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 14 31 17 478.98 0.56 2 14 36 22 396.63 41.59 3 14 55 41 271.05 41.68 4 14 58 44 270.67 41.65 5 14 59 45 270.68 41.65 6 15 59 44 270.69 41.65 7 15 61 46 270.48 41.59 8 15 64 49 268.95 41.87 9 15 67 52 267.75 42.26 10 16 48 32 284.98 37.76 11 16 51 35 284.45 37.95 12 16 58 42 271.01 41.67 13 16 59 43 270.86 41.66 14 16 60 44 270.66 41.64 15 16 61 45 270.66 41.65 16 16 67 51 268.93 41.86 17 17 67 50 268.97 41.87 18 17 68 51 268.89 41.84 19 17 71 54 267.50 42.15 20 18 44 26 285.73 37.84 21 18 47 29 285.76 37.82 22 18 48 30 285.62 37.87 23 19 75 56 267.56 42.17 24 20 75 55 268.41 41.76 25 21 40 19 396.55 41.43 26 21 75 54 267.56 42.18 27 21 79 58 266.21 42.55 28 22 79 57 266.23 42.55 29 22 168 146 45.11 0.12 30 23 40 17 396.54 41.43 31 23 78 55 267.10 42.27 32 23 142 119 142.86 0.62 33 23 165 142 51.31 0.74 34 23 168 145 45.11 0.12 35 23 169 146 44.34 0.24 36 23 172 149 39.15 0.06 37 25 40 15 396.44 41.48 38 25 41 16 396.32 41.51 39 25 42 17 395.09 41.54 40 25 44 19 390.02 43.66 41 25 47 22 318.86 34.79 42 26 39 13 396.60 41.55 43 26 40 14 396.33 41.54 44 26 47 21 287.67 38.76 45 26 75 49 267.36 42.20 46 26 78 52 266.36 42.62 47 27 38 11 396.70 41.52 48 27 39 12 396.44 41.48 49 27 47 20 285.62 37.88 50 27 48 21 285.61 37.88 51 27 51 24 285.58 37.88 52 28 35 7 461.80 9.10 53 28 37 9 396.68 41.57 54 28 38 10 396.55 41.54 55 28 67 39 268.93 41.86 56 28 71 43 267.46 42.15 57 28 74 46 267.37 42.11 58 29 35 6 417.38 31.26 59 29 36 7 396.72 41.56 60 29 37 8 396.63 41.56 61 29 51 22 284.94 37.76 62 30 34 4 461.79 9.10 63 30 35 5 396.68 41.59 64 30 36 6 396.66 41.58 65 30 67 37 267.75 42.26 66 30 70 40 267.38 42.11 67 31 34 3 488.67 3.20 68 31 36 5 396.74 41.55 69 31 90 59 143.19 0.58 70 31 92 61 143.12 0.60 71 33 88 55 143.39 0.59 72 33 90 57 143.22 0.57 73 34 88 54 143.35 0.61 74 34 89 55 143.31 0.60 75 34 90 56 143.22 0.57 76 35 38 3 570.16 4.73 77 35 74 39 267.26 42.16 78 35 85 50 143.65 0.69 79 35 87 52 143.47 0.64 80 35 88 53 143.41 0.65 81 35 89 54 143.16 0.60 82 35 90 55 143.16 0.60 83 35 140 105 142.73 0.60 84 36 55 19 272.48 41.77 85 36 90 54 143.16 0.60 86 36 140 104 142.72 0.61 87 37 51 14 285.30 37.93 88 37 55 18 274.13 41.70 89 37 139 102 142.62 0.62 90 37 140 103 142.72 0.60 91 38 74 36 267.26 42.17 92 38 78 40 264.32 43.45 93 38 85 47 143.83 0.72 94 38 139 101 142.74 0.60 95 38 140 102 142.74 0.60 96 38 141 103 142.72 0.60 97 38 143 105 142.48 0.58 98 38 161 123 58.79 0.44 99 39 47 8 285.65 37.90 100 39 50 11 285.60 37.88 101 39 51 12 285.58 37.88 102 39 54 15 285.41 37.93 103 39 139 100 142.76 0.61 104 39 161 122 58.68 0.49 105 40 47 7 316.39 36.01 106 40 141 101 142.77 0.61 107 40 142 102 142.77 0.61 108 40 161 121 58.66 0.51 109 40 165 125 51.41 0.73 110 41 47 6 393.32 2.44 111 41 165 124 52.19 0.37 112 42 165 123 53.44 0.83 113 43 46 3 497.56 0.01 114 43 47 4 487.42 1.78 115 44 47 3 494.14 2.33 116 44 48 4 483.44 0.58 117 45 48 3 494.15 2.33 118 45 49 4 486.23 1.19 119 46 49 3 493.71 2.55 120 46 50 4 486.69 1.18 121 47 50 3 489.11 2.28 122 47 51 4 486.76 1.14 123 48 51 3 488.85 0.10 124 48 52 4 484.47 0.03 125 49 52 3 484.94 0.20 126 49 53 4 484.48 0.03 127 50 53 3 498.79 1.57 128 50 54 4 493.31 1.17 129 50 160 110 58.80 0.47 130 50 161 111 58.76 0.47 131 51 54 3 498.79 1.57 132 51 55 4 484.88 0.22 133 51 58 7 271.75 41.64 134 52 55 3 484.88 0.23 135 52 56 4 409.38 22.89 136 54 139 85 142.25 0.62 137 54 160 106 58.80 0.46 138 55 58 3 496.11 5.98 139 61 64 3 487.80 2.10 140 61 67 6 373.53 8.38 141 61 68 7 393.89 18.57 142 62 68 6 422.11 4.46 143 64 67 3 502.38 2.67 144 64 68 4 485.15 1.89 145 65 68 3 500.99 3.37 146 65 69 4 486.28 1.32 147 66 69 3 492.40 1.74 148 66 70 4 486.38 1.27 149 67 70 3 487.28 1.72 150 67 71 4 483.69 0.03 151 68 71 3 497.32 3.30 152 68 72 4 477.31 4.44 153 69 72 3 487.04 2.31 154 69 73 4 478.42 5.00 155 70 73 3 483.55 2.66 156 70 74 4 478.10 5.16 157 70 87 17 143.43 0.66 158 71 74 3 500.38 2.10 159 71 75 4 475.56 3.88 160 72 75 3 487.62 0.41 161 72 76 4 486.20 0.30 162 73 76 3 492.63 0.73 163 73 77 4 487.56 0.38 164 73 87 14 143.62 0.70 165 74 77 3 503.99 0.01 166 74 78 4 486.25 0.28 167 74 85 11 143.72 0.73 168 74 87 13 143.66 0.71 169 75 78 3 488.51 1.09 170 75 79 4 485.99 0.15 171 76 79 3 499.71 4.11 172 76 80 4 485.98 0.15 173 77 80 3 492.61 3.16 174 77 83 6 143.81 0.70 175 77 84 7 143.80 0.71 176 77 85 8 143.75 0.73 177 78 142 64 142.73 0.63 178 78 143 65 142.71 0.63 179 78 172 94 38.95 0.18 180 79 172 93 38.90 0.15 181 80 83 3 505.68 5.80 182 80 172 92 38.83 0.12 183 81 109 28 139.90 0.71 184 81 172 91 38.74 0.09 185 81 173 92 38.29 0.12 186 81 175 94 37.28 0.30 187 82 109 27 139.86 0.72 188 85 89 4 510.91 1.41 189 85 143 58 142.06 0.56 190 89 105 16 214.87 31.85 191 89 140 51 214.81 31.82 192 89 143 54 214.81 31.87 193 91 98 7 409.62 0.47 194 91 101 10 394.69 0.93 195 91 105 14 295.27 24.85 196 91 140 49 215.37 31.87 197 91 144 53 215.26 31.84 198 92 101 9 429.56 0.09 199 92 139 47 250.30 34.62 200 93 97 4 467.51 9.84 201 93 98 5 451.31 4.36 202 93 101 8 442.84 6.71 203 94 97 3 485.78 0.71 204 94 98 4 485.78 0.71 205 95 98 3 487.44 1.54 206 95 99 4 485.80 0.70 207 96 99 3 492.51 3.02 208 96 100 4 486.84 0.18 209 96 122 26 270.56 37.27 210 96 124 28 270.52 37.27 211 96 130 34 270.17 37.17 212 96 131 35 270.15 37.17 213 96 134 38 269.99 37.14 214 97 100 3 488.49 1.01 215 97 101 4 488.49 1.01 216 97 134 37 269.70 37.26 217 97 137 40 269.31 37.23 218 98 101 3 492.51 3.02 219 98 102 4 482.22 1.22 220 99 102 3 485.54 0.47 221 99 103 4 482.22 1.22 222 100 103 3 485.61 1.52 223 100 104 4 483.17 0.71 224 100 118 18 270.50 37.26 225 100 122 22 270.60 37.27 226 100 131 31 270.18 37.17 227 100 134 34 270.17 37.17 228 100 135 35 270.14 37.16 229 101 104 3 490.96 1.17 230 101 105 4 490.97 1.17 231 101 134 33 270.18 37.17 232 101 137 36 269.68 37.23 233 101 138 37 269.27 37.23 234 101 144 43 268.76 37.09 235 102 105 3 490.98 1.17 236 102 106 4 490.98 1.17 237 103 106 3 490.98 1.17 238 103 107 4 490.98 1.17 239 103 118 15 270.57 37.27 240 103 122 19 270.62 37.27 241 104 107 3 493.58 2.46 242 104 118 14 270.62 37.28 243 104 135 31 270.19 37.18 244 104 144 40 268.80 37.09 245 104 145 41 268.77 37.09 246 104 146 42 268.75 37.09 247 104 149 45 266.06 36.48 248 105 144 39 268.80 37.09 249 105 145 40 268.79 37.09 250 107 111 4 460.73 0.47 251 107 113 6 281.53 31.89 252 107 148 41 268.38 37.12 253 107 149 42 268.35 37.12 254 108 111 3 509.67 2.75 255 108 148 40 268.79 37.08 256 109 148 39 268.82 37.09 257 109 173 64 38.73 0.07 258 110 173 63 38.73 0.07 259 111 148 37 268.62 37.09 260 112 148 36 267.67 36.82 261 112 150 38 267.53 36.81 262 112 170 58 49.48 0.49 263 113 117 4 460.30 8.48 264 113 118 5 455.67 10.79 265 113 148 35 267.67 36.82 266 113 149 36 267.32 36.71 267 113 150 37 267.13 36.62 268 114 117 3 488.87 0.73 269 114 118 4 473.56 7.79 270 114 149 35 267.11 36.62 271 114 150 36 266.00 36.52 272 114 152 38 257.33 35.72 273 115 118 3 487.64 1.34 274 115 119 4 472.36 8.39 275 115 128 13 273.36 36.61 276 115 131 16 273.28 36.59 277 115 132 17 273.25 36.56 278 115 135 20 273.24 36.59 279 115 149 34 266.19 36.48 280 115 150 35 266.00 36.52 281 115 151 36 260.41 36.91 282 115 158 43 59.45 0.30 283 116 119 3 472.88 5.45 284 116 120 4 469.67 7.04 285 116 125 9 292.55 28.72 286 116 128 12 273.39 36.59 287 117 120 3 475.05 5.79 288 117 121 4 468.27 6.34 289 118 121 3 488.33 1.34 290 118 122 4 472.93 8.68 291 118 131 13 273.35 36.60 292 118 135 17 273.31 36.62 293 118 149 31 266.73 36.74 294 119 122 3 489.88 0.94 295 119 123 4 472.53 9.25 296 119 124 5 420.18 9.95 297 119 125 6 297.32 26.34 298 119 128 9 273.92 36.33 299 119 131 12 273.35 36.60 300 120 123 3 493.76 1.75 301 120 125 5 298.91 25.55 302 122 131 9 287.19 29.72 303 124 127 3 498.40 1.99 304 125 128 3 527.36 4.67 305 127 130 3 487.35 2.56 306 127 131 4 475.29 2.62 307 128 131 3 486.87 2.79 308 128 132 4 475.43 2.69 309 129 132 3 488.45 2.23 310 129 133 4 481.05 0.12 311 130 133 3 486.18 2.45 312 130 134 4 475.36 2.75 313 131 134 3 489.38 1.48 314 131 135 4 481.27 5.71 315 132 135 3 497.05 2.35 316 132 136 4 490.34 1.18 317 133 136 3 497.13 2.40 318 133 137 4 476.87 7.91 319 134 137 3 494.91 3.52 320 134 138 4 487.92 2.39 321 135 138 3 501.92 0.02 322 135 146 11 267.44 36.77 323 135 149 14 265.98 36.51 324 136 158 22 59.32 0.31 325 136 160 24 59.29 0.28 326 137 160 23 59.29 0.28 327 138 141 3 535.28 1.90 328 138 144 6 291.54 25.75 329 138 146 8 268.32 37.20 330 138 160 22 59.27 0.29 331 138 161 23 59.28 0.28 332 139 160 21 59.20 0.26 333 140 143 3 505.81 1.72 334 140 144 4 426.52 19.32 335 141 161 20 58.79 0.44 336 142 145 3 457.87 3.66 337 142 147 5 415.73 9.43 338 142 169 27 44.26 0.29 339 142 172 30 38.79 0.07 340 145 148 3 499.47 0.35 341 146 149 3 501.94 0.41 342 146 159 13 59.36 0.30 343 146 161 15 59.35 0.30 344 147 159 12 59.37 0.30 345 147 166 19 51.32 0.77 346 147 169 22 44.52 0.24 347 147 170 23 44.41 0.21 348 147 173 26 38.74 0.07 349 148 170 22 44.44 0.21 350 148 173 25 39.46 0.29 351 149 166 17 59.12 0.23 352 150 156 6 59.43 0.33 353 150 166 16 59.20 0.24 354 150 170 20 51.40 0.72 355 151 155 4 329.49 15.04 356 151 157 6 59.48 0.30 357 156 163 7 140.08 40.58 358 156 166 10 59.29 0.21 359 156 167 11 59.25 0.19 360 156 170 14 51.41 0.72 361 157 166 9 145.90 43.24 362 159 162 3 453.70 16.12 363 159 165 6 404.87 6.20 364 159 166 7 164.39 49.84 365 159 169 10 314.36 25.14 366 161 165 4 488.89 1.43 367 162 165 3 497.25 5.40 368 162 166 4 465.12 6.24 369 163 166 3 484.01 1.01 370 163 167 4 464.04 6.79 371 164 167 3 487.01 0.62 372 164 168 4 465.14 6.25 373 165 168 3 469.21 8.28 374 165 169 4 465.17 6.25 375 166 169 3 473.60 7.25 376 166 170 4 465.21 6.27 377 167 170 3 483.56 2.91 378 167 171 4 473.23 2.25 379 168 171 3 489.70 1.78 380 168 172 4 473.24 2.26 381 169 172 3 491.62 1.12 382 169 173 4 476.52 6.15 383 170 173 3 490.96 0.79 384 170 174 4 471.06 3.35 385 171 174 3 496.65 2.43 386 172 175 3 490.31 0.74