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 65.73 7.04 2 2 121 119 66.28 7.35 3 2 124 122 63.63 6.45 4 2 125 123 62.19 6.94 5 2 126 124 62.12 6.92 6 2 130 128 62.16 6.93 7 3 127 124 62.20 6.93 8 3 130 127 62.34 6.87 9 4 124 120 65.84 7.04 10 4 125 121 63.92 6.33 11 4 127 123 63.01 6.58 12 5 110 105 63.50 6.38 13 5 124 119 66.23 7.23 14 5 125 120 65.80 7.07 15 6 110 104 66.19 7.42 16 6 121 115 75.53 9.47 17 6 122 116 73.10 8.26 18 6 123 117 71.91 8.65 19 6 124 118 66.23 7.23 20 6 125 119 65.86 7.05 21 7 11 4 352.25 5.05 22 7 110 103 66.22 7.40 23 7 111 104 66.29 7.36 24 7 112 105 70.45 9.35 25 7 120 113 75.70 9.46 26 7 121 114 75.61 9.46 27 7 122 115 75.55 9.48 28 7 125 118 71.87 8.67 29 8 11 3 358.85 3.99 30 8 109 101 70.33 9.40 31 8 110 102 70.47 9.36 32 8 122 114 98.52 0.32 33 9 14 5 346.31 4.58 34 9 122 113 99.17 0.01 35 10 13 3 366.52 0.14 36 10 14 4 346.31 4.58 37 11 14 3 371.51 2.64 38 11 15 4 346.29 4.58 39 11 39 28 118.16 0.71 40 11 42 31 118.11 0.73 41 11 46 35 118.11 0.72 42 11 109 98 101.09 0.75 43 11 111 100 111.91 0.37 44 11 120 109 115.42 0.62 45 12 15 3 353.81 0.83 46 12 16 4 348.93 2.82 47 12 39 27 118.16 0.71 48 13 16 3 348.93 2.81 49 13 17 4 348.91 2.81 50 14 17 3 359.30 3.68 51 14 18 4 342.66 5.88 52 14 109 95 118.17 0.73 53 15 18 3 392.37 14.44 54 15 19 4 348.83 2.77 55 15 38 23 318.62 0.43 56 15 39 24 211.91 37.47 57 15 42 27 137.49 0.25 58 15 61 46 137.49 0.26 59 15 105 90 118.16 0.73 60 16 19 3 346.48 4.54 61 16 20 4 515.70 8.14 62 16 35 19 341.89 6.20 63 16 36 20 341.88 6.20 64 16 39 23 211.91 37.47 65 18 104 86 137.72 0.36 66 18 105 87 137.73 0.36 67 18 106 88 137.74 0.36 68 18 107 89 137.73 0.36 69 18 109 91 137.74 0.36 70 19 38 19 361.20 7.88 71 19 101 82 137.75 0.36 72 19 105 86 137.75 0.36 73 22 67 45 143.31 1.08 74 22 95 73 142.97 1.10 75 22 99 77 142.97 1.10 76 22 100 78 142.97 1.10 77 22 101 79 142.97 1.10 78 22 104 82 142.98 1.10 79 25 90 65 143.01 1.13 80 25 91 66 142.97 1.11 81 25 104 79 143.32 1.08 82 26 67 41 143.37 1.11 83 26 101 75 143.34 1.08 84 30 67 37 143.55 1.15 85 30 68 38 143.43 1.08 86 33 64 31 145.25 0.98 87 33 65 32 144.12 0.72 88 33 66 33 144.28 0.79 89 33 67 34 143.46 1.05 90 33 101 68 143.37 1.07 91 34 38 4 529.88 2.91 92 35 38 3 362.34 2.01 93 35 39 4 352.44 3.50 94 36 39 3 368.63 0.24 95 36 40 4 363.79 2.17 96 37 40 3 363.79 2.17 97 37 41 4 363.79 2.17 98 37 64 27 145.53 0.90 99 38 41 3 368.90 0.39 100 38 42 4 354.26 2.54 101 38 61 23 145.49 0.92 102 38 64 26 145.53 0.90 103 38 65 27 145.47 0.92 104 38 101 63 145.47 0.92 105 39 42 3 353.31 1.02 106 39 43 4 358.82 3.81 107 39 46 7 343.91 5.42 108 40 43 3 367.68 1.00 109 40 44 4 363.94 2.86 110 41 44 3 383.62 4.32 111 41 60 19 149.12 0.21 112 41 61 20 149.06 0.20 113 41 64 23 149.12 0.21 114 42 45 3 444.51 2.27 115 42 58 16 222.16 36.73 116 42 61 19 149.12 0.21 117 42 111 69 149.18 0.18 118 42 139 97 149.12 0.21 119 43 46 3 374.70 8.78 120 43 47 4 357.35 0.10 121 44 47 3 372.58 1.19 122 44 48 4 366.92 1.32 123 44 57 13 222.46 36.78 124 45 48 3 366.92 1.32 125 45 53 8 222.45 36.78 126 45 58 13 222.48 36.79 127 45 135 90 222.44 36.77 128 46 111 65 337.54 9.15 129 46 112 66 338.31 8.44 130 46 113 67 345.62 5.12 131 46 120 74 363.44 3.21 132 47 113 66 371.10 0.85 133 48 52 4 512.82 7.40 134 48 53 5 489.26 15.55 135 48 57 9 439.43 37.91 136 48 113 65 382.17 4.67 137 49 113 64 386.38 4.37 138 50 112 62 384.04 3.75 139 50 113 63 396.26 0.56 140 50 114 64 405.22 0.18 141 50 115 65 405.20 0.18 142 50 126 76 412.51 2.92 143 50 134 84 386.41 2.96 144 50 135 85 383.35 4.08 145 51 133 82 416.44 5.45 146 52 133 81 449.44 0.14 147 53 134 81 446.83 1.44 148 53 135 82 416.54 5.40 149 53 138 85 412.56 3.48 150 54 138 84 412.76 3.52 151 55 138 83 417.18 1.43 152 55 141 86 411.93 3.18 153 55 142 87 411.41 2.92 154 58 138 80 444.59 6.05 155 58 139 81 434.56 2.00 156 58 142 84 427.94 4.83 157 59 142 83 429.61 4.44 158 62 142 80 433.18 2.71 159 62 143 81 433.02 2.77 160 62 146 84 427.31 5.42 161 66 146 80 429.55 4.40 162 66 150 84 426.87 5.59 163 69 147 78 433.05 2.77 164 69 150 81 427.30 5.45 165 71 152 81 426.90 5.63 166 71 153 82 426.79 5.67 167 71 188 117 268.00 3.06 168 72 152 80 426.93 5.64 169 72 153 81 423.55 7.29 170 72 154 82 419.98 9.05 171 72 156 84 419.87 9.10 172 74 147 73 436.16 1.64 173 74 151 77 427.61 5.31 174 74 155 81 391.01 23.57 175 74 156 82 376.35 30.89 176 75 147 72 436.43 1.56 177 75 156 81 376.10 31.02 178 75 157 82 376.08 31.03 179 75 158 83 376.02 31.04 180 75 193 118 261.98 5.26 181 76 147 71 436.44 1.56 182 76 148 72 436.17 1.66 183 76 151 75 428.25 5.11 184 76 155 79 398.38 19.89 185 76 156 80 376.11 31.02 186 76 157 81 375.87 31.11 187 76 158 82 375.87 31.11 188 76 174 98 270.41 2.52 189 76 178 102 270.41 2.52 190 76 182 106 270.30 2.50 191 77 157 80 376.01 31.03 192 77 158 81 375.68 31.03 193 78 158 80 375.99 31.02 194 78 159 81 375.37 30.93 195 78 160 82 375.18 31.02 196 78 169 91 270.75 2.46 197 78 174 96 270.38 2.52 198 79 160 81 375.16 31.01 199 79 163 84 331.80 20.24 200 79 169 90 270.75 2.46 201 80 158 78 375.77 30.93 202 80 159 79 375.19 31.02 203 80 160 80 375.00 31.06 204 83 158 75 375.58 30.82 205 83 195 112 260.94 5.57 206 83 234 151 60.97 7.08 207 83 237 154 55.37 4.37 208 83 238 155 54.22 4.39 209 84 158 74 375.56 30.82 210 86 237 151 54.85 4.53 211 87 158 71 375.61 30.77 212 87 193 106 262.00 5.25 213 87 231 144 176.72 3.95 214 87 233 146 66.17 9.10 215 87 234 147 59.08 6.24 216 87 237 150 54.31 4.38 217 94 156 62 389.34 16.30 218 94 193 99 262.05 5.24 219 95 147 52 434.72 2.01 220 96 147 51 432.45 3.08 221 97 143 46 436.42 1.58 222 97 144 47 436.18 1.69 223 97 147 50 428.25 5.00 224 100 147 47 428.29 4.99 225 102 143 41 433.09 2.76 226 102 146 44 429.59 4.43 227 102 147 45 428.25 5.00 228 128 137 9 420.25 3.41 229 131 134 3 444.12 0.07 230 132 141 9 412.01 3.14 231 133 138 5 420.27 3.00 232 134 137 3 435.75 1.41 233 134 138 4 431.58 1.78 234 135 138 3 435.91 1.33 235 135 139 4 431.78 1.68 236 136 139 3 435.91 1.33 237 136 140 4 433.81 2.18 238 137 140 3 436.18 1.19 239 137 141 4 433.48 2.52 240 138 141 3 433.56 2.49 241 138 142 4 432.36 3.08 242 139 142 3 432.36 3.08 243 139 143 4 431.96 3.28 244 140 143 3 431.96 3.28 245 140 144 4 428.37 5.05 246 140 173 33 270.27 2.54 247 141 144 3 432.69 2.85 248 141 145 4 428.16 5.11 249 141 173 32 270.20 2.53 250 141 177 36 270.10 2.58 251 142 145 3 428.19 5.04 252 142 146 4 427.37 5.45 253 143 146 3 428.15 5.06 254 143 147 4 427.36 5.45 255 144 147 3 427.36 5.46 256 144 148 4 426.87 5.62 257 144 173 29 270.32 2.54 258 144 177 33 270.23 2.58 259 144 178 34 270.10 2.58 260 145 148 3 426.85 5.62 261 145 149 4 426.74 5.62 262 145 177 32 270.30 2.54 263 145 181 36 269.94 2.59 264 146 149 3 426.48 5.73 265 146 150 4 421.83 8.01 266 147 150 3 422.31 7.75 267 147 151 4 419.81 8.99 268 148 151 3 420.19 8.79 269 148 178 30 270.31 2.54 270 148 181 33 270.12 2.58 271 148 182 34 269.33 2.67 272 149 181 32 270.12 2.58 273 149 183 34 269.31 2.67 274 149 186 37 268.22 2.98 275 150 186 36 268.37 3.08 276 151 155 4 389.89 10.54 277 151 186 35 268.38 3.08 278 152 186 34 268.38 3.08 279 152 187 35 267.73 3.18 280 153 186 33 269.32 2.65 281 153 187 34 267.77 3.18 282 153 188 35 265.86 4.11 283 154 188 34 265.83 4.12 284 154 189 35 265.05 4.44 285 154 191 37 262.66 4.98 286 155 182 27 270.42 2.51 287 155 187 32 267.74 3.20 288 155 189 34 263.51 4.67 289 155 190 35 262.13 5.24 290 155 191 36 262.12 5.23 291 156 191 35 262.10 5.24 292 156 193 37 261.98 5.26 293 157 174 17 270.65 2.52 294 157 190 33 262.13 5.23 295 157 191 34 262.10 5.24 296 157 192 35 261.98 5.26 297 157 193 36 261.97 5.27 298 158 193 35 261.54 5.48 299 158 195 37 261.01 5.59 300 158 234 76 69.70 10.36 301 159 167 8 270.99 2.44 302 159 192 33 261.98 5.27 303 159 193 34 261.56 5.48 304 159 194 35 261.11 5.62 305 159 195 36 260.92 5.65 306 159 211 52 247.16 0.18 307 159 214 55 247.31 0.21 308 160 163 3 359.43 0.16 309 160 167 7 270.99 2.44 310 160 195 35 260.92 5.65 311 161 167 6 271.00 2.44 312 161 194 33 261.50 5.50 313 161 195 34 261.25 5.61 314 161 196 35 260.86 5.68 315 161 203 42 247.28 0.18 316 161 204 43 245.97 0.20 317 162 196 34 261.14 5.66 318 162 197 35 260.94 5.67 319 162 201 39 247.41 0.17 320 162 203 41 247.34 0.18 321 163 166 3 353.48 3.23 322 163 203 40 247.38 0.18 323 164 203 39 247.83 0.35 324 166 203 37 247.92 0.38 325 166 204 38 247.88 0.38 326 166 210 44 248.00 0.39 327 167 194 27 261.49 5.50 328 167 204 37 247.86 0.38 329 167 210 43 248.00 0.39 330 167 211 44 247.98 0.39 331 168 174 6 277.82 0.06 332 168 175 7 275.22 1.38 333 168 179 11 275.19 1.37 334 168 210 42 247.95 0.37 335 168 213 45 248.00 0.38 336 168 214 46 247.97 0.38 337 168 217 49 248.01 0.39 338 169 175 6 278.37 0.15 339 170 175 5 279.40 0.36 340 170 213 43 247.84 0.32 341 171 176 5 287.55 1.23 342 172 175 3 366.18 5.58 343 172 176 4 336.56 2.73 344 173 176 3 364.54 0.48 345 173 177 4 313.60 14.21 346 173 178 5 313.61 14.21 347 174 178 4 333.35 4.35 348 174 179 5 333.40 4.32 349 174 214 40 247.47 0.26 350 175 179 4 334.12 3.96 351 175 180 5 336.48 2.85 352 175 217 42 247.35 0.20 353 176 180 4 352.59 5.18 354 177 180 3 390.23 7.41 355 177 181 4 352.62 5.20 356 178 181 3 361.66 0.67 357 178 182 4 352.62 5.20 358 179 182 3 362.60 2.33 359 179 214 35 247.27 0.23 360 179 217 38 247.31 0.21 361 179 218 39 247.20 0.27 362 179 221 42 247.10 0.32 363 180 217 37 247.26 0.24 364 180 221 41 247.10 0.32 365 182 187 5 310.22 9.33 366 182 190 8 269.40 1.60 367 182 223 41 241.93 0.78 368 183 186 3 370.74 5.25 369 183 187 4 346.71 6.42 370 184 187 3 361.52 0.94 371 184 221 37 242.62 0.78 372 184 223 39 241.93 0.78 373 187 190 3 502.19 1.52 374 187 223 36 241.96 0.79 375 188 224 36 241.87 0.81 376 189 224 35 241.86 0.81 377 190 218 28 243.97 0.32 378 190 223 33 242.49 0.73 379 190 224 34 241.93 0.79 380 190 225 35 241.07 1.09 381 190 226 36 239.05 0.75 382 191 226 35 236.87 3.19 383 191 228 37 220.47 1.81 384 192 211 19 245.09 0.79 385 192 214 22 247.15 0.18 386 192 218 26 247.12 0.18 387 192 225 33 241.87 0.81 388 192 226 34 241.14 1.15 389 192 227 35 226.28 0.99 390 192 228 36 216.24 2.41 391 193 228 35 208.56 0.96 392 193 231 38 161.09 3.90 393 193 234 41 70.67 10.29 394 194 204 10 246.26 0.09 395 194 205 11 241.87 0.82 396 194 206 12 241.52 0.98 397 194 211 17 247.14 0.20 398 194 227 33 235.50 2.54 399 194 228 34 213.27 0.96 400 194 229 35 203.66 0.83 401 194 230 36 198.50 1.32 402 195 230 35 182.80 2.33 403 195 231 36 182.80 2.33 404 195 234 39 70.62 10.31 405 195 235 40 70.98 10.50 406 195 238 43 69.04 10.79 407 196 202 6 247.36 0.17 408 196 204 8 247.27 0.19 409 196 205 9 247.14 0.21 410 196 229 33 207.79 0.75 411 196 230 34 199.94 1.03 412 196 235 39 71.17 10.58 413 196 238 42 69.09 10.79 414 197 200 3 299.79 16.91 415 197 238 41 69.09 10.79 416 198 235 37 106.09 28.04 417 198 238 40 69.12 10.78 418 198 239 41 69.06 10.79 419 198 242 44 69.03 10.77 420 198 245 47 69.00 10.77 421 198 247 49 68.95 10.81 422 198 248 50 68.96 10.80 423 199 245 46 69.03 10.79 424 199 247 48 68.96 10.81 425 202 205 3 443.62 2.14 426 205 229 24 216.40 2.72 427 206 228 22 507.80 1.70 428 206 229 23 328.83 5.03 429 228 231 3 359.81 1.16 430 230 235 5 311.55 14.55 431 231 234 3 366.38 2.27 432 231 235 4 343.35 1.21 433 232 235 3 352.76 4.78 434 232 236 4 344.86 0.48 435 233 236 3 355.91 1.62 436 233 237 4 346.94 1.16 437 234 237 3 358.22 4.48 438 234 238 4 359.19 1.55 439 235 238 3 359.49 1.41 440 235 239 4 345.62 1.25 441 236 239 3 357.66 0.78