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 50 98 48 84.60 0.04 2 50 99 49 84.60 0.04 3 50 172 122 84.60 0.05 4 50 173 123 84.59 0.05 5 50 174 124 84.59 0.04 6 50 179 129 84.63 0.04 7 51 175 124 84.70 0.07 8 51 178 127 85.20 0.32 9 51 179 128 85.20 0.32 10 52 172 120 86.11 0.58 11 52 173 121 85.22 0.32 12 52 175 123 85.21 0.32 13 52 179 127 85.36 0.29 14 53 158 105 85.64 0.40 15 53 172 119 86.20 0.59 16 53 173 120 86.12 0.58 17 54 158 104 86.13 0.57 18 54 169 115 87.83 0.39 19 54 170 116 87.82 0.39 20 54 171 117 87.78 0.40 21 54 172 118 86.20 0.59 22 54 173 119 86.20 0.59 23 55 59 4 329.33 0.60 24 55 158 103 86.13 0.57 25 55 159 104 86.11 0.56 26 55 160 105 86.90 0.24 27 55 168 113 94.27 0.90 28 55 169 114 89.56 1.23 29 55 170 115 89.64 1.19 30 55 173 118 87.75 0.41 31 56 59 3 347.92 4.98 32 56 157 101 87.42 0.42 33 56 158 102 87.48 0.46 34 56 170 114 97.55 0.45 35 57 170 113 99.19 0.16 36 58 61 3 352.98 1.73 37 58 62 4 331.69 3.68 38 59 62 3 337.20 1.59 39 59 63 4 331.69 3.68 40 59 86 27 116.90 0.56 41 59 89 30 116.66 0.43 42 59 93 34 117.30 0.36 43 59 157 98 98.99 0.04 44 59 159 100 99.25 0.07 45 59 168 109 116.95 0.54 46 59 170 111 116.89 0.52 47 60 63 3 355.01 1.59 48 60 64 4 331.69 3.69 49 60 86 26 116.84 0.53 50 60 168 108 119.93 0.58 51 60 170 110 119.58 0.76 52 61 64 3 354.17 1.17 53 61 65 4 331.78 3.65 54 62 65 3 355.17 1.68 55 62 66 4 331.78 3.65 56 62 157 95 116.90 0.56 57 63 66 3 342.91 4.34 58 63 67 4 331.79 3.65 59 63 86 23 206.73 38.64 60 63 89 26 127.53 0.56 61 63 153 90 116.87 0.55 62 63 157 94 117.31 0.73 63 64 67 3 339.18 1.98 64 64 68 4 519.35 1.70 65 64 82 18 325.97 1.34 66 64 83 19 314.73 6.95 67 64 86 22 128.51 0.55 68 66 152 86 128.48 0.55 69 66 153 87 128.50 0.56 70 66 154 88 128.53 0.57 71 66 155 89 128.50 0.56 72 66 157 91 128.54 0.57 73 67 85 18 336.93 1.50 74 67 149 82 128.55 0.57 75 67 153 86 128.55 0.57 76 69 152 83 134.48 0.86 77 70 115 45 134.57 0.89 78 70 147 77 134.46 0.86 79 70 148 78 134.47 0.86 80 70 149 79 134.47 0.86 81 70 152 82 134.47 0.86 82 71 149 78 134.50 0.85 83 77 113 36 134.95 0.72 84 77 114 37 134.90 0.75 85 77 115 38 134.81 0.79 86 77 149 72 134.80 0.80 87 80 112 32 135.57 0.58 88 80 149 69 134.78 0.89 89 81 85 4 538.26 2.54 90 82 85 3 351.30 6.36 91 82 86 4 336.31 1.19 92 83 86 3 359.57 0.65 93 83 87 4 342.33 2.10 94 84 87 3 345.91 0.32 95 84 88 4 342.33 2.10 96 84 112 28 136.42 0.65 97 85 88 3 344.85 3.88 98 85 89 4 337.75 0.32 99 85 109 24 136.42 0.65 100 85 112 27 136.43 0.65 101 85 149 64 136.40 0.65 102 85 153 68 136.40 0.65 103 86 89 3 337.75 0.32 104 86 90 4 339.57 0.60 105 86 168 82 312.62 1.14 106 87 90 3 344.64 1.93 107 87 91 4 337.00 1.92 108 88 91 3 351.73 0.30 109 88 92 4 346.60 2.88 110 88 108 20 143.05 0.40 111 88 109 21 142.78 0.41 112 88 112 24 142.92 0.34 113 89 92 3 361.19 2.54 114 89 93 4 354.60 0.76 115 89 106 17 143.76 0.51 116 89 109 20 142.97 0.36 117 89 153 64 142.93 0.34 118 89 154 65 142.78 0.41 119 89 159 70 143.82 0.49 120 90 93 3 361.28 0.18 121 90 94 4 346.57 2.87 122 91 96 5 347.74 2.80 123 92 96 4 367.87 3.05 124 92 101 9 143.84 0.49 125 92 105 13 143.80 0.51 126 92 106 14 143.79 0.51 127 93 96 3 368.05 3.14 128 93 101 8 223.86 32.99 129 93 159 66 309.92 0.15 130 93 160 67 309.92 0.15 131 93 161 68 345.19 3.59 132 93 168 75 386.95 0.66 133 93 184 91 143.81 0.50 134 94 166 72 399.21 0.69 135 94 167 73 399.20 0.69 136 94 168 74 391.23 0.35 137 95 162 67 399.44 0.62 138 95 163 68 399.71 0.49 139 95 165 70 399.55 0.56 140 95 166 71 399.43 0.61 141 96 101 5 382.91 0.90 142 96 105 9 377.51 1.90 143 96 162 66 399.73 0.50 144 96 163 67 399.73 0.50 145 97 100 3 399.36 0.59 146 97 101 4 397.54 1.51 147 97 163 66 402.06 0.63 148 98 101 3 434.42 1.28 149 98 160 62 399.60 0.56 150 98 161 63 402.06 0.63 151 98 162 64 402.14 0.66 152 98 174 76 405.76 0.55 153 98 182 84 411.66 0.79 154 98 183 85 399.45 0.58 155 98 184 86 399.37 0.61 156 99 174 75 497.08 10.18 157 99 182 83 411.88 0.90 158 99 183 84 405.22 0.47 159 100 182 82 522.31 0.59 160 101 105 4 428.75 3.57 161 101 106 5 436.63 0.46 162 101 183 82 509.70 0.84 163 101 184 83 447.64 1.20 164 101 187 86 405.80 0.47 165 102 105 3 436.73 0.41 166 102 187 85 412.90 2.86 167 103 106 3 437.76 0.10 168 103 107 4 438.26 0.29 169 103 187 84 417.98 2.75 170 103 190 87 406.11 0.54 171 103 191 88 405.93 0.51 172 103 194 91 405.95 0.52 173 104 107 3 441.94 1.55 174 104 108 4 445.30 0.81 175 105 108 3 482.10 1.38 176 106 109 3 446.42 0.23 177 106 110 4 433.95 0.95 178 106 188 82 561.61 0.05 179 107 110 3 441.05 1.25 180 107 111 4 435.11 0.14 181 107 191 84 463.28 1.33 182 108 111 3 438.75 0.84 183 108 112 4 435.49 0.04 184 109 112 3 444.65 0.70 185 109 113 4 435.48 0.04 186 110 113 3 442.05 0.49 187 110 114 4 438.90 2.07 188 110 195 85 447.14 0.60 189 111 114 3 442.09 0.52 190 120 202 82 557.99 4.01 191 120 203 83 458.57 0.35 192 122 204 82 458.47 0.42 193 122 205 83 458.44 0.41 194 123 205 82 458.43 0.42 195 123 206 83 458.41 0.41 196 123 207 84 458.30 0.45 197 123 241 118 257.06 0.07 198 124 204 80 459.19 0.18 199 124 205 81 458.47 0.43 200 124 206 82 458.37 0.42 201 124 207 83 458.38 0.42 202 124 222 98 262.16 0.29 203 124 226 102 262.10 0.29 204 124 230 106 261.93 0.34 205 125 206 81 458.44 0.43 206 125 207 82 458.38 0.42 207 125 222 97 262.12 0.31 208 126 207 81 458.47 0.42 209 126 208 82 458.32 0.45 210 126 209 83 458.30 0.45 211 126 220 94 262.43 0.26 212 126 222 96 262.09 0.30 213 127 209 82 458.31 0.45 214 127 212 85 395.24 8.46 215 127 217 90 262.81 0.17 216 127 220 93 262.43 0.26 217 128 207 79 458.49 0.42 218 128 208 80 458.31 0.44 219 128 209 81 458.25 0.43 220 128 243 115 256.23 0.12 221 129 155 26 557.18 0.04 222 129 156 27 557.16 0.04 223 131 207 76 458.38 0.41 224 131 243 112 256.20 0.12 225 131 281 150 39.63 1.52 226 131 284 153 39.64 1.52 227 131 285 154 39.61 1.52 228 132 207 75 458.29 0.42 229 133 155 22 557.18 0.04 230 134 285 151 39.62 1.52 231 135 207 72 458.28 0.43 232 135 241 106 257.27 0.14 233 135 284 149 39.65 1.53 234 135 285 150 39.61 1.52 235 135 288 153 39.53 1.52 236 138 288 150 39.57 1.54 237 138 289 151 39.54 1.56 238 139 288 149 39.54 1.56 239 142 205 63 441.05 0.37 240 142 241 99 257.35 0.12 241 145 151 6 560.24 1.58 242 145 189 44 456.15 5.08 243 146 151 5 560.25 1.58 244 146 152 6 560.25 1.58 245 146 155 9 553.61 1.69 246 146 189 43 545.25 5.35 247 176 186 10 557.31 0.24 248 180 183 3 486.01 0.64 249 181 186 5 412.91 2.86 250 182 187 5 412.86 2.88 251 183 186 3 451.25 1.27 252 183 187 4 426.88 1.03 253 184 188 4 448.44 3.85 254 185 188 3 458.56 1.02 255 185 189 4 457.05 0.46 256 186 189 3 457.69 0.21 257 186 190 4 455.45 0.75 258 187 190 3 460.43 1.58 259 187 191 4 456.04 0.46 260 188 191 3 468.67 2.54 261 188 192 4 455.05 0.94 262 189 192 3 469.04 1.54 263 189 193 4 448.97 0.90 264 190 193 3 469.04 1.54 265 190 194 4 453.82 0.32 266 190 225 35 261.72 0.31 267 191 194 3 472.32 3.03 268 191 195 4 454.44 0.06 269 192 195 3 472.21 3.08 270 192 196 4 454.69 0.15 271 193 196 3 469.81 2.04 272 193 197 4 454.93 0.04 273 193 221 28 261.87 0.32 274 193 225 32 261.75 0.31 275 193 226 33 261.72 0.32 276 194 197 3 466.03 0.15 277 194 198 4 454.96 0.01 278 194 225 31 261.75 0.31 279 194 229 35 261.58 0.28 280 195 198 3 457.39 0.83 281 195 199 4 454.74 0.09 282 196 199 3 458.08 0.48 283 196 200 4 455.18 0.28 284 197 200 3 458.11 0.41 285 197 226 29 261.75 0.30 286 197 229 32 261.67 0.30 287 197 230 33 261.57 0.28 288 198 229 31 261.69 0.29 289 198 231 33 261.00 0.32 290 198 234 36 260.26 0.42 291 199 234 35 260.34 0.39 292 200 204 4 410.42 0.66 293 200 230 30 261.71 0.29 294 200 234 34 260.35 0.39 295 200 235 35 260.22 0.42 296 201 204 3 457.72 0.25 297 201 234 33 260.27 0.42 298 201 235 34 260.22 0.42 299 202 234 32 261.01 0.32 300 202 235 33 260.23 0.43 301 202 236 34 260.21 0.43 302 202 237 35 260.15 0.45 303 203 237 34 259.26 0.50 304 203 239 36 258.16 0.37 305 204 230 26 261.94 0.33 306 204 235 31 260.22 0.43 307 204 237 33 258.88 0.45 308 204 238 34 257.38 0.10 309 204 239 35 257.37 0.10 310 205 239 34 257.26 0.08 311 205 241 36 257.07 0.06 312 206 222 16 262.50 0.29 313 206 238 32 257.37 0.10 314 206 239 33 257.26 0.07 315 206 240 34 256.92 0.01 316 206 241 35 256.86 0.04 317 207 241 34 256.83 0.04 318 207 243 36 256.27 0.12 319 207 284 77 40.68 1.39 320 208 215 7 263.06 0.25 321 208 216 8 263.03 0.26 322 208 222 14 262.72 0.18 323 208 240 32 256.94 0.03 324 208 241 33 256.82 0.04 325 208 242 34 256.44 0.08 326 208 243 35 256.27 0.12 327 208 259 51 254.62 0.32 328 208 262 54 254.86 0.27 329 209 212 3 365.67 3.12 330 209 215 6 263.07 0.25 331 209 243 34 256.24 0.12 332 210 215 5 263.08 0.25 333 210 242 32 256.77 0.05 334 210 243 33 256.60 0.01 335 210 253 43 249.84 1.18 336 211 245 34 256.26 0.12 337 212 215 3 323.39 4.62 338 214 217 3 344.87 1.43 339 214 258 44 255.08 0.14 340 215 242 27 256.63 0.12 341 215 253 38 253.40 0.44 342 215 256 41 254.65 0.05 343 215 258 43 255.10 0.13 344 215 259 44 255.06 0.10 345 216 222 6 270.91 1.93 346 216 223 7 270.35 2.21 347 216 227 11 270.27 2.19 348 216 258 42 255.00 0.09 349 216 259 43 255.08 0.09 350 216 261 45 255.21 0.09 351 216 262 46 255.21 0.09 352 216 265 49 255.27 0.07 353 217 220 3 347.39 0.14 354 217 223 6 270.35 2.21 355 218 223 5 270.36 2.21 356 218 224 6 277.31 5.60 357 218 261 43 255.19 0.09 358 218 265 47 255.25 0.08 359 219 224 5 288.61 8.05 360 220 223 3 336.03 3.08 361 220 224 4 319.36 4.99 362 221 224 3 345.94 1.05 363 221 225 4 319.36 4.99 364 221 226 5 319.37 5.00 365 222 226 4 317.67 5.85 366 222 227 5 318.31 5.54 367 222 238 16 257.37 0.10 368 222 262 40 255.18 0.09 369 223 227 4 319.47 4.98 370 223 228 5 346.54 0.39 371 224 228 4 351.38 1.86 372 225 228 3 359.75 4.25 373 225 229 4 351.38 1.86 374 226 229 3 351.86 1.63 375 226 230 4 347.49 0.09 376 227 230 3 374.22 0.78 377 227 262 35 255.01 0.10 378 227 265 38 255.00 0.10 379 227 266 39 254.97 0.10 380 227 269 42 254.79 0.01 381 228 265 37 255.03 0.11 382 228 269 41 254.70 0.05 383 229 269 40 254.70 0.05 384 230 235 5 273.43 7.08 385 230 238 8 257.22 0.07 386 230 266 36 254.73 0.19 387 230 269 39 253.86 0.03 388 230 271 41 250.53 0.90 389 231 234 3 345.83 2.22 390 231 235 4 298.08 1.12 391 232 269 37 250.87 0.85 392 232 271 39 249.86 1.18 393 235 271 36 250.50 0.87 394 236 271 35 250.55 0.90 395 236 272 36 250.24 1.00 396 237 271 34 250.85 0.84 397 237 272 35 249.99 1.11 398 237 273 36 249.84 1.17 399 237 274 37 249.62 1.28 400 238 262 24 254.56 0.29 401 238 266 28 253.77 0.68 402 238 271 33 250.86 0.85 403 238 272 34 250.50 0.92 404 238 273 35 249.66 1.26 405 238 274 36 249.16 1.51 406 239 274 35 248.60 1.46 407 239 276 37 245.03 0.93 408 240 262 22 254.61 0.30 409 240 273 33 249.92 1.21 410 240 274 34 249.13 1.50 411 240 275 35 244.44 1.76 412 240 276 36 242.94 1.42 413 241 276 35 220.75 0.20 414 241 278 37 174.97 0.76 415 241 284 43 43.65 0.27 416 242 253 11 249.95 1.22 417 242 254 12 249.84 1.17 418 242 259 17 254.62 0.31 419 242 275 33 248.88 1.62 420 242 276 34 231.16 1.04 421 242 277 35 214.75 1.40 422 242 278 36 192.12 4.87 423 243 278 35 174.97 0.76 424 243 281 38 97.70 29.93 425 244 250 6 254.36 0.18 426 244 251 7 254.36 0.18 427 244 253 9 252.16 0.14 428 244 277 33 232.95 3.95 429 244 278 34 215.56 1.13 430 244 279 35 170.30 1.19 431 244 281 37 101.73 28.02 432 250 279 29 247.46 0.96 433 251 279 28 248.89 1.64 434 252 277 25 248.97 1.61 435 252 279 27 247.91 1.18 436 253 277 24 281.19 7.01 437 254 276 22 497.81 5.08 438 254 277 23 357.36 13.13 439 278 281 3 357.69 2.74 440 278 284 6 291.60 0.40 441 280 283 3 346.85 0.45 442 280 284 4 336.40 1.29 443 281 284 3 342.22 0.56 444 281 285 4 337.29 0.85 445 282 285 3 363.53 2.97 446 282 286 4 336.41 1.27 447 283 286 3 359.03 5.22 448 283 287 4 336.40 1.28 449 283 295 12 339.89 0.45 450 284 287 3 351.97 0.69 451 284 288 4 547.32 5.48