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 2 136 134 23.81 0.66 2 3 7 4 485.04 2.76 3 3 75 72 26.70 0.78 4 3 78 75 26.79 0.76 5 3 79 76 26.79 0.76 6 3 136 133 26.84 0.70 7 3 137 134 26.84 0.70 8 4 7 3 515.69 5.74 9 4 8 4 506.31 1.05 10 4 79 75 33.30 0.45 11 5 8 3 516.71 5.24 12 5 9 4 490.88 0.05 13 5 79 74 43.12 3.06 14 6 9 3 498.78 2.73 15 6 10 4 501.48 1.24 16 7 10 3 508.54 1.22 17 7 11 4 502.20 1.60 18 7 129 122 58.04 3.67 19 7 132 125 51.32 0.32 20 7 133 126 50.55 0.04 21 7 136 129 50.57 0.04 22 8 11 3 502.54 1.44 23 8 12 4 502.20 1.60 24 8 76 68 50.58 0.06 25 8 79 71 50.58 0.06 26 9 12 3 505.11 3.05 27 9 13 4 502.20 1.60 28 10 13 3 505.73 0.34 29 10 14 4 499.37 3.50 30 10 129 119 67.86 0.43 31 10 130 120 67.85 0.43 32 11 14 3 504.86 0.78 33 11 15 4 504.84 0.77 34 11 72 61 67.62 0.52 35 11 75 64 67.63 0.52 36 11 133 122 67.84 0.42 37 11 134 123 67.82 0.43 38 12 15 3 510.22 1.90 39 12 16 4 510.41 2.00 40 12 72 60 67.83 0.43 41 12 76 64 67.82 0.43 42 13 16 3 512.12 1.21 43 13 17 4 510.41 2.00 44 14 17 3 512.05 1.18 45 14 18 4 510.41 2.00 46 14 118 104 72.23 0.60 47 14 122 108 81.42 0.04 48 14 130 116 75.02 2.00 49 14 134 120 69.75 0.48 50 15 18 3 508.82 0.43 51 15 19 4 503.49 0.66 52 15 68 53 69.61 0.41 53 15 69 54 69.75 0.48 54 15 72 57 69.60 0.41 55 15 134 119 72.44 0.72 56 16 19 3 506.38 0.79 57 16 20 4 503.49 0.66 58 17 20 3 513.02 1.62 59 17 25 8 467.17 12.24 60 17 121 104 100.64 1.05 61 17 122 105 100.52 1.10 62 17 125 108 100.56 1.10 63 18 21 3 530.01 1.37 64 18 22 4 510.34 2.94 65 18 25 7 347.33 4.39 66 18 26 8 384.06 3.66 67 18 65 47 148.00 23.03 68 18 68 50 99.01 0.70 69 18 117 99 100.64 1.04 70 18 118 100 100.44 1.09 71 18 121 103 100.71 1.03 72 19 22 3 517.13 0.46 73 21 24 3 520.77 3.39 74 21 25 4 498.05 0.83 75 22 25 3 513.75 4.53 76 22 26 4 495.80 1.98 77 22 61 39 155.91 23.17 78 22 65 43 152.31 24.73 79 23 27 4 495.80 1.99 80 23 61 38 175.54 13.38 81 24 27 3 513.84 3.98 82 24 28 4 492.78 4.80 83 25 28 3 496.57 2.91 84 25 29 4 502.22 1.19 85 25 117 92 144.49 2.64 86 25 121 96 146.84 3.82 87 26 29 3 505.17 2.67 88 26 30 4 506.32 0.23 89 26 60 34 184.18 9.09 90 26 61 35 184.02 9.14 91 26 64 38 176.02 13.11 92 26 65 39 178.91 11.62 93 27 30 3 509.95 0.28 94 27 31 4 503.42 1.68 95 27 53 26 188.78 10.76 96 27 54 27 188.75 10.75 97 27 55 28 186.91 9.85 98 27 60 33 184.52 9.21 99 28 31 3 503.43 1.67 100 28 32 4 502.38 1.14 101 28 120 92 167.22 0.47 102 29 32 3 511.88 5.88 103 29 33 4 502.39 1.14 104 29 64 35 184.71 8.84 105 29 68 39 184.06 8.98 106 29 110 81 167.90 0.91 107 29 113 84 167.84 0.86 108 29 114 85 167.84 0.87 109 29 117 88 167.64 0.76 110 30 33 3 503.14 1.51 111 30 34 4 509.49 1.67 112 30 44 14 211.95 22.21 113 30 46 16 211.95 22.21 114 30 47 17 211.96 22.21 115 30 53 23 188.97 10.71 116 30 60 30 186.81 9.85 117 30 63 33 185.51 9.21 118 30 64 34 184.81 8.87 119 31 34 3 525.39 0.88 120 31 35 4 509.49 1.67 121 31 53 22 188.86 10.76 122 32 35 3 504.26 1.09 123 32 36 4 503.12 0.53 124 32 113 81 168.03 0.78 125 32 116 84 167.90 0.70 126 32 117 85 167.96 0.65 127 33 36 3 520.61 1.06 128 33 37 4 490.94 4.22 129 33 40 7 344.98 2.12 130 33 109 76 168.23 0.77 131 33 113 80 168.03 0.77 132 34 37 3 491.73 5.96 133 34 38 4 412.57 2.12 134 34 40 6 394.87 27.17 135 34 41 7 324.78 2.89 136 34 47 13 213.93 23.14 137 34 53 19 198.80 15.58 138 36 109 73 168.39 0.74 139 36 112 76 168.38 0.71 140 36 113 77 168.33 0.69 141 37 40 3 519.96 0.89 142 37 109 72 168.42 0.73 143 38 41 3 536.39 1.48 144 39 42 3 537.97 2.83 145 40 43 3 532.77 0.23 146 40 44 4 519.12 0.19 147 41 44 3 530.88 2.88 148 41 47 6 372.88 28.09 149 41 48 7 335.59 9.43 150 41 50 9 300.74 7.99 151 42 48 6 308.62 4.07 152 43 48 5 473.32 5.37 153 43 100 57 168.47 0.79 154 43 101 58 168.56 0.73 155 43 106 63 168.55 0.69 156 44 47 3 525.38 0.19 157 44 48 4 501.97 1.40 158 44 63 19 201.33 16.73 159 45 48 3 519.94 2.91 160 46 50 4 528.31 1.28 161 46 54 8 210.53 21.00 162 46 57 11 207.27 19.43 163 46 59 13 202.61 17.12 164 46 60 14 201.59 16.64 165 46 63 17 201.59 16.64 166 47 50 3 510.19 2.70 167 47 53 6 223.97 27.72 168 47 54 7 223.97 27.73 169 47 60 13 202.62 17.11 170 50 54 4 501.07 4.58 171 53 60 7 421.29 23.18 172 54 57 3 521.85 1.16 173 54 60 6 462.04 5.88 174 56 61 5 479.79 3.54 175 57 60 3 514.04 1.38 176 57 61 4 489.03 1.08 177 58 61 3 500.10 0.74 178 58 62 4 500.36 0.88 179 59 62 3 524.61 3.91 180 59 63 4 508.82 3.33 181 60 63 3 511.61 1.94 182 60 64 4 508.84 3.32 183 61 64 3 524.44 0.34 184 61 65 4 508.84 3.32 185 62 65 3 509.10 3.19 186 62 66 4 500.36 0.92 187 63 66 3 515.21 0.12 188 63 67 4 511.86 1.58 189 64 67 3 511.86 1.59 190 64 68 4 511.88 1.58 191 65 68 3 522.03 1.08 192 65 69 4 511.90 1.58 193 66 69 3 521.97 1.05 194 66 70 4 511.90 1.59 195 67 70 3 525.69 4.39 196 67 71 4 509.94 2.56 197 67 110 43 183.65 6.93 198 67 114 47 192.52 11.41 199 68 71 3 524.10 5.20 200 68 72 4 502.91 0.70 201 68 114 46 192.45 11.43 202 68 117 49 193.22 11.80 203 68 118 50 193.21 11.83 204 68 134 66 192.31 12.31 205 69 72 3 502.95 0.68 206 69 73 4 497.71 3.29 207 70 73 3 508.85 2.23 208 70 74 4 497.75 3.32 209 70 93 23 183.28 6.58 210 70 141 71 182.74 16.27 211 71 74 3 502.79 2.51 212 71 75 4 499.78 4.03 213 71 114 43 193.34 11.78 214 71 134 63 192.37 12.35 215 71 137 66 192.00 12.44 216 71 138 67 191.16 12.09 217 71 141 70 182.76 16.29 218 72 75 3 510.57 1.36 219 72 76 4 502.45 2.69 220 72 134 62 192.37 12.34 221 73 76 3 511.46 4.14 222 73 77 4 499.82 4.01 223 74 77 3 509.21 0.69 224 74 78 4 499.82 4.01 225 74 84 10 253.48 2.68 226 74 141 67 190.10 12.63 227 75 78 3 508.12 1.21 228 75 79 4 499.93 3.98 229 75 137 62 192.26 12.39 230 76 79 3 502.44 2.73 231 76 80 4 499.94 3.98 232 77 80 3 514.57 3.34 233 77 81 4 491.51 1.09 234 77 82 5 473.88 8.97 235 77 83 6 362.27 8.12 236 77 84 7 270.29 1.79 237 77 85 8 270.45 1.87 238 78 82 4 468.39 6.27 239 78 83 5 331.37 0.33 240 78 84 6 328.80 0.26 241 78 136 58 206.63 19.32 242 78 137 59 200.09 16.07 243 78 140 62 192.43 12.51 244 84 90 6 497.39 2.88 245 84 140 56 207.86 20.27 246 84 141 57 207.88 20.29 247 84 144 60 206.94 20.62 248 85 90 5 503.20 5.78 249 86 90 4 497.41 2.88 250 86 91 5 497.40 2.88 251 86 144 58 206.87 20.81 252 86 148 62 198.73 24.87 253 87 90 3 517.34 1.28 254 87 91 4 508.70 3.02 255 88 91 3 510.82 3.52 256 88 92 4 502.91 0.14 257 89 92 3 514.17 5.20 258 89 93 4 503.22 5.78 259 90 93 3 502.07 0.21 260 90 94 4 498.16 1.58 261 90 141 51 208.27 20.91 262 90 144 54 200.05 24.95 263 90 145 55 200.03 24.96 264 90 148 58 198.20 25.85 265 91 94 3 509.99 0.71 266 91 95 4 505.64 2.00 267 91 148 57 196.97 26.46 268 92 95 3 515.99 0.60 269 92 96 4 501.50 0.07 270 93 96 3 505.53 2.06 271 93 97 4 502.36 0.51 272 93 145 52 200.00 25.00 273 94 97 3 517.47 0.64 274 94 98 4 508.72 3.69 275 94 148 54 191.78 29.09 276 94 149 55 188.14 30.90 277 94 152 58 186.41 30.61 278 95 98 3 511.59 2.27 279 95 99 4 505.78 5.17 280 95 152 57 187.02 30.91 281 96 99 3 519.03 1.46 282 96 100 4 516.78 0.34 283 97 100 3 519.03 1.47 284 97 101 4 516.77 0.35 285 97 102 5 475.24 5.98 286 97 145 48 199.91 25.16 287 97 149 52 188.19 30.93 288 98 101 3 504.88 0.83 289 98 149 51 188.19 30.93 290 98 152 54 187.53 31.17 291 98 153 55 187.31 31.07 292 101 106 5 521.56 1.54 293 102 106 4 521.53 1.53 294 102 107 5 521.53 1.53 295 102 149 47 188.34 31.11 296 103 106 3 529.75 0.60 297 103 107 4 529.75 0.60 298 103 149 46 188.36 31.10 299 104 107 3 532.76 0.90 300 104 108 4 530.82 0.07 301 104 146 42 196.40 27.53 302 105 108 3 546.20 0.01 303 106 109 3 525.76 0.33 304 106 110 4 522.71 0.98 305 107 110 3 525.64 0.27 306 107 111 4 509.43 1.68 307 107 138 31 210.80 21.93 308 107 142 35 200.88 25.42 309 107 145 38 197.41 27.16 310 107 146 39 196.52 27.59 311 107 149 42 189.56 31.07 312 108 111 3 508.53 2.13 313 108 112 4 508.09 2.35 314 109 112 3 523.85 1.21 315 109 113 4 501.40 0.99 316 110 113 3 507.62 1.74 317 110 114 4 516.03 8.32 318 110 138 28 210.85 21.95 319 111 114 3 522.83 4.92 320 111 115 4 516.02 8.32 321 111 135 24 211.03 21.89 322 111 138 27 210.84 21.96 323 111 139 28 210.83 21.96 324 112 115 3 526.64 3.02 325 112 116 4 493.81 1.39 326 113 116 3 522.84 4.92 327 113 117 4 504.84 1.90 328 114 117 3 504.85 1.90 329 114 118 4 504.85 1.90 330 114 134 20 211.40 21.97 331 114 138 24 210.84 21.96 332 115 118 3 512.46 4.12 333 115 119 4 504.85 1.90 334 115 131 16 211.52 21.98 335 115 134 19 211.24 21.89 336 115 135 20 211.09 21.94 337 116 119 3 500.31 0.32 338 116 120 4 500.34 0.32 339 117 120 3 505.74 3.00 340 117 121 4 505.76 3.01 341 118 121 3 505.76 3.01 342 118 122 4 505.76 3.01 343 118 130 12 241.94 7.07 344 118 134 16 211.40 21.99 345 119 122 3 521.51 0.35 346 119 123 4 505.75 3.02 347 119 126 7 255.14 5.21 348 120 123 3 514.45 1.33 349 122 125 3 507.69 3.57 350 122 126 4 415.26 0.73 351 122 130 8 356.89 23.89 352 123 126 3 520.38 0.09 353 126 130 4 511.81 5.11 354 126 131 5 503.47 0.93 355 127 130 3 511.81 5.11 356 127 131 4 503.49 0.93 357 128 131 3 510.60 2.06 358 128 132 4 507.35 2.85 359 129 132 3 516.70 2.66 360 129 133 4 507.35 2.85 361 130 133 3 516.84 1.89 362 130 134 4 516.84 1.89 363 131 134 3 511.35 4.74 364 131 135 4 498.18 1.39 365 132 135 3 497.08 0.85 366 132 136 4 496.81 0.98 367 133 136 3 509.31 1.33 368 133 137 4 498.17 0.28 369 134 137 3 504.65 3.52 370 134 138 4 499.18 0.78 371 135 138 3 521.40 0.11 372 135 139 4 497.51 5.50 373 136 139 3 505.18 1.66 374 136 140 4 505.17 1.66 375 137 140 3 517.20 1.99 376 137 141 4 504.16 4.53 377 138 141 3 516.27 2.13 378 138 142 4 506.04 3.59 379 139 142 3 509.70 5.42 380 139 143 4 500.35 0.73 381 140 143 3 523.75 1.60 382 140 144 4 508.68 3.43 383 141 144 3 523.02 1.45 384 141 145 4 517.83 1.15 385 142 145 3 517.84 1.15 386 142 146 4 517.83 1.15 387 143 146 3 517.86 1.16 388 143 147 4 515.97 2.08 389 144 147 3 515.98 2.08 390 144 148 4 515.97 2.08 391 145 148 3 516.10 2.15 392 145 149 4 508.96 1.55 393 146 149 3 508.96 1.55 394 146 150 4 491.50 10.29 395 147 150 3 519.81 0.30 396 147 151 4 489.84 11.12 397 148 151 3 490.16 10.96 398 148 152 4 458.44 4.83 399 149 152 3 490.09 10.99 400 149 153 4 471.76 1.79