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 27.41 0.84 2 1 81 80 25.63 0.71 3 1 84 83 25.49 0.67 4 1 132 131 25.73 0.69 5 1 136 135 25.41 0.65 6 2 6 4 468.31 2.00 7 2 7 5 465.67 0.69 8 2 78 76 27.54 0.78 9 2 79 77 27.59 0.75 10 2 129 127 27.20 0.04 11 2 132 130 25.73 0.69 12 2 133 131 25.73 0.69 13 2 136 134 25.73 0.69 14 3 6 3 478.78 4.34 15 3 7 4 471.23 0.54 16 3 79 76 34.12 0.70 17 4 7 3 481.83 0.46 18 4 8 4 475.92 2.77 19 4 79 75 35.79 0.83 20 5 8 3 501.95 2.27 21 5 9 4 484.20 1.70 22 6 9 3 492.56 2.20 23 6 10 4 492.66 5.92 24 6 129 123 43.77 0.43 25 6 132 126 43.79 0.43 26 7 10 3 492.66 5.92 27 7 11 4 492.66 5.92 28 7 78 71 44.44 0.41 29 7 79 72 50.62 2.68 30 8 11 3 500.36 2.07 31 8 12 4 484.21 1.69 32 9 12 3 500.29 2.11 33 9 13 4 485.28 1.15 34 9 123 114 74.13 1.12 35 9 124 115 71.05 0.42 36 9 125 116 70.24 0.12 37 9 126 117 63.65 1.78 38 10 13 3 491.69 2.19 39 10 14 4 485.12 1.07 40 10 75 65 64.00 1.58 41 10 129 119 62.97 1.43 42 10 130 120 61.06 0.48 43 11 14 3 490.61 1.07 44 11 15 4 485.40 1.21 45 11 75 64 64.75 1.24 46 12 15 3 508.59 1.97 47 12 16 4 504.62 0.02 48 12 123 111 87.66 0.73 49 13 16 3 524.16 0.25 50 13 17 4 501.69 1.44 51 13 116 103 87.63 0.74 52 13 122 109 87.66 0.73 53 13 123 110 87.67 0.73 54 13 126 113 87.56 0.71 55 13 130 117 87.10 0.49 56 14 17 3 501.00 1.79 57 14 18 4 491.65 0.00 58 14 68 54 87.73 0.70 59 14 71 57 87.65 0.73 60 14 72 58 87.60 0.72 61 14 75 61 87.55 0.70 62 14 112 98 87.63 0.73 63 14 130 116 87.62 0.73 64 15 18 3 489.87 0.89 65 15 19 4 487.59 2.02 66 16 19 3 485.57 0.83 67 16 119 103 88.28 0.96 68 16 120 104 88.28 0.96 69 17 20 3 516.62 5.15 70 17 24 7 288.20 0.51 71 17 68 51 88.23 0.95 72 17 115 98 88.28 0.96 73 17 116 99 88.28 0.96 74 17 119 102 88.30 0.95 75 18 21 3 474.87 2.02 76 18 68 50 88.22 0.95 77 18 72 54 88.22 0.94 78 20 23 3 506.25 1.14 79 20 24 4 469.37 0.38 80 21 24 3 493.09 0.76 81 21 25 4 472.45 1.17 82 21 65 44 122.03 0.06 83 21 68 47 108.96 0.67 84 21 69 48 109.73 0.29 85 22 25 3 492.17 2.71 86 22 26 4 472.95 0.92 87 22 61 39 130.99 0.66 88 23 26 3 490.50 3.54 89 23 27 4 481.38 3.28 90 24 27 3 481.49 3.23 91 24 28 4 481.43 3.29 92 24 68 44 131.06 0.62 93 24 115 91 131.19 0.64 94 24 119 95 141.59 0.08 95 25 28 3 493.04 5.22 96 25 29 4 481.43 3.30 97 25 64 39 131.09 0.61 98 25 68 43 131.06 0.62 99 26 29 3 496.46 0.55 100 26 30 4 488.20 0.07 101 26 60 34 142.60 0.30 102 26 61 35 142.61 0.30 103 26 64 38 141.94 0.01 104 27 30 3 488.47 0.21 105 27 31 4 488.20 0.07 106 27 115 88 142.52 0.29 107 28 31 3 490.61 1.28 108 28 32 4 479.94 4.05 109 28 67 39 143.22 0.32 110 28 68 40 143.00 0.32 111 28 108 80 142.50 0.28 112 28 111 83 142.52 0.29 113 28 112 84 142.52 0.29 114 28 115 87 142.56 0.30 115 29 32 3 499.96 0.64 116 29 33 4 475.06 0.24 117 29 46 17 190.32 23.14 118 29 60 31 143.41 0.31 119 29 63 34 143.29 0.33 120 29 64 35 143.25 0.33 121 29 67 38 143.25 0.34 122 30 33 3 495.28 4.76 123 30 34 4 476.37 0.42 124 30 51 21 143.68 0.41 125 30 55 25 143.46 0.31 126 30 60 30 143.41 0.32 127 31 34 3 490.16 7.32 128 31 35 4 479.09 1.78 129 31 111 80 142.84 0.14 130 32 35 3 498.76 3.01 131 32 36 4 473.69 0.90 132 32 39 7 406.07 0.70 133 32 108 76 142.84 0.14 134 32 111 79 142.86 0.15 135 33 36 3 490.87 1.97 136 33 37 4 461.41 7.02 137 33 39 6 406.07 0.71 138 33 40 7 333.85 20.70 139 33 43 10 338.63 5.28 140 33 46 13 252.89 1.03 141 33 51 18 144.22 0.17 142 33 54 21 144.18 0.20 143 34 37 3 505.10 2.62 144 34 51 17 144.22 0.17 145 35 111 76 143.21 0.29 146 36 39 3 507.48 0.73 147 36 107 71 142.88 0.14 148 36 110 74 143.26 0.30 149 36 111 75 143.27 0.30 150 37 40 3 509.00 0.03 151 38 41 3 506.61 0.27 152 38 42 4 506.57 0.28 153 39 42 3 507.41 0.66 154 39 43 4 506.58 0.67 155 40 43 3 506.59 0.67 156 40 46 6 280.58 9.17 157 40 47 7 255.87 0.49 158 40 54 14 194.11 25.12 159 41 47 6 255.87 0.49 160 41 48 7 255.88 0.49 161 42 99 57 143.05 0.23 162 42 100 58 143.06 0.23 163 42 104 62 143.28 0.29 164 43 46 3 485.35 0.05 165 43 47 4 408.50 18.96 166 43 63 20 144.17 0.25 167 45 49 4 515.22 1.88 168 45 59 14 144.39 0.28 169 46 49 3 490.49 3.11 170 46 54 8 268.23 2.40 171 46 59 13 144.40 0.29 172 46 60 14 144.39 0.28 173 46 63 17 144.22 0.24 174 49 53 4 443.54 15.43 175 49 54 5 442.60 15.01 176 50 53 3 485.53 5.56 177 50 54 4 456.62 8.89 178 51 54 3 487.89 2.41 179 51 55 4 460.92 11.04 180 52 55 3 492.49 0.14 181 52 56 4 476.35 0.98 182 53 56 3 495.92 1.60 183 53 57 4 468.09 2.28 184 54 57 3 492.69 0.01 185 54 60 6 335.91 26.55 186 55 60 5 401.99 6.50 187 57 60 3 483.59 3.72 188 59 62 3 499.15 2.75 189 59 63 4 487.67 1.85 190 60 63 3 493.12 1.53 191 60 64 4 486.96 1.50 192 61 64 3 494.34 0.92 193 61 65 4 486.59 1.68 194 62 65 3 497.97 3.38 195 62 66 4 490.28 3.48 196 63 66 3 499.19 2.77 197 63 67 4 490.58 0.32 198 64 67 3 502.90 2.83 199 64 68 4 490.55 0.33 200 65 68 3 493.62 1.81 201 65 69 4 479.55 0.47 202 66 69 3 495.25 0.42 203 66 70 4 481.35 1.36 204 67 70 3 499.87 2.73 205 67 71 4 475.90 1.35 206 68 71 3 490.18 1.18 207 68 72 4 479.56 3.19 208 68 115 47 209.68 4.94 209 69 72 3 492.26 2.22 210 69 73 4 479.57 3.20 211 70 73 3 491.22 0.67 212 70 74 4 487.92 0.98 213 70 91 21 205.36 5.16 214 70 94 24 205.67 5.71 215 71 74 3 491.24 0.67 216 71 75 4 487.93 0.99 217 71 112 41 209.74 4.98 218 71 130 59 210.15 4.85 219 72 75 3 486.06 1.93 220 72 76 4 483.32 3.31 221 73 76 3 483.32 3.31 222 73 77 4 483.32 3.31 223 73 87 14 238.41 0.63 224 74 77 3 493.01 1.53 225 74 78 4 468.98 1.80 226 74 84 10 294.95 6.37 227 74 87 13 238.43 0.64 228 74 88 14 229.54 5.07 229 74 91 17 229.53 5.07 230 74 133 59 210.09 4.87 231 74 137 63 209.99 4.86 232 75 78 3 493.11 1.57 233 75 130 55 210.28 4.86 234 75 133 58 210.17 4.86 235 77 80 3 494.78 1.72 236 77 83 6 308.28 6.74 237 77 84 7 294.99 6.37 238 77 87 10 294.95 6.37 239 78 84 6 330.61 14.16 240 78 133 55 210.25 4.83 241 80 83 3 505.68 1.21 242 80 84 4 484.62 0.68 243 81 84 3 498.10 5.00 244 81 85 4 489.54 3.13 245 82 85 3 502.20 2.94 246 82 86 4 504.05 2.02 247 83 86 3 497.92 1.04 248 83 87 4 486.56 4.61 249 84 87 3 497.90 1.05 250 84 88 4 481.17 2.40 251 84 133 49 225.31 0.71 252 84 136 52 225.08 0.78 253 85 88 3 497.88 1.06 254 85 89 4 488.53 0.41 255 86 89 3 498.69 1.31 256 86 90 4 485.73 1.80 257 87 90 3 496.20 2.56 258 87 91 4 485.69 1.78 259 88 91 3 498.54 1.39 260 88 92 4 485.74 1.76 261 88 136 48 225.27 0.72 262 88 137 49 225.13 0.79 263 88 140 52 224.12 0.42 264 89 92 3 489.97 0.90 265 89 93 4 485.76 1.71 266 90 93 3 487.85 0.69 267 90 94 4 485.77 1.72 268 91 94 3 495.40 3.02 269 91 95 4 485.74 1.73 270 91 105 14 242.92 3.10 271 91 137 46 225.40 0.72 272 92 95 3 494.33 0.51 273 92 96 4 489.10 0.04 274 92 140 48 225.16 0.78 275 92 141 49 224.38 0.49 276 92 144 52 224.16 0.39 277 93 96 3 502.67 2.06 278 93 97 4 489.18 0.14 279 94 97 3 506.04 1.12 280 94 98 4 489.17 0.14 281 95 98 3 492.36 1.45 282 95 99 4 488.97 0.06 283 95 100 5 448.78 3.97 284 95 105 10 401.64 15.52 285 95 141 46 225.45 0.71 286 96 99 3 483.73 2.65 287 96 100 4 475.02 1.69 288 96 141 45 225.44 0.71 289 96 144 48 225.34 0.73 290 96 146 50 224.25 0.40 291 100 104 4 487.54 3.29 292 100 105 5 484.97 0.38 293 100 141 41 227.34 1.24 294 101 104 3 507.67 0.03 295 101 105 4 497.93 1.91 296 101 141 40 227.32 1.24 297 101 146 45 225.58 0.86 298 102 105 3 492.56 3.20 299 102 106 4 480.95 2.40 300 102 138 36 227.36 1.24 301 102 141 39 227.36 1.24 302 102 142 40 227.34 1.24 303 102 146 44 225.65 0.86 304 103 106 3 496.62 1.16 305 103 107 4 480.95 2.39 306 104 107 3 494.94 0.32 307 104 108 4 484.04 0.84 308 105 108 3 494.42 4.96 309 105 109 4 487.55 1.52 310 105 137 32 227.75 1.21 311 105 138 33 227.73 1.23 312 105 141 36 227.70 1.21 313 106 109 3 496.36 2.89 314 106 110 4 489.47 0.56 315 106 138 32 227.76 1.22 316 107 110 3 493.51 1.47 317 107 111 4 490.41 0.09 318 108 111 3 503.56 0.88 319 108 112 4 489.45 0.56 320 108 134 26 228.46 1.01 321 109 112 3 508.35 1.52 322 109 113 4 508.35 1.52 323 109 131 22 228.47 0.99 324 109 134 25 228.45 0.99 325 109 135 26 228.46 0.99 326 109 138 29 228.41 1.00 327 110 113 3 561.10 3.11 328 111 114 3 506.99 0.43 329 111 115 4 491.38 0.35 330 112 115 3 501.59 0.87 331 112 116 4 487.49 0.58 332 112 130 18 229.09 1.06 333 112 134 22 228.94 1.11 334 113 116 3 491.78 1.54 335 113 117 4 481.95 0.01 336 113 127 14 229.21 1.10 337 113 131 18 229.15 1.08 338 114 117 3 486.92 2.38 339 114 118 4 488.45 3.27 340 115 118 3 494.54 0.24 341 115 119 4 494.54 0.24 342 116 119 3 496.06 0.53 343 116 120 4 488.45 3.27 344 116 122 6 374.24 20.07 345 117 120 3 496.06 0.53 346 117 122 5 393.56 10.40 347 122 126 4 439.13 9.73 348 122 127 5 411.02 0.81 349 123 126 3 498.50 4.39 350 125 128 3 494.55 5.45 351 125 129 4 485.32 1.64 352 126 129 3 486.12 1.24 353 126 130 4 484.67 1.96 354 127 130 3 485.71 1.44 355 127 131 4 484.70 1.95 356 128 131 3 503.85 4.41 357 128 132 4 484.68 1.93 358 129 132 3 501.43 5.62 359 129 133 4 485.52 2.35 360 130 133 3 490.21 0.01 361 130 134 4 485.52 2.35 362 131 134 3 492.06 0.92 363 131 135 4 485.45 2.39 364 132 135 3 493.00 1.39 365 132 136 4 494.42 2.10 366 133 136 3 498.34 0.15 367 133 137 4 491.82 3.41 368 134 137 3 495.06 1.79 369 134 138 4 491.81 3.41 370 135 138 3 495.06 1.79 371 135 139 4 492.88 2.88 372 136 139 3 487.36 1.50 373 136 140 4 478.56 1.19 374 137 140 3 489.81 2.38 375 137 141 4 478.59 1.20 376 138 141 3 494.80 0.02 377 138 142 4 485.41 4.61 378 139 142 3 497.16 1.16 379 139 143 4 483.22 5.70 380 140 143 3 498.57 0.45 381 140 144 4 476.86 8.88 382 141 144 3 481.07 6.78 383 141 145 4 469.44 5.17 384 141 146 5 420.86 3.74 385 142 145 3 489.19 3.31 386 142 146 4 445.61 16.12