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 28.19 0.41 2 1 81 80 25.52 0.52 3 1 84 83 25.20 0.65 4 1 136 135 24.03 0.22 5 2 6 4 458.38 6.86 6 2 7 5 439.02 0.12 7 2 10 8 437.76 0.50 8 2 78 76 30.44 0.35 9 2 79 77 31.19 0.03 10 2 129 127 31.07 1.69 11 2 132 130 25.22 0.66 12 2 133 131 25.21 0.65 13 2 136 134 25.22 0.66 14 3 6 3 480.25 3.16 15 3 7 4 478.38 1.76 16 3 79 76 32.37 0.22 17 4 7 3 495.25 3.18 18 4 8 4 478.06 1.93 19 4 79 75 36.59 0.04 20 5 8 3 494.11 0.15 21 5 9 4 494.26 0.09 22 6 9 3 494.26 0.08 23 6 10 4 494.26 0.08 24 6 129 123 46.69 0.59 25 6 132 126 46.69 0.59 26 7 10 3 495.69 0.64 27 7 11 4 501.33 3.46 28 7 78 71 47.04 0.73 29 7 79 72 47.45 0.53 30 8 11 3 501.34 3.46 31 8 12 4 496.68 5.79 32 9 12 3 502.79 2.73 33 9 13 4 496.68 5.78 34 9 124 115 69.67 0.79 35 9 125 116 67.03 0.64 36 9 126 117 65.94 0.32 37 9 129 120 63.18 0.87 38 10 13 3 502.79 2.73 39 10 14 4 496.69 5.76 40 10 129 119 64.21 1.18 41 10 130 120 63.36 0.78 42 11 14 3 503.21 2.50 43 11 15 4 496.67 5.75 44 11 75 64 64.20 1.18 45 12 16 4 499.00 0.24 46 12 123 111 82.78 1.01 47 13 16 3 523.99 3.07 48 13 17 4 498.80 0.14 49 13 116 103 82.78 0.98 50 13 122 109 82.81 1.02 51 13 123 110 82.83 1.01 52 13 126 113 82.51 0.97 53 13 130 117 82.33 0.91 54 14 17 3 500.76 0.84 55 14 18 4 489.03 2.00 56 14 68 54 83.07 0.98 57 14 71 57 82.75 1.00 58 14 72 58 82.73 0.98 59 14 75 61 82.34 0.87 60 14 112 98 82.94 0.93 61 14 130 116 82.68 1.02 62 15 18 3 500.30 5.61 63 15 19 4 488.95 2.01 64 16 19 3 499.88 5.82 65 16 119 103 88.67 1.81 66 16 120 104 86.16 0.55 67 17 20 3 507.34 2.09 68 17 24 7 292.94 7.76 69 17 68 51 86.06 0.53 70 17 115 98 86.13 0.54 71 17 116 99 86.09 0.55 72 17 119 102 86.18 0.55 73 18 21 3 481.02 1.82 74 18 68 50 86.05 0.55 75 18 72 54 84.11 1.49 76 20 23 3 501.19 2.16 77 20 24 4 479.63 2.07 78 21 24 3 504.05 8.58 79 21 25 4 471.24 6.25 80 21 65 44 121.83 0.99 81 21 68 47 111.22 1.63 82 21 69 48 111.23 1.62 83 22 25 3 502.28 2.71 84 22 26 4 487.50 3.19 85 22 61 39 128.62 0.18 86 23 26 3 500.79 3.45 87 23 27 4 482.30 0.74 88 24 27 3 488.12 2.88 89 24 28 4 483.63 1.99 90 24 68 44 129.70 0.34 91 24 115 91 136.18 2.46 92 24 119 95 141.14 0.29 93 25 28 3 489.42 2.23 94 25 29 4 485.96 0.82 95 25 64 39 137.83 1.35 96 25 68 43 128.66 0.18 97 26 29 3 496.66 1.40 98 26 30 4 485.96 0.83 99 26 60 34 143.56 0.84 100 26 61 35 143.55 0.83 101 26 64 38 142.31 0.73 102 27 30 3 495.76 4.02 103 27 31 4 486.01 0.83 104 27 115 88 143.03 1.04 105 28 31 3 502.90 0.45 106 28 32 4 495.74 4.03 107 28 67 39 143.62 0.90 108 28 68 40 143.55 0.86 109 28 108 80 143.00 1.03 110 28 111 83 143.03 1.03 111 28 112 84 143.02 1.04 112 28 115 87 143.03 1.04 113 29 32 3 502.90 0.45 114 29 33 4 495.73 4.03 115 29 46 17 204.06 29.50 116 29 60 31 143.90 0.94 117 29 63 34 143.75 0.88 118 29 64 35 143.66 0.88 119 29 67 38 143.66 0.89 120 30 33 3 495.74 4.04 121 30 34 4 488.67 0.51 122 30 51 21 144.32 0.91 123 30 55 25 144.13 0.90 124 30 60 30 143.90 0.95 125 31 34 3 487.60 2.18 126 31 35 4 484.32 2.68 127 31 111 80 143.19 0.97 128 32 35 3 498.46 2.62 129 32 36 4 476.28 2.90 130 32 39 7 397.43 8.20 131 32 108 76 143.10 0.99 132 32 111 79 143.10 0.99 133 33 36 3 499.49 1.77 134 33 37 4 438.87 2.48 135 33 39 6 426.97 6.57 136 33 40 7 386.19 13.81 137 33 43 10 350.38 4.10 138 33 46 13 204.20 29.55 139 33 51 18 144.69 0.84 140 33 54 21 144.69 0.83 141 34 37 3 499.42 1.74 142 34 51 17 144.71 0.84 143 36 39 3 512.72 3.60 144 36 107 71 143.14 0.97 145 36 110 74 143.46 0.89 146 36 111 75 143.47 0.89 147 37 40 3 515.22 2.35 148 38 41 3 510.82 2.14 149 38 42 4 505.50 0.53 150 39 42 3 510.84 2.14 151 39 43 4 502.25 2.16 152 40 43 3 512.24 2.84 153 40 46 6 320.41 19.73 154 40 47 7 206.40 29.19 155 40 54 14 195.22 26.02 156 41 47 6 206.40 29.19 157 41 48 7 206.43 29.18 158 42 99 57 142.21 0.34 159 42 100 58 142.22 0.34 160 42 104 62 143.31 0.84 161 43 46 3 485.74 1.35 162 43 47 4 459.39 3.37 163 43 63 20 144.33 0.91 164 44 47 3 510.86 2.19 165 45 49 4 514.59 0.33 166 45 59 14 144.91 0.94 167 46 49 3 501.38 1.54 168 46 54 8 274.50 2.33 169 46 57 11 195.23 26.03 170 46 59 13 145.03 1.01 171 46 60 14 144.83 0.98 172 46 63 17 144.81 0.97 173 49 53 4 472.65 1.90 174 49 54 5 456.64 6.14 175 49 57 8 386.95 7.36 176 50 53 3 476.26 3.67 177 50 54 4 472.70 1.87 178 51 54 3 489.12 0.97 179 51 55 4 472.70 1.86 180 52 55 3 482.30 2.93 181 52 56 4 482.30 2.93 182 53 56 3 491.44 1.65 183 53 57 4 482.26 2.94 184 54 57 3 485.98 1.08 185 54 60 6 312.84 3.98 186 55 60 5 381.88 13.11 187 57 60 3 491.31 2.89 188 59 62 3 493.75 1.81 189 59 63 4 484.98 0.17 190 60 63 3 492.62 2.38 191 60 64 4 481.00 1.79 192 61 64 3 500.13 2.76 193 61 65 4 481.01 1.79 194 62 65 3 500.93 4.09 195 62 66 4 485.37 1.24 196 63 66 3 500.01 4.55 197 63 67 4 485.58 1.35 198 64 67 3 489.60 0.66 199 64 68 4 485.36 1.25 200 65 68 3 487.76 1.57 201 65 69 4 483.48 2.52 202 66 69 3 486.88 1.14 203 66 70 4 486.81 1.17 204 67 70 3 492.65 2.36 205 67 71 4 486.82 1.16 206 68 71 3 486.83 1.16 207 68 72 4 486.56 1.04 208 68 115 47 209.21 6.75 209 69 72 3 486.58 1.03 210 69 73 4 486.57 1.04 211 70 73 3 487.03 1.26 212 70 74 4 486.55 1.04 213 70 91 21 186.38 1.82 214 71 74 3 487.00 1.27 215 71 75 4 484.84 0.19 216 71 112 41 209.22 6.75 217 71 130 59 209.28 6.77 218 72 75 3 497.37 3.88 219 72 76 4 484.82 0.21 220 73 76 3 491.90 3.72 221 73 77 4 484.81 0.23 222 73 87 14 242.91 10.08 223 74 77 3 509.11 3.66 224 74 78 4 467.84 2.84 225 74 84 10 264.26 0.51 226 74 87 13 242.91 10.08 227 74 88 14 242.93 10.09 228 74 91 17 242.91 10.09 229 74 133 59 209.25 6.75 230 74 137 63 209.19 6.78 231 75 78 3 491.34 4.26 232 75 130 55 209.34 6.75 233 77 80 3 499.73 0.07 234 77 83 6 312.32 21.41 235 77 84 7 291.20 2.05 236 77 87 10 278.27 4.40 237 78 84 6 327.83 7.27 238 78 133 55 209.34 6.75 239 80 83 3 499.59 1.02 240 80 84 4 477.38 0.11 241 81 84 3 492.34 2.60 242 81 85 4 488.29 0.58 243 82 85 3 502.54 2.50 244 82 86 4 491.66 0.64 245 83 86 3 495.29 1.34 246 83 87 4 484.78 2.80 247 84 87 3 490.29 0.04 248 84 88 4 489.84 0.18 249 84 133 49 249.34 5.10 250 84 136 52 248.93 5.22 251 85 88 3 493.79 2.10 252 85 89 4 489.81 0.19 253 86 89 3 495.50 3.08 254 86 90 4 483.60 3.29 255 87 90 3 501.93 2.53 256 87 91 4 476.44 0.29 257 88 91 3 493.99 6.50 258 88 92 4 474.12 1.44 259 88 136 48 249.41 5.14 260 88 137 49 249.05 5.13 261 88 140 52 248.53 5.26 262 89 92 3 490.16 2.59 263 89 93 4 486.25 4.62 264 90 93 3 489.77 6.12 265 90 94 4 483.12 6.20 266 91 94 3 492.84 1.39 267 91 95 4 492.84 1.42 268 91 105 14 250.81 5.08 269 91 137 46 249.55 5.21 270 92 95 3 493.97 1.99 271 92 96 4 492.84 1.42 272 92 140 48 249.05 5.27 273 92 141 49 248.55 5.26 274 92 144 52 248.53 5.26 275 93 96 3 499.38 1.32 276 93 97 4 492.85 1.41 277 93 144 51 248.55 5.29 278 94 97 3 498.17 1.01 279 94 98 4 492.86 1.42 280 95 98 3 492.12 1.38 281 95 99 4 480.94 0.99 282 95 100 5 413.95 4.65 283 95 105 10 306.64 0.46 284 95 141 46 249.73 5.12 285 96 99 3 490.81 7.71 286 96 100 4 450.82 4.67 287 96 141 45 249.74 5.12 288 96 144 48 249.02 5.32 289 96 146 50 248.62 5.31 290 100 104 4 487.84 3.77 291 100 105 5 486.61 4.41 292 101 104 3 500.88 0.61 293 101 105 4 488.88 3.27 294 101 141 40 250.38 4.88 295 101 146 45 248.91 5.38 296 102 105 3 496.72 0.64 297 102 106 4 488.90 3.27 298 102 138 36 250.39 4.89 299 102 141 39 250.39 4.89 300 102 142 40 250.38 4.89 301 102 146 44 248.96 5.37 302 103 106 3 492.37 1.54 303 103 107 4 488.92 3.27 304 104 107 3 494.51 0.46 305 104 108 4 488.91 3.26 306 105 108 3 483.53 2.47 307 105 109 4 479.36 1.51 308 105 137 32 250.82 5.03 309 105 138 33 250.78 5.03 310 105 141 36 250.73 5.05 311 106 109 3 486.34 4.99 312 106 110 4 483.03 3.33 313 106 138 32 250.87 5.00 314 107 110 3 487.51 1.76 315 107 111 4 489.19 0.92 316 108 111 3 491.50 2.08 317 108 112 4 484.12 1.62 318 108 134 26 252.49 4.91 319 109 112 3 484.93 1.23 320 109 113 4 488.56 0.60 321 109 131 22 252.49 4.91 322 109 134 25 252.48 4.91 323 109 135 26 252.47 4.91 324 109 138 29 252.46 4.91 325 111 114 3 498.88 1.29 326 111 115 4 479.09 1.97 327 112 115 3 481.65 0.69 328 112 116 4 480.20 1.42 329 112 130 18 252.69 4.95 330 112 134 22 252.61 4.95 331 113 116 3 482.85 1.85 332 113 117 4 477.88 1.35 333 113 127 14 252.69 4.94 334 113 131 18 252.69 4.94 335 114 117 3 483.98 1.69 336 114 118 4 477.89 1.36 337 115 118 3 499.20 3.68 338 115 119 4 493.65 0.90 339 116 119 3 502.22 2.17 340 116 120 4 482.89 3.87 341 116 122 6 338.45 16.42 342 117 120 3 487.92 3.77 343 117 122 5 437.81 7.99 344 122 126 4 450.43 8.66 345 122 127 5 400.22 12.43 346 123 126 3 493.41 1.28 347 125 128 3 498.32 4.54 348 125 129 4 480.00 4.62 349 126 129 3 498.32 4.54 350 126 130 4 479.99 4.61 351 127 130 3 496.04 0.88 352 127 131 4 482.22 3.48 353 128 131 3 484.10 2.52 354 128 132 4 475.53 6.78 355 129 132 3 486.26 1.44 356 129 133 4 481.33 3.92 357 130 133 3 487.82 0.68 358 130 134 4 476.84 6.12 359 131 134 3 487.37 2.56 360 131 135 4 477.64 2.00 361 132 135 3 484.00 0.88 362 132 136 4 485.68 1.72 363 133 136 3 488.07 0.57 364 133 137 4 481.39 3.85 365 134 137 3 485.54 5.93 366 134 138 4 477.82 2.08 367 135 138 3 486.56 6.44 368 135 139 4 477.84 2.08 369 136 139 3 500.32 0.09 370 136 140 4 477.85 2.09 371 137 140 3 487.19 6.48 372 137 141 4 472.41 4.83 373 138 141 3 488.86 0.01 374 138 142 4 472.41 4.83 375 139 142 3 476.23 7.49 376 139 143 4 471.64 5.21 377 140 143 3 492.32 0.55 378 140 144 4 476.19 7.51 379 141 144 3 492.33 0.56 380 141 145 4 486.25 2.48 381 141 146 5 423.00 2.92 382 142 145 3 492.33 0.55 383 142 146 4 437.43 5.25