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 65.69 7.41 2 2 124 122 64.10 7.56 3 2 125 123 63.86 7.62 4 2 126 124 63.86 7.62 5 2 130 128 64.04 7.53 6 3 127 124 63.96 7.58 7 3 130 127 64.05 7.53 8 4 124 120 65.81 7.57 9 4 125 121 64.45 7.71 10 4 126 122 64.59 7.63 11 4 127 123 64.09 7.55 12 5 110 105 64.78 7.92 13 5 124 119 65.92 7.53 14 5 125 120 65.84 7.58 15 6 110 104 66.39 7.74 16 6 121 115 69.54 8.14 17 6 122 116 69.47 8.14 18 6 123 117 69.02 7.88 19 6 124 118 65.84 7.58 20 6 125 119 65.84 7.57 21 7 110 103 66.40 7.74 22 7 111 104 66.42 7.75 23 7 112 105 66.98 7.48 24 7 120 113 77.52 11.71 25 7 121 114 72.09 9.15 26 7 122 115 69.61 8.15 27 7 125 118 67.39 7.68 28 8 11 3 361.21 5.05 29 8 109 101 66.42 7.75 30 8 110 102 66.44 7.75 31 8 122 114 78.84 12.38 32 9 14 5 349.06 2.43 33 9 122 113 78.88 12.39 34 10 13 3 368.91 1.21 35 10 14 4 349.06 2.43 36 11 14 3 363.08 1.57 37 11 15 4 349.07 2.43 38 11 39 28 114.48 0.56 39 11 42 31 114.29 0.61 40 11 46 35 114.86 0.57 41 11 109 98 102.28 0.78 42 11 111 100 108.94 0.93 43 11 120 109 114.59 0.43 44 12 15 3 356.50 3.12 45 12 16 4 349.07 2.43 46 12 39 27 114.48 0.56 47 13 16 3 353.51 4.61 48 13 17 4 340.04 1.29 49 14 17 3 352.14 1.17 50 14 18 4 348.14 2.90 51 14 109 95 114.67 0.47 52 15 18 3 372.80 7.88 53 15 19 4 336.12 3.11 54 15 38 23 308.46 0.68 55 15 39 24 303.23 1.90 56 15 42 27 136.45 1.12 57 15 61 46 136.75 1.07 58 15 105 90 115.73 1.18 59 16 19 3 353.68 4.71 60 16 20 4 535.70 3.61 61 16 35 19 326.05 1.47 62 16 36 20 317.45 0.20 63 16 39 23 304.20 1.41 64 18 104 86 136.81 1.07 65 18 105 87 136.81 1.06 66 18 106 88 136.85 1.07 67 18 107 89 136.81 1.06 68 18 109 91 136.87 1.08 69 19 38 19 374.81 3.33 70 19 101 82 136.91 1.07 71 19 105 86 136.90 1.07 72 22 67 45 141.66 0.26 73 22 91 69 140.74 0.04 74 22 99 77 140.73 0.04 75 22 100 78 140.74 0.04 76 22 101 79 140.75 0.04 77 22 104 82 140.75 0.04 78 25 90 65 140.77 0.04 79 25 91 66 140.75 0.03 80 25 104 79 141.60 0.24 81 26 67 41 141.63 0.24 82 26 101 75 141.60 0.24 83 30 67 37 141.75 0.24 84 30 68 38 141.75 0.24 85 33 64 31 143.37 0.27 86 33 65 32 141.86 0.23 87 33 66 33 143.25 0.32 88 33 101 68 141.83 0.24 89 34 38 4 504.33 2.63 90 35 38 3 368.24 0.04 91 35 39 4 360.57 1.10 92 36 39 3 366.33 1.78 93 36 40 4 365.45 1.34 94 37 40 3 366.33 1.78 95 37 41 4 359.34 4.40 96 37 64 27 143.95 0.29 97 38 41 3 377.36 3.73 98 38 42 4 354.37 1.99 99 38 61 23 143.75 0.18 100 38 64 26 143.94 0.27 101 38 65 27 143.72 0.20 102 38 101 63 143.74 0.20 103 39 42 3 371.44 6.69 104 39 43 4 350.86 0.23 105 39 46 7 343.06 4.09 106 40 43 3 365.77 4.20 107 40 44 4 354.23 1.86 108 41 44 3 383.31 0.99 109 41 60 19 144.90 0.12 110 41 61 20 144.88 0.12 111 41 64 23 144.90 0.12 112 42 45 3 440.23 4.42 113 42 58 16 144.90 0.13 114 42 61 19 144.88 0.12 115 42 111 69 296.38 4.92 116 42 139 97 144.89 0.12 117 43 46 3 368.21 3.08 118 44 47 3 368.53 3.24 119 44 48 4 359.12 0.61 120 44 57 13 222.62 38.68 121 45 48 3 369.36 2.82 122 45 53 8 224.55 39.65 123 45 58 13 222.66 38.70 124 45 135 90 145.09 0.10 125 46 111 65 309.73 4.78 126 46 112 66 309.95 4.68 127 46 113 67 350.70 0.12 128 46 120 74 376.53 3.57 129 47 113 66 381.37 1.28 130 48 52 4 521.87 1.28 131 48 53 5 522.08 1.17 132 48 57 9 448.41 35.47 133 48 113 65 400.53 2.25 134 49 53 4 574.36 0.08 135 49 113 64 403.97 2.19 136 50 112 62 400.53 2.23 137 50 113 63 403.97 2.18 138 50 114 64 405.19 2.43 139 50 115 65 405.25 2.41 140 50 126 76 422.55 0.79 141 50 134 84 404.09 2.09 142 50 135 85 400.49 2.23 143 51 126 75 487.10 14.05 144 51 133 82 423.90 0.41 145 51 134 83 410.87 0.16 146 52 133 81 444.62 0.12 147 53 133 80 574.38 0.33 148 53 134 81 441.88 1.21 149 53 135 82 425.98 1.45 150 53 138 85 421.39 0.18 151 54 138 84 421.42 0.18 152 55 138 83 421.89 0.41 153 55 141 86 416.12 0.53 154 55 142 87 414.58 1.24 155 58 138 80 438.98 1.93 156 58 139 81 426.26 0.48 157 58 142 84 422.66 0.53 158 59 142 83 423.82 0.10 159 61 139 78 571.93 0.41 160 62 142 80 426.76 0.74 161 62 143 81 425.41 0.87 162 62 146 84 420.51 1.42 163 66 146 80 424.60 1.27 164 66 150 84 410.81 0.11 165 69 147 78 426.20 0.48 166 69 150 81 411.73 0.35 167 69 151 82 409.62 0.73 168 71 152 81 410.30 1.06 169 71 153 82 409.38 0.81 170 71 188 117 261.75 1.85 171 72 152 80 410.32 1.06 172 72 153 81 405.59 0.83 173 72 154 82 403.74 1.72 174 72 156 84 398.38 3.48 175 74 147 73 427.17 0.89 176 74 151 77 410.79 0.83 177 74 155 81 355.05 2.46 178 74 156 82 354.91 2.40 179 75 147 72 427.67 0.65 180 75 156 81 354.83 2.41 181 75 157 82 354.81 2.40 182 75 158 83 354.79 2.40 183 75 193 118 252.46 1.59 184 76 147 71 427.70 0.66 185 76 148 72 427.60 0.67 186 76 151 75 420.82 1.31 187 76 155 79 363.74 1.87 188 76 156 80 354.83 2.41 189 76 157 81 354.68 2.46 190 76 158 82 354.58 2.41 191 76 174 98 264.82 2.52 192 76 178 102 264.77 2.51 193 76 182 106 264.71 2.50 194 77 157 80 354.74 2.38 195 77 158 81 354.57 2.42 196 78 158 80 354.65 2.42 197 78 159 81 354.28 2.50 198 78 160 82 354.13 2.52 199 78 169 91 265.38 2.64 200 78 172 94 265.26 2.68 201 78 173 95 265.22 2.68 202 78 174 96 264.77 2.50 203 79 160 81 353.83 2.66 204 79 163 84 319.29 13.98 205 79 169 90 265.52 2.56 206 80 158 78 354.53 2.41 207 83 158 75 354.74 2.39 208 83 195 112 251.17 1.46 209 83 234 151 63.65 8.07 210 83 237 154 56.55 4.92 211 83 238 155 54.26 3.91 212 84 158 74 354.68 2.37 213 86 237 151 54.40 3.85 214 87 158 71 354.82 2.39 215 87 193 106 252.61 1.60 216 87 231 144 161.75 4.22 217 87 233 146 68.79 10.61 218 87 234 147 59.25 6.04 219 87 237 150 54.27 3.91 220 94 156 62 368.86 0.68 221 94 193 99 252.74 1.55 222 95 147 52 426.93 0.82 223 96 147 51 424.67 1.24 224 97 143 46 428.37 1.02 225 97 144 47 427.62 0.67 226 97 147 50 420.83 1.32 227 100 147 47 420.85 1.31 228 102 143 41 426.19 0.48 229 102 146 44 422.67 0.47 230 102 147 45 420.81 1.32 231 128 137 9 424.61 0.30 232 131 134 3 444.19 0.03 233 132 141 9 417.72 0.28 234 133 138 5 422.51 0.74 235 134 137 3 435.56 2.00 236 134 138 4 425.99 0.61 237 135 138 3 428.66 1.14 238 135 139 4 425.99 0.61 239 136 139 3 427.54 0.65 240 136 140 4 426.00 0.61 241 137 140 3 426.55 0.89 242 137 141 4 425.99 0.61 243 137 173 36 264.58 2.57 244 138 141 3 426.78 0.20 245 138 142 4 425.95 0.60 246 139 142 3 424.99 1.09 247 139 143 4 422.79 2.19 248 140 143 3 423.44 1.85 249 140 144 4 422.78 2.19 250 140 173 33 264.60 2.56 251 141 144 3 425.60 0.18 252 141 145 4 420.93 1.27 253 141 173 32 264.60 2.57 254 141 177 36 264.50 2.58 255 142 145 3 425.59 0.18 256 142 146 4 420.78 1.34 257 143 146 3 420.78 1.34 258 143 147 4 420.77 1.34 259 144 147 3 420.78 1.34 260 144 148 4 420.75 1.35 261 144 177 33 264.59 2.57 262 144 178 34 264.55 2.56 263 145 148 3 415.18 1.43 264 145 149 4 409.42 0.80 265 145 177 32 264.61 2.58 266 145 181 36 262.92 1.83 267 146 149 3 409.21 0.75 268 146 150 4 403.81 1.73 269 147 150 3 409.14 0.72 270 147 151 4 403.79 1.73 271 148 151 3 403.78 1.73 272 148 178 30 264.62 2.56 273 148 181 33 264.11 2.33 274 148 182 34 262.69 1.75 275 149 181 32 264.30 2.43 276 149 183 34 262.36 1.67 277 149 186 37 261.77 1.84 278 150 186 36 261.78 1.84 279 151 155 4 386.38 2.42 280 151 186 35 261.78 1.84 281 152 155 3 444.88 1.02 282 152 186 34 261.77 1.84 283 152 187 35 261.64 1.86 284 153 186 33 262.25 1.62 285 153 187 34 261.69 1.84 286 153 188 35 261.62 1.87 287 154 188 34 261.47 1.94 288 154 189 35 260.35 2.19 289 154 191 37 253.06 1.48 290 155 182 27 264.77 2.50 291 155 187 32 261.68 1.84 292 155 189 34 256.01 0.66 293 155 190 35 252.90 1.52 294 155 191 36 252.85 1.54 295 156 191 35 252.68 1.58 296 156 193 37 252.53 1.63 297 157 174 17 265.31 2.66 298 157 190 33 252.84 1.54 299 157 191 34 252.68 1.58 300 157 192 35 252.34 1.64 301 157 193 36 252.31 1.62 302 158 193 35 252.20 1.60 303 158 195 37 252.06 1.58 304 158 234 76 69.45 10.79 305 159 167 8 265.69 2.53 306 159 168 9 265.69 2.52 307 159 192 33 252.39 1.63 308 159 193 34 252.28 1.64 309 159 194 35 252.08 1.57 310 159 195 36 252.08 1.57 311 159 211 52 249.69 1.53 312 159 214 55 250.01 1.43 313 160 163 3 365.75 1.65 314 160 167 7 265.68 2.54 315 160 195 35 252.06 1.58 316 161 167 6 265.83 2.56 317 161 194 33 252.09 1.57 318 161 195 34 252.09 1.57 319 161 196 35 251.70 1.47 320 161 202 41 249.79 1.54 321 161 203 42 249.59 1.52 322 161 204 43 248.43 1.80 323 162 196 34 252.06 1.59 324 162 197 35 252.02 1.60 325 162 201 39 249.91 1.50 326 162 203 41 249.69 1.53 327 163 166 3 360.11 0.09 328 163 203 40 249.87 1.49 329 164 203 39 249.91 1.51 330 166 204 38 249.68 1.51 331 166 210 44 249.92 1.49 332 167 194 27 252.08 1.57 333 167 204 37 249.47 1.46 334 167 210 43 249.89 1.51 335 167 211 44 249.86 1.51 336 168 174 6 281.59 3.44 337 168 175 7 282.07 3.68 338 168 179 11 281.58 3.45 339 168 210 42 249.83 1.51 340 168 213 45 250.05 1.42 341 168 214 46 250.03 1.43 342 168 217 49 250.05 1.43 343 169 172 3 359.66 2.13 344 169 175 6 282.37 3.59 345 170 175 5 282.69 3.65 346 170 213 43 250.07 1.42 347 171 176 5 283.69 4.03 348 172 175 3 358.92 0.53 349 172 176 4 328.93 3.33 350 173 176 3 369.45 5.79 351 173 177 4 284.20 4.26 352 173 178 5 284.23 4.28 353 174 178 4 284.23 4.28 354 174 179 5 311.01 9.12 355 174 214 40 250.03 1.42 356 175 179 4 326.35 1.48 357 175 180 5 326.65 1.56 358 175 217 42 249.97 1.41 359 176 180 4 361.68 2.90 360 177 180 3 405.22 12.09 361 177 181 4 362.72 2.38 362 178 181 3 363.42 2.03 363 178 182 4 361.69 2.90 364 179 182 3 381.64 7.08 365 179 214 35 249.91 1.42 366 179 217 38 249.81 1.36 367 179 218 39 249.67 1.34 368 179 221 42 249.06 1.24 369 180 217 37 249.81 1.37 370 180 221 41 249.01 1.17 371 182 187 5 335.83 1.23 372 182 190 8 252.87 1.54 373 182 223 41 246.74 1.01 374 183 186 3 372.99 6.37 375 183 187 4 346.46 6.54 376 184 187 3 362.35 1.35 377 184 221 37 245.43 1.68 378 184 222 38 245.16 1.81 379 184 223 39 244.91 1.89 380 187 190 3 496.65 2.21 381 187 223 36 244.88 1.94 382 188 224 36 244.53 2.10 383 189 224 35 244.53 2.10 384 190 218 28 248.73 1.16 385 190 223 33 244.93 1.93 386 190 224 34 244.82 1.96 387 190 225 35 243.97 1.96 388 190 226 36 243.86 2.02 389 191 226 35 241.00 2.56 390 191 228 37 232.84 2.03 391 192 211 19 249.34 1.55 392 192 214 22 249.75 1.40 393 192 218 26 249.75 1.38 394 192 225 33 244.80 1.97 395 192 226 34 244.06 2.00 396 192 227 35 226.44 0.92 397 192 228 36 216.26 0.17 398 193 228 35 210.12 1.80 399 193 231 38 161.80 4.21 400 193 234 41 71.36 10.90 401 194 204 10 248.22 1.36 402 194 205 11 245.16 1.81 403 194 206 12 244.78 1.96 404 194 211 17 249.64 1.49 405 194 227 33 239.09 2.08 406 194 228 34 218.72 1.54 407 194 229 35 184.47 0.92 408 194 230 36 182.00 1.36 409 195 230 35 176.27 1.51 410 195 231 36 173.02 0.12 411 195 234 39 70.14 11.09 412 195 235 40 70.14 11.09 413 195 238 43 69.53 11.20 414 196 202 6 249.93 1.46 415 196 204 8 249.61 1.50 416 196 205 9 249.41 1.49 417 196 229 33 206.38 0.06 418 196 230 34 182.93 1.07 419 196 235 39 70.46 11.26 420 196 238 42 69.57 11.22 421 197 200 3 329.39 10.56 422 197 201 4 329.38 10.56 423 197 238 41 69.58 11.21 424 198 235 37 70.50 11.23 425 198 238 40 69.59 11.22 426 198 239 41 69.58 11.21 427 198 242 44 69.59 11.22 428 198 245 47 69.51 11.19 429 198 247 49 69.55 11.20 430 198 248 50 69.50 11.19 431 199 245 46 69.56 11.21 432 199 247 48 69.51 11.22 433 202 205 3 437.56 0.37 434 205 229 24 272.23 2.91 435 206 228 22 497.39 3.69 436 206 229 23 314.75 3.48 437 228 231 3 364.11 1.08 438 230 235 5 289.40 3.82 439 231 234 3 368.88 1.02 440 231 235 4 332.53 4.02 441 232 235 3 353.67 4.89 442 232 236 4 335.24 2.67 443 233 236 3 369.29 1.21 444 233 237 4 341.83 5.42 445 234 237 3 368.67 1.52 446 234 238 4 343.01 6.54 447 235 238 3 358.48 2.94 448 235 239 4 332.86 1.48 449 236 239 3 355.62 1.51 450 236 240 4 572.76 0.54