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 7 5 475.92 3.54 2 2 10 8 473.67 3.53 3 2 130 128 44.99 1.08 4 2 133 131 33.49 0.55 5 2 134 132 32.91 0.68 6 2 137 135 32.91 0.68 7 3 6 3 512.96 2.61 8 3 7 4 513.26 2.46 9 4 7 3 515.97 3.64 10 4 8 4 513.27 2.46 11 4 79 75 59.81 1.37 12 5 8 3 513.62 2.64 13 5 9 4 513.29 2.44 14 6 9 3 527.15 4.13 15 6 10 4 505.33 1.68 16 6 130 124 67.38 1.29 17 6 133 127 67.43 1.27 18 7 10 3 506.91 2.46 19 7 11 4 505.32 1.67 20 7 76 69 70.73 0.36 21 7 79 72 70.71 0.35 22 7 80 73 70.73 0.36 23 7 134 127 67.47 1.27 24 7 137 130 70.76 0.35 25 8 11 3 526.58 1.64 26 8 12 4 513.13 2.23 27 9 12 3 526.58 1.64 28 9 13 4 514.08 1.77 29 9 126 117 82.94 0.73 30 9 127 118 82.85 0.70 31 9 130 121 82.78 0.69 32 10 13 3 529.42 0.21 33 10 14 4 515.40 1.10 34 10 76 66 82.86 0.70 35 10 130 120 82.85 0.70 36 10 131 121 82.83 0.71 37 10 134 124 82.75 0.68 38 11 14 3 515.42 1.10 39 11 15 4 515.40 1.10 40 11 76 65 82.88 0.70 41 11 77 66 82.88 0.70 42 11 79 68 82.89 0.69 43 12 15 3 519.81 0.84 44 12 16 4 520.36 3.58 45 12 122 110 90.71 0.96 46 13 16 3 523.89 2.89 47 13 17 4 515.91 1.35 48 13 115 102 90.63 0.91 49 13 122 109 90.64 0.92 50 13 123 110 90.56 0.95 51 13 131 118 89.79 1.20 52 14 17 3 518.71 0.04 53 14 18 4 518.71 0.04 54 14 69 55 90.50 0.97 55 14 72 58 90.41 0.94 56 14 73 59 89.43 1.42 57 14 76 62 89.43 1.43 58 14 77 63 90.07 1.12 59 14 131 117 90.51 0.97 60 15 18 3 523.15 2.18 61 15 19 4 519.99 0.59 62 16 19 3 518.70 0.05 63 16 119 103 98.53 1.22 64 16 122 106 93.42 0.30 65 17 20 3 530.19 0.52 66 17 21 4 493.30 3.16 67 17 24 7 422.00 15.93 68 17 69 52 132.95 22.11 69 17 115 98 96.82 2.06 70 17 119 102 113.24 0.48 71 18 21 3 515.19 1.71 72 18 77 59 90.77 0.90 73 20 23 3 526.90 2.88 74 20 24 4 507.59 5.24 75 20 118 98 134.79 0.64 76 21 24 3 519.79 0.85 77 21 25 4 505.86 4.37 78 21 66 45 152.49 13.03 79 21 69 48 148.45 14.83 80 22 25 3 514.31 2.04 81 22 26 4 514.14 1.96 82 22 62 40 173.35 3.33 83 22 66 44 153.69 12.45 84 23 26 3 512.42 1.09 85 23 27 4 512.02 0.90 86 23 118 95 163.95 0.59 87 24 27 3 522.09 4.75 88 24 28 4 512.02 0.90 89 24 69 45 157.27 10.74 90 24 114 90 163.69 0.62 91 24 115 91 162.62 0.01 92 24 118 94 163.95 0.59 93 24 119 95 164.04 0.56 94 25 28 3 511.54 0.54 95 25 29 4 511.52 0.55 96 25 65 40 172.74 3.02 97 25 69 44 155.34 11.71 98 26 29 3 513.40 0.39 99 26 30 4 511.21 0.40 100 26 56 30 209.71 2.64 101 26 62 36 173.85 3.17 102 27 30 3 519.12 0.93 103 27 31 4 507.69 2.15 104 27 114 87 167.19 0.74 105 27 118 91 167.13 0.77 106 28 31 3 508.76 1.61 107 28 32 4 507.70 2.14 108 28 69 41 173.99 3.05 109 28 107 79 167.68 0.78 110 28 110 82 167.44 0.85 111 28 111 83 167.43 0.85 112 28 114 86 167.22 0.75 113 29 32 3 515.39 1.70 114 29 33 4 507.69 2.15 115 29 61 32 194.16 6.89 116 29 64 35 174.13 3.04 117 29 65 36 174.12 3.05 118 29 107 78 167.69 0.78 119 30 33 3 513.07 0.56 120 30 34 4 506.74 2.60 121 30 52 22 210.53 2.51 122 30 55 25 210.18 2.41 123 30 56 26 210.12 2.46 124 31 34 3 511.48 2.08 125 31 35 4 504.53 2.98 126 31 110 79 167.44 0.85 127 31 113 82 167.41 0.85 128 32 35 3 508.73 0.88 129 32 36 4 504.50 2.98 130 32 39 7 425.66 9.09 131 32 106 74 167.76 0.80 132 32 107 75 167.69 0.77 133 32 110 78 167.45 0.85 134 33 36 3 514.39 2.02 135 33 37 4 493.01 3.53 136 33 39 6 400.97 3.27 137 33 40 7 362.98 0.77 138 33 43 10 347.99 6.73 139 33 46 13 263.29 2.29 140 33 55 22 212.58 1.50 141 33 61 28 210.98 2.23 142 34 37 3 525.44 4.05 143 34 52 18 214.61 0.74 144 36 39 3 524.18 5.67 145 36 106 70 168.10 0.90 146 37 40 3 527.35 4.08 147 37 41 4 512.35 0.97 148 38 41 3 533.95 0.64 149 38 103 65 168.34 0.84 150 38 106 68 168.35 0.85 151 39 42 3 530.79 2.27 152 39 43 4 527.46 2.61 153 39 103 64 168.28 0.83 154 39 106 67 168.28 0.82 155 40 43 3 526.51 1.46 156 40 46 6 381.21 9.55 157 40 47 7 345.01 27.62 158 40 49 9 280.86 1.40 159 40 55 15 243.94 0.86 160 41 47 6 328.22 16.89 161 42 97 55 169.25 0.91 162 42 98 56 169.22 0.92 163 42 99 57 169.14 0.88 164 42 100 58 169.21 0.92 165 42 103 61 168.92 0.89 166 43 46 3 522.04 2.10 167 43 47 4 503.08 4.97 168 43 64 21 228.88 1.55 169 44 47 3 526.67 1.39 170 45 48 3 586.75 1.88 171 45 60 15 229.08 1.50 172 46 49 3 534.12 0.64 173 46 60 14 229.08 1.50 174 46 61 15 229.07 1.50 175 46 64 18 229.06 1.50 176 49 54 5 445.50 18.68 177 49 55 6 328.66 7.21 178 49 58 9 284.17 1.39 179 49 61 12 264.06 6.77 180 50 54 4 502.09 2.07 181 51 54 3 499.93 0.99 182 51 55 4 491.18 1.50 183 52 55 3 501.13 1.42 184 52 56 4 495.81 0.81 185 53 56 3 507.42 0.22 186 53 57 4 499.56 1.06 187 54 57 3 504.62 3.09 188 54 58 4 499.11 0.83 189 55 58 3 515.25 3.27 190 55 61 6 430.45 9.12 191 58 61 3 533.14 2.79 192 58 62 4 505.95 2.46 193 59 62 3 511.59 0.35 194 59 63 4 502.79 4.06 195 60 63 3 509.09 0.97 196 60 64 4 502.79 4.06 197 61 64 3 517.36 3.22 198 61 65 4 504.59 3.19 199 62 65 3 523.35 0.22 200 62 66 4 512.63 0.26 201 63 66 3 526.60 2.48 202 63 67 4 512.65 0.26 203 64 67 3 512.70 0.28 204 64 68 4 512.67 0.27 205 65 68 3 515.92 1.89 206 65 69 4 512.73 0.29 207 66 69 3 519.13 0.29 208 66 70 4 510.69 1.33 209 67 70 3 520.51 1.10 210 67 71 4 510.70 1.34 211 68 71 3 523.24 0.26 212 68 72 4 511.99 0.70 213 68 107 39 168.22 0.92 214 69 72 3 519.66 1.53 215 69 73 4 512.01 0.71 216 70 73 3 527.12 0.54 217 70 74 4 512.02 0.71 218 71 74 3 520.83 3.69 219 71 75 4 512.02 0.71 220 72 75 3 520.33 1.76 221 72 76 4 512.34 0.56 222 72 111 39 168.23 0.92 223 72 135 63 166.83 0.81 224 72 138 66 166.72 0.79 225 73 76 3 512.34 0.55 226 73 77 4 509.49 0.88 227 74 78 4 509.49 0.86 228 75 78 3 536.29 0.35 229 75 82 7 248.65 0.31 230 75 85 10 206.95 10.56 231 75 86 11 201.23 7.71 232 75 89 14 201.11 7.65 233 75 138 63 166.78 0.79 234 76 79 3 536.29 0.35 235 76 134 58 166.90 0.82 236 78 81 3 502.78 2.45 237 78 82 4 362.85 1.49 238 78 85 7 299.99 0.14 239 80 137 57 167.05 0.81 240 82 85 3 509.18 1.06 241 82 86 4 506.31 2.49 242 82 137 55 167.06 0.80 243 82 141 59 166.06 0.70 244 83 86 3 519.91 1.91 245 83 87 4 509.00 1.16 246 84 88 4 519.81 1.86 247 85 88 3 544.45 0.42 248 86 89 3 528.44 2.46 249 86 90 4 511.00 1.25 250 86 138 52 166.81 0.78 251 86 141 55 165.44 0.42 252 86 142 56 163.12 0.14 253 86 145 59 157.21 0.47 254 87 90 3 526.02 1.25 255 87 91 4 512.12 1.81 256 88 91 3 515.97 0.10 257 88 92 4 512.16 1.79 258 89 92 3 519.25 0.77 259 89 93 4 512.16 1.79 260 89 138 49 166.77 0.80 261 89 142 53 162.08 0.17 262 90 93 3 519.25 0.76 263 90 94 4 512.16 1.79 264 90 142 52 160.97 0.36 265 90 145 55 155.81 0.01 266 90 146 56 151.60 0.09 267 91 94 3 518.88 0.66 268 91 95 4 506.06 1.26 269 91 149 58 148.69 0.20 270 92 95 3 513.87 0.96 271 92 96 4 480.68 4.63 272 92 97 5 465.13 3.14 273 93 97 4 365.55 5.48 274 93 98 5 365.54 5.48 275 93 99 6 323.56 6.95 276 93 146 53 151.58 0.10 277 94 98 4 365.54 5.48 278 94 146 52 150.90 0.33 279 94 151 57 70.97 0.08 280 95 98 3 520.87 1.86 281 95 149 54 148.50 0.10 282 95 151 56 118.84 2.31 283 98 151 53 84.75 1.10 284 99 103 4 513.72 0.78 285 99 104 5 509.93 2.67 286 99 146 47 150.88 0.33 287 100 103 3 524.38 0.28 288 100 104 4 514.19 1.02 289 100 146 46 150.90 0.33 290 100 153 53 28.71 3.71 291 101 104 3 518.26 1.02 292 101 105 4 510.01 2.64 293 101 139 38 164.65 0.48 294 101 142 41 159.74 0.35 295 101 143 42 155.07 0.18 296 101 146 45 150.82 0.36 297 101 153 52 27.55 4.28 298 102 105 3 521.49 3.10 299 102 106 4 509.99 2.65 300 103 106 3 519.31 2.06 301 103 107 4 509.90 2.64 302 104 107 3 521.85 2.86 303 104 108 4 513.37 1.00 304 104 138 34 165.32 0.36 305 104 142 38 158.61 0.15 306 105 108 3 519.57 4.00 307 105 109 4 513.13 1.12 308 105 139 34 164.69 0.58 309 106 109 3 519.37 4.04 310 106 110 4 511.81 1.79 311 107 110 3 511.80 1.79 312 107 111 4 508.75 2.50 313 108 111 3 519.10 2.65 314 108 112 4 506.20 1.00 315 108 135 27 165.77 0.54 316 108 139 31 164.71 0.58 317 109 112 3 513.69 0.81 318 109 113 4 504.00 0.07 319 110 113 3 504.83 1.12 320 110 114 4 503.23 0.32 321 111 114 3 515.00 2.71 322 111 115 4 506.52 1.78 323 111 135 24 165.81 0.55 324 112 115 3 515.00 2.71 325 112 116 4 508.25 0.67 326 112 123 11 278.12 1.86 327 112 131 19 174.78 3.41 328 112 132 20 166.24 0.63 329 112 135 23 165.79 0.54 330 113 116 3 515.00 2.71 331 113 117 4 508.31 0.64 332 114 117 3 512.18 1.30 333 114 118 4 507.83 0.39 334 115 118 3 522.36 3.00 335 115 119 4 503.56 0.35 336 115 123 8 317.31 11.28 337 115 131 16 222.65 0.85 338 116 119 3 520.51 3.92 339 116 120 4 497.06 2.08 340 116 123 7 278.12 1.86 341 116 128 12 261.07 0.07 342 117 120 3 538.19 3.27 343 119 122 3 517.01 5.09 344 119 123 4 470.85 9.71 345 120 123 3 516.27 6.95 346 120 124 4 494.93 1.82 347 122 127 5 473.08 12.91 348 123 127 4 486.17 6.36 349 123 128 5 481.60 1.29 350 123 131 8 463.14 7.94 351 124 127 3 512.33 2.02 352 124 128 4 500.28 3.99 353 125 128 3 508.32 0.03 354 125 129 4 503.86 2.19 355 126 129 3 510.87 1.28 356 126 130 4 505.76 1.26 357 127 130 3 504.30 0.52 358 127 131 4 502.39 1.46 359 128 131 3 506.45 1.59 360 128 132 4 497.28 1.10 361 129 132 3 515.54 0.14 362 129 133 4 504.94 5.44 363 130 133 3 514.82 0.70 364 130 134 4 511.23 2.29 365 131 134 3 516.50 0.15 366 131 135 4 502.14 1.82 367 132 135 3 514.07 1.07 368 132 136 4 502.14 1.82 369 133 136 3 507.76 0.56 370 133 137 4 505.79 0.00 371 134 137 3 509.20 1.36 372 134 138 4 503.54 1.13 373 135 138 3 506.20 0.14 374 135 139 4 504.38 1.52 375 136 139 3 513.13 2.58 376 136 140 4 503.60 1.12 377 137 140 3 510.91 1.73 378 137 141 4 503.94 1.19 379 138 141 3 520.37 3.42 380 138 142 4 506.56 0.45 381 139 142 3 513.47 0.05 382 139 143 4 507.62 0.94 383 140 143 3 514.95 2.72 384 140 144 4 507.72 0.89 385 141 144 3 514.16 3.12 386 141 145 4 506.94 0.50 387 142 145 3 513.46 0.99 388 142 146 4 506.94 0.50 389 143 146 3 507.19 0.38 390 143 147 4 506.81 0.55 391 143 152 9 243.41 11.20 392 144 147 3 515.27 2.87 393 144 148 4 502.88 1.34 394 145 148 3 510.59 1.96 395 145 149 4 495.44 2.37 396 146 149 3 511.44 0.62 397 146 150 4 495.35 2.42 398 146 151 5 400.02 38.63 399 146 152 6 261.81 2.25 400 146 153 7 330.87 7.99 401 147 150 3 495.94 7.12 402 147 152 5 261.68 2.18