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 2 115 113 82.48 0.65 2 2 124 122 80.75 0.42 3 2 125 123 80.53 0.47 4 2 126 124 80.39 0.41 5 2 130 128 80.55 0.38 6 3 127 124 80.83 0.47 7 3 129 126 80.84 0.47 8 3 130 127 80.78 0.45 9 4 124 120 83.30 0.24 10 4 125 121 80.85 0.47 11 4 126 122 80.85 0.47 12 4 127 123 80.83 0.47 13 5 110 105 80.50 0.40 14 5 124 119 83.93 0.04 15 5 125 120 83.25 0.26 16 6 110 104 83.92 0.06 17 6 121 115 95.54 0.51 18 6 122 116 93.92 2.56 19 6 123 117 87.75 0.73 20 6 124 118 83.39 0.23 21 6 125 119 83.39 0.23 22 7 11 4 356.93 2.12 23 7 110 103 83.93 0.06 24 7 111 104 83.93 0.06 25 7 112 105 86.98 1.11 26 7 120 113 97.84 0.60 27 7 121 114 97.81 0.61 28 7 122 115 97.81 0.61 29 7 125 118 87.66 0.80 30 8 11 3 371.13 2.16 31 8 109 101 86.56 1.25 32 8 110 102 86.56 1.25 33 8 122 114 99.20 0.02 34 9 14 5 353.98 0.73 35 9 122 113 99.27 0.05 36 10 13 3 368.00 0.59 37 10 14 4 359.31 1.94 38 11 14 3 372.00 1.41 39 11 15 4 346.35 8.42 40 11 39 28 115.55 2.02 41 11 42 31 115.50 2.04 42 11 46 35 116.03 1.77 43 11 109 98 101.77 1.08 44 11 111 100 108.73 1.96 45 11 120 109 113.64 0.57 46 12 15 3 360.86 2.71 47 12 16 4 350.66 6.26 48 12 39 27 115.55 2.02 49 13 16 3 371.54 8.56 50 13 17 4 358.69 2.21 51 14 17 3 376.69 5.99 52 14 18 4 358.73 2.21 53 14 109 95 115.62 2.01 54 15 18 3 365.48 0.38 55 15 19 4 357.83 2.64 56 15 38 23 224.53 43.77 57 15 39 24 137.72 0.37 58 15 42 27 137.38 0.24 59 15 61 46 137.47 0.27 60 15 105 90 115.62 2.00 61 16 19 3 364.39 0.61 62 16 20 4 534.52 2.01 63 16 35 19 335.24 8.65 64 16 36 20 238.40 39.72 65 16 39 23 211.91 37.46 66 18 104 86 137.72 0.36 67 18 105 87 137.73 0.36 68 18 106 88 137.74 0.36 69 18 107 89 137.73 0.36 70 18 109 91 137.74 0.36 71 19 38 19 359.42 2.08 72 19 101 82 137.75 0.36 73 19 105 86 137.77 0.37 74 22 67 45 143.46 1.19 75 22 91 69 142.96 1.11 76 22 95 73 142.97 1.10 77 22 99 77 142.97 1.11 78 22 100 78 142.97 1.10 79 22 101 79 142.99 1.10 80 22 104 82 142.98 1.10 81 25 90 65 143.01 1.14 82 25 91 66 142.99 1.12 83 25 104 79 143.49 1.19 84 26 67 41 143.47 1.19 85 26 101 75 143.52 1.18 86 30 67 37 143.58 1.17 87 30 68 38 143.57 1.17 88 33 64 31 144.97 0.88 89 33 65 32 143.61 1.13 90 33 66 33 144.04 1.34 91 33 67 34 143.59 1.12 92 33 101 68 144.16 0.67 93 34 38 4 534.66 5.20 94 35 38 3 365.19 0.81 95 35 39 4 359.41 2.08 96 36 39 3 371.93 8.34 97 36 40 4 356.78 0.77 98 37 40 3 361.69 3.22 99 37 41 4 356.77 0.77 100 37 64 27 145.58 0.86 101 38 41 3 360.88 2.96 102 38 42 4 352.24 1.30 103 38 61 23 145.71 0.94 104 38 64 26 145.59 0.86 105 38 65 27 145.52 0.90 106 38 101 63 145.52 0.90 107 39 42 3 353.37 0.74 108 39 43 4 352.25 1.30 109 39 46 7 333.07 1.24 110 40 43 3 371.88 1.26 111 40 44 4 371.10 1.50 112 41 44 3 385.04 0.77 113 41 60 19 148.37 0.24 114 41 61 20 148.21 0.32 115 41 64 23 148.21 0.32 116 42 45 3 437.39 1.28 117 42 58 16 148.38 0.24 118 42 61 19 148.37 0.24 119 42 111 69 226.84 39.44 120 42 139 97 148.38 0.23 121 43 46 3 371.10 1.49 122 43 47 4 362.62 2.74 123 44 47 3 369.13 2.65 124 44 48 4 357.64 0.04 125 44 57 13 148.48 0.23 126 45 48 3 367.44 1.06 127 45 53 8 148.47 0.23 128 45 58 13 148.47 0.23 129 45 135 90 148.45 0.23 130 46 111 65 227.47 39.43 131 46 112 66 318.44 6.04 132 46 113 67 339.08 3.43 133 46 120 74 365.97 3.36 134 47 113 66 371.63 3.14 135 48 53 5 506.08 4.25 136 48 57 9 437.80 38.37 137 48 113 65 383.14 6.46 138 49 113 64 392.39 6.47 139 50 112 62 388.74 6.20 140 50 113 63 393.66 5.84 141 50 114 64 402.89 1.30 142 50 115 65 406.91 3.31 143 50 126 76 425.26 0.57 144 50 134 84 388.97 6.05 145 50 135 85 385.75 7.67 146 51 126 75 547.15 4.24 147 51 133 82 418.75 6.79 148 52 133 81 451.10 0.69 149 53 133 80 573.13 1.69 150 53 134 81 446.89 1.42 151 53 135 82 427.79 0.18 152 53 138 85 413.27 3.98 153 54 138 84 414.51 4.58 154 55 138 83 424.85 0.36 155 55 141 86 410.30 2.46 156 55 142 87 410.21 2.47 157 58 138 80 445.00 5.85 158 58 139 81 431.89 0.07 159 58 142 84 422.97 0.92 160 59 142 83 428.92 0.89 161 61 139 78 569.66 4.55 162 62 142 80 429.86 1.30 163 62 143 81 429.06 0.96 164 62 146 84 419.48 2.21 165 66 146 80 428.75 0.83 166 66 150 84 416.64 3.62 167 69 147 78 431.31 0.18 168 69 150 81 419.39 2.30 169 71 152 81 416.67 3.63 170 71 153 82 416.23 3.81 171 71 186 115 293.20 9.96 172 71 188 117 293.06 10.00 173 72 152 80 418.20 2.89 174 72 153 81 414.87 4.54 175 72 154 82 407.52 8.10 176 72 156 84 404.90 9.40 177 74 147 73 432.91 0.25 178 74 151 77 418.22 2.90 179 74 155 81 393.54 15.11 180 74 156 82 390.67 16.54 181 75 147 72 433.19 0.32 182 75 156 81 390.53 16.48 183 75 157 82 390.51 16.48 184 75 158 83 390.41 16.52 185 75 193 118 289.50 11.73 186 76 147 71 443.02 5.23 187 76 148 72 432.93 0.25 188 76 151 75 419.95 2.27 189 76 155 79 395.66 14.10 190 76 156 80 390.56 16.48 191 76 157 81 390.39 16.52 192 76 158 82 390.39 16.52 193 76 174 98 294.15 9.69 194 76 178 102 293.86 9.71 195 76 182 106 293.77 9.76 196 77 157 80 390.39 16.52 197 77 158 81 390.34 16.55 198 78 158 80 390.26 16.52 199 78 159 81 390.15 16.52 200 78 160 82 389.84 16.37 201 78 169 91 294.51 9.61 202 78 172 94 294.37 9.62 203 78 173 95 294.28 9.67 204 78 174 96 294.15 9.73 205 79 160 81 385.99 14.76 206 79 163 84 294.82 9.67 207 79 169 90 294.55 9.61 208 80 158 78 390.06 16.44 209 83 158 75 389.88 16.29 210 83 195 112 279.38 6.90 211 83 234 151 45.97 1.26 212 83 237 154 44.68 1.08 213 83 238 155 44.01 1.02 214 84 158 74 386.38 14.59 215 86 237 151 44.30 1.14 216 87 158 71 387.25 14.83 217 87 193 106 285.61 9.80 218 87 231 144 103.33 23.66 219 87 233 146 49.11 0.43 220 87 234 147 45.15 0.85 221 87 237 150 44.40 1.09 222 94 156 62 389.11 10.84 223 94 193 99 270.62 2.29 224 95 147 52 432.30 0.07 225 96 147 51 428.87 0.84 226 97 143 46 443.05 4.98 227 97 144 47 432.88 0.24 228 97 147 50 420.06 2.36 229 100 147 47 423.68 0.86 230 102 143 41 431.31 0.17 231 102 146 44 424.39 0.43 232 102 147 45 419.95 2.41 233 128 137 9 426.50 0.30 234 131 134 3 453.07 1.67 235 132 141 9 415.57 1.92 236 133 138 5 425.82 0.01 237 134 137 3 436.69 1.44 238 134 138 4 428.00 0.23 239 135 138 3 433.12 0.35 240 135 139 4 431.05 0.41 241 136 139 3 433.22 0.29 242 136 140 4 431.29 0.29 243 137 140 3 433.22 0.30 244 137 141 4 428.97 0.88 245 137 173 36 251.72 11.29 246 138 141 3 429.55 0.59 247 138 142 4 428.94 0.89 248 139 142 3 428.71 0.78 249 139 143 4 426.07 0.54 250 140 143 3 426.08 0.54 251 140 144 4 424.16 0.38 252 140 173 33 254.86 9.72 253 141 144 3 426.36 0.41 254 141 145 4 419.98 2.46 255 141 173 32 254.87 9.72 256 141 177 36 254.87 9.70 257 142 145 3 419.98 2.46 258 142 146 4 416.67 3.64 259 143 146 3 417.25 3.34 260 143 147 4 416.65 3.63 261 144 147 3 416.66 3.62 262 144 148 4 416.63 3.62 263 144 177 33 254.91 9.70 264 144 178 34 254.86 9.70 265 145 148 3 416.28 3.72 266 145 149 4 415.55 4.01 267 145 177 32 254.91 9.70 268 145 181 36 272.19 0.61 269 146 149 3 413.23 5.14 270 146 150 4 413.15 5.11 271 147 150 3 413.58 4.89 272 147 151 4 408.39 7.43 273 148 151 3 409.45 6.93 274 148 178 30 272.75 0.78 275 148 181 33 274.35 0.41 276 148 182 34 274.29 0.44 277 149 181 32 275.81 1.11 278 149 183 34 289.57 8.09 279 149 186 37 293.06 10.00 280 150 186 36 293.11 9.99 281 151 155 4 392.84 5.73 282 151 186 35 293.12 10.00 283 152 155 3 453.80 1.01 284 152 186 34 293.11 9.99 285 152 187 35 292.87 10.10 286 153 186 33 293.20 9.96 287 153 187 34 292.87 10.10 288 153 188 35 292.83 10.11 289 153 189 36 292.82 10.11 290 154 188 34 292.82 10.12 291 154 189 35 292.46 10.27 292 155 182 27 293.80 9.69 293 155 187 32 292.91 10.12 294 155 189 34 290.98 11.04 295 155 190 35 289.62 11.69 296 155 191 36 289.62 11.69 297 156 191 35 289.56 11.72 298 156 193 37 289.49 11.72 299 157 174 17 294.44 9.58 300 157 190 33 289.69 11.72 301 157 191 34 289.59 11.72 302 157 192 35 289.51 11.74 303 157 193 36 289.48 11.72 304 158 193 35 289.49 11.74 305 158 195 37 289.26 11.79 306 158 234 76 49.23 0.47 307 159 167 8 294.66 9.59 308 159 168 9 294.64 9.59 309 159 192 33 289.62 11.73 310 159 193 34 289.56 11.74 311 159 194 35 289.38 11.76 312 159 195 36 289.28 11.80 313 159 211 52 255.50 1.20 314 159 214 55 255.64 1.21 315 160 163 3 365.62 3.05 316 160 167 7 294.73 9.57 317 160 195 35 289.32 11.83 318 161 167 6 294.75 9.58 319 161 194 33 289.55 11.76 320 161 195 34 289.51 11.76 321 161 196 35 289.32 11.83 322 161 202 41 255.58 1.18 323 161 203 42 255.52 1.20 324 161 204 43 253.25 0.69 325 162 196 34 289.49 11.76 326 162 197 35 289.48 11.76 327 162 201 39 255.64 1.15 328 162 203 41 255.53 1.19 329 163 166 3 359.51 0.21 330 163 203 40 255.64 1.15 331 164 203 39 255.65 1.15 332 166 203 37 255.65 1.16 333 166 204 38 255.54 1.19 334 166 210 44 255.66 1.16 335 167 194 27 289.55 11.77 336 167 204 37 255.43 1.19 337 167 210 43 255.65 1.16 338 167 211 44 255.59 1.18 339 168 174 6 296.92 8.79 340 168 175 7 297.70 8.39 341 168 179 11 296.78 8.86 342 168 210 42 255.64 1.17 343 168 211 43 255.58 1.20 344 168 213 45 255.72 1.19 345 168 214 46 255.69 1.21 346 168 217 49 255.72 1.20 347 169 172 3 353.86 2.78 348 169 175 6 298.09 8.59 349 170 175 5 300.86 7.36 350 170 213 43 255.71 1.19 351 171 176 5 303.70 6.69 352 172 175 3 351.61 1.71 353 172 176 4 339.93 4.42 354 173 176 3 364.62 8.21 355 173 177 4 304.28 6.41 356 173 178 5 308.87 8.71 357 174 178 4 308.88 8.71 358 174 179 5 310.12 8.07 359 174 214 40 255.61 1.24 360 175 179 4 318.10 4.09 361 175 180 5 323.48 1.42 362 175 217 42 255.67 1.22 363 176 180 4 357.45 0.28 364 177 180 3 378.89 0.10 365 177 181 4 356.83 0.58 366 178 181 3 363.00 0.01 367 178 182 4 356.83 0.59 368 179 182 3 375.83 9.98 369 179 214 35 255.50 1.27 370 179 217 38 255.46 1.29 371 179 218 39 255.20 1.39 372 179 221 42 255.44 1.29 373 180 217 37 255.46 1.29 374 180 221 41 255.04 1.38 375 182 187 5 310.21 9.33 376 182 190 8 289.68 11.72 377 182 223 41 239.56 1.86 378 183 186 3 359.00 0.62 379 183 187 4 344.22 7.67 380 184 187 3 360.40 0.07 381 184 221 37 239.77 1.72 382 184 223 39 239.36 1.75 383 187 190 3 491.03 4.06 384 187 223 36 239.35 1.76 385 188 224 36 239.32 1.76 386 189 224 35 239.28 1.78 387 190 218 28 252.35 2.25 388 190 223 33 239.58 1.79 389 190 224 34 239.36 1.76 390 190 225 35 239.18 1.78 391 190 226 36 239.00 1.83 392 191 226 35 237.19 1.68 393 191 228 37 226.93 1.32 394 192 211 19 254.93 1.28 395 192 214 22 255.40 1.25 396 192 218 26 255.06 1.30 397 192 225 33 239.41 1.79 398 192 226 34 239.22 1.75 399 192 227 35 226.96 0.66 400 192 228 36 222.15 1.07 401 193 228 35 208.56 0.96 402 193 231 38 152.00 0.65 403 193 234 41 49.46 0.48 404 194 204 10 254.48 1.30 405 194 205 11 239.53 1.82 406 194 206 12 239.36 1.75 407 194 211 17 255.40 1.22 408 194 227 33 236.49 2.06 409 194 228 34 213.62 0.78 410 194 229 35 197.05 2.04 411 194 230 36 175.43 3.59 412 195 230 35 175.18 3.59 413 195 231 36 175.18 3.59 414 195 234 39 49.45 0.49 415 195 235 40 49.36 0.47 416 195 238 43 46.98 1.61 417 196 202 6 255.59 1.17 418 196 204 8 255.43 1.22 419 196 205 9 255.28 1.20 420 196 230 34 192.83 3.85 421 196 235 39 49.54 0.54 422 196 238 42 47.04 1.60 423 197 200 3 255.65 1.15 424 197 238 41 47.02 1.61 425 198 235 37 49.59 0.58 426 198 238 40 47.36 1.45 427 198 239 41 47.01 1.61 428 198 242 44 46.98 1.63 429 198 245 47 46.91 1.65 430 198 247 49 46.64 1.67 431 198 248 50 46.63 1.67 432 199 245 46 46.91 1.65 433 199 247 48 46.66 1.66 434 202 205 3 436.85 0.55 435 205 229 24 255.82 13.71 436 206 228 22 501.09 0.42 437 206 229 23 320.14 1.10 438 228 231 3 375.87 1.99 439 230 235 5 306.81 7.10 440 231 234 3 365.02 2.95 441 231 235 4 346.79 0.59 442 232 235 3 348.93 0.48 443 232 236 4 336.78 5.59 444 233 236 3 357.49 4.70 445 233 237 4 348.04 0.03 446 234 237 3 357.64 4.76 447 234 238 4 346.70 0.61 448 235 238 3 356.88 4.38 449 235 239 4 346.67 0.60 450 236 239 3 352.10 2.00 451 236 240 4 575.97 0.74