 0.89 93 34 44 10 152.84 1.12 94 34 45 11 152.84 1.12 95 34 48 14 152.81 1.10 96 35 41 6 153.19 1.10 97 37 44 7 361.60 25.61 98 37 48 11 157.94 1.26 99 39 43 4 544.33 5.24 100 39 44 5 523.98 4.21 101 40 43 3 547.20 3.81 102 40 44 4 542.69 1.52 103 41 44 3 543.00 1.62 104 41 45 4 542.71 1.51 105 42 45 3 547.28 3.77 106 42 46 4 547.27 3.77 107 42 150 108 61.95 0.74 108 42 154 112 61.84 0.72 109 43 46 3 544.67 2.46 110 43 47 4 542.06 1.17 111 44 47 3 545.81 3.04 112 44 48 4 542.06 1.17 113 45 48 3 551.64 1.66 114 45 49 4 544.61 2.49 115 46 49 3 547.28 3.83 116 46 144 98 70.99 0.33 117 46 145 99 69.75 0.29 118 46 148 102 68.53 0.58 119 46 150 104 62.22 0.81 120 47 50 3 556.36 1.90 121 47 51 4 549.18 2.87 122 47 138 91 99.31 1.57 123 47 139 92 84.73 0.58 124 48 51 3 549.18 2.87 125 48 52 4 545.82 1.19 126 48 91 43 394.71 0.54 127 48 93 45 395.79 0.00 128 49 52 3 558.95 2.02 129 50 55 5 495.74 1.34 130 50 59 9 458.45 3.73 131 50 135 85 242.34 2.44 132 50 139 89 84.71 0.59 133 50 144 94 70.99 0.33 134 51 91 40 396.81 0.02 135 51 92 41 396.28 0.04 136 52 55 3 539.97 0.85 137 52 56 4 538.29 1.69 138 52 88 36 398.48 0.11 139 52 89 37 398.38 0.14 140 53 56 3 548.84 1.84 141 53 57 4 539.80 0.02 142 53 73 20 400.01 0.38 143 53 80 27 397.88 0.01 144 53 85 32 398.47 0.10 145 53 87 34 398.51 0.12 146 53 88 35 398.48 0.11 147 53 90 37 398.31 0.12 148 53 91 38 398.25 0.10 149 53 92 39 398.10 0.03 150 54 57 3 541.54 0.89 151 54 58 4 538.42 1.75 152 54 69 15 400.05 0.39 153 54 70 16 400.05 0.39 154 54 73 19 400.05 0.39 155 55 58 3 549.09 4.66 156 55 59 4 530.41 1.29 157 56 59 3 536.92 2.50 158 56 60 4 533.46 4.23 159 56 92 36 398.32 0.12 160 56 98 42 396.95 0.03 161 56 124 68 291.81 1.45 162 56 135 79 291.25 1.16 163 57 60 3 553.21 2.60 164 57 61 4 533.27 4.32 165 57 62 5 486.60 1.88 166 57 63 6 435.34 8.77 167 57 69 12 400.22 0.42 168 57 72 15 400.22 0.42 169 57 73 16 400.12 0.37 170 57 78 21 398.74 0.02 171 58 61 3 540.87 0.51 172 58 63 5 425.17 3.69 173 58 64 6 422.49 2.35 174 58 65 7 413.47 6.84 175 58 69 11 400.12 0.38 176 59 121 62 291.86 1.46 177 59 124 65 291.81 1.45 178 60 98 38 397.18 0.02 179 60 120 60 292.19 1.29 180 60 124 64 292.16 1.28 181 60 126 66 292.13 1.25 182 60 133 73 292.04 1.21 183 61 113 52 300.06 0.11 184 61 114 53 300.03 0.12 185 62 72 10 406.99 3.60 186 62 98 36 397.41 0.01 187 62 100 38 396.81 0.03 188 62 110 48 300.90 0.18 189 62 113 51 300.08 0.12 190 62 114 52 300.04 0.12 191 62 126 64 292.34 1.21 192 63 68 5 412.67 0.78 193 63 69 6 406.99 3.60 194 63 72 9 406.99 3.60 195 63 113 50 300.78 0.24 196 64 68 4 530.44 3.50 197 64 112 48 300.99 0.19 198 64 113 49 300.81 0.24 199 64 116 52 297.50 0.33 200 65 68 3 533.55 1.95 201 65 69 4 529.38 4.05 202 66 69 3 537.07 0.22 203 66 70 4 529.36 4.04 204 67 70 3 547.13 3.42 205 67 71 4 537.43 0.10 206 68 71 3 567.26 6.73 207 68 72 4 537.42 0.10 208 68 109 41 301.26 0.10 209 69 72 3 546.10 4.21 210 69 73 4 546.10 4.21 211 70 73 3 550.26 3.70 212 70 74 4 536.58 0.29 213 70 88 18 398.75 0.26 214 71 74 3 549.89 2.33 215 71 75 4 526.32 0.85 216 72 75 3 544.00 1.80 217 72 76 4 532.62 2.30 218 72 77 5 509.88 5.44 219 72 78 6 473.00 4.44 220 72 107 35 305.51 1.91 221 72 109 37 301.69 0.11 222 72 110 38 301.67 0.11 223 73 76 3 532.62 2.30 224 73 85 12 399.04 0.21 225 73 86 13 399.03 0.21 226 73 87 14 399.03 0.22 227 73 88 15 398.88 0.29 228 74 86 12 399.01 0.22 229 76 84 8 399.30 0.27 230 76 86 10 399.11 0.23 231 76 101 25 397.14 0.04 232 77 100 23 397.19 0.04 233 77 101 24 397.05 0.07 234 77 104 27 353.06 4.95 235 77 107 30 327.62 10.66 236 78 83 5 405.66 1.49 237 78 84 6 400.14 0.09 238 78 85 7 399.37 0.24 239 78 98 20 397.50 0.02 240 78 99 21 397.41 0.01 241 78 100 22 397.19 0.03 242 79 82 3 519.96 0.70 243 79 83 4 404.31 2.16 244 79 84 5 400.15 0.09 245 79 98 19 397.50 0.01 246 79 99 20 397.41 0.01 247 79 100 21 397.40 0.01 248 79 101 22 397.30 0.01 249 79 102 23 397.39 0.01 250 80 83 3 501.91 4.82 251 80 85 5 400.17 0.09 252 80 92 12 398.95 0.28 253 80 96 16 398.34 0.09 254 80 97 17 397.85 0.14 255 80 98 18 397.50 0.01 256 81 96 15 398.22 0.04 257 81 97 16 398.16 0.01 258 84 101 17 397.31 0.01 259 85 90 5 438.56 19.02 260 87 90 3 537.33 0.01 261 92 96 4 546.62 1.91 262 92 98 6 401.81 2.15 263 92 135 43 289.96 0.55 264 93 96 3 571.93 3.79 265 94 135 41 291.17 1.14 266 94 137 43 289.67 0.43 267 94 138 44 287.96 0.34 268 95 135 40 291.54 1.03 269 96 134 38 291.55 1.03 270 96 135 39 291.54 1.03 271 97 132 35 292.11 1.21 272 97 133 36 292.06 1.22 273 97 134 37 291.55 1.03 274 97 135 38 291.54 1.03 275 98 132 34 292.10 1.22 276 98 133 35 291.99 1.18 277 99 131 32 292.25 1.17 278 99 132 33 292.10 1.22 279 100 104 4 520.14 4.41 280 100 105 5 443.67 1.45 281 100 110 10 350.84 24.64 282 100 131 31 292.30 1.19 283 101 104 3 522.93 5.80 284 101 105 4 520.13 4.40 285 102 105 3 539.89 0.96 286 104 107 3 546.79 1.36 287 104 110 6 469.86 4.74 288 105 111 6 493.93 8.80 289 105 131 26 292.61 1.12 290 106 111 5 520.90 4.22 291 107 110 3 543.85 2.31 292 107 111 4 521.73 3.81 293 108 111 3 540.33 2.00 294 108 112 4 523.20 3.12 295 109 112 3 546.81 1.24 296 109 113 4 540.76 1.05 297 110 113 3 541.01 0.93 298 110 114 4 541.59 1.21 299 110 131 21 292.71 1.18 300 111 114 3 557.84 0.18 301 111 115 4 554.34 1.46 302 111 131 20 292.74 1.18 303 112 115 3 568.12 1.66 304 112 116 4 547.28 0.99 305 113 116 3 550.34 0.54 306 113 117 4 546.69 1.29 307 114 117 3 554.64 1.26 308 114 126 12 292.64 1.19 309 114 131 17 292.74 1.18 310 117 120 3 588.88 1.16 311 119 143 24 196.46 14.40 312 120 124 4 540.21 2.00 313 120 126 6 293.23 1.27 314 121 124 3 545.45 2.65 315 123 135 12 293.17 1.21 316 123 136 13 293.10 1.20 317 123 137 14 292.92 1.27 318 123 138 15 292.71 1.20 319 123 139 16 292.16 1.44 320 123 143 20 202.37 4.65 321 124 134 10 293.32 1.27 322 124 135 11 293.17 1.21 323 124 136 12 293.17 1.21 324 125 132 7 293.98 1.05 325 125 133 8 293.50 1.28 326 125 134 9 293.38 1.25 327 125 136 11 293.28 1.26 328 126 131 5 418.75 6.63 329 126 132 6 293.98 1.05 330 126 133 7 293.50 1.28 331 127 130 3 550.07 3.68 332 127 131 4 483.00 2.31 333 127 132 5 350.78 27.34 334 128 131 3 483.00 2.31 335 135 138 3 610.60 1.17 336 135 139 4 575.66 3.19 337 140 143 3 565.57 5.17 338 140 144 4 547.89 2.69 339 141 144 3 549.53 1.86 340 141 148 7 294.13 1.01 341 141 149 8 128.78 14.10 342 141 150 9 127.28 14.69 343 145 148 3 550.73 0.04 344 149 152 3 602.81 2.46 345 149 153 4 554.22 2.52 346 150 153 3 551.15 1.16 347 150 154 4 547.87 0.47 348 151 154 3 547.87 0.47 349 151 155 4 547.87 0.47 350 152 156 4 539.74 0.77 351 153 156 3 540.18 0.95 352 153 157 4 546.11 1.69 353 154 157 3 568.86 3.71 354 155 158 3 545.39 2.05 355 155 159 4 544.51 1.61 356 156 159 3 555.45 2.98