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 2 143 141 36.34 0.89 2 2 217 215 36.18 0.82 3 3 14 11 36.38 0.87 4 3 57 54 36.37 0.87 5 3 139 136 37.20 0.82 6 3 143 140 36.37 0.89 7 3 144 141 36.34 0.89 8 3 147 144 36.34 0.89 9 3 216 213 36.36 0.86 10 3 217 214 36.36 0.86 11 4 139 135 38.63 0.80 12 4 217 213 37.12 0.86 13 5 9 4 291.63 2.14 14 5 11 6 298.19 1.15 15 5 137 132 118.31 40.38 16 5 139 134 39.68 1.06 17 6 137 131 208.37 0.41 18 6 138 132 203.69 1.41 19 7 136 129 223.41 0.42 20 7 137 130 217.99 2.04 21 8 11 3 526.49 2.21 22 8 62 54 266.79 0.01 23 8 64 56 266.87 0.12 24 8 65 57 266.34 0.17 25 8 85 77 265.37 0.28 26 8 86 78 261.12 0.93 27 8 136 128 233.78 0.55 28 8 137 129 223.43 0.42 29 10 62 52 268.10 0.34 30 10 63 53 268.12 0.35 31 10 64 54 268.09 0.35 32 11 14 3 630.10 1.61 33 11 59 48 268.12 0.35 34 11 60 49 268.71 0.63 35 11 61 50 268.39 0.28 36 11 62 51 268.10 0.34 37 11 137 126 267.89 0.28 38 11 139 128 267.63 0.35 39 11 213 202 170.61 1.48 40 12 212 200 170.62 1.47 41 12 213 201 170.61 1.48 42 12 226 214 118.39 0.29 43 13 59 46 269.50 0.31 44 13 60 47 269.50 0.31 45 13 210 197 170.55 1.44 46 13 211 198 170.68 1.45 47 13 212 199 170.62 1.47 48 13 213 200 170.62 1.48 49 13 226 213 118.40 0.28 50 13 227 214 118.50 0.27 51 13 228 215 118.39 0.28 52 14 57 43 270.19 0.06 53 14 58 44 269.68 0.23 54 14 59 45 269.50 0.31 55 14 139 125 269.17 0.44 56 14 210 196 170.72 1.45 57 14 211 197 170.69 1.44 58 14 213 199 170.71 1.49 59 14 216 202 170.69 1.53 60 15 57 42 270.42 0.12 61 15 58 43 270.21 0.04 62 15 208 193 170.42 1.30 63 15 209 194 170.72 1.45 64 15 210 195 170.72 1.45 65 16 56 40 270.68 0.01 66 16 57 41 270.43 0.12 67 16 148 132 255.15 0.20 68 16 151 135 249.61 0.21 69 16 155 139 236.46 0.96 70 16 207 191 170.72 1.45 71 16 208 192 170.72 1.46 72 16 209 193 170.72 1.45 73 16 211 195 170.81 1.47 74 17 55 38 270.80 0.02 75 17 56 39 270.69 0.01 76 17 58 41 270.69 0.01 77 17 206 189 170.69 1.44 78 17 207 190 170.73 1.46 79 17 208 191 170.72 1.45 80 18 52 34 272.23 0.31 81 18 53 35 271.09 0.06 82 18 54 36 270.81 0.02 83 18 55 37 270.81 0.02 84 18 152 134 249.64 0.21 85 18 155 137 245.48 1.53 86 18 206 188 170.72 1.46 87 18 207 189 170.74 1.46 88 18 209 191 170.82 1.46 89 19 24 5 395.43 0.21 90 19 51 32 272.81 0.14 91 19 52 33 272.75 0.13 92 19 53 34 271.31 0.11 93 19 55 36 270.91 0.04 94 19 205 186 170.72 1.46 95 19 206 187 170.73 1.46 96 20 23 3 462.69 0.68 97 20 24 4 417.20 9.18 98 20 48 28 273.01 0.12 99 20 51 31 272.81 0.14 100 20 52 32 272.76 0.14 101 20 164 144 180.72 4.92 102 20 168 148 180.38 4.75 103 20 204 184 170.72 1.46 104 20 205 185 170.73 1.46 105 20 206 186 170.78 1.46 106 20 240 220 79.38 0.53 107 20 241 221 73.20 0.78 108 21 24 3 448.87 6.65 109 21 25 4 408.31 6.61 110 21 42 21 290.69 0.24 111 21 51 30 272.81 0.14 112 21 53 32 272.79 0.14 113 21 117 96 272.83 0.09 114 22 25 3 459.89 1.14 115 22 26 4 605.59 0.04 116 22 42 20 291.03 0.39 117 22 51 29 272.81 0.14 118 22 241 219 73.21 0.78 119 22 242 220 73.00 0.84 120 22 243 221 64.30 1.77 121 23 203 180 170.79 1.46 122 23 204 181 170.81 1.46 123 23 205 182 170.81 1.46 124 23 241 218 73.27 0.81 125 24 205 181 170.81 1.46 126 25 42 17 427.10 0.84 127 25 245 220 58.55 0.96 128 26 203 177 170.81 1.46 129 26 241 215 78.98 0.72 130 26 244 218 64.72 1.48 131 26 245 219 57.48 1.28 132 27 198 171 118.63 0.28 133 27 203 176 170.85 1.47 134 27 205 178 170.88 1.47 135 29 245 216 58.48 0.97 136 30 203 173 170.91 1.48 137 31 198 167 118.77 0.32 138 35 245 210 64.36 1.82 139 37 122 85 272.97 0.02 140 38 42 4 557.74 3.19 141 38 117 79 272.95 0.04 142 38 118 80 272.96 0.04 143 38 123 85 272.97 0.04 144 39 42 3 422.29 3.25 145 39 245 206 59.17 0.80 146 42 51 9 286.97 1.19 147 43 51 8 309.17 9.72 148 44 48 4 463.77 0.40 149 44 51 7 330.80 1.08 150 44 168 124 180.71 4.82 151 44 243 199 72.67 0.72 152 45 48 3 477.93 5.45 153 45 51 6 357.00 13.99 154 47 50 3 465.81 0.60 155 48 51 3 465.53 0.47 156 48 165 117 180.75 4.90 157 48 168 120 180.59 4.83 158 49 52 3 471.39 2.46 159 49 156 107 249.37 0.34 160 49 161 112 195.61 1.12 161 49 165 116 180.78 4.88 162 50 53 3 491.32 1.46 163 50 156 106 249.38 0.34 164 51 168 117 180.59 4.84 165 51 243 192 67.14 0.42 166 52 152 100 253.58 0.22 167 52 155 103 249.44 0.30 168 52 156 104 248.06 0.08 169 52 164 112 180.74 4.89 170 52 207 155 170.83 1.47 171 53 115 62 275.08 0.24 172 53 117 64 276.44 0.86 173 53 152 99 251.21 0.96 174 54 115 61 276.33 0.85 175 54 116 62 276.38 0.88 176 54 148 94 271.11 3.44 177 54 149 95 269.68 3.24 178 54 152 98 262.63 6.74 179 55 116 61 276.70 0.76 180 55 125 70 277.61 0.73 181 55 129 74 277.70 0.77 182 55 206 151 170.72 1.46 183 56 129 73 277.74 0.75 184 56 148 92 267.95 5.10 185 57 133 76 279.30 0.71 186 57 144 87 275.74 1.25 187 57 147 90 268.01 5.11 188 57 148 91 266.45 5.86 189 57 151 94 263.68 7.24 190 57 216 159 170.80 1.50 191 58 129 71 279.31 0.72 192 58 133 75 279.31 0.71 193 58 208 150 170.72 1.46 194 59 75 16 305.08 4.94 195 59 133 74 279.34 0.71 196 59 137 78 279.35 0.72 197 59 139 80 279.35 0.71 198 60 75 15 309.75 2.60 199 61 65 4 425.06 2.54 200 61 66 5 417.12 1.43 201 61 70 9 352.18 8.22 202 61 71 10 333.44 1.17 203 61 72 11 331.97 0.46 204 61 75 14 310.09 2.44 205 62 65 3 431.88 1.52 206 62 66 4 423.56 1.79 207 62 75 13 332.00 0.47 208 62 137 75 289.07 1.48 209 63 66 3 425.43 2.36 210 63 67 4 423.57 1.79 211 64 67 3 449.00 5.76 212 64 68 4 423.60 1.79 213 64 85 21 355.93 6.53 214 65 68 3 449.60 3.33 215 65 70 5 359.74 4.66 216 65 75 10 352.49 8.26 217 65 82 17 352.56 8.24 218 65 85 20 353.28 7.82 219 65 86 21 352.50 8.21 220 66 69 3 439.86 2.68 221 66 70 4 356.01 6.51 222 68 84 16 412.49 1.63 223 68 85 17 410.70 1.91 224 69 74 5 439.09 0.62 225 70 74 4 427.99 2.88 226 70 75 5 427.93 2.85 227 70 82 12 423.33 0.62 228 70 83 13 424.77 1.28 229 70 84 14 426.12 1.96 230 70 85 15 423.30 0.60 231 71 74 3 469.68 4.88 232 71 75 4 433.87 1.32 233 72 75 3 453.85 4.25 234 72 76 4 453.44 3.47 235 73 76 3 461.62 0.61 236 73 77 4 463.02 1.32 237 74 77 3 467.91 1.11 238 74 78 4 463.03 1.32 239 74 82 8 463.07 1.30 240 75 78 3 467.92 1.11 241 75 79 4 453.38 3.47 242 75 80 5 461.59 0.60 243 75 82 7 490.45 0.12 244 75 86 11 630.63 1.16 245 75 136 61 463.08 1.30 246 75 137 62 461.58 0.60 247 76 132 56 633.26 0.47 248 102 141 39 547.53 1.67 249 102 145 43 465.28 3.99 250 103 141 38 548.97 1.05 251 104 141 37 549.01 1.07 252 104 142 38 547.71 1.67 253 104 145 41 508.16 17.34 254 105 142 37 549.01 1.07 255 108 142 34 547.70 1.66 256 108 145 37 546.98 1.91 257 108 146 38 456.41 0.46 258 112 145 33 456.34 0.45 259 112 149 37 453.45 0.83 260 115 149 34 453.48 0.83 261 115 152 37 434.16 0.99 262 115 156 41 407.45 0.36 263 116 145 29 465.15 3.96 264 116 148 32 453.78 0.75 265 126 145 19 454.98 1.12 266 130 139 9 614.11 3.45 267 130 141 11 505.90 17.23 268 130 144 14 455.00 1.11 269 130 145 15 454.98 1.11 270 133 139 6 611.27 1.19 271 133 144 11 454.98 1.12 272 134 139 5 551.07 3.48 273 134 144 10 454.99 1.12 274 139 144 5 455.00 1.12 275 140 143 3 464.67 4.82 276 140 144 4 455.84 0.71 277 141 144 3 464.16 3.28 278 141 145 4 455.83 0.71 279 142 146 4 455.82 0.71 280 143 146 3 459.92 1.16 281 143 147 4 455.78 0.73 282 144 147 3 461.20 0.52 283 144 148 4 455.69 0.69 284 145 148 3 458.11 1.90 285 145 149 4 446.63 3.84 286 146 149 3 452.07 1.56 287 146 150 4 442.31 1.68 288 147 150 3 445.45 3.25 289 147 151 4 440.37 2.00 290 147 216 69 170.77 1.48 291 148 151 3 451.62 1.84 292 148 152 4 439.68 2.35 293 149 152 3 444.72 4.73 294 149 153 4 424.03 1.54 295 150 153 3 448.06 9.22 296 150 154 4 424.04 1.50 297 150 216 66 170.97 1.44 298 150 217 67 170.96 1.44 299 150 218 68 170.91 1.45 300 150 219 69 170.77 1.49 301 151 154 3 448.07 9.22 302 151 155 4 425.34 2.15 303 151 211 60 170.94 1.46 304 151 216 65 170.97 1.44 305 151 220 69 170.56 1.59 306 152 155 3 456.39 0.58 307 152 156 4 418.63 5.50 308 153 156 3 429.09 0.14 309 153 157 4 410.59 0.12 310 154 157 3 435.77 6.67 311 154 158 4 409.45 0.69 312 154 219 65 170.93 1.45 313 154 220 66 170.88 1.43 314 155 158 3 437.93 8.04 315 155 160 5 386.81 0.76 316 155 161 6 366.37 3.50 317 155 209 54 170.94 1.46 318 155 220 65 170.93 1.45 319 156 161 5 358.41 7.48 320 158 161 3 444.02 7.29 321 158 162 4 414.99 4.95 322 158 184 26 170.91 1.45 323 158 185 27 170.92 1.45 324 159 162 3 420.16 2.37 325 159 163 4 414.93 4.92 326 159 180 21 170.85 1.49 327 159 183 24 170.93 1.45 328 159 184 25 170.93 1.45 329 160 163 3 420.11 2.34 330 160 164 4 421.49 3.03 331 160 180 20 170.85 1.52 332 160 181 21 170.81 1.51 333 161 164 3 444.87 4.88 334 161 165 4 442.70 6.49 335 162 165 3 463.55 1.73 336 162 166 4 442.68 6.48 337 163 166 3 461.49 2.91 338 163 167 4 442.69 6.49 339 163 172 9 171.15 1.47 340 163 176 13 171.01 1.49 341 163 177 14 170.94 1.51 342 163 180 17 171.00 1.47 343 164 167 3 460.39 5.08 344 164 168 4 430.49 12.59 345 164 204 40 170.84 1.45 346 164 207 43 171.02 1.47 347 164 240 76 79.78 0.77 348 165 168 3 443.79 5.93 349 167 170 3 417.14 2.67 350 167 172 5 355.24 5.37 351 167 240 73 84.17 1.04 352 168 240 72 85.20 0.49 353 168 241 73 83.14 0.54 354 168 242 74 79.91 0.73 355 168 243 75 79.98 0.77 356 169 239 70 89.39 1.17 357 169 240 71 86.70 0.13 358 169 242 73 79.91 0.73 359 170 239 69 90.33 0.70 360 170 240 70 88.42 0.69 361 171 237 66 118.01 0.38 362 171 238 67 100.82 1.22 363 171 239 68 90.81 0.94 364 172 237 65 116.50 1.11 365 172 238 66 98.58 0.95 366 172 240 68 89.36 1.17 367 173 176 3 425.75 2.83 368 173 177 4 410.64 0.40 369 173 236 63 117.50 0.61 370 173 237 64 92.73 1.06 371 174 177 3 428.92 0.43 372 174 178 4 411.32 0.06 373 174 193 19 170.89 1.44 374 174 195 21 170.77 1.44 375 174 231 57 170.50 1.33 376 174 235 61 118.34 0.27 377 174 236 62 105.95 2.95 378 174 238 64 90.32 0.71 379 175 178 3 448.13 8.79 380 175 179 4 411.32 0.06 381 176 179 3 444.32 0.18 382 176 180 4 406.39 2.41 383 177 180 3 457.61 2.25 384 177 181 4 427.36 12.87 385 177 193 16 170.85 1.43 386 177 195 18 170.68 1.39 387 177 207 30 171.19 1.52 388 177 238 61 90.30 0.70 389 178 181 3 457.60 2.25 390 178 182 4 420.95 5.42 391 178 190 12 170.93 1.42 392 179 182 3 438.37 7.62 393 179 183 4 416.62 3.25 394 180 183 3 448.39 3.68 395 180 184 4 448.39 3.68 396 181 184 3 451.99 3.66 397 181 185 4 425.88 14.93 398 181 189 8 358.79 1.75 399 181 190 9 330.75 6.78 400 181 193 12 170.78 1.43 401 181 209 28 246.41 36.08 402 181 225 44 359.01 1.83 403 182 185 3 428.76 13.49 404 182 186 4 358.81 1.74 405 182 187 5 358.79 1.76 406 182 190 8 340.53 10.86 407 185 189 4 456.79 0.42 408 185 220 35 512.94 1.22 409 185 221 36 468.63 0.59 410 185 222 37 446.36 10.52 411 185 225 40 433.65 11.98 412 186 189 3 467.48 0.04 413 186 190 4 456.80 0.42 414 187 190 3 466.25 0.58 415 189 192 3 463.62 1.96 416 190 193 3 473.94 0.31 417 191 227 36 633.18 1.51 418 191 228 37 574.64 0.56 419 192 228 36 633.16 1.51 420 194 231 37 541.56 4.05 421 194 232 38 521.32 0.17 422 195 232 37 576.09 5.30 423 195 233 38 550.25 3.89 424 195 234 39 505.92 0.58 425 195 238 43 386.08 2.80 426 196 233 37 632.28 1.07 427 196 234 38 593.39 1.44 428 197 238 41 407.19 5.05 429 202 238 36 446.97 4.62 430 202 239 37 436.75 9.72 431 203 238 35 398.92 9.19 432 203 239 36 386.05 2.83 433 203 241 38 372.94 2.93 434 204 238 34 398.90 9.20 435 204 239 35 386.04 2.83 436 204 240 36 372.65 3.11 437 234 237 3 491.22 3.31 438 234 238 4 400.16 8.56