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 1 185 267 82 75.44 0.14 2 185 268 83 75.97 0.09 3 185 270 85 75.98 0.08 4 186 215 29 76.00 0.09 5 186 216 30 76.02 0.09 6 186 267 81 76.33 0.24 7 187 212 25 76.01 0.09 8 187 215 28 76.08 0.06 9 187 265 78 76.01 0.09 10 187 266 79 76.33 0.24 11 187 267 80 76.83 0.00 12 187 270 83 81.50 1.44 13 187 271 84 76.32 0.24 14 187 272 85 75.92 0.08 15 188 214 26 94.42 0.37 16 188 215 27 94.54 0.46 17 188 272 84 76.42 0.29 18 189 272 83 84.55 2.15 19 190 212 22 96.84 0.73 20 190 272 82 88.88 0.01 21 191 212 21 96.84 0.73 22 191 272 81 93.97 0.58 23 191 273 82 88.88 0.01 24 191 274 83 82.14 1.13 25 192 210 18 97.31 0.73 26 192 211 19 97.08 0.84 27 192 212 20 96.81 0.74 28 192 263 71 96.78 0.72 29 192 265 73 95.09 0.30 30 192 272 80 94.76 0.41 31 192 273 81 94.34 0.45 32 192 274 82 87.34 0.75 33 193 210 17 97.34 0.74 34 193 211 18 97.31 0.73 35 194 208 14 97.68 0.89 36 194 209 15 97.66 0.88 37 194 210 16 97.36 0.74 38 194 225 31 97.36 0.74 39 194 261 67 97.47 0.78 40 194 263 69 97.34 0.74 41 194 274 80 94.77 0.41 42 194 276 82 94.29 0.46 43 195 208 13 97.69 0.88 44 195 209 14 97.67 0.88 45 196 208 12 97.69 0.89 46 196 261 65 97.72 0.88 47 196 278 82 94.35 0.46 48 197 207 10 99.75 0.12 49 197 278 81 94.39 0.44 50 198 276 78 95.16 0.31 51 198 278 80 94.38 0.44 52 198 279 81 94.38 0.44 53 199 278 79 94.49 0.42 54 199 279 80 94.40 0.45 55 199 281 82 94.34 0.45 56 199 350 135 90.86 0.06 57 199 351 136 94.19 0.47 58 199 353 138 90.51 0.11 59 199 355 140 78.09 1.06 60 200 204 4 384.66 0.72 61 200 205 5 377.98 1.02 62 200 206 6 278.37 27.95 63 200 249 49 359.07 0.06 64 200 251 51 376.11 1.96 65 200 278 78 94.92 0.37 66 200 279 79 94.55 0.45 67 200 280 80 94.34 0.45 68 200 281 81 94.33 0.46 69 201 204 3 393.30 1.76 70 201 281 80 94.34 0.45 71 201 357 140 88.74 0.96 72 202 252 50 442.18 6.67 73 202 253 51 492.42 6.04 74 202 256 54 405.75 0.55 75 202 280 78 94.63 0.46 76 202 281 79 94.39 0.45 77 202 282 80 94.31 0.47 78 203 251 48 492.99 18.39 79 203 252 49 520.38 4.70 80 204 250 46 535.89 2.87 81 204 251 47 536.46 3.15 82 205 248 43 546.14 0.83 83 205 249 44 545.29 1.26 84 205 250 45 537.49 2.64 85 206 249 43 545.32 1.25 86 208 225 17 523.88 9.47 87 227 278 51 94.98 0.32 88 251 280 29 94.64 0.36 89 255 280 25 94.94 0.36 90 256 280 24 94.97 0.35 91 256 282 26 94.88 0.38 92 257 279 22 95.11 0.39 93 257 280 23 94.98 0.36 94 258 277 19 95.34 0.35 95 258 278 20 95.25 0.35 96 258 279 21 95.01 0.35 97 259 277 18 95.27 0.35 98 259 278 19 95.10 0.38 99 259 280 21 94.88 0.37 100 260 275 15 95.33 0.35 101 260 276 16 95.29 0.35 102 261 275 14 95.26 0.34 103 261 276 15 95.10 0.35 104 261 278 17 94.86 0.37 105 262 274 12 95.26 0.34 106 262 275 13 95.07 0.36 107 263 273 10 95.25 0.34 108 263 274 11 95.14 0.35 109 264 272 8 95.34 0.33 110 264 273 9 95.24 0.34 111 265 271 6 95.34 0.33 112 265 272 7 95.31 0.32 113 266 270 4 129.74 0.32 114 266 271 5 95.35 0.33 115 267 270 3 384.64 6.16 116 279 350 55 301.68 0.24 117 279 351 56 316.72 0.04 118 281 348 51 320.79 0.99 119 281 350 53 320.82 0.99 120 281 355 58 319.81 1.07 121 282 348 50 320.99 0.97 122 283 346 47 320.81 0.98 123 283 347 48 321.01 0.97 124 283 348 49 321.01 0.98 125 283 355 56 321.03 0.95 126 283 356 57 320.95 0.97 127 283 357 58 306.33 0.75 128 284 307 23 321.43 0.54 129 285 307 22 321.88 0.58 130 285 357 56 321.31 0.80 131 286 307 21 321.88 0.58 132 286 344 42 320.72 0.97 133 286 346 44 321.81 0.61 134 286 357 55 321.74 0.63 135 286 358 56 321.68 0.60 136 286 359 57 318.92 0.70 137 287 305 18 321.88 0.58 138 287 306 19 321.90 0.59 139 287 344 41 321.85 0.58 140 287 359 56 321.73 0.59 141 288 303 15 321.91 0.59 142 288 304 16 321.92 0.59 143 288 342 38 321.69 0.56 144 288 343 39 321.85 0.58 145 288 344 40 321.87 0.58 146 288 359 55 321.81 0.60 147 288 360 56 321.75 0.58 148 288 361 57 318.95 0.55 149 289 303 14 321.94 0.58 150 289 304 15 321.95 0.58 151 289 306 17 321.97 0.58 152 290 293 3 376.62 3.58 153 290 302 12 322.02 0.55 154 290 303 13 322.01 0.55 155 290 342 36 321.89 0.59 156 290 361 55 321.86 0.59 157 290 362 56 321.85 0.59 158 290 363 57 320.74 0.96 159 291 301 10 322.05 0.53 160 291 302 11 322.06 0.54 161 292 295 3 386.78 1.48 162 292 363 55 321.87 0.59 163 293 361 52 321.97 0.60 164 293 363 54 321.81 0.60 165 293 364 55 321.81 0.61 166 294 364 54 321.81 0.60 167 294 366 56 321.78 0.61 168 295 299 4 372.25 1.39 169 295 301 6 337.24 8.04 170 295 333 22 375.23 0.10 171 295 364 53 321.89 0.61 172 295 365 54 321.79 0.61 173 295 366 55 321.78 0.61 174 296 299 3 396.19 2.94 175 296 365 53 321.87 0.61 176 296 366 54 321.78 0.61 177 297 333 20 435.35 7.25 178 297 335 22 403.13 1.99 179 297 365 52 321.91 0.61 180 297 366 53 321.81 0.59 181 297 367 54 321.74 0.59 182 297 395 82 200.69 0.45 183 298 332 18 547.24 0.27 184 298 333 19 546.84 0.42 185 301 363 46 322.00 0.65 186 333 365 32 335.35 6.09 187 334 365 31 335.43 6.05 188 335 365 30 335.48 6.02 189 335 367 32 335.17 6.11 190 335 395 60 200.53 0.40 191 337 363 26 336.43 5.57 192 337 365 28 335.53 5.93 193 338 363 25 336.43 5.57 194 338 364 26 336.08 5.66 195 338 365 27 335.44 5.88 196 338 367 29 335.83 5.69 197 338 397 59 200.46 0.42 198 339 362 23 336.64 5.46 199 339 363 24 336.64 5.46 200 340 362 22 336.62 5.46 201 340 363 23 336.61 5.46 202 341 360 19 336.67 5.46 203 341 361 20 336.62 5.46 204 341 362 21 336.31 5.47 205 342 360 18 336.64 5.46 206 342 361 19 336.61 5.45 207 342 363 21 336.24 5.49 208 343 359 16 336.69 5.43 209 343 360 17 336.48 5.37 210 344 358 14 336.72 5.42 211 344 359 15 336.62 5.39 212 345 357 12 336.75 5.42 213 345 358 13 336.69 5.41 214 346 356 10 336.88 5.39 215 346 357 11 336.75 5.41 216 347 354 7 337.09 5.38 217 347 355 8 337.04 5.37 218 347 356 9 336.93 5.41 219 348 354 6 337.12 5.37 220 348 355 7 337.06 5.37 221 349 352 3 389.59 0.53 222 349 353 4 343.10 3.90 223 349 354 5 337.12 5.37 224 350 353 3 370.36 1.46 225 350 355 5 343.08 3.27 226 365 397 32 200.47 0.36 227 366 397 31 200.47 0.36 228 366 398 32 200.59 0.40 229 366 436 70 200.55 0.39 230 367 395 28 200.59 0.40 231 367 396 29 200.55 0.42 232 367 397 30 200.61 0.40 233 368 395 27 200.83 0.42 234 368 436 68 200.57 0.39 235 369 395 26 200.82 0.42 236 369 400 31 200.56 0.41 237 369 432 63 200.52 0.39 238 369 434 65 201.00 0.35 239 369 436 67 201.18 0.31 240 369 437 68 201.10 0.31 241 369 438 69 200.62 0.38 242 369 439 70 200.52 0.39 243 370 394 24 200.88 0.39 244 370 395 25 200.94 0.39 245 371 376 5 344.82 1.95 246 371 392 21 268.25 34.07 247 371 393 22 263.41 31.62 248 371 394 23 200.94 0.39 249 371 402 31 201.14 0.31 250 371 430 59 200.58 0.40 251 371 432 61 201.15 0.31 252 371 439 68 201.15 0.32 253 371 441 70 200.56 0.39 254 372 375 3 383.66 3.43 255 372 376 4 369.62 1.08 256 372 441 69 201.16 0.32 257 373 376 3 382.63 3.94 258 373 377 4 411.06 1.01 259 373 441 68 201.21 0.33 260 375 393 18 383.90 2.89 261 376 430 54 211.55 1.48 262 376 441 65 209.55 0.59 263 376 443 67 209.39 0.60 264 377 443 66 209.43 0.58 265 378 441 63 209.80 0.59 266 378 442 64 209.57 0.63 267 378 443 65 209.43 0.58 268 378 444 66 209.40 0.60 269 379 444 65 209.39 0.59 270 380 443 63 209.88 0.60 271 380 444 64 209.59 0.53 272 380 445 65 209.38 0.59 273 380 446 66 209.34 0.58 274 381 446 65 209.36 0.58 275 381 448 67 209.27 0.59 276 382 420 38 287.67 4.96 277 382 424 42 284.89 3.97 278 382 445 63 209.85 0.62 279 382 446 64 209.46 0.61 280 382 447 65 209.31 0.60 281 382 448 66 209.28 0.59 282 383 420 37 287.72 4.94 283 383 448 65 209.28 0.61 284 384 420 36 287.72 4.94 285 384 422 38 287.70 4.94 286 384 447 63 209.61 0.55 287 384 448 64 209.40 0.61 288 384 449 65 209.24 0.59 289 384 450 66 188.47 1.95 290 385 419 34 287.75 4.95 291 385 420 35 287.74 4.95 292 386 419 33 287.70 4.96 293 386 420 34 287.73 4.96 294 387 417 30 287.47 5.03 295 387 418 31 287.61 4.96 296 388 417 29 287.31 4.98 297 388 418 30 287.44 5.01 298 388 420 32 287.47 4.99 299 389 415 26 277.56 0.46 300 389 416 27 283.07 3.20 301 389 417 28 283.31 3.09 302 390 412 22 251.44 0.92 303 390 413 23 251.44 0.92 304 390 414 24 251.44 0.92 305 390 415 25 275.45 1.41 306 390 416 26 283.07 3.20 307 390 418 28 287.35 5.04 308 391 415 24 255.25 2.73 309 392 402 10 216.52 1.01 310 392 404 12 211.56 1.48 311 392 414 22 246.98 3.15 312 392 430 38 211.58 1.48 313 393 402 9 216.76 0.93 314 394 400 6 238.00 0.96 315 394 402 8 217.67 0.78 316 394 432 38 213.54 0.48 317 395 400 5 299.34 19.84 318 396 399 3 376.83 0.04 319 396 400 4 354.18 0.70 320 397 436 39 213.34 0.58 321 398 434 36 213.63 0.53 322 398 435 37 213.56 0.49 323 398 436 38 213.35 0.58 324 400 432 32 217.11 0.45 325 400 433 33 214.56 0.16 326 400 434 34 213.72 0.50 327 401 431 30 345.49 2.35 328 401 432 31 223.55 2.70 329 401 433 32 214.83 0.12 330 402 430 28 416.50 1.06 331 402 431 29 344.93 2.63 332 402 432 30 222.56 0.35 333 403 430 27 540.41 0.72 334 403 431 28 381.01 1.04 335 412 443 31 210.75 0.30 336 412 445 33 209.72 0.68 337 420 447 27 209.80 0.64 338 421 447 26 209.84 0.62 339 422 447 25 209.90 0.59 340 422 449 27 209.81 0.64 341 424 445 21 210.34 0.53 342 424 447 23 210.06 0.62 343 425 445 20 210.34 0.53 344 425 446 21 210.12 0.62 345 425 447 22 210.06 0.60 346 426 444 18 210.95 0.38 347 426 445 19 210.40 0.56 348 427 442 15 211.86 0.14 349 427 443 16 211.46 0.27 350 427 444 17 210.86 0.33 351 428 442 14 211.86 0.15 352 428 443 15 211.23 0.15 353 428 445 17 210.89 0.32 354 429 440 11 212.24 0.07 355 429 441 12 212.08 0.14 356 429 442 13 211.86 0.15 357 430 440 10 212.23 0.07 358 430 441 11 211.96 0.19 359 430 443 13 211.81 0.14 360 431 438 7 212.86 0.28 361 431 439 8 212.47 0.14 362 431 440 9 212.24 0.07 363 432 438 6 212.83 0.29 364 432 439 7 212.46 0.14 365 433 437 4 270.50 28.54 366 433 438 5 212.53 0.19 367 434 437 3 377.11 1.90