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 1 80 79 28.23 0.43 2 1 81 80 25.84 0.33 3 1 84 83 25.84 0.33 4 1 132 131 25.86 0.34 5 1 136 135 24.75 0.12 6 2 6 4 453.77 0.76 7 2 7 5 445.45 4.54 8 2 10 8 445.45 4.54 9 2 78 76 31.39 0.14 10 2 79 77 31.41 0.14 11 2 129 127 29.93 0.94 12 2 132 130 25.87 0.34 13 2 133 131 25.87 0.34 14 2 136 134 25.87 0.34 15 3 6 3 485.57 4.26 16 3 7 4 479.04 1.43 17 3 79 76 32.40 0.24 18 4 7 3 492.63 7.79 19 4 8 4 479.48 1.21 20 4 79 75 34.36 1.21 21 5 8 3 501.31 3.45 22 5 9 4 481.84 2.82 23 6 9 3 496.19 2.75 24 6 10 4 479.76 1.09 25 6 129 123 45.26 0.10 26 6 132 126 45.27 0.12 27 7 10 3 495.69 0.64 28 7 11 4 482.73 2.53 29 7 78 71 45.83 0.15 30 7 79 72 45.84 0.15 31 8 11 3 490.50 2.74 32 8 12 4 486.79 4.56 33 9 12 3 496.62 5.78 34 9 13 4 490.50 2.70 35 9 123 114 74.05 2.08 36 9 124 115 73.56 1.83 37 9 125 116 70.76 0.45 38 9 126 117 64.45 1.02 39 10 13 3 498.57 4.80 40 10 14 4 489.28 2.06 41 10 129 119 66.61 1.19 42 10 130 120 63.32 0.46 43 11 14 3 491.20 1.10 44 11 15 4 491.19 1.11 45 11 75 64 67.25 0.90 46 12 15 3 508.69 4.21 47 12 16 4 501.58 0.65 48 12 123 111 86.79 0.83 49 13 16 3 523.99 3.07 50 13 17 4 500.74 1.07 51 13 116 103 86.75 0.83 52 13 122 109 86.79 0.83 53 13 123 110 86.80 0.83 54 13 126 113 86.70 0.82 55 13 130 117 86.70 0.83 56 14 17 3 499.25 1.81 57 14 18 4 490.89 0.98 58 14 68 54 87.17 0.96 59 14 71 57 86.80 0.81 60 14 72 58 86.83 0.82 61 14 75 61 86.76 0.83 62 14 112 98 86.78 0.83 63 14 130 116 86.76 0.83 64 15 18 3 500.22 5.65 65 15 19 4 488.22 0.35 66 16 19 3 488.25 0.34 67 16 119 103 91.72 1.14 68 16 120 104 87.60 0.92 69 17 20 3 507.34 2.09 70 17 24 7 294.12 1.35 71 17 68 51 87.51 0.92 72 17 115 98 87.53 0.91 73 17 116 99 87.52 0.91 74 17 119 102 87.64 0.96 75 18 21 3 481.02 1.82 76 18 68 50 87.47 0.92 77 18 72 54 87.47 0.92 78 20 23 3 501.19 2.16 79 20 24 4 469.12 1.91 80 21 24 3 504.05 8.58 81 21 25 4 469.03 1.96 82 21 65 44 119.69 1.51 83 21 68 47 111.20 1.63 84 21 69 48 111.20 1.62 85 22 25 3 500.79 3.46 86 22 26 4 477.33 2.19 87 22 61 39 124.80 0.21 88 23 26 3 500.79 3.46 89 23 27 4 479.34 3.21 90 24 27 3 489.81 2.03 91 24 28 4 478.64 3.56 92 24 68 44 125.30 0.20 93 24 115 91 128.82 0.29 94 24 119 95 134.26 0.20 95 25 28 3 489.81 2.03 96 25 29 4 486.68 0.47 97 25 64 39 130.59 2.21 98 25 68 43 125.29 0.19 99 26 29 3 496.66 1.40 100 26 30 4 486.69 0.48 101 26 60 34 136.28 0.36 102 26 61 35 136.28 0.36 103 26 64 38 134.23 0.44 104 27 30 3 495.72 4.04 105 27 31 4 477.68 4.99 106 27 115 88 135.78 0.21 107 28 31 3 495.75 4.04 108 28 32 4 495.74 4.04 109 28 67 39 136.66 0.22 110 28 68 40 136.65 0.23 111 28 108 80 135.47 0.10 112 28 111 83 135.48 0.10 113 28 112 84 135.48 0.10 114 28 115 87 135.53 0.08 115 29 32 3 502.90 0.46 116 29 33 4 495.74 4.04 117 29 60 31 136.86 0.24 118 29 63 34 136.79 0.24 119 29 64 35 136.68 0.23 120 29 67 38 136.68 0.23 121 30 33 3 495.74 4.04 122 30 34 4 477.51 5.08 123 30 51 21 137.82 0.50 124 30 55 25 136.91 0.23 125 30 60 30 136.87 0.24 126 31 34 3 487.60 2.18 127 31 35 4 484.36 2.65 128 32 35 3 498.46 2.62 129 32 36 4 480.00 0.48 130 32 39 7 412.56 0.68 131 32 108 76 136.16 0.21 132 32 111 79 136.34 0.33 133 33 36 3 499.49 1.77 134 33 37 4 457.60 2.23 135 33 39 6 396.07 8.93 136 33 40 7 389.10 12.41 137 33 43 10 335.80 6.53 138 33 46 13 264.57 0.56 139 33 51 18 138.38 0.39 140 33 54 21 138.37 0.38 141 34 37 3 505.16 2.12 142 34 51 17 138.41 0.38 143 35 111 76 136.75 0.24 144 36 39 3 505.60 0.44 145 36 107 71 136.37 0.10 146 36 110 74 136.75 0.24 147 36 111 75 136.81 0.27 148 37 40 3 509.01 1.75 149 38 41 3 510.82 2.15 150 38 42 4 505.50 0.53 151 39 42 3 510.84 2.14 152 39 43 4 502.25 2.16 153 40 43 3 512.24 2.84 154 40 46 6 320.41 19.73 155 40 47 7 264.75 0.47 156 40 54 14 243.56 1.85 157 41 47 6 264.72 0.48 158 41 48 7 265.03 0.33 159 42 99 57 136.42 0.12 160 42 100 58 136.44 0.14 161 42 104 62 136.71 0.22 162 43 46 3 487.80 0.33 163 43 47 4 469.49 6.50 164 43 63 20 138.25 0.24 165 43 66 23 138.25 0.25 166 44 47 3 492.44 2.23 167 45 49 4 508.78 3.24 168 45 59 14 230.65 3.29 169 46 49 3 499.59 0.64 170 46 54 8 277.12 5.82 171 46 57 11 256.37 4.00 172 46 59 13 242.77 2.77 173 46 60 14 230.61 3.27 174 46 63 17 230.48 3.23 175 49 53 4 468.25 4.10 176 49 54 5 452.14 3.95 177 49 57 8 387.98 14.08 178 50 53 3 472.66 1.90 179 50 54 4 472.65 1.90 180 51 54 3 481.81 2.68 181 51 55 4 472.64 1.90 182 52 55 3 491.14 6.94 183 52 56 4 486.00 1.06 184 53 56 3 491.44 1.65 185 53 57 4 476.66 3.60 186 54 57 3 486.00 1.06 187 54 60 6 328.09 6.73 188 55 60 5 369.30 25.25 189 57 60 3 492.62 2.23 190 59 62 3 499.84 1.23 191 59 63 4 486.85 0.77 192 60 63 3 494.71 0.78 193 60 64 4 485.63 1.37 194 61 64 3 497.68 1.54 195 61 65 4 485.62 1.38 196 62 65 3 499.88 4.62 197 62 66 4 485.63 1.38 198 63 66 3 499.88 4.62 199 63 67 4 487.36 0.48 200 64 67 3 489.63 0.65 201 64 68 4 481.53 3.40 202 65 68 3 489.62 0.65 203 65 69 4 487.36 0.48 204 66 69 3 486.81 1.17 205 66 70 4 486.81 1.17 206 67 70 3 488.70 0.22 207 67 71 4 486.81 1.16 208 68 71 3 486.81 1.17 209 68 72 4 486.48 1.01 210 68 115 47 185.67 2.92 211 69 72 3 492.00 1.86 212 69 73 4 486.45 1.02 213 70 73 3 490.73 2.50 214 70 74 4 486.96 1.29 215 70 87 17 233.50 1.99 216 70 91 21 184.60 2.98 217 70 94 24 185.35 2.79 218 71 74 3 486.64 1.45 219 71 75 4 486.64 1.45 220 71 112 41 185.86 2.91 221 71 134 63 185.71 2.94 222 72 75 3 497.36 3.88 223 72 76 4 482.20 2.46 224 73 76 3 485.37 0.89 225 73 77 4 481.28 1.99 226 73 87 14 248.30 2.62 227 74 77 3 494.65 1.71 228 74 78 4 469.62 3.83 229 74 84 10 248.34 2.75 230 74 87 13 241.59 5.98 231 74 88 14 241.57 5.97 232 74 91 17 233.62 2.01 233 74 133 59 186.07 2.96 234 74 137 63 185.87 2.85 235 75 78 3 491.34 4.26 236 75 130 55 186.09 2.96 237 77 80 3 499.96 0.18 238 77 83 6 294.91 0.20 239 77 84 7 294.88 0.21 240 77 87 10 276.56 9.37 241 78 84 6 352.30 18.43 242 78 133 55 186.15 2.94 243 80 83 3 499.59 1.02 244 80 84 4 476.39 0.39 245 81 84 3 484.76 1.16 246 81 85 4 476.39 0.39 247 82 85 3 497.29 0.13 248 82 86 4 485.73 2.33 249 83 86 3 485.74 2.33 250 83 87 4 480.36 4.51 251 84 87 3 490.29 0.04 252 84 88 4 489.78 0.20 253 84 133 49 215.28 3.66 254 84 136 52 214.96 3.70 255 85 88 3 493.69 2.15 256 85 89 4 483.65 3.29 257 86 89 3 496.95 0.04 258 86 90 4 483.62 3.31 259 87 90 3 501.93 2.53 260 87 91 4 483.62 3.31 261 88 91 3 489.79 0.23 262 88 92 4 483.62 3.31 263 88 136 48 215.17 3.63 264 88 137 49 215.08 3.65 265 88 140 52 214.86 3.70 266 89 92 3 487.26 1.14 267 89 93 4 474.78 1.11 268 90 93 3 489.49 6.27 269 90 94 4 473.88 2.72 270 91 94 3 502.69 5.38 271 91 95 4 492.84 1.43 272 91 105 14 232.88 1.09 273 91 137 46 215.32 3.68 274 92 95 3 494.01 1.97 275 92 96 4 492.84 1.39 276 92 140 48 215.14 3.62 277 92 141 49 214.93 3.66 278 92 144 52 214.84 3.69 279 93 96 3 500.13 0.73 280 93 97 4 492.84 1.40 281 94 97 3 505.39 1.20 282 94 98 4 492.86 1.41 283 95 98 3 495.29 0.21 284 95 99 4 500.94 2.65 285 95 100 5 462.75 3.25 286 95 105 10 328.14 16.76 287 95 141 46 215.27 3.68 288 96 99 3 492.75 6.74 289 96 100 4 471.35 0.47 290 96 141 45 215.28 3.69 291 96 144 48 215.17 3.64 292 96 146 50 214.94 3.72 293 100 104 4 487.87 3.79 294 100 105 5 486.64 4.40 295 100 141 41 219.00 3.55 296 101 104 3 500.87 0.61 297 101 105 4 487.87 3.79 298 101 141 40 219.00 3.55 299 101 146 45 214.99 3.74 300 102 105 3 487.87 3.79 301 102 106 4 486.64 4.40 302 102 138 36 219.22 3.45 303 102 141 39 219.02 3.55 304 102 142 40 219.00 3.56 305 102 146 44 215.08 3.79 306 103 106 3 487.87 3.79 307 103 107 4 486.63 4.41 308 104 107 3 488.87 3.27 309 104 108 4 487.89 3.73 310 105 108 3 479.50 0.46 311 105 109 4 478.06 1.43 312 105 137 32 219.52 3.56 313 105 138 33 219.50 3.56 314 105 141 36 219.32 3.61 315 106 109 3 495.41 0.46 316 106 110 4 483.11 3.96 317 106 138 32 219.53 3.56 318 106 142 36 219.52 3.56 319 107 110 3 489.82 3.25 320 107 111 4 487.17 1.93 321 108 111 3 501.62 1.90 322 108 112 4 485.78 1.35 323 108 134 26 220.03 3.60 324 109 112 3 507.14 0.86 325 109 113 4 504.70 0.35 326 109 131 22 220.03 3.58 327 109 134 25 220.03 3.60 328 109 135 26 220.03 3.60 329 109 138 29 219.93 3.54 330 110 113 3 563.76 0.52 331 111 114 3 500.57 0.44 332 111 115 4 489.11 0.88 333 112 115 3 489.13 0.86 334 112 116 4 489.11 0.88 335 112 130 18 220.34 3.60 336 112 134 22 220.22 3.63 337 113 116 3 485.29 3.07 338 113 117 4 481.73 2.82 339 113 127 14 220.41 3.62 340 113 131 18 220.41 3.62 341 114 117 3 485.29 3.07 342 114 118 4 481.73 2.81 343 115 118 3 482.90 3.88 344 115 119 4 485.50 2.56 345 116 119 3 502.21 2.17 346 116 120 4 481.07 4.78 347 116 122 6 381.75 20.03 348 117 120 3 487.92 3.77 349 117 122 5 393.09 16.41 350 122 126 4 432.73 3.83 351 122 127 5 404.00 10.54 352 123 126 3 493.41 1.28 353 125 128 3 498.20 4.60 354 125 129 4 482.12 3.44 355 126 129 3 498.21 4.60 356 126 130 4 482.13 3.44 357 127 130 3 482.31 3.53 358 127 131 4 482.16 3.46 359 128 131 3 482.30 3.53 360 128 132 4 477.01 6.03 361 129 132 3 487.93 0.72 362 129 133 4 476.85 6.12 363 130 133 3 493.11 3.31 364 130 134 4 487.78 0.66 365 131 134 3 479.94 4.57 366 131 135 4 479.94 4.57 367 132 135 3 479.13 5.06 368 132 136 4 479.14 5.06 369 133 136 3 486.25 1.54 370 133 137 4 479.19 5.07 371 134 137 3 479.19 5.07 372 134 138 4 479.17 5.07 373 135 138 3 479.29 5.02 374 135 139 4 479.28 5.01 375 136 139 3 484.75 7.71 376 136 140 4 477.43 5.94 377 137 140 3 484.74 7.70 378 137 141 4 477.36 5.91 379 138 141 3 489.26 0.20 380 138 142 4 478.38 6.42 381 139 142 3 478.39 6.42 382 139 143 4 478.39 6.43 383 140 143 3 492.34 0.55 384 140 144 4 478.39 6.43 385 141 144 3 491.12 0.07 386 141 145 4 486.26 2.50 387 141 146 5 433.68 3.20 388 142 145 3 489.24 1.01 389 142 146 4 436.69 4.71