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 83.20 0.96 2 2 121 119 83.26 0.99 3 2 124 122 81.48 0.83 4 2 125 123 81.38 0.84 5 2 126 124 81.29 0.89 6 2 130 128 81.42 0.81 7 3 127 124 81.39 0.83 8 3 129 126 81.50 0.81 9 3 130 127 81.50 0.81 10 4 124 120 83.21 0.96 11 4 125 121 81.53 0.80 12 4 126 122 82.26 1.16 13 4 127 123 81.51 0.81 14 5 110 105 82.48 0.79 15 5 124 119 83.25 0.96 16 5 125 120 83.20 0.95 17 6 110 104 83.17 0.95 18 6 121 115 88.72 0.46 19 6 122 116 88.70 0.46 20 6 123 117 87.50 0.86 21 6 124 118 83.28 0.97 22 6 125 119 83.28 0.96 23 7 110 103 83.18 0.95 24 7 111 104 83.18 0.95 25 7 112 105 85.22 0.04 26 7 120 113 96.00 1.56 27 7 121 114 94.72 2.16 28 7 122 115 94.72 2.16 29 7 125 118 87.25 0.98 30 8 11 3 359.03 3.31 31 8 109 101 83.19 0.95 32 8 110 102 87.14 0.96 33 8 122 114 100.61 0.22 34 9 14 5 349.82 5.10 35 9 122 113 101.97 0.82 36 10 13 3 363.26 1.62 37 10 14 4 348.66 5.68 38 11 14 3 356.17 1.94 39 11 15 4 348.66 5.68 40 11 39 28 111.67 0.49 41 11 42 31 110.52 0.79 42 11 46 35 110.33 0.72 43 11 109 98 101.89 0.93 44 11 111 100 104.33 0.01 45 12 15 3 356.10 1.97 46 12 16 4 348.64 5.68 47 12 39 27 111.67 0.49 48 13 16 3 356.11 1.97 49 13 17 4 348.01 5.41 50 14 17 3 361.57 0.76 51 14 18 4 348.74 5.66 52 14 109 95 114.68 1.96 53 15 18 3 394.43 15.67 54 15 19 4 344.89 6.98 55 15 38 23 321.63 2.52 56 15 39 24 292.15 2.15 57 15 42 27 211.06 38.40 58 15 61 46 135.62 0.65 59 15 105 90 114.66 1.95 60 16 19 3 360.98 1.06 61 16 20 4 514.77 0.57 62 16 35 19 325.91 4.06 63 16 36 20 331.36 6.79 64 16 39 23 298.16 0.85 65 18 104 86 135.65 0.66 66 18 105 87 135.68 0.67 67 18 106 88 135.74 0.65 68 18 107 89 135.69 0.67 69 18 109 91 135.75 0.65 70 19 38 19 355.07 4.42 71 19 101 82 135.78 0.62 72 19 105 86 135.77 0.64 73 22 67 45 139.52 0.57 74 22 99 77 136.84 0.72 75 22 100 78 136.92 0.76 76 22 101 79 137.83 1.16 77 22 104 82 136.84 0.72 78 25 90 65 137.88 1.18 79 25 104 79 138.06 1.24 80 26 67 41 139.58 0.59 81 26 101 75 138.08 1.24 82 30 67 37 140.08 0.39 83 30 68 38 140.08 0.39 84 33 64 31 141.69 0.12 85 33 65 32 140.85 0.10 86 33 66 33 140.87 0.10 87 33 67 34 140.77 0.07 88 33 101 68 140.74 0.07 89 34 38 4 524.73 2.75 90 35 38 3 359.92 6.84 91 35 39 4 353.96 4.98 92 36 39 3 365.34 4.13 93 36 40 4 353.94 4.99 94 37 40 3 361.11 1.41 95 37 41 4 353.93 4.99 96 37 64 27 141.83 0.06 97 38 41 3 363.98 2.06 98 38 42 4 347.57 6.13 99 38 61 23 141.83 0.06 100 38 64 26 141.83 0.06 101 38 65 27 141.73 0.10 102 38 101 63 141.81 0.07 103 39 42 3 357.53 3.17 104 39 43 4 352.52 3.63 105 39 46 7 346.40 6.66 106 40 43 3 365.12 2.91 107 40 44 4 355.51 2.16 108 41 44 3 368.00 4.34 109 41 60 19 142.88 0.10 110 41 61 20 142.84 0.10 111 41 64 23 142.88 0.10 112 42 45 3 410.73 10.33 113 42 58 16 142.88 0.10 114 42 61 19 142.88 0.09 115 42 111 69 302.74 1.75 116 42 139 97 142.88 0.10 117 43 46 3 368.90 3.23 118 43 47 4 361.53 2.19 119 44 47 3 365.10 0.41 120 44 48 4 358.42 3.74 121 44 57 13 221.38 39.34 122 45 48 3 361.74 0.70 123 45 53 8 216.36 36.83 124 45 58 13 286.72 6.67 125 46 111 65 319.18 6.42 126 46 112 66 326.42 5.41 127 46 113 67 340.85 7.71 128 46 120 74 364.69 3.58 129 47 113 66 372.47 0.96 130 48 52 4 519.25 12.22 131 48 53 5 493.06 13.09 132 48 57 9 444.30 37.41 133 48 113 65 385.35 4.09 134 49 52 3 574.20 0.45 135 49 53 4 573.16 0.70 136 49 113 64 387.36 4.33 137 50 112 62 385.41 4.07 138 50 113 63 389.02 4.66 139 50 114 64 390.93 4.77 140 50 115 65 403.23 2.78 141 50 126 76 413.82 3.58 142 50 134 84 388.69 3.67 143 50 135 85 385.38 4.08 144 51 126 75 499.81 10.48 145 51 133 82 418.24 2.93 146 52 133 81 450.19 1.75 147 53 133 80 570.04 0.59 148 53 134 81 444.38 0.37 149 53 135 82 415.28 5.11 150 53 138 85 411.03 3.04 151 54 138 84 413.13 4.01 152 55 138 83 412.00 3.45 153 55 141 86 411.09 3.00 154 55 142 87 409.04 3.98 155 58 138 80 436.84 4.75 156 58 139 81 435.19 4.94 157 58 142 84 431.00 3.50 158 59 142 83 434.32 5.16 159 61 139 78 566.72 0.83 160 62 142 80 435.34 5.03 161 62 143 81 435.05 5.00 162 62 146 84 430.94 6.96 163 66 146 80 434.53 5.26 164 66 150 84 429.31 7.74 165 69 147 78 435.33 5.04 166 69 150 81 429.35 7.78 167 69 151 82 429.34 7.78 168 71 152 81 429.31 7.79 169 71 153 82 429.19 7.81 170 71 188 117 267.37 1.27 171 72 152 80 429.34 7.80 172 72 153 81 426.06 9.39 173 72 154 82 426.01 9.39 174 72 156 84 425.48 9.65 175 74 147 73 436.78 4.77 176 74 151 77 429.35 7.80 177 74 155 81 410.88 16.98 178 74 156 82 392.43 26.20 179 75 147 72 436.97 4.81 180 75 156 81 386.10 29.36 181 75 157 82 381.61 31.59 182 75 158 83 381.60 31.59 183 75 193 118 262.08 2.85 184 76 147 71 436.98 4.81 185 76 148 72 436.76 4.75 186 76 151 75 431.74 6.74 187 76 155 79 392.45 26.21 188 76 156 80 389.93 27.44 189 76 157 81 381.30 31.57 190 76 158 82 381.28 31.57 191 76 174 98 268.43 1.30 192 76 178 102 268.43 1.30 193 76 182 106 268.36 1.27 194 77 157 80 381.38 31.48 195 77 158 81 381.13 31.50 196 78 158 80 381.12 31.51 197 78 159 81 380.96 31.50 198 78 160 82 380.80 31.58 199 78 169 91 269.12 1.40 200 78 172 94 268.89 1.41 201 78 173 95 268.85 1.43 202 78 174 96 268.61 1.38 203 79 160 81 380.60 31.61 204 79 163 84 332.99 19.32 205 79 169 90 269.41 1.38 206 80 158 78 380.97 31.50 207 80 159 79 380.71 31.55 208 80 160 80 380.56 31.59 209 83 158 75 381.13 31.36 210 83 195 112 261.58 2.88 211 83 234 151 47.38 0.80 212 83 237 154 46.55 1.00 213 83 238 155 45.54 0.60 214 84 158 74 380.95 31.41 215 86 237 151 46.38 0.96 216 87 158 71 381.10 31.32 217 87 193 106 262.12 2.84 218 87 231 144 161.75 4.22 219 87 233 146 48.17 0.88 220 87 234 147 47.15 0.71 221 87 237 150 45.59 0.58 222 94 156 62 392.31 15.54 223 94 193 99 262.13 2.83 224 95 147 52 436.36 4.66 225 96 147 51 435.20 5.09 226 97 140 43 573.55 0.48 227 97 143 46 440.32 3.16 228 97 144 47 436.89 4.82 229 97 147 50 433.34 5.87 230 100 147 47 433.32 5.86 231 102 143 41 435.17 5.04 232 102 146 44 433.41 5.83 233 102 147 45 431.55 6.71 234 103 140 37 573.53 0.48 235 128 137 9 421.32 1.30 236 131 134 3 447.36 0.58 237 132 141 9 411.55 3.19 238 133 138 5 417.38 3.27 239 134 137 3 435.47 4.61 240 134 138 4 434.53 5.05 241 135 138 3 436.10 4.30 242 135 139 4 434.54 5.05 243 136 139 3 435.62 4.53 244 136 140 4 434.69 4.97 245 137 140 3 434.28 4.02 246 137 141 4 434.44 5.02 247 138 141 3 435.54 4.58 248 138 142 4 433.93 5.42 249 139 142 3 434.50 5.24 250 139 143 4 433.33 5.87 251 140 143 3 433.87 5.61 252 140 144 4 433.32 5.87 253 140 173 33 268.17 1.29 254 141 144 3 433.34 5.87 255 141 145 4 433.32 5.87 256 141 173 32 268.14 1.28 257 141 177 36 268.11 1.29 258 142 145 3 431.94 6.57 259 142 146 4 431.76 6.65 260 143 146 3 431.86 6.55 261 143 147 4 431.30 6.83 262 144 147 3 430.56 7.17 263 144 148 4 430.50 7.14 264 144 173 29 268.23 1.31 265 144 177 33 268.16 1.30 266 144 178 34 268.12 1.29 267 145 148 3 430.23 7.27 268 145 149 4 429.00 7.59 269 145 177 32 268.16 1.30 270 145 181 36 267.93 1.27 271 146 149 3 429.00 7.59 272 146 150 4 425.69 9.21 273 147 150 3 426.12 9.21 274 147 151 4 425.13 8.94 275 148 151 3 425.13 8.94 276 148 178 30 268.17 1.30 277 148 181 33 268.06 1.29 278 148 182 34 267.94 1.26 279 149 181 32 268.08 1.28 280 149 183 34 267.92 1.27 281 149 186 37 267.12 1.14 282 150 186 36 267.13 1.14 283 151 155 4 402.19 12.62 284 151 186 35 267.14 1.14 285 152 155 3 450.39 0.60 286 152 186 34 267.14 1.14 287 153 186 33 267.69 1.16 288 153 187 34 267.02 1.14 289 153 188 35 266.92 1.09 290 154 188 34 266.85 1.04 291 154 189 35 265.91 1.50 292 155 182 27 268.37 1.29 293 155 187 32 267.04 1.15 294 155 189 34 265.53 1.65 295 155 190 35 262.24 2.84 296 155 191 36 262.24 2.84 297 156 191 35 262.17 2.83 298 156 193 37 262.12 2.84 299 157 174 17 269.02 1.44 300 157 190 33 262.24 2.83 301 157 191 34 262.14 2.85 302 157 192 35 262.06 2.87 303 157 193 36 262.06 2.87 304 158 193 35 261.99 2.85 305 158 195 37 261.74 2.93 306 158 234 76 48.59 0.79 307 159 167 8 269.52 1.39 308 159 168 9 269.52 1.39 309 159 192 33 262.09 2.85 310 159 193 34 262.00 2.85 311 159 194 35 261.81 2.90 312 159 195 36 261.81 2.90 313 159 211 52 256.66 1.66 314 159 214 55 256.93 1.69 315 160 163 3 376.94 4.33 316 160 167 7 269.54 1.39 317 160 195 35 261.83 2.91 318 161 167 6 269.56 1.38 319 161 194 33 261.88 2.90 320 161 195 34 261.86 2.89 321 161 196 35 261.77 2.89 322 161 201 40 256.99 1.69 323 161 202 41 256.69 1.68 324 161 203 42 256.52 1.69 325 161 204 43 254.77 1.29 326 162 196 34 261.84 2.90 327 162 197 35 261.80 2.88 328 162 201 39 256.95 1.68 329 162 203 41 256.62 1.73 330 163 166 3 361.06 0.56 331 163 203 40 256.90 1.66 332 164 203 39 256.92 1.67 333 166 203 37 256.88 1.64 334 166 204 38 256.56 1.72 335 166 210 44 256.87 1.64 336 167 194 27 261.84 2.90 337 167 204 37 256.18 1.75 338 167 210 43 256.90 1.66 339 167 211 44 256.86 1.65 340 168 174 6 279.50 0.09 341 168 175 7 279.52 0.10 342 168 179 11 279.49 0.09 343 168 210 42 256.77 1.66 344 168 211 43 256.75 1.68 345 168 213 45 256.93 1.69 346 168 214 46 256.93 1.69 347 168 217 49 257.00 1.66 348 169 172 3 347.52 8.20 349 169 175 6 284.78 2.48 350 170 175 5 292.32 6.25 351 170 176 6 285.30 2.23 352 170 213 43 256.91 1.69 353 171 176 5 292.83 6.00 354 172 175 3 359.48 2.23 355 172 176 4 342.18 3.29 356 173 176 3 358.88 0.51 357 173 177 4 292.85 6.00 358 173 178 5 290.31 0.58 359 174 178 4 290.31 0.58 360 174 179 5 310.37 9.45 361 174 214 40 256.81 1.71 362 175 179 4 330.00 0.36 363 175 180 5 330.25 0.24 364 175 217 42 256.70 1.71 365 176 180 4 356.05 5.72 366 177 180 3 374.83 4.16 367 177 181 4 353.88 6.80 368 178 181 3 360.25 3.62 369 178 182 4 353.88 6.80 370 179 182 3 365.25 1.12 371 179 214 35 256.51 1.80 372 179 217 38 256.49 1.81 373 179 218 39 256.42 1.84 374 179 221 42 256.08 2.00 375 180 217 37 256.45 1.82 376 180 221 41 255.81 1.87 377 182 187 5 328.31 2.52 378 182 190 8 270.57 1.47 379 182 223 41 248.25 1.02 380 183 186 3 372.99 6.37 381 183 187 4 348.95 5.29 382 184 187 3 360.89 0.68 383 184 221 37 248.72 1.12 384 184 222 38 248.31 1.01 385 184 223 39 248.27 1.00 386 187 190 3 484.14 1.97 387 187 223 36 248.29 1.01 388 188 224 36 248.09 0.99 389 189 224 35 247.98 1.04 390 190 218 28 251.53 0.35 391 190 223 33 248.32 1.02 392 190 224 34 248.16 0.99 393 190 225 35 247.35 1.04 394 190 226 36 246.66 1.30 395 191 226 35 246.57 1.27 396 191 228 37 232.59 1.90 397 192 211 19 255.92 1.71 398 192 214 22 256.22 1.85 399 192 218 26 255.97 1.80 400 192 225 33 248.12 0.98 401 192 226 34 247.78 0.97 402 192 227 35 229.65 0.43 403 192 228 36 221.54 0.11 404 193 228 35 206.58 0.03 405 193 231 38 161.80 4.21 406 193 234 41 48.66 0.77 407 194 204 10 254.41 1.14 408 194 205 11 248.31 1.01 409 194 206 12 248.19 0.96 410 194 211 17 256.45 1.75 411 194 227 33 246.56 1.27 412 194 228 34 215.41 0.12 413 194 229 35 201.53 1.90 414 194 230 36 178.10 2.38 415 195 230 35 177.72 2.44 416 195 231 36 177.72 2.44 417 195 234 39 48.64 0.78 418 195 235 40 48.62 0.79 419 195 238 43 47.45 1.28 420 196 202 6 256.70 1.72 421 196 204 8 256.35 1.70 422 196 205 9 256.05 1.57 423 196 229 33 208.77 1.26 424 196 230 34 189.25 4.23 425 196 235 39 48.64 0.80 426 196 238 42 47.48 1.29 427 197 200 3 274.78 4.41 428 197 201 4 307.13 8.56 429 198 235 37 48.63 0.81 430 198 238 40 47.57 1.25 431 198 239 41 47.47 1.29 432 198 242 44 47.47 1.29 433 198 245 47 47.47 1.29 434 198 247 49 47.34 1.33 435 198 248 50 47.34 1.33 436 199 245 46 47.41 1.31 437 199 247 48 47.31 1.32 438 202 205 3 431.87 9.14 439 205 229 24 218.47 1.69 440 206 228 22 498.72 2.60 441 206 229 23 300.03 10.84 442 228 231 3 365.87 0.24 443 230 235 5 311.57 14.43 444 231 234 3 368.56 7.03 445 231 235 4 345.69 2.34 446 232 235 3 348.24 2.18 447 232 236 4 345.69 2.34 448 233 236 3 347.97 3.20 449 233 237 4 346.81 2.90 450 234 237 3 355.19 0.46 451 234 238 4 353.23 1.44 452 235 238 3 361.44 2.68 453 235 239 4 346.75 2.93 454 236 239 3 359.90 1.90