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 81.81 0.60 2 2 124 122 80.71 0.40 3 2 125 123 80.42 0.45 4 2 126 124 80.32 0.44 5 2 130 128 80.56 0.40 6 3 127 124 80.58 0.40 7 3 129 126 80.70 0.39 8 3 130 127 80.70 0.39 9 4 124 120 82.17 0.44 10 4 125 121 80.75 0.41 11 4 126 122 80.75 0.41 12 4 127 123 80.75 0.40 13 5 110 105 80.66 0.38 14 5 124 119 82.20 0.43 15 5 125 120 82.18 0.44 16 6 110 104 82.48 0.62 17 6 121 115 91.65 1.42 18 6 122 116 90.73 1.05 19 6 123 117 87.77 0.74 20 6 124 118 82.19 0.43 21 6 125 119 82.31 0.49 22 7 11 4 353.49 6.67 23 7 110 103 82.48 0.62 24 7 111 104 82.48 0.62 25 7 112 105 87.66 0.80 26 7 120 113 97.79 0.60 27 7 121 114 95.43 0.41 28 7 122 115 97.74 0.65 29 7 125 118 87.67 0.80 30 8 11 3 358.97 3.93 31 8 109 101 86.52 1.36 32 8 110 102 86.52 1.36 33 8 122 114 99.16 0.01 34 9 14 5 346.36 4.54 35 9 122 113 99.18 0.01 36 10 13 3 362.84 1.99 37 10 14 4 346.38 4.53 38 11 14 3 357.16 0.85 39 11 15 4 345.91 4.31 40 11 39 28 201.25 40.84 41 11 42 31 114.68 2.44 42 11 46 35 116.01 1.78 43 11 109 98 101.29 1.01 44 11 111 100 108.77 1.93 45 11 120 109 116.07 1.79 46 12 15 3 353.80 0.83 47 12 16 4 345.93 4.31 48 12 39 27 115.50 2.04 49 13 16 3 366.24 7.15 50 13 17 4 345.88 4.32 51 14 17 3 358.44 3.59 52 14 18 4 343.51 5.50 53 14 109 95 115.62 2.01 54 15 18 3 421.42 0.09 55 15 19 4 341.35 6.54 56 15 38 23 322.36 3.00 57 15 39 24 300.03 8.55 58 15 42 27 209.94 36.49 59 15 61 46 135.65 0.67 60 15 105 90 115.62 2.01 61 16 19 3 364.36 0.64 62 16 20 4 518.20 10.12 63 16 35 19 336.06 9.14 64 16 36 20 331.56 6.90 65 16 39 23 312.47 7.89 66 18 104 86 135.67 0.66 67 18 105 87 135.67 0.66 68 18 106 88 135.72 0.65 69 18 107 89 135.68 0.67 70 18 109 91 135.75 0.62 71 19 38 19 367.64 4.66 72 19 101 82 135.79 0.60 73 19 105 86 135.76 0.62 74 22 67 45 143.97 0.94 75 22 91 69 143.68 0.82 76 22 95 73 143.04 1.13 77 22 99 77 143.04 1.13 78 22 100 78 143.05 1.13 79 22 101 79 143.07 1.14 80 22 104 82 143.05 1.13 81 25 90 65 143.72 0.81 82 25 91 66 143.71 0.80 83 25 104 79 144.03 0.90 84 26 67 41 144.02 0.92 85 26 101 75 144.03 0.90 86 30 67 37 144.05 0.91 87 30 68 38 144.05 0.91 88 33 64 31 145.17 0.78 89 33 65 32 144.34 0.75 90 33 66 33 144.97 0.69 91 33 101 68 144.28 0.59 92 34 38 4 532.18 4.06 93 35 38 3 367.64 4.66 94 35 39 4 354.32 2.00 95 36 39 3 363.72 2.71 96 36 40 4 358.31 0.01 97 37 40 3 363.72 2.71 98 37 41 4 363.72 2.71 99 37 64 27 145.41 0.84 100 38 41 3 352.70 1.44 101 38 42 4 352.61 1.41 102 38 61 23 145.42 0.84 103 38 64 26 145.42 0.84 104 38 65 27 145.41 0.84 105 38 101 63 145.41 0.84 106 39 42 3 356.69 0.64 107 39 43 4 352.61 1.41 108 39 46 7 341.48 4.08 109 40 43 3 362.19 2.12 110 40 44 4 356.78 0.72 111 41 44 3 383.62 4.33 112 41 60 19 148.58 0.04 113 41 61 20 148.50 0.01 114 41 64 23 148.56 0.04 115 42 45 3 436.51 1.73 116 42 58 16 148.58 0.04 117 42 61 19 148.56 0.04 118 42 111 69 301.03 2.48 119 42 139 97 148.58 0.03 120 43 46 3 375.08 8.59 121 43 47 4 363.73 2.92 122 44 47 3 372.29 1.36 123 44 48 4 363.74 2.92 124 44 57 13 222.40 36.91 125 45 48 3 404.56 17.50 126 45 53 8 223.96 37.69 127 45 58 13 222.37 36.90 128 45 135 90 222.37 36.90 129 46 111 65 326.95 4.09 130 46 112 66 326.92 4.12 131 46 113 67 337.24 5.96 132 46 120 74 365.55 2.80 133 47 113 66 380.83 3.51 134 48 53 5 467.71 10.47 135 48 57 9 426.53 28.52 136 48 113 65 385.17 3.24 137 49 53 4 569.84 3.99 138 49 113 64 393.97 7.27 139 50 112 62 391.64 6.39 140 50 113 63 396.17 7.81 141 50 114 64 408.25 5.18 142 50 115 65 412.18 7.12 143 50 126 76 424.42 2.50 144 50 134 84 399.81 6.00 145 50 135 85 391.63 6.29 146 51 126 75 495.40 17.98 147 51 133 82 422.44 1.12 148 51 134 83 405.84 4.20 149 52 133 81 450.87 3.40 150 53 134 81 447.48 1.30 151 53 135 82 423.55 1.29 152 53 138 85 421.74 1.07 153 54 138 84 421.85 1.02 154 55 138 83 422.08 0.91 155 55 141 86 418.79 0.05 156 55 142 87 414.57 1.82 157 58 138 80 428.87 0.88 158 58 139 81 423.37 1.23 159 58 142 84 420.46 0.80 160 59 142 83 422.38 0.88 161 61 139 78 568.28 5.12 162 62 142 80 422.57 0.85 163 62 143 81 422.48 0.83 164 62 146 84 418.82 0.29 165 66 146 80 422.29 0.78 166 66 150 84 413.16 3.10 167 69 147 78 422.57 0.87 168 69 150 81 415.93 1.79 169 71 152 81 412.74 2.87 170 71 153 82 412.43 2.81 171 71 188 117 269.69 4.67 172 72 152 80 413.20 3.10 173 72 153 81 409.39 3.61 174 72 154 82 408.46 4.07 175 72 156 84 407.13 4.73 176 74 147 73 424.47 0.86 177 74 151 77 415.32 2.04 178 74 155 81 384.28 16.15 179 74 156 82 373.50 21.53 180 75 147 72 424.58 0.86 181 75 156 81 365.26 25.66 182 75 157 82 365.24 25.66 183 75 158 83 365.20 25.64 184 75 193 118 264.69 6.62 185 76 147 71 424.64 0.88 186 76 148 72 424.51 0.84 187 76 151 75 418.92 0.33 188 76 155 79 383.35 16.64 189 76 156 80 365.25 25.65 190 76 157 81 365.05 25.70 191 76 158 82 365.05 25.71 192 76 174 98 271.24 4.59 193 76 178 102 271.22 4.59 194 76 182 106 271.16 4.61 195 77 157 80 365.05 25.70 196 77 158 81 364.89 25.64 197 78 158 80 365.03 25.71 198 78 159 81 364.56 25.71 199 78 160 82 364.54 25.70 200 78 167 89 271.75 4.48 201 78 169 91 271.68 4.51 202 78 174 96 271.19 4.62 203 79 160 81 364.19 25.66 204 79 163 84 318.72 17.05 205 80 158 78 364.74 25.63 206 80 160 80 362.94 25.27 207 83 158 75 364.93 25.55 208 83 195 112 264.18 6.83 209 83 234 151 45.87 0.69 210 83 237 154 44.59 1.02 211 83 238 155 43.74 0.90 212 84 158 74 363.98 25.17 213 86 237 151 43.79 0.90 214 87 158 71 364.15 25.09 215 87 193 106 264.70 6.59 216 87 231 144 112.10 28.05 217 87 233 146 47.02 0.74 218 87 234 147 45.06 0.95 219 87 237 150 43.99 0.78 220 94 156 62 389.04 11.67 221 94 193 99 264.76 6.57 222 95 147 52 423.39 1.27 223 96 147 51 422.55 0.88 224 97 143 46 440.18 6.52 225 97 144 47 424.53 0.88 226 97 147 50 418.93 0.33 227 100 147 47 419.03 0.29 228 102 143 41 423.19 1.17 229 102 146 44 419.32 0.23 230 102 147 45 418.93 0.34 231 128 137 9 422.88 1.17 232 131 134 3 447.04 1.48 233 132 141 9 419.29 0.10 234 133 138 5 422.06 0.98 235 134 137 3 431.30 2.11 236 134 138 4 424.32 0.80 237 135 138 3 431.26 2.12 238 135 139 4 424.92 1.10 239 136 139 3 424.94 1.09 240 136 140 4 424.92 1.09 241 137 140 3 428.64 0.76 242 137 141 4 423.36 1.27 243 137 173 36 271.05 4.62 244 138 141 3 423.88 0.99 245 138 142 4 423.35 1.26 246 139 142 3 423.10 1.14 247 139 143 4 421.45 0.32 248 140 143 3 421.46 0.33 249 140 144 4 420.22 0.29 250 140 173 33 271.06 4.62 251 141 144 3 420.44 1.14 252 141 145 4 416.36 1.62 253 141 173 32 271.05 4.62 254 141 177 36 271.04 4.62 255 142 145 3 417.31 2.40 256 142 146 4 415.93 1.76 257 143 146 3 415.94 1.75 258 143 147 4 415.58 1.92 259 144 147 3 415.61 1.91 260 144 148 4 415.57 1.92 261 144 177 33 271.05 4.62 262 144 178 34 271.04 4.62 263 145 148 3 419.87 0.23 264 145 149 4 412.41 2.80 265 145 177 32 271.05 4.62 266 145 181 36 270.41 4.46 267 146 149 3 420.31 1.13 268 146 150 4 408.45 4.06 269 147 150 3 409.13 3.73 270 147 151 4 408.11 4.21 271 148 151 3 408.36 4.07 272 148 178 30 271.08 4.62 273 148 181 33 270.63 4.49 274 148 182 34 270.35 4.48 275 149 181 32 270.59 4.48 276 149 183 34 270.29 4.47 277 149 186 37 268.07 5.51 278 150 186 36 270.10 4.50 279 151 155 4 378.18 6.38 280 151 186 35 270.10 4.50 281 152 186 34 269.95 4.57 282 153 186 33 270.23 4.48 283 153 187 34 267.94 5.51 284 153 188 35 267.88 5.52 285 154 188 34 267.48 5.71 286 154 189 35 267.04 5.91 287 154 191 37 265.08 6.42 288 155 182 27 271.20 4.60 289 155 187 32 267.91 5.54 290 155 189 34 266.16 6.02 291 155 190 35 264.90 6.51 292 155 191 36 264.81 6.55 293 156 191 35 264.75 6.58 294 156 193 37 264.74 6.58 295 157 174 17 271.51 4.53 296 157 190 33 264.94 6.61 297 157 191 34 264.76 6.59 298 157 192 35 264.68 6.62 299 157 193 36 264.67 6.62 300 158 193 35 264.29 6.80 301 158 195 37 263.75 7.05 302 158 234 76 47.68 0.83 303 159 167 8 271.85 4.48 304 159 168 9 271.85 4.47 305 159 192 33 264.69 6.63 306 159 193 34 264.29 6.82 307 159 194 35 264.25 6.83 308 159 195 36 263.75 7.06 309 159 211 52 247.72 0.35 310 159 214 55 248.02 0.39 311 160 163 3 377.64 8.95 312 160 167 7 271.84 4.47 313 160 195 35 263.68 7.10 314 161 167 6 271.89 4.45 315 161 194 33 264.27 6.82 316 161 195 34 264.25 6.83 317 161 196 35 263.49 7.20 318 161 202 41 247.92 0.40 319 161 203 42 247.77 0.41 320 161 204 43 246.61 0.03 321 162 195 33 264.26 6.83 322 162 196 34 263.52 7.18 323 162 197 35 263.31 7.28 324 162 201 39 247.90 0.41 325 162 203 41 247.87 0.39 326 163 166 3 353.48 3.23 327 163 203 40 247.94 0.40 328 164 203 39 247.93 0.41 329 166 204 38 247.79 0.42 330 166 210 44 247.95 0.41 331 167 194 27 264.26 6.83 332 167 204 37 247.61 0.51 333 167 210 43 247.94 0.40 334 167 211 44 247.88 0.39 335 168 174 6 287.44 1.30 336 168 175 7 287.76 1.15 337 168 179 11 281.80 1.52 338 168 210 42 247.89 0.35 339 168 213 45 248.02 0.38 340 168 214 46 248.02 0.39 341 168 217 49 248.06 0.40 342 169 175 6 291.68 0.15 343 170 175 5 291.76 0.12 344 170 213 43 248.02 0.38 345 171 175 4 343.98 4.69 346 171 176 5 302.85 5.65 347 172 175 3 367.14 5.09 348 172 176 4 311.44 9.83 349 173 176 3 368.64 4.33 350 173 177 4 302.97 5.58 351 173 178 5 292.08 0.10 352 174 178 4 292.09 0.10 353 174 179 5 308.33 8.21 354 174 214 40 247.99 0.38 355 175 179 4 336.89 3.09 356 175 180 5 336.90 3.09 357 175 217 42 247.87 0.32 358 176 180 4 352.32 5.33 359 177 180 3 399.86 12.52 360 177 181 4 353.81 4.60 361 178 181 3 358.01 2.50 362 178 182 4 353.81 4.60 363 179 182 3 371.06 4.04 364 179 214 35 247.86 0.32 365 179 217 38 247.63 0.21 366 179 218 39 247.61 0.20 367 179 221 42 247.44 0.14 368 180 217 37 247.63 0.20 369 180 221 41 247.04 0.02 370 182 187 5 311.16 8.86 371 182 190 8 270.83 3.54 372 182 223 41 242.16 0.66 373 183 186 3 360.21 0.34 374 183 187 4 326.06 1.42 375 184 187 3 360.05 0.26 376 184 221 37 242.27 0.47 377 184 223 39 241.71 0.67 378 187 190 3 502.60 1.31 379 187 223 36 241.99 0.54 380 188 224 36 241.96 0.56 381 189 224 35 241.84 0.50 382 190 218 28 242.83 0.17 383 190 223 33 242.10 0.53 384 190 224 34 241.95 0.56 385 190 225 35 241.49 0.62 386 190 226 36 241.29 0.52 387 191 226 35 240.47 0.46 388 191 228 37 228.91 2.31 389 192 211 19 247.53 0.29 390 192 214 22 247.81 0.30 391 192 218 26 246.89 0.10 392 192 225 33 241.94 0.56 393 192 226 34 241.47 0.62 394 192 227 35 227.40 1.55 395 192 228 36 218.90 1.08 396 193 228 35 208.56 0.96 397 193 231 38 109.28 29.59 398 193 234 41 49.00 0.49 399 194 204 10 247.03 0.24 400 194 205 11 242.15 0.56 401 194 206 12 241.72 0.70 402 194 211 17 247.71 0.35 403 194 227 33 240.07 0.27 404 194 228 34 216.00 0.41 405 194 229 35 198.49 1.32 406 194 230 36 180.52 2.11 407 195 230 35 168.38 0.09 408 195 231 36 161.00 3.78 409 195 234 39 48.28 0.61 410 195 235 40 47.80 0.83 411 195 238 43 45.23 1.12 412 196 202 6 247.93 0.40 413 196 204 8 247.80 0.39 414 196 205 9 247.72 0.40 415 196 230 34 193.30 4.12 416 196 235 39 48.01 0.93 417 196 238 42 45.29 1.14 418 197 200 3 256.38 3.83 419 197 238 41 45.27 1.13 420 198 235 37 48.66 0.64 421 198 238 40 45.31 1.15 422 198 239 41 45.27 1.13 423 198 242 44 45.27 1.15 424 198 245 47 45.23 1.11 425 198 247 49 45.12 1.12 426 198 248 50 45.12 1.12 427 199 245 46 45.23 1.11 428 199 247 48 45.12 1.11 429 202 205 3 443.62 2.14 430 205 229 24 225.12 1.64 431 206 228 22 505.89 0.99 432 206 229 23 342.06 9.88 433 228 231 3 373.12 3.85 434 230 235 5 330.29 5.07 435 231 234 3 368.57 3.14 436 231 235 4 351.60 5.35 437 232 235 3 351.41 4.99 438 232 236 4 345.38 2.25 439 233 236 3 359.19 1.55 440 233 237 4 345.67 2.11 441 234 237 3 363.97 0.83 442 234 238 4 351.86 5.21 443 235 238 3 355.13 3.58 444 235 239 4 351.58 5.36 445 236 239 3 344.47 0.66