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 61 64 3 660.58 0.28 2 61 65 4 660.15 0.07 3 62 65 3 662.85 1.28 4 62 66 4 660.15 0.07 5 63 66 3 663.90 0.18 6 63 67 4 660.29 0.14 7 64 67 3 667.49 1.08 8 64 68 4 663.08 1.12 9 65 68 3 665.94 1.20 10 65 69 4 660.66 0.08 11 65 83 18 155.28 0.94 12 65 84 19 155.22 0.92 13 65 87 22 155.31 0.93 14 65 89 24 155.20 0.93 15 66 69 3 660.58 0.01 16 66 70 4 660.59 0.00 17 66 105 39 147.94 1.79 18 67 70 3 673.72 2.46 19 67 71 4 660.61 0.03 20 68 71 3 663.25 1.23 21 68 72 4 663.15 1.27 22 68 83 15 156.18 0.49 23 69 72 3 679.61 0.48 24 69 73 4 663.16 1.27 25 69 80 11 172.47 9.58 26 70 73 3 679.61 0.48 27 70 74 4 660.59 0.03 28 70 105 35 148.05 1.75 29 70 106 36 148.03 1.76 30 71 74 3 660.58 0.03 31 71 75 4 657.36 1.12 32 72 75 3 670.22 3.12 33 72 76 4 651.28 3.33 34 72 79 7 471.80 10.12 35 72 80 8 426.51 6.87 36 73 76 3 659.23 2.08 37 73 77 4 623.68 2.39 38 73 78 5 623.68 2.39 39 73 80 7 533.62 20.79 40 73 81 8 544.08 15.56 41 73 100 27 155.21 0.81 42 73 101 28 155.04 0.84 43 73 107 34 148.04 1.76 44 73 108 35 148.01 1.77 45 73 111 38 147.74 1.69 46 74 108 34 148.00 1.77 47 76 79 3 667.29 0.36 48 77 111 34 147.76 1.68 49 78 81 3 666.95 0.84 50 78 82 4 659.83 0.04 51 79 82 3 662.51 1.38 52 79 83 4 659.85 0.04 53 80 83 3 662.52 1.38 54 80 84 4 658.98 0.40 55 81 84 3 671.51 5.87 56 81 85 4 658.97 0.40 57 81 97 16 159.11 0.94 58 81 100 19 158.24 0.70 59 81 101 20 155.15 0.79 60 82 85 3 671.51 5.87 61 82 86 4 633.74 0.46 62 83 86 3 656.38 0.25 63 83 87 4 651.88 2.00 64 84 87 3 655.75 2.02 65 84 88 4 640.15 3.87 66 84 89 5 519.22 6.12 67 84 90 6 478.72 6.86 68 84 100 16 178.35 2.21 69 85 88 3 651.47 1.69 70 85 90 5 478.73 6.86 71 85 91 6 478.72 6.86 72 85 92 7 428.09 1.40 73 85 97 12 189.05 1.39 74 90 96 6 521.86 5.01 75 90 97 7 500.32 15.78 76 90 100 10 429.82 1.31 77 91 95 4 572.72 10.82 78 91 96 5 521.86 5.01 79 91 97 6 521.86 5.01 80 92 95 3 670.11 1.80 81 92 97 5 526.54 7.36 82 94 97 3 649.98 3.89 83 94 122 28 106.00 0.29 84 94 125 31 105.39 0.49 85 94 126 32 105.39 0.49 86 94 129 35 104.88 0.64 87 95 98 3 682.64 2.68 88 95 130 35 104.87 0.64 89 96 99 3 664.90 5.12 90 96 100 4 646.91 4.29 91 97 100 3 657.00 0.76 92 97 101 4 613.40 3.27 93 97 102 5 623.51 1.80 94 97 122 25 106.04 0.30 95 97 126 29 105.39 0.49 96 98 102 4 591.91 7.04 97 98 126 28 105.40 0.49 98 98 129 31 104.88 0.64 99 98 130 32 104.64 0.74 100 98 133 35 92.20 1.49 101 99 133 34 92.19 1.49 102 100 103 3 655.06 1.40 103 100 104 4 479.45 5.53 104 100 107 7 474.74 16.91 105 101 107 6 473.32 17.62 106 101 112 11 158.50 7.04 107 101 115 14 158.50 7.04 108 101 126 25 105.40 0.49 109 102 112 10 158.58 7.00 110 102 115 13 158.52 7.04 111 102 116 14 158.45 7.03 112 102 133 31 92.18 1.48 113 102 134 32 92.18 1.48 114 103 107 4 612.13 9.38 115 103 112 9 166.27 3.16 116 103 133 30 92.18 1.48 117 104 107 3 667.08 1.04 118 107 112 5 634.68 3.52 119 108 111 3 659.44 3.62 120 108 112 4 649.91 1.18 121 109 112 3 664.67 3.81 122 109 113 4 647.02 2.62 123 109 151 42 38.37 1.34 124 110 113 3 665.65 2.73 125 110 114 4 647.01 2.62 126 111 114 3 661.73 2.61 127 111 115 4 648.72 3.48 128 112 115 3 664.24 4.29 129 112 116 4 646.94 2.65 130 113 116 3 659.81 1.47 131 113 152 39 35.94 2.56 132 114 118 4 653.33 1.18 133 115 118 3 701.09 0.55 134 115 123 8 424.39 1.17 135 115 126 11 437.10 7.53 136 116 123 7 446.15 4.15 137 116 127 11 261.50 77.48 138 118 123 5 648.29 0.77 139 118 160 42 62.53 1.07 140 119 123 4 662.87 3.12 141 119 124 5 621.49 2.51 142 120 123 3 665.78 1.66 143 120 124 4 653.25 1.70 144 122 125 3 666.51 4.79 145 122 126 4 652.66 2.94 146 123 126 3 652.89 2.83 147 123 127 4 652.10 3.23 148 124 127 3 673.78 0.87 149 124 128 4 652.56 3.00 150 125 128 3 660.54 0.20 151 125 129 4 647.54 5.50 152 126 129 3 659.98 1.31 153 127 130 3 682.62 1.68 154 127 131 4 654.48 1.43 155 127 164 37 81.25 3.67 156 128 131 3 694.99 4.25 157 128 167 39 99.36 4.20 158 128 171 43 100.57 4.58 159 129 171 42 100.62 4.58 160 130 133 3 710.38 1.30 161 130 171 41 100.61 4.60 162 131 167 36 100.48 4.63 163 131 168 37 100.45 4.63 164 131 171 40 100.58 4.58 165 131 172 41 100.58 4.58 166 132 174 42 398.52 4.84 167 134 148 14 99.64 5.02 168 135 139 4 658.75 5.78 169 136 139 3 637.99 0.54 170 136 144 8 447.14 4.29 171 136 168 32 409.73 2.71 172 136 172 36 409.73 2.70 173 137 172 35 409.73 2.70 174 137 175 38 409.68 2.69 175 139 143 4 650.71 2.44 176 140 143 3 662.21 5.43 177 140 144 4 650.72 2.43 178 140 235 95 313.55 6.94 179 141 144 3 651.51 2.08 180 141 145 4 650.77 2.45 181 141 168 27 410.24 2.60 182 141 172 31 410.25 2.60 183 141 180 39 410.17 2.64 184 141 186 45 409.91 2.71 185 141 189 48 409.88 2.71 186 141 190 49 409.79 2.74 187 141 193 52 409.73 2.71 188 141 235 94 313.67 6.95 189 142 145 3 652.11 1.79 190 142 146 4 650.77 2.46 191 142 193 51 409.72 2.71 192 142 235 93 313.68 6.95 193 142 236 94 313.67 6.95 194 142 238 96 313.61 6.98 195 142 239 97 313.54 7.00 196 143 146 3 661.64 0.17 197 143 238 95 313.55 7.00 198 144 148 4 618.84 8.03 199 145 148 3 687.34 0.40 200 145 165 20 410.24 2.61 201 145 190 45 409.95 2.72 202 145 193 48 409.75 2.71 203 145 194 49 409.73 2.71 204 145 245 100 303.48 8.63 205 146 149 3 815.64 5.17 206 146 239 93 313.55 7.00 207 146 242 96 310.37 6.55 208 146 243 97 308.61 7.25 209 146 244 98 308.19 7.42 210 146 245 99 303.13 8.55 211 147 244 97 308.28 7.40 212 148 165 17 410.35 2.62 213 148 194 46 410.07 2.67 214 149 152 3 720.71 1.34 215 149 161 12 410.34 2.62 216 149 245 96 307.85 7.27 217 149 246 97 303.06 8.52 218 149 247 98 303.06 8.52 219 150 153 3 690.48 3.56 220 150 244 94 308.49 7.29 221 150 247 97 303.06 8.52 222 150 248 98 303.11 8.53 223 153 247 94 302.99 8.49 224 154 157 3 687.62 0.77 225 154 160 6 428.71 11.61 226 154 161 7 410.62 2.61 227 154 247 93 302.99 8.48 228 160 163 3 682.09 2.15 229 160 164 4 643.00 2.69 230 161 164 3 663.50 7.16 231 161 165 4 643.00 2.69 232 161 194 33 410.69 2.73 233 162 165 3 660.73 2.79 234 162 166 4 646.73 0.84 235 162 187 25 412.76 2.48 236 162 191 29 410.90 2.82 237 163 166 3 651.16 1.39 238 163 167 4 646.71 0.84 239 164 168 4 635.79 1.20 240 165 168 3 635.79 1.20 241 165 169 4 646.52 4.25 242 165 187 22 412.76 2.47 243 165 190 25 412.37 2.67 244 165 194 29 412.12 2.54 245 166 170 4 646.55 4.23 246 166 187 21 412.77 2.48 247 167 170 3 646.69 4.25 248 167 171 4 632.53 2.79 249 168 171 3 663.03 0.29 250 168 172 4 632.38 2.83 251 168 186 18 413.19 2.60 252 168 190 22 413.05 2.54 253 169 172 3 647.41 2.79 254 169 173 4 632.40 2.85 255 169 183 14 413.26 2.58 256 169 186 17 413.11 2.56 257 169 187 18 413.07 2.54 258 170 183 13 413.28 2.58 259 171 174 3 692.99 3.04 260 172 175 3 678.89 7.88 261 172 186 14 413.37 2.59 262 173 176 3 679.31 4.69 263 173 177 4 580.78 8.64 264 173 182 9 419.12 0.24 265 173 183 10 413.42 2.60 266 176 179 3 662.41 4.66 267 176 180 4 662.41 4.66 268 178 181 3 651.96 7.19 269 179 227 48 326.29 2.50 270 180 185 5 506.67 5.88 271 180 186 6 480.18 7.37 272 180 189 9 480.18 7.37 273 180 227 47 326.29 2.50 274 180 235 55 323.44 3.33 275 181 185 4 627.55 4.24 276 181 222 41 327.37 2.89 277 181 225 44 326.48 2.57 278 183 186 3 647.41 2.73 279 183 187 4 643.43 0.73 280 184 187 3 656.30 1.47 281 184 188 4 647.69 2.85 282 185 188 3 654.25 0.43 283 185 189 4 647.70 2.85 284 185 221 36 327.69 2.92 285 185 222 37 327.38 2.89 286 185 227 42 327.36 2.90 287 186 189 3 659.86 3.22 288 186 190 4 651.42 0.99 289 187 190 3 652.99 0.21 290 187 191 4 653.00 0.21 291 188 191 3 674.12 2.21 292 188 192 4 653.00 0.20 293 188 221 33 327.74 2.93 294 189 192 3 653.44 0.09 295 189 193 4 652.94 0.17 296 189 214 25 328.04 2.90 297 189 218 29 327.80 2.93 298 189 221 32 327.75 2.93 299 190 193 3 662.65 4.70 300 190 194 4 652.94 0.16 301 191 194 3 651.93 0.34 302 191 195 4 645.37 0.39 303 192 195 3 662.95 2.87 304 192 196 4 645.36 0.40 305 192 214 22 328.06 2.89 306 192 217 25 327.95 2.89 307 193 196 3 645.36 0.40 308 193 197 4 641.91 1.33 309 193 214 21 328.06 2.89 310 193 239 46 313.89 6.84 311 194 198 4 641.76 1.26 312 194 245 51 307.29 7.55 313 195 198 3 649.98 1.77 314 195 199 4 640.16 2.06 315 196 199 3 659.00 2.75 316 196 200 4 637.53 0.77 317 196 209 13 328.76 2.96 318 196 214 18 328.09 2.88 319 196 236 40 321.06 4.92 320 197 200 3 654.91 0.67 321 197 201 4 648.61 2.48 322 197 239 42 314.63 7.21 323 197 243 46 310.82 6.32 324 197 244 47 309.63 6.75 325 197 245 48 308.56 7.25 326 198 201 3 673.20 1.21 327 198 202 4 618.19 6.62 328 198 205 7 371.00 22.16 329 198 245 47 308.56 7.25 330 199 202 3 663.89 5.86 331 199 205 6 366.73 21.07 332 199 207 8 329.39 3.11 333 199 208 9 329.24 3.06 334 199 209 10 329.23 3.07 335 200 208 8 329.07 2.99 336 200 209 9 329.07 2.99 337 200 236 36 326.81 2.73 338 200 239 39 315.98 7.14 339 200 240 40 314.82 7.16 340 201 240 39 315.37 7.43 341 201 243 42 312.88 7.19 342 202 205 3 644.22 2.96 343 202 206 4 518.92 13.51 344 209 236 27 326.90 2.73 345 210 213 3 668.37 6.36 346 210 214 4 656.24 0.29 347 210 236 26 326.87 2.75 348 211 214 3 661.95 3.15 349 211 215 4 656.23 0.29 350 211 232 21 327.39 2.89 351 211 233 22 327.35 2.88 352 211 236 25 326.87 2.75 353 212 215 3 663.85 3.51 354 212 216 4 662.16 4.34 355 213 216 3 661.60 4.63 356 213 217 4 661.59 4.63 357 214 217 3 640.04 0.08 358 214 218 4 639.77 0.21 359 214 232 18 327.38 2.89 360 215 218 3 639.77 0.21 361 215 219 4 638.45 0.86 362 215 229 14 327.43 2.89 363 215 232 17 327.39 2.89 364 216 219 3 653.17 0.44 365 217 221 4 642.43 1.16 366 218 221 3 657.91 0.46 367 218 222 4 602.55 6.50 368 218 226 8 330.52 2.37 369 218 227 9 330.01 2.62 370 218 232 14 327.38 2.90 371 220 223 3 678.86 0.27 372 222 225 3 654.34 3.85 373 222 226 4 542.19 0.82 374 222 227 5 512.46 1.93 375 227 231 4 642.15 4.61 376 227 232 5 634.30 0.69 377 228 231 3 653.59 1.10 378 228 232 4 648.53 1.43 379 229 232 3 648.53 1.43 380 229 233 4 648.52 1.43 381 230 233 3 660.99 3.02 382 230 234 4 636.17 0.24 383 231 234 3 647.61 1.42 384 231 235 4 636.17 0.24 385 232 235 3 649.61 0.42 386 232 236 4 636.05 0.30 387 233 237 4 635.04 0.26 388 234 237 3 635.59 0.53 389 234 238 4 636.41 0.42 390 235 238 3 664.24 4.74 391 236 239 3 659.68 2.44 392 236 240 4 653.00 0.05 393 237 240 3 653.62 0.26 394 237 241 4 623.13 5.66 395 238 242 4 617.91 3.06 396 239 242 3 631.16 1.61 397 239 243 4 601.12 16.64 398 240 243 3 658.56 2.72 399 244 249 5 444.22 8.19 400 245 249 4 637.45 1.25 401 246 249 3 701.42 1.26 402 250 253 3 661.94 1.06 403 252 255 3 683.25 2.12