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 80 79 26.15 0.32 2 1 81 80 24.34 0.12 3 1 84 83 24.04 0.29 4 1 132 131 24.30 0.15 5 1 136 135 23.74 0.26 6 2 6 4 469.48 7.75 7 2 7 5 459.33 2.91 8 2 78 76 26.37 0.20 9 2 79 77 26.44 0.23 10 2 129 127 26.88 0.14 11 2 132 130 24.33 0.14 12 2 133 131 24.30 0.15 13 2 136 134 24.33 0.14 14 3 6 3 491.50 3.22 15 3 7 4 468.62 1.11 16 3 79 76 32.33 0.34 17 4 7 3 492.42 3.21 18 4 8 4 469.11 0.89 19 4 79 75 37.09 0.56 20 5 8 3 500.70 2.90 21 5 9 4 486.70 0.73 22 6 9 3 501.86 6.84 23 6 10 4 495.09 3.46 24 6 129 123 42.28 0.30 25 6 132 126 43.95 0.53 26 7 10 3 495.10 3.46 27 7 11 4 491.39 5.31 28 7 78 71 44.43 0.42 29 7 79 72 46.62 1.51 30 8 11 3 499.12 1.45 31 8 12 4 489.12 6.44 32 9 12 3 501.97 0.03 33 9 13 4 484.80 0.41 34 9 123 114 72.36 2.18 35 9 124 115 72.36 2.18 36 9 125 116 66.69 2.00 37 9 126 117 64.86 2.81 38 9 129 120 64.88 2.83 39 10 13 3 501.97 0.03 40 10 14 4 486.74 0.57 41 10 75 65 64.86 2.83 42 10 129 119 64.88 2.83 43 10 130 120 64.84 2.82 44 11 14 3 489.19 1.78 45 11 15 4 486.77 0.57 46 11 75 64 64.91 2.83 47 12 15 3 505.57 0.46 48 12 16 4 502.66 1.92 49 12 123 111 86.06 1.17 50 13 16 3 523.19 0.73 51 13 17 4 500.45 0.82 52 13 116 103 85.98 1.17 53 13 122 109 86.07 1.17 54 13 123 110 86.08 1.16 55 13 126 113 85.98 1.16 56 13 130 117 85.96 1.17 57 14 17 3 499.87 1.11 58 14 18 4 493.39 2.12 59 14 68 54 86.44 1.18 60 14 71 57 86.00 1.15 61 14 72 58 86.17 1.18 62 14 75 61 85.97 1.16 63 14 112 98 86.08 1.16 64 14 130 116 86.00 1.17 65 15 18 3 499.86 1.11 66 15 19 4 486.32 1.41 67 16 19 3 490.37 0.64 68 16 119 103 86.73 1.27 69 16 120 104 86.70 1.26 70 17 20 3 515.37 4.53 71 17 24 7 215.97 25.49 72 17 68 51 86.63 1.26 73 17 115 98 86.73 1.27 74 17 116 99 86.63 1.25 75 17 119 102 86.75 1.26 76 18 21 3 469.48 3.84 77 18 68 50 86.60 1.25 78 18 72 54 86.60 1.25 79 20 23 3 505.00 1.77 80 20 24 4 469.34 0.47 81 21 24 3 488.47 0.30 82 21 25 4 469.38 0.42 83 21 65 44 121.14 0.86 84 21 68 47 112.59 0.14 85 21 69 48 113.50 0.60 86 22 25 3 487.89 0.57 87 22 26 4 474.35 1.96 88 22 61 39 128.88 0.46 89 23 26 3 496.81 3.91 90 23 27 4 481.86 1.80 91 24 27 3 486.21 1.39 92 24 28 4 481.89 1.81 93 24 68 44 129.88 0.00 94 24 115 91 130.07 0.07 95 24 119 95 143.80 0.03 96 25 28 3 500.27 0.35 97 25 29 4 486.66 4.20 98 25 64 39 129.99 0.04 99 25 68 43 129.84 0.02 100 26 29 3 500.23 0.03 101 26 30 4 491.67 1.66 102 26 60 34 143.91 0.14 103 26 61 35 143.83 0.17 104 26 64 38 139.73 1.11 105 27 30 3 494.31 2.98 106 27 31 4 491.67 1.66 107 27 115 88 143.96 0.04 108 28 31 3 498.11 1.56 109 28 32 4 477.62 2.83 110 28 67 39 144.22 0.12 111 28 68 40 144.21 0.12 112 28 108 80 143.90 0.01 113 28 111 83 143.91 0.03 114 28 112 84 143.92 0.03 115 28 115 87 143.93 0.03 116 29 32 3 493.88 1.16 117 29 33 4 477.63 2.82 118 29 46 17 145.50 0.47 119 29 60 31 144.48 0.01 120 29 63 34 144.30 0.09 121 29 64 35 144.24 0.11 122 29 67 38 144.24 0.10 123 30 33 3 500.49 2.16 124 30 34 4 477.63 2.82 125 30 51 21 145.78 0.50 126 30 55 25 145.58 0.42 127 30 60 30 144.47 0.00 128 31 34 3 491.33 0.36 129 31 35 4 487.64 2.20 130 31 111 80 143.97 0.06 131 32 35 3 491.68 2.17 132 32 36 4 470.78 0.57 133 32 39 7 410.03 0.51 134 32 108 76 143.91 0.01 135 32 111 79 143.97 0.00 136 33 36 3 493.32 0.74 137 33 37 4 440.75 7.97 138 33 39 6 407.84 0.58 139 33 40 7 385.13 10.54 140 33 43 10 387.64 9.28 141 33 46 13 145.91 0.50 142 33 51 18 145.89 0.50 143 33 54 21 145.87 0.48 144 34 37 3 497.73 0.76 145 34 51 17 145.91 0.49 146 35 111 76 144.12 0.01 147 36 39 3 506.23 1.35 148 36 107 71 143.91 0.01 149 36 110 74 144.15 0.01 150 36 111 75 144.16 0.01 151 37 40 3 506.30 1.32 152 38 41 3 506.25 1.33 153 38 42 4 507.01 0.85 154 39 42 3 507.02 0.85 155 39 43 4 505.73 1.10 156 40 43 3 506.62 0.66 157 40 46 6 298.34 10.67 158 40 47 7 298.33 10.67 159 40 54 14 146.37 0.48 160 41 47 6 298.34 10.67 161 41 48 7 298.34 10.67 162 42 99 57 143.62 0.18 163 42 100 58 143.62 0.18 164 42 104 62 143.96 0.12 165 43 46 3 486.69 3.89 166 43 47 4 462.03 7.25 167 43 63 20 145.87 0.49 168 43 66 23 145.87 0.48 169 43 67 24 145.83 0.51 170 44 47 3 501.17 0.81 171 45 49 4 512.70 3.14 172 45 59 14 146.49 0.40 173 45 63 18 146.34 0.46 174 46 49 3 489.24 2.48 175 46 54 8 211.44 31.25 176 46 57 11 146.58 0.40 177 46 59 13 146.50 0.39 178 46 60 14 146.47 0.40 179 46 63 17 146.31 0.44 180 49 53 4 443.11 3.40 181 49 54 5 446.17 8.87 182 50 53 3 488.57 2.79 183 50 54 4 475.49 0.55 184 51 54 3 493.18 0.48 185 51 55 4 479.79 1.60 186 52 55 3 491.44 0.62 187 52 56 4 486.61 1.80 188 53 56 3 491.88 0.40 189 53 57 4 482.30 3.96 190 54 57 3 491.44 0.61 191 54 60 6 379.85 17.56 192 55 60 5 393.14 10.93 193 57 60 3 489.25 0.89 194 59 62 3 497.90 2.12 195 59 63 4 487.54 0.02 196 60 63 3 493.67 0.00 197 60 64 4 485.82 0.83 198 61 64 3 493.68 0.00 199 61 65 4 485.88 0.77 200 62 65 3 496.73 2.75 201 62 66 4 487.16 0.15 202 63 66 3 493.43 1.09 203 63 67 4 489.31 0.95 204 64 67 3 492.98 0.89 205 64 68 4 487.13 0.13 206 65 68 3 490.81 1.97 207 65 69 4 485.22 0.83 208 66 69 3 494.12 5.28 209 66 70 4 485.20 0.83 210 67 70 3 491.63 1.40 211 67 71 4 486.79 1.60 212 68 71 3 494.88 2.44 213 68 72 4 486.79 1.60 214 68 115 47 231.39 13.98 215 69 72 3 497.87 3.29 216 69 73 4 486.79 1.60 217 70 73 3 490.42 0.21 218 70 74 4 486.73 1.63 219 70 87 17 231.37 13.96 220 70 91 21 231.30 13.99 221 70 94 24 231.30 13.99 222 71 74 3 489.26 0.38 223 71 75 4 486.72 1.62 224 71 112 41 231.44 13.98 225 71 130 59 231.53 13.94 226 71 134 63 231.40 13.98 227 72 75 3 491.75 0.90 228 72 76 4 491.76 0.91 229 73 76 3 491.76 0.91 230 73 77 4 491.76 0.91 231 73 87 14 231.41 13.96 232 74 77 3 491.28 1.15 233 74 78 4 469.55 0.14 234 74 84 10 257.92 0.71 235 74 87 13 231.41 13.96 236 74 88 14 231.41 13.96 237 74 91 17 231.41 13.96 238 74 133 59 231.56 13.93 239 74 137 63 231.48 13.95 240 75 78 3 490.09 1.83 241 75 130 55 231.69 13.91 242 75 133 58 231.66 13.89 243 77 80 3 491.74 1.84 244 77 83 6 311.13 0.86 245 77 84 7 311.13 0.85 246 77 87 10 289.16 3.51 247 78 84 6 373.80 30.48 248 78 133 55 231.70 13.90 249 80 83 3 499.20 4.45 250 80 84 4 485.52 1.79 251 81 84 3 496.15 5.98 252 81 85 4 486.66 2.35 253 82 85 3 502.14 2.98 254 82 86 4 502.80 2.65 255 83 86 3 500.16 2.18 256 83 87 4 486.20 0.27 257 84 87 3 500.15 2.18 258 84 88 4 486.20 0.27 259 84 133 49 267.95 9.30 260 84 136 52 267.85 9.32 261 85 88 3 496.64 0.43 262 85 89 4 487.89 0.56 263 86 89 3 490.48 4.17 264 86 90 4 484.43 1.16 265 87 90 3 498.66 1.45 266 87 91 4 485.16 1.52 267 88 91 3 498.66 1.45 268 88 92 4 485.22 1.48 269 88 136 48 267.94 9.35 270 88 137 49 267.87 9.31 271 88 140 52 266.92 9.77 272 89 92 3 491.87 1.62 273 89 93 4 484.50 1.08 274 90 93 3 491.98 2.65 275 90 94 4 484.51 1.08 276 91 94 3 502.27 1.54 277 91 95 4 484.50 1.09 278 91 105 14 271.02 9.03 279 91 137 46 268.06 9.33 280 92 95 3 496.25 1.34 281 92 96 4 484.44 1.12 282 92 140 48 267.93 9.35 283 92 141 49 267.42 9.47 284 92 144 52 266.90 9.77 285 93 97 4 485.69 1.90 286 94 97 3 501.55 0.12 287 94 98 4 487.85 0.82 288 95 98 3 487.86 0.83 289 95 99 4 481.92 3.79 290 95 100 5 415.69 2.36 291 95 105 10 331.21 4.07 292 95 141 46 268.11 9.31 293 96 99 3 481.91 3.78 294 96 100 4 454.99 1.04 295 96 141 45 268.20 9.36 296 96 144 48 267.98 9.38 297 96 146 50 267.31 9.63 298 100 104 4 483.07 1.64 299 100 105 5 483.08 1.64 300 100 141 41 269.12 9.12 301 100 146 46 267.79 9.52 302 101 104 3 506.42 0.65 303 101 105 4 496.68 1.28 304 101 141 40 269.12 9.12 305 101 146 45 267.66 9.59 306 102 105 3 495.29 0.58 307 102 106 4 483.09 1.64 308 102 138 36 269.18 9.12 309 102 141 39 269.15 9.11 310 102 142 40 269.13 9.12 311 102 146 44 268.04 9.45 312 103 106 3 496.93 0.24 313 103 107 4 490.97 1.67 314 104 107 3 503.44 2.11 315 104 108 4 496.00 4.18 316 105 108 3 496.00 4.17 317 105 109 4 483.84 1.90 318 105 137 32 269.47 9.22 319 105 138 33 269.42 9.23 320 105 141 36 269.42 9.23 321 106 109 3 492.94 3.35 322 106 110 4 488.22 1.19 323 106 138 32 269.47 9.22 324 107 110 3 492.28 0.84 325 107 111 4 493.65 0.53 326 108 111 3 507.46 1.07 327 108 112 4 489.38 1.61 328 108 134 26 270.01 9.07 329 109 112 3 507.46 1.07 330 109 113 4 512.59 1.85 331 109 131 22 270.04 9.04 332 109 134 25 269.99 9.06 333 109 135 26 270.00 9.05 334 109 138 29 269.98 9.06 335 110 113 3 560.37 3.48 336 111 114 3 504.75 1.04 337 111 115 4 495.01 1.20 338 112 115 3 500.38 1.48 339 112 116 4 495.01 1.20 340 112 130 18 270.51 9.11 341 112 134 22 270.48 9.10 342 113 116 3 496.12 0.63 343 113 117 4 495.69 0.81 344 113 127 14 270.56 9.10 345 113 131 18 270.56 9.09 346 114 117 3 495.69 0.81 347 114 118 4 495.69 0.81 348 115 118 3 495.69 0.81 349 115 119 4 495.69 0.81 350 116 119 3 497.19 0.04 351 116 120 4 494.81 1.15 352 117 120 3 494.81 1.15 353 117 122 5 424.46 23.30 354 122 126 4 465.67 8.20 355 122 127 5 407.05 0.70 356 123 126 3 506.50 0.39 357 125 128 3 505.41 0.02 358 125 129 4 485.26 1.66 359 126 129 3 485.25 1.65 360 126 130 4 485.24 1.65 361 127 130 3 502.99 4.83 362 127 131 4 485.24 1.65 363 128 131 3 502.61 5.03 364 128 132 4 483.42 2.55 365 129 132 3 502.61 5.03 366 129 133 4 484.31 2.96 367 130 133 3 491.38 0.58 368 130 134 4 484.31 2.95 369 131 134 3 490.82 0.29 370 131 135 4 484.32 2.95 371 132 135 3 491.46 0.61 372 132 136 4 493.12 1.45 373 133 136 3 493.12 1.45 374 133 137 4 490.85 2.59 375 134 137 3 490.89 2.62 376 134 138 4 491.03 2.66 377 135 138 3 495.60 0.38 378 135 139 4 491.04 2.67 379 136 139 3 499.57 1.60 380 136 140 4 491.04 2.67 381 137 140 3 493.36 1.51 382 137 141 4 493.34 1.50 383 138 141 3 495.59 0.38 384 138 142 4 493.34 1.50 385 139 142 3 496.20 0.39 386 139 143 4 490.84 2.75 387 140 143 3 497.20 0.24 388 140 144 4 490.81 2.75 389 141 144 3 493.20 1.74 390 141 145 4 490.73 2.75 391 141 146 5 458.30 8.52 392 142 145 3 490.70 2.75 393 142 146 4 480.23 2.44