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 1 125 124 252.52 4.56 2 1 126 125 253.48 4.79 3 2 123 121 293.50 1.20 4 2 124 122 277.80 0.80 5 3 110 107 254.56 4.34 6 3 111 108 254.56 4.34 7 3 121 118 296.31 0.93 8 3 122 119 296.31 0.93 9 3 123 120 297.04 0.54 10 3 124 121 295.54 0.89 11 3 125 122 281.15 2.49 12 4 7 3 377.33 2.11 13 4 10 6 343.15 5.66 14 4 109 105 267.52 2.12 15 4 110 106 278.39 3.32 16 4 122 118 297.51 0.68 17 5 10 5 359.72 2.06 18 5 122 117 297.77 0.62 19 6 9 3 374.19 1.49 20 6 10 4 359.74 2.08 21 6 122 116 301.11 2.08 22 7 10 3 372.70 2.52 23 7 11 4 359.76 2.08 24 7 38 31 338.48 2.79 25 7 41 34 329.57 0.94 26 7 45 38 328.64 0.71 27 7 109 102 328.73 0.76 28 7 111 104 328.18 0.82 29 8 11 3 375.35 1.19 30 8 12 4 359.77 2.09 31 8 38 30 331.50 1.31 32 9 12 3 365.91 0.30 33 9 13 4 359.95 2.17 34 10 13 3 364.17 4.26 35 10 14 4 363.74 4.04 36 10 109 99 352.61 0.12 37 11 14 3 377.95 1.72 38 11 15 4 364.12 4.24 39 11 37 26 355.29 0.77 40 11 38 27 355.11 0.82 41 11 41 30 354.76 0.86 42 11 61 50 355.12 0.82 43 11 105 94 353.60 0.28 44 11 106 95 353.67 0.32 45 12 15 3 376.95 1.78 46 12 16 4 535.38 11.68 47 12 34 22 361.72 3.04 48 12 35 23 361.72 3.04 49 12 38 26 355.38 0.71 50 14 104 90 396.51 0.26 51 14 105 91 384.06 1.99 52 14 107 93 396.50 0.25 53 14 109 95 380.86 0.39 54 15 37 22 410.49 1.06 55 15 105 90 396.51 0.25 56 17 104 87 433.00 1.11 57 18 67 49 448.36 1.74 58 18 99 81 437.99 1.08 59 18 100 82 438.60 0.78 60 18 101 83 435.24 0.02 61 18 104 86 433.01 1.12 62 22 104 82 439.10 0.78 63 23 90 67 448.33 1.79 64 23 99 76 446.04 0.68 65 26 70 44 448.67 1.77 66 26 91 65 448.50 1.76 67 26 95 69 448.56 1.79 68 27 67 40 448.55 1.72 69 27 69 42 448.66 1.77 70 27 70 43 448.67 1.77 71 27 95 68 448.61 1.76 72 27 99 72 448.50 1.76 73 28 67 39 448.56 1.72 74 28 68 40 448.61 1.70 75 30 64 34 447.40 1.64 76 30 65 35 447.75 1.47 77 30 66 36 448.11 1.48 78 30 67 37 448.12 1.47 79 30 101 71 448.07 1.46 80 32 64 32 444.97 0.62 81 33 37 4 538.48 1.35 82 34 37 3 410.50 1.05 83 34 38 4 410.51 1.06 84 35 38 3 421.99 0.68 85 35 39 4 422.04 0.70 86 36 39 3 423.27 0.53 87 36 40 4 422.27 0.83 88 37 40 3 428.24 2.32 89 37 41 4 423.59 0.17 90 37 61 24 438.80 0.87 91 37 64 27 445.13 0.56 92 37 65 28 445.32 0.60 93 37 101 64 448.60 1.71 94 37 105 68 445.31 0.64 95 38 41 3 432.73 1.99 96 38 42 4 428.06 2.41 97 39 42 3 438.03 0.20 98 39 43 4 433.92 0.95 99 40 43 3 439.28 0.74 100 40 44 4 441.86 2.00 101 40 60 20 446.20 1.04 102 40 61 21 447.60 1.56 103 40 64 24 448.92 1.76 104 41 44 3 445.14 0.36 105 41 45 4 445.25 0.40 106 41 58 17 447.24 1.45 107 41 61 20 448.79 1.74 108 41 106 65 500.68 24.21 109 41 111 70 446.79 1.07 110 41 139 98 312.14 1.34 111 42 45 3 447.08 1.31 112 42 46 4 441.71 1.96 113 42 118 76 567.18 0.05 114 42 120 78 445.12 0.49 115 43 46 3 447.10 1.30 116 43 60 17 486.25 0.70 117 44 48 4 447.69 1.52 118 44 53 9 439.15 1.36 119 44 57 13 448.79 1.74 120 44 58 14 449.01 1.84 121 45 48 3 447.75 1.48 122 45 53 8 444.96 0.48 123 45 58 13 520.17 12.69 124 45 111 66 566.98 0.04 125 45 112 67 551.93 0.62 126 45 113 68 540.87 5.84 127 45 120 75 567.21 0.07 128 48 52 4 534.32 1.83 129 51 135 84 314.45 1.05 130 53 134 81 314.45 1.11 131 53 135 82 313.67 1.44 132 53 138 85 313.19 1.61 133 54 134 80 314.43 1.12 134 54 138 84 313.19 1.61 135 55 134 79 550.00 2.25 136 55 137 82 313.67 1.44 137 55 138 83 313.19 1.61 138 55 141 86 312.52 1.44 139 55 142 87 312.17 1.31 140 55 178 123 197.22 0.48 141 57 138 81 312.72 1.38 142 58 138 80 312.56 1.44 143 58 139 81 312.17 1.33 144 59 142 83 311.61 1.49 145 61 139 78 312.16 1.33 146 62 139 77 312.16 1.33 147 62 142 80 310.62 1.90 148 62 143 81 309.42 1.36 149 62 146 84 302.16 3.11 150 66 146 80 302.16 3.11 151 66 150 84 289.52 0.92 152 69 147 78 308.02 1.17 153 69 150 81 290.74 1.50 154 69 151 82 289.52 0.92 155 71 152 81 285.96 2.69 156 71 153 82 285.87 2.71 157 72 152 80 289.52 0.92 158 72 153 81 285.35 2.88 159 72 154 82 280.97 1.49 160 74 147 73 308.72 1.08 161 74 151 77 289.17 1.10 162 74 155 81 257.63 3.38 163 74 156 82 257.62 3.39 164 75 147 72 308.73 1.08 165 75 156 81 257.51 3.35 166 75 158 83 257.43 3.34 167 76 147 71 308.74 1.08 168 76 148 72 308.64 1.08 169 76 155 79 257.69 3.36 170 76 156 80 257.51 3.35 171 76 157 81 257.41 3.33 172 76 158 82 257.42 3.34 173 76 175 99 197.19 0.46 174 76 179 103 197.12 0.43 175 76 183 107 193.05 0.85 176 77 158 81 257.40 3.33 177 78 157 79 257.50 3.35 178 78 158 80 257.43 3.34 179 78 159 81 257.40 3.33 180 78 160 82 257.40 3.34 181 78 170 92 197.43 0.53 182 79 160 81 257.39 3.34 183 79 197 118 178.52 0.76 184 80 158 78 257.44 3.33 185 80 159 79 257.41 3.34 186 80 160 80 257.38 3.35 187 80 195 115 178.45 0.78 188 80 197 117 175.97 0.27 189 83 195 112 178.71 0.86 190 83 197 114 173.88 0.74 191 83 237 154 66.28 1.27 192 83 238 155 66.25 1.27 193 84 158 74 257.44 3.33 194 86 237 151 66.26 1.27 195 87 158 71 257.52 3.38 196 87 193 106 178.84 0.84 197 87 233 146 69.56 0.13 198 87 234 147 66.34 1.31 199 87 237 150 66.17 1.31 200 94 156 62 257.64 3.37 201 95 147 52 308.41 1.03 202 96 147 51 307.56 0.70 203 97 140 43 311.14 1.26 204 97 143 46 308.94 1.07 205 97 144 47 308.92 1.06 206 97 147 50 301.95 3.21 207 100 147 47 299.18 1.87 208 103 140 37 310.63 1.25 209 106 139 33 310.55 1.20 210 106 140 34 310.53 1.20 211 107 140 33 310.53 1.20 212 111 139 28 311.19 0.99 213 128 136 8 316.07 0.77 214 129 136 7 363.44 1.90 215 131 135 4 339.46 7.39 216 131 136 5 319.51 2.56 217 132 135 3 375.22 2.00 218 132 136 4 345.95 10.63 219 133 136 3 345.97 10.63 220 133 137 4 328.82 2.08 221 134 137 3 363.78 1.69 222 134 138 4 319.57 2.52 223 135 138 3 369.04 0.91 224 137 141 4 315.24 0.06 225 137 174 37 197.25 0.47 226 137 177 40 197.25 0.47 227 137 178 41 197.22 0.48 228 138 142 4 354.82 8.35 229 139 142 3 375.47 1.96 230 139 143 4 364.85 3.35 231 140 143 3 369.25 1.15 232 140 144 4 367.41 2.08 233 140 174 34 197.23 0.47 234 141 144 3 369.50 1.02 235 141 145 4 364.86 3.35 236 141 174 33 197.22 0.47 237 141 178 37 197.19 0.47 238 142 145 3 376.26 2.35 239 142 146 4 354.81 8.38 240 143 146 3 376.28 2.35 241 143 147 4 365.43 3.08 242 144 147 3 365.44 3.07 243 144 148 4 355.43 3.54 244 144 174 30 197.23 0.47 245 144 178 34 197.12 0.45 246 144 179 35 197.00 0.48 247 145 148 3 368.29 2.01 248 145 149 4 360.38 1.07 249 145 178 33 197.11 0.46 250 145 182 37 187.58 2.00 251 146 149 3 371.97 0.18 252 146 150 4 365.27 3.52 253 147 150 3 375.50 1.96 254 147 151 4 365.28 3.52 255 148 151 3 370.97 0.69 256 148 178 30 197.15 0.44 257 148 179 31 196.90 0.43 258 148 182 34 187.65 1.97 259 148 183 35 187.48 2.00 260 149 182 33 187.58 1.98 261 149 184 35 187.25 2.06 262 149 186 37 185.87 1.39 263 150 186 36 185.76 1.35 264 151 155 4 338.36 0.71 265 151 186 35 185.77 1.36 266 151 187 36 185.70 1.35 267 152 186 34 185.75 1.35 268 152 187 35 185.71 1.35 269 153 186 33 185.92 1.41 270 153 187 34 185.71 1.35 271 153 188 35 185.41 1.21 272 153 189 36 185.27 1.15 273 154 188 34 185.66 1.33 274 154 189 35 184.75 1.04 275 154 191 37 179.56 0.58 276 155 183 28 193.08 0.85 277 155 187 32 185.74 1.34 278 155 189 34 184.75 1.04 279 155 190 35 181.12 1.67 280 155 191 36 179.21 0.74 281 156 191 35 179.21 0.74 282 156 193 37 179.02 0.73 283 157 168 11 197.70 0.45 284 157 175 18 197.21 0.46 285 157 191 34 179.21 0.74 286 157 192 35 179.05 0.73 287 157 193 36 179.03 0.73 288 157 214 57 149.25 0.35 289 158 193 35 178.81 0.83 290 158 195 37 178.56 0.75 291 158 234 76 70.40 0.23 292 159 168 9 197.63 0.43 293 159 192 33 179.21 0.75 294 159 193 34 179.03 0.73 295 159 194 35 178.77 0.83 296 159 195 36 178.75 0.84 297 159 211 52 149.36 0.39 298 160 163 3 415.95 2.46 299 160 168 8 197.65 0.42 300 160 195 35 178.65 0.79 301 160 197 37 178.49 0.74 302 161 194 33 179.05 0.71 303 161 195 34 178.78 0.83 304 161 196 35 178.77 0.83 305 161 202 41 149.75 0.35 306 161 203 42 149.41 0.40 307 161 204 43 148.49 0.04 308 162 196 34 178.75 0.83 309 162 197 35 178.75 0.83 310 162 201 39 149.94 0.32 311 162 202 40 149.75 0.35 312 162 203 41 149.60 0.30 313 163 166 3 374.53 4.21 314 163 203 40 149.83 0.31 315 164 201 37 160.59 0.60 316 164 203 39 149.85 0.32 317 166 170 4 386.20 3.44 318 167 170 3 408.21 0.28 319 167 204 37 149.44 0.38 320 167 210 43 149.41 0.39 321 168 204 36 149.16 0.29 322 168 210 42 149.40 0.39 323 168 211 43 149.35 0.39 324 169 175 6 210.46 1.43 325 169 176 7 211.37 1.88 326 169 210 41 149.32 0.38 327 169 214 45 149.18 0.40 328 169 217 48 149.28 0.35 329 170 173 3 376.24 0.86 330 170 176 6 213.06 1.03 331 171 176 5 217.08 3.04 332 171 177 6 219.00 2.20 333 172 177 5 220.42 1.88 334 173 176 3 373.55 2.82 335 173 177 4 320.99 1.20 336 174 177 3 351.51 1.01 337 174 178 4 221.59 2.44 338 174 179 5 220.67 1.98 339 175 179 4 221.60 2.44 340 175 180 5 224.37 0.45 341 175 181 6 224.72 0.62 342 175 214 39 149.16 0.40 343 176 181 5 323.87 2.82 344 177 181 4 350.36 4.94 345 178 181 3 383.19 0.01 346 178 182 4 350.37 4.94 347 179 182 3 364.52 2.14 348 179 183 4 364.51 2.14 349 180 183 3 370.47 0.19 350 180 214 34 149.02 0.42 351 180 217 37 148.80 0.35 352 180 218 38 147.48 0.25 353 180 221 41 147.44 0.24 354 181 221 40 147.43 0.24 355 183 187 4 338.61 0.48 356 183 190 7 184.66 1.02 357 183 223 40 147.27 0.24 358 184 187 3 368.39 0.58 359 184 223 39 147.31 0.22 360 185 223 38 147.25 0.25 361 187 190 3 507.15 1.74 362 187 223 36 147.25 0.25 363 188 224 36 147.08 0.33 364 189 224 35 147.08 0.33 365 189 226 37 146.53 0.59 366 190 218 28 148.36 0.51 367 190 223 33 147.47 0.26 368 190 224 34 147.33 0.23 369 190 225 35 147.03 0.34 370 190 226 36 146.52 0.59 371 191 226 35 144.16 0.41 372 191 228 37 135.90 0.92 373 192 211 19 149.34 0.39 374 192 214 22 149.34 0.37 375 192 225 33 147.37 0.24 376 192 226 34 146.52 0.59 377 192 227 35 135.90 0.92 378 192 228 36 132.13 2.80 379 193 228 35 113.41 1.03 380 193 231 38 78.60 1.02 381 193 234 41 70.48 0.20 382 194 204 10 149.16 0.29 383 194 206 12 147.60 0.21 384 194 211 17 149.38 0.39 385 194 227 33 142.68 0.09 386 194 228 34 130.02 0.38 387 194 229 35 79.60 1.47 388 194 230 36 79.68 1.36 389 195 230 35 79.43 1.42 390 195 234 39 70.48 0.20 391 195 238 43 69.97 0.18 392 196 202 6 149.71 0.34 393 196 204 8 149.40 0.35 394 196 229 33 87.79 0.74 395 196 230 34 79.68 1.42 396 196 238 42 70.02 0.18 397 197 200 3 377.79 2.10 398 198 235 37 70.62 0.28 399 198 238 40 70.00 0.19 400 198 239 41 69.93 0.20 401 198 242 44 69.89 0.19 402 198 245 47 69.14 0.10 403 198 247 49 68.72 0.29 404 198 248 50 68.70 0.28 405 199 247 48 69.85 0.20 406 202 205 3 477.40 0.60 407 205 229 24 319.75 0.14 408 206 228 22 491.34 3.83 409 206 229 23 378.70 2.58 410 228 231 3 394.44 5.02 411 230 235 5 223.29 2.06 412 230 238 8 141.12 35.37 413 231 234 3 377.10 3.90 414 231 235 4 353.32 5.62 415 232 235 3 366.96 1.19 416 232 236 4 352.53 5.21 417 233 236 3 369.76 0.35 418 233 237 4 352.53 5.21 419 234 237 3 373.43 2.19 420 234 238 4 351.89 5.54 421 235 238 3 355.16 3.92 422 235 239 4 349.41 6.78 423 235 247 12 349.41 6.78 424 236 239 3 342.88 10.06 425 236 240 4 506.69 4.17