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 47 169 122 88.84 0.70 2 47 171 124 93.62 0.10 3 48 97 49 91.36 0.55 4 49 172 123 93.73 0.09 5 50 97 47 93.81 0.09 6 50 98 48 93.78 0.07 7 50 99 49 93.78 0.07 8 50 172 122 93.75 0.10 9 50 173 123 93.73 0.09 10 50 174 124 93.72 0.10 11 50 179 129 93.75 0.08 12 51 175 124 93.77 0.09 13 51 178 127 93.77 0.08 14 51 179 128 93.78 0.07 15 52 172 120 95.23 0.06 16 52 173 121 93.78 0.07 17 52 175 123 93.78 0.08 18 53 158 105 95.01 0.07 19 53 172 119 95.29 0.04 20 53 173 120 95.10 0.01 21 54 158 104 95.09 0.04 22 54 170 116 102.20 1.82 23 54 171 117 96.83 0.70 24 54 172 118 95.29 0.04 25 54 173 119 95.23 0.06 26 55 59 4 360.68 2.14 27 55 158 103 95.11 0.03 28 55 159 104 95.09 0.04 29 55 160 105 95.28 0.02 30 55 168 113 105.14 0.35 31 55 169 114 103.28 1.28 32 55 170 115 102.72 1.57 33 55 173 118 96.80 0.71 34 56 59 3 364.53 0.21 35 56 157 101 95.26 0.02 36 56 158 102 95.28 0.03 37 56 170 114 109.68 1.84 38 57 170 113 111.59 0.92 39 58 61 3 364.82 3.48 40 58 62 4 350.00 1.25 41 58 170 112 126.20 0.46 42 59 62 3 357.31 0.09 43 59 63 4 351.14 1.82 44 59 86 27 126.55 0.35 45 59 89 30 126.55 0.35 46 59 93 34 126.56 0.35 47 59 157 98 109.83 1.93 48 59 159 100 117.09 2.81 49 59 168 109 126.59 0.35 50 60 63 3 359.01 1.33 51 60 64 4 357.13 0.46 52 60 86 26 126.54 0.35 53 60 168 108 126.61 0.35 54 60 170 110 126.60 0.35 55 61 64 3 367.32 0.16 56 61 65 4 357.36 0.36 57 62 65 3 365.28 3.58 58 62 66 4 357.34 0.37 59 62 157 95 126.56 0.36 60 63 66 3 361.38 1.60 61 63 67 4 357.34 0.37 62 63 86 23 137.46 0.28 63 63 89 26 137.30 0.24 64 63 153 90 126.55 0.37 65 63 157 94 126.62 0.38 66 64 67 3 357.35 0.37 67 64 68 4 511.87 5.42 68 64 82 18 350.12 1.26 69 64 83 19 349.47 0.93 70 64 86 22 329.96 3.60 71 66 152 86 137.75 0.29 72 66 153 87 137.78 0.29 73 66 154 88 137.85 0.26 74 66 155 89 137.81 0.28 75 66 157 91 137.85 0.27 76 67 85 18 361.82 0.07 77 67 149 82 137.84 0.28 78 67 153 86 137.84 0.28 79 69 152 83 140.30 0.28 80 70 115 45 140.47 0.34 81 70 147 77 140.28 0.28 82 70 148 78 140.30 0.28 83 70 149 79 140.30 0.28 84 70 152 82 140.30 0.28 85 77 114 37 140.62 0.34 86 77 115 38 140.48 0.35 87 77 149 72 140.56 0.30 88 80 149 69 140.47 0.26 89 81 85 4 555.67 3.41 90 82 85 3 366.52 2.27 91 82 86 4 361.82 0.07 92 83 86 3 366.52 2.27 93 83 87 4 360.04 0.48 94 84 87 3 367.49 0.87 95 84 88 4 360.51 0.71 96 84 112 28 143.31 0.39 97 85 88 3 365.44 1.89 98 85 89 4 356.85 0.60 99 85 109 24 143.30 0.40 100 85 112 27 143.31 0.39 101 85 153 68 143.31 0.39 102 86 89 3 360.47 0.73 103 86 90 4 358.71 0.06 104 86 168 82 336.88 0.03 105 87 90 3 363.06 0.51 106 87 91 4 360.69 0.71 107 88 91 3 364.36 1.08 108 88 92 4 363.14 0.47 109 88 108 20 148.72 1.56 110 88 109 21 148.69 1.55 111 88 112 24 148.71 1.56 112 89 92 3 379.32 3.32 113 89 93 4 375.42 1.22 114 89 106 17 148.85 1.53 115 89 109 20 148.72 1.57 116 89 153 64 148.74 1.58 117 89 154 65 148.73 1.57 118 89 159 70 306.75 5.98 119 90 93 3 383.19 1.39 120 90 94 4 360.38 0.85 121 91 96 5 370.02 1.48 122 92 96 4 393.49 3.06 123 92 101 9 219.62 36.53 124 92 105 13 149.58 1.52 125 92 106 14 149.53 1.51 126 93 96 3 393.98 2.82 127 93 101 8 309.62 7.34 128 93 159 66 317.69 4.69 129 93 160 67 313.48 2.63 130 93 161 68 345.29 1.00 131 93 168 75 404.91 0.24 132 93 184 91 219.45 36.44 133 94 161 67 368.93 3.48 134 94 165 71 405.49 0.48 135 94 166 72 405.45 0.49 136 94 167 73 405.30 0.42 137 94 168 74 405.25 0.42 138 95 162 67 405.37 0.45 139 95 163 68 405.44 0.46 140 95 164 69 405.50 0.48 141 95 165 70 405.49 0.48 142 96 101 5 401.95 0.53 143 96 105 9 388.25 1.32 144 96 162 66 405.50 0.47 145 96 163 67 405.51 0.48 146 97 100 3 438.87 7.09 147 97 101 4 412.70 3.23 148 97 163 66 411.07 2.18 149 98 101 3 444.65 4.20 150 98 160 62 405.49 0.48 151 98 161 63 406.58 0.07 152 98 162 64 415.34 0.09 153 98 174 76 419.39 1.28 154 98 183 85 405.44 0.48 155 98 184 86 405.42 0.47 156 99 174 75 515.13 0.09 157 99 182 83 429.44 6.38 158 100 182 82 540.34 2.24 159 101 105 4 445.72 0.78 160 101 106 5 445.71 0.78 161 101 183 82 553.43 2.64 162 101 184 83 457.40 2.46 163 101 187 86 419.42 1.35 164 102 105 3 453.12 2.79 165 102 187 85 429.62 6.45 166 103 106 3 448.87 0.67 167 103 107 4 446.16 0.56 168 103 187 84 437.19 2.66 169 103 191 88 417.06 0.32 170 104 107 3 448.85 0.67 171 104 108 4 458.16 1.63 172 105 108 3 491.41 3.33 173 106 109 3 450.42 0.70 174 106 110 4 443.56 1.39 175 106 188 82 571.83 1.52 176 107 110 3 446.50 0.32 177 107 111 4 449.44 1.55 178 108 111 3 454.92 0.53 179 108 112 4 450.13 1.80 180 109 112 3 456.88 0.45 181 109 113 4 450.13 1.80 182 110 113 3 455.46 0.86 183 110 114 4 450.89 1.42 184 110 195 85 466.37 2.52 185 111 114 3 456.06 1.16 186 122 204 82 473.51 2.35 187 122 205 83 473.47 2.33 188 123 205 82 473.44 2.34 189 123 206 83 473.44 2.34 190 123 207 84 473.32 2.33 191 123 241 118 265.42 0.21 192 124 204 80 473.67 2.37 193 124 205 81 473.51 2.35 194 124 206 82 473.42 2.35 195 124 207 83 473.42 2.35 196 124 222 98 274.85 0.52 197 124 226 102 274.73 0.55 198 124 230 106 274.62 0.54 199 125 206 81 473.47 2.36 200 125 207 82 473.37 2.32 201 126 207 81 473.47 2.36 202 126 208 82 473.38 2.33 203 126 209 83 473.36 2.32 204 126 222 96 274.77 0.52 205 127 209 82 473.34 2.34 206 127 212 85 420.16 2.04 207 127 217 90 275.83 0.33 208 127 219 92 275.78 0.33 209 127 220 93 275.53 0.27 210 128 207 79 473.44 2.35 211 128 208 80 473.34 2.34 212 128 209 81 473.16 2.30 213 128 243 115 264.60 0.24 214 129 155 26 571.80 3.60 215 129 156 27 565.15 2.48 216 131 207 76 473.35 2.33 217 131 243 112 264.83 0.07 218 131 281 150 38.62 1.16 219 131 285 154 35.62 0.63 220 132 207 75 473.25 2.30 221 134 285 151 35.59 0.65 222 135 207 72 473.23 2.29 223 135 241 106 265.46 0.23 224 135 284 149 35.66 0.62 225 135 285 150 35.62 0.63 226 135 288 153 29.46 0.90 227 138 285 147 35.65 0.62 228 138 288 150 29.53 0.86 229 138 289 151 28.89 0.67 230 139 288 149 29.82 0.71 231 142 205 63 456.51 0.97 232 145 151 6 575.16 1.91 233 145 189 44 557.58 2.40 234 146 151 5 575.18 1.91 235 146 152 6 575.33 1.83 236 146 155 9 561.45 4.33 237 176 186 10 554.92 7.54 238 176 219 43 274.67 0.59 239 180 183 3 516.93 14.76 240 181 186 5 429.62 6.44 241 182 187 5 429.62 6.45 242 182 190 8 429.57 6.46 243 183 186 3 468.43 2.56 244 183 187 4 437.46 2.54 245 184 188 4 456.32 1.80 246 185 188 3 471.47 2.13 247 185 189 4 462.50 1.29 248 186 189 3 471.57 2.40 249 186 190 4 465.11 2.02 250 187 190 3 471.82 1.86 251 187 191 4 468.78 1.75 252 188 191 3 470.79 1.89 253 188 192 4 469.67 1.78 254 189 192 3 474.79 1.57 255 189 193 4 464.77 0.29 256 190 193 3 475.07 0.20 257 190 194 4 469.10 1.40 258 190 225 35 274.47 0.59 259 191 194 3 475.71 0.52 260 191 195 4 470.70 2.18 261 192 195 3 475.05 0.83 262 192 196 4 470.81 2.23 263 193 196 3 474.34 0.48 264 193 197 4 470.80 2.25 265 193 221 28 274.73 0.56 266 193 225 32 274.60 0.58 267 193 226 33 274.48 0.59 268 194 197 3 474.66 1.09 269 194 198 4 468.50 3.39 270 194 225 31 274.60 0.58 271 194 229 35 274.08 0.58 272 195 198 3 472.10 2.35 273 195 199 4 468.97 3.16 274 196 199 3 473.34 2.88 275 196 200 4 463.62 0.49 276 197 200 3 473.44 2.83 277 197 226 29 274.65 0.56 278 197 229 32 274.56 0.58 279 197 230 33 274.06 0.61 280 198 229 31 274.58 0.57 281 198 231 33 273.88 0.53 282 198 234 36 273.51 0.52 283 199 234 35 273.53 0.53 284 200 204 4 401.04 5.48 285 200 230 30 274.58 0.56 286 200 234 34 273.54 0.53 287 200 235 35 273.47 0.53 288 201 234 33 273.53 0.53 289 201 235 34 273.48 0.53 290 202 234 32 273.81 0.53 291 202 235 33 273.50 0.52 292 202 236 34 273.47 0.53 293 202 237 35 273.44 0.53 294 203 236 33 273.47 0.54 295 203 237 34 270.44 0.99 296 203 239 36 266.23 0.33 297 204 230 26 274.68 0.55 298 204 235 31 273.48 0.53 299 204 237 33 270.40 0.99 300 204 238 34 265.88 0.35 301 204 239 35 265.72 0.28 302 205 239 34 265.69 0.28 303 205 241 36 265.43 0.21 304 206 222 16 275.47 0.29 305 206 238 32 265.72 0.28 306 206 239 33 265.68 0.28 307 206 240 34 265.31 0.26 308 206 241 35 265.25 0.23 309 207 241 34 265.22 0.21 310 207 243 36 264.62 0.25 311 207 284 77 40.68 0.86 312 208 215 7 275.95 0.29 313 208 216 8 275.94 0.29 314 208 222 14 275.66 0.30 315 208 240 32 265.34 0.25 316 208 241 33 265.22 0.21 317 208 242 34 264.63 0.26 318 208 243 35 264.63 0.26 319 208 259 51 262.32 0.79 320 208 262 54 262.37 0.79 321 209 212 3 371.26 1.55 322 209 215 6 276.09 0.22 323 210 215 5 276.13 0.24 324 210 242 32 264.94 0.12 325 210 243 33 264.92 0.12 326 210 253 43 260.41 0.40 327 211 245 34 263.44 0.60 328 211 247 36 262.70 0.68 329 212 215 3 345.47 2.52 330 214 217 3 366.37 0.92 331 214 258 44 262.56 0.70 332 215 242 27 265.00 0.15 333 215 253 38 261.86 0.37 334 215 256 41 262.51 0.68 335 215 258 43 262.54 0.69 336 215 259 44 262.54 0.69 337 216 222 6 285.33 0.77 338 216 223 7 284.62 1.11 339 216 258 42 262.47 0.65 340 216 259 43 262.49 0.66 341 216 261 45 262.57 0.69 342 216 262 46 262.55 0.70 343 216 265 49 262.61 0.70 344 217 220 3 371.81 0.42 345 217 223 6 284.64 1.10 346 218 223 5 284.64 1.10 347 218 224 6 294.76 5.46 348 218 261 43 262.56 0.69 349 220 223 3 357.86 4.28 350 220 224 4 326.38 3.28 351 221 224 3 360.70 2.85 352 221 225 4 326.24 3.35 353 221 226 5 313.22 3.18 354 222 226 4 334.41 3.97 355 222 227 5 327.16 3.79 356 222 238 16 265.70 0.28 357 222 262 40 262.44 0.74 358 223 227 4 334.47 4.00 359 223 228 5 337.22 3.60 360 224 228 4 356.10 0.52 361 225 228 3 362.41 2.63 362 225 229 4 352.31 2.41 363 226 229 3 361.06 1.96 364 226 230 4 350.79 3.18 365 227 230 3 373.14 2.40 366 227 238 11 265.69 0.28 367 227 262 35 262.37 0.75 368 227 265 38 262.35 0.76 369 227 266 39 262.33 0.76 370 227 269 42 262.37 0.73 371 228 265 37 262.39 0.73 372 228 269 41 262.30 0.70 373 229 269 40 262.30 0.70 374 230 235 5 280.84 2.06 375 230 238 8 265.70 0.28 376 230 266 36 262.29 0.74 377 230 269 39 262.15 0.72 378 230 271 41 261.31 0.70 379 231 234 3 353.91 2.55 380 231 235 4 293.41 0.19 381 232 235 3 344.29 1.61 382 232 269 37 261.33 0.81 383 232 270 38 261.20 0.76 384 232 271 39 260.73 0.66 385 235 271 36 260.98 0.77 386 236 271 35 261.02 0.77 387 236 272 36 260.75 0.68 388 237 271 34 261.16 0.79 389 237 272 35 260.75 0.68 390 237 274 37 259.33 0.42 391 238 262 24 261.92 0.98 392 238 266 28 261.80 0.97 393 238 271 33 261.26 0.77 394 238 272 34 261.14 0.80 395 238 273 35 260.25 0.83 396 238 274 36 259.31 0.42 397 239 274 35 255.88 1.99 398 239 276 37 252.06 0.95 399 240 262 22 262.33 0.80 400 240 273 33 260.39 0.77 401 240 274 34 260.12 0.82 402 240 275 35 252.09 0.96 403 240 276 36 251.93 0.89 404 241 276 35 242.38 0.47 405 241 278 37 194.68 0.36 406 241 284 43 44.74 0.38 407 242 253 11 261.11 0.73 408 242 259 17 262.31 0.79 409 242 275 33 258.40 0.73 410 242 276 34 251.87 1.06 411 242 277 35 225.55 3.48 412 242 278 36 214.49 5.95 413 243 278 35 194.67 0.36 414 243 281 38 49.80 0.27 415 244 251 7 262.13 0.69 416 244 253 9 260.83 0.59 417 244 277 33 251.22 1.01 418 244 278 34 225.33 3.60 419 244 279 35 192.71 0.65 420 244 281 37 160.96 0.27 421 250 279 29 260.12 0.93 422 251 279 28 260.32 0.86 423 252 277 25 268.27 4.44 424 252 279 27 260.71 0.66 425 253 277 24 288.95 2.35 426 254 276 22 499.67 3.98 427 254 277 23 350.48 2.63 428 278 281 3 387.53 0.65 429 278 284 6 280.29 0.09 430 280 283 3 354.08 3.52 431 280 284 4 333.89 0.88 432 281 284 3 333.89 0.88 433 281 285 4 337.64 2.75 434 282 286 4 337.71 2.71 435 283 286 3 345.47 0.22 436 283 287 4 344.19 0.86 437 284 287 3 365.77 2.21 438 284 288 4 345.19 0.09 439 285 288 3 352.08 2.62 440 285 289 4 342.25 1.55 441 286 289 3 348.52 0.83 442 286 290 4 328.04 8.65 443 287 291 4 308.91 4.33 444 288 291 3 359.84 0.86