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 11 14 3 642.64 2.75 2 11 15 4 624.17 3.62 3 12 15 3 634.50 1.41 4 12 16 4 627.06 2.17 5 13 16 3 634.56 1.22 6 13 17 4 625.49 2.94 7 14 17 3 624.34 3.52 8 14 18 4 628.00 1.68 9 15 18 3 629.59 1.06 10 15 19 4 627.99 1.67 11 16 19 3 627.90 1.62 12 17 75 58 37.27 0.31 13 17 76 59 37.27 0.31 14 24 41 17 357.20 70.41 15 24 42 18 357.28 70.36 16 24 108 84 133.21 1.07 17 24 109 85 127.43 0.82 18 25 40 15 543.84 0.13 19 26 38 12 680.26 0.29 20 26 39 13 615.81 1.62 21 26 40 14 543.85 0.14 22 26 98 72 142.47 8.61 23 26 100 74 140.74 0.34 24 26 109 83 133.19 1.07 25 26 111 85 114.64 1.50 26 27 38 11 747.37 5.92 27 27 39 12 639.88 1.85 28 28 98 70 157.46 6.53 29 28 111 83 133.55 1.09 30 28 113 85 121.42 0.14 31 28 118 90 105.72 0.14 32 29 118 89 105.73 0.14 33 29 120 91 100.35 0.10 34 29 208 179 101.36 0.20 35 30 115 85 111.91 1.02 36 30 118 88 109.68 0.12 37 30 119 89 105.90 0.06 38 30 120 90 105.58 0.19 39 31 120 89 106.73 0.44 40 31 121 90 105.38 0.20 41 31 122 91 103.70 0.35 42 32 122 90 109.06 0.07 43 32 146 114 109.80 0.18 44 32 147 115 109.80 0.18 45 32 149 117 109.93 0.18 46 33 92 59 196.94 2.44 47 33 116 83 127.33 0.52 48 33 119 86 113.70 1.89 49 33 149 116 110.08 0.10 50 33 200 167 110.20 0.14 51 33 205 172 125.81 0.24 52 34 87 53 215.72 0.41 53 34 90 56 200.20 0.92 54 35 90 55 200.06 0.88 55 36 84 48 216.59 0.05 56 36 85 49 216.41 0.14 57 36 90 54 194.63 0.02 58 36 96 60 167.58 3.73 59 36 113 77 133.57 1.09 60 36 115 79 113.73 1.95 61 36 118 82 109.96 0.07 62 37 82 45 217.05 0.06 63 37 83 46 217.01 0.04 64 37 84 47 216.41 0.14 65 38 55 17 217.09 0.11 66 38 82 44 217.03 0.07 67 38 83 45 217.00 0.07 68 38 98 60 157.63 6.61 69 39 80 41 217.52 0.23 70 39 81 42 217.12 0.08 71 39 82 43 217.01 0.04 72 40 53 13 217.58 0.26 73 40 55 15 217.54 0.25 74 40 69 29 217.53 0.24 75 40 80 40 217.53 0.23 76 40 81 41 217.40 0.18 77 40 100 60 157.59 6.46 78 40 108 68 135.41 1.98 79 40 109 69 135.25 1.94 80 41 74 33 217.91 0.14 81 41 79 38 217.75 0.21 82 41 80 39 217.53 0.23 83 42 53 11 218.03 0.20 84 42 78 36 218.01 0.16 85 42 79 37 217.81 0.21 86 42 81 39 217.78 0.21 87 42 108 66 135.46 2.01 88 43 78 35 218.03 0.15 89 43 79 36 218.03 0.16 90 44 79 35 218.03 0.16 91 45 48 3 625.91 2.96 92 48 52 4 614.15 0.99 93 48 71 23 244.31 0.42 94 48 81 33 244.30 0.42 95 49 52 3 643.69 1.90 96 49 71 22 244.31 0.42 97 49 81 32 244.30 0.42 98 50 53 3 663.06 4.29 99 50 69 19 244.31 0.42 100 50 70 20 244.31 0.42 101 50 71 21 244.31 0.42 102 50 81 31 244.30 0.42 103 51 103 52 157.77 6.46 104 52 102 50 157.89 6.46 105 52 103 51 157.67 6.43 106 53 69 16 248.36 0.07 107 53 81 28 248.99 0.40 108 53 100 47 158.16 6.45 109 53 101 48 157.90 6.47 110 53 102 49 157.80 6.48 111 53 103 50 157.66 6.43 112 53 108 55 137.38 1.06 113 54 66 12 249.21 0.37 114 54 100 46 158.28 6.50 115 54 101 47 157.94 6.50 116 55 66 11 249.29 0.34 117 55 67 12 249.16 0.39 118 55 69 14 249.11 0.35 119 55 83 28 249.03 0.38 120 55 98 43 164.83 3.55 121 55 99 44 162.16 4.58 122 55 100 45 158.17 6.46 123 56 64 8 249.84 0.12 124 56 65 9 249.72 0.17 125 56 66 10 249.22 0.37 126 56 98 42 165.94 4.09 127 56 99 43 164.56 3.42 128 57 62 5 619.06 1.52 129 57 64 7 374.66 62.53 130 57 65 8 249.75 0.17 131 57 66 9 249.74 0.18 132 57 67 10 249.71 0.18 133 57 85 28 248.30 0.11 134 57 86 29 248.27 0.09 135 57 89 32 243.39 0.17 136 57 96 39 168.58 3.56 137 57 97 40 168.37 3.56 138 57 98 41 165.94 4.09 139 58 62 4 609.19 6.46 140 58 64 6 376.29 61.72 141 58 96 38 176.00 0.15 142 58 97 39 168.37 3.56 143 59 62 3 620.64 1.46 144 59 89 30 242.65 0.21 145 59 91 32 241.22 0.06 146 59 94 35 193.25 0.57 147 59 95 36 190.55 1.82 148 59 96 37 176.78 0.46 149 60 94 34 198.80 2.50 150 60 95 35 190.62 1.80 151 64 97 33 175.99 0.16 152 64 99 35 168.51 3.56 153 67 85 18 613.73 0.50 154 85 89 4 636.78 4.70 155 85 90 5 607.43 3.72 156 85 96 11 168.46 3.58 157 86 89 3 643.51 1.35 158 86 90 4 636.79 4.70 159 87 90 3 643.50 1.34 160 90 115 25 133.25 1.07 161 91 94 3 673.94 1.47 162 91 115 24 133.55 1.08 163 92 115 23 133.55 1.08 164 92 116 24 133.31 1.10 165 93 114 21 135.56 1.60 166 93 116 23 134.00 1.31 167 93 205 112 133.58 1.11 168 94 114 20 135.94 1.54 169 95 112 17 136.58 1.29 170 95 113 18 136.15 1.47 171 95 114 19 136.11 1.45 172 96 112 16 136.22 1.47 173 96 113 17 136.11 1.45 174 96 115 19 135.99 1.39 175 97 110 13 137.20 1.14 176 97 111 14 136.84 1.30 177 97 112 15 136.23 1.46 178 98 110 12 137.20 1.14 179 98 111 13 136.82 1.30 180 98 113 15 136.70 1.25 181 99 109 10 137.24 1.12 182 99 110 11 136.84 1.30 183 100 108 8 309.28 84.89 184 100 109 9 309.12 84.82 185 101 105 4 585.50 9.24 186 101 106 5 555.00 7.54 187 101 107 6 508.31 1.26 188 101 108 7 492.43 6.69 189 102 105 3 613.64 1.44 190 102 106 4 557.70 6.19 191 114 117 3 632.06 1.55 192 114 118 4 630.97 0.53 193 115 118 3 639.58 0.41 194 116 119 3 658.76 5.30 195 116 204 88 355.02 0.64 196 116 205 89 340.17 0.06 197 116 206 90 343.61 0.54 198 117 206 89 350.31 0.25 199 118 206 88 357.41 0.44 200 118 207 89 357.26 0.47 201 118 208 90 357.33 0.43 202 119 200 81 357.19 0.41 203 119 205 86 357.63 0.44 204 119 206 87 357.53 0.40 205 119 207 88 357.40 0.43 206 119 208 89 357.40 0.43 207 120 208 88 357.40 0.43 208 120 209 89 357.40 0.43 209 121 145 24 359.75 0.53 210 121 148 27 361.31 0.93 211 121 200 79 358.74 0.88 212 121 210 89 357.47 0.42 213 122 145 23 361.10 0.86 214 122 210 88 357.56 0.39 215 123 145 22 365.68 0.43 216 123 146 23 366.01 0.42 217 123 210 87 357.88 0.55 218 123 211 88 357.58 0.39 219 123 212 89 357.55 0.39 220 123 213 90 357.45 0.41 221 124 142 18 365.85 0.49 222 124 143 19 365.89 0.51 223 124 145 21 365.75 0.47 224 124 156 32 359.60 0.46 225 124 196 72 357.58 0.40 226 124 197 73 359.32 0.58 227 124 198 74 359.62 0.46 228 124 210 86 360.13 0.35 229 124 213 89 357.54 0.40 230 125 142 17 366.23 0.34 231 125 143 18 366.16 0.38 232 125 144 19 366.05 0.43 233 125 146 21 366.14 0.40 234 126 141 15 366.50 0.36 235 126 142 16 366.31 0.34 236 127 140 13 366.67 0.36 237 127 141 14 366.54 0.34 238 127 142 15 366.46 0.35 239 127 194 67 360.06 0.42 240 127 195 68 360.19 0.38 241 127 196 69 360.22 0.39 242 127 213 86 360.24 0.38 243 127 214 87 360.21 0.38 244 127 215 88 360.12 0.39 245 127 216 89 358.25 0.39 246 128 140 12 366.76 0.39 247 128 141 13 366.62 0.36 248 128 216 88 359.97 0.40 249 129 139 10 488.07 1.88 250 129 140 11 366.76 0.38 251 129 194 65 360.22 0.39 252 129 216 87 360.20 0.39 253 129 218 89 358.04 0.49 254 130 137 7 536.26 2.19 255 130 138 8 515.38 2.76 256 130 139 9 493.28 0.70 257 130 218 88 360.19 0.38 258 131 136 5 546.30 2.19 259 131 137 6 536.25 2.19 260 131 138 7 515.46 2.77 261 132 135 3 634.02 0.55 262 132 136 4 585.63 1.91 263 132 137 5 536.26 2.19 264 132 139 7 536.24 2.19 265 133 136 3 628.00 0.16 266 137 182 45 462.81 1.04 267 137 184 47 462.25 1.01 268 138 182 44 462.84 1.03 269 138 183 45 462.50 1.09 270 138 186 48 462.39 1.05 271 138 194 56 462.14 0.96 272 138 218 80 360.20 0.38 273 139 180 41 464.66 0.89 274 139 181 42 463.62 1.28 275 139 182 43 462.89 1.06 276 140 158 18 463.46 1.26 277 140 180 40 464.67 0.89 278 140 181 41 463.64 1.29 279 140 183 43 464.47 0.84 280 140 194 54 462.19 0.94 281 141 179 38 465.17 0.69 282 141 180 39 464.68 0.89 283 142 156 14 465.24 0.73 284 142 158 16 465.04 0.71 285 142 174 32 465.37 0.72 286 142 179 37 465.19 0.70 287 142 180 38 465.19 0.70 288 142 181 39 465.19 0.70 289 142 196 54 462.19 0.94 290 144 151 7 473.21 3.16 291 144 154 10 465.42 0.73 292 144 156 12 465.36 0.71 293 144 179 35 465.37 0.71 294 145 148 3 639.71 3.13 295 145 154 9 507.45 13.97 296 145 198 53 462.18 0.93 297 148 151 3 657.78 2.77 298 148 154 6 611.80 2.56 299 150 153 3 640.87 0.52 300 150 154 4 632.67 2.53 301 150 200 50 462.28 0.90 302 150 205 55 458.14 0.91 303 151 154 3 630.80 1.16 304 152 176 24 478.18 2.11 305 152 177 25 477.52 1.93 306 153 176 23 478.32 2.15 307 153 200 47 462.00 0.95 308 153 201 48 461.45 0.94 309 154 176 22 478.38 2.14 310 154 177 23 478.39 2.13 311 154 198 44 462.35 0.91 312 154 199 45 462.14 0.95 313 154 200 46 462.06 0.92 314 155 176 21 478.39 2.13 315 155 198 43 462.29 0.89 316 155 199 44 462.11 0.94 317 155 201 46 461.23 0.80 318 155 202 47 461.99 0.96 319 156 174 18 478.56 2.08 320 156 178 22 478.43 2.14 321 156 179 23 478.41 2.14 322 156 196 40 462.43 0.88 323 156 197 41 462.40 0.89 324 156 198 42 462.11 0.94 325 156 209 53 372.03 0.95 326 157 171 14 479.86 2.16 327 157 172 15 479.41 2.25 328 157 196 39 462.44 0.87 329 157 197 40 462.41 0.88 330 157 209 52 372.03 0.95 331 157 212 55 370.19 1.02 332 158 171 13 479.86 2.16 333 158 172 14 479.55 2.19 334 158 174 16 479.39 2.25 335 158 181 23 478.18 2.29 336 158 195 37 462.49 0.86 337 158 196 38 462.37 0.83 338 159 170 11 480.00 2.20 339 159 171 12 479.99 2.20 340 159 194 35 462.58 0.88 341 159 195 36 462.54 0.88 342 159 212 53 369.56 1.08 343 160 170 10 480.00 2.19 344 160 172 12 480.00 2.20 345 160 183 23 477.93 2.44 346 160 192 32 465.75 0.01 347 160 193 33 465.50 0.07 348 160 194 34 462.62 0.88 349 161 192 31 465.81 0.01 350 161 193 32 465.54 0.07 351 162 166 4 598.87 4.27 352 162 167 5 506.20 6.30 353 162 190 28 466.66 0.21 354 162 191 29 466.51 0.15 355 162 192 30 466.09 0.15 356 163 166 3 616.23 0.45 357 163 190 27 466.66 0.21 358 163 191 28 466.50 0.15 359 166 187 21 476.19 1.92 360 170 183 13 478.04 2.38 361 171 212 41 369.88 1.18 362 172 183 11 478.00 2.34 363 174 178 4 617.86 4.23 364 174 181 7 483.80 4.99 365 175 178 3 644.20 1.26 366 176 201 25 460.87 0.78 367 183 186 3 721.85 3.79 368 183 194 11 463.12 1.15 369 186 192 6 569.56 4.12 370 186 220 34 360.79 0.26 371 187 190 3 648.36 3.11 372 187 192 5 620.55 0.83 373 187 220 33 361.40 0.52 374 188 220 32 361.56 0.34 375 189 219 30 364.10 0.16 376 189 220 31 363.08 0.21 377 190 218 28 365.05 0.44 378 190 219 29 364.17 0.20 379 190 220 30 364.06 0.25 380 191 217 26 365.25 0.53 381 191 218 27 364.93 0.49 382 191 219 28 364.24 0.23 383 192 217 25 365.08 0.44 384 192 218 26 364.88 0.52 385 192 220 28 364.17 0.20 386 193 215 22 366.14 0.27 387 193 216 23 365.07 0.45 388 193 217 24 364.19 0.19 389 194 215 21 365.25 0.52 390 194 216 22 364.92 0.49 391 194 218 24 364.85 0.52 392 195 212 17 368.64 0.93 393 195 213 18 368.05 0.67 394 195 215 20 364.86 0.51 395 196 212 16 368.53 0.87 396 196 213 17 368.48 0.86 397 197 209 12 372.03 0.95 398 197 210 13 371.22 1.11 399 197 211 14 371.19 1.11 400 197 212 15 369.47 1.05 401 198 209 11 372.03 0.95 402 198 210 12 371.69 0.99 403 199 207 8 372.17 0.95 404 199 208 9 372.12 0.94 405 199 209 10 372.05 0.94 406 200 205 5 560.53 1.17 407 201 205 4 616.61 0.48 408 202 205 3 651.59 3.86