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 2 6 4 488.66 2.38 2 2 7 5 460.54 0.84 3 2 10 8 458.55 1.11 4 2 73 71 30.99 1.41 5 2 132 130 20.93 1.66 6 2 133 131 20.93 1.66 7 3 6 3 499.43 4.97 8 3 7 4 490.95 3.60 9 4 7 3 491.31 3.42 10 4 8 4 489.02 2.27 11 5 8 3 495.56 1.32 12 5 9 4 497.42 0.36 13 6 9 3 500.88 2.10 14 6 10 4 489.98 1.81 15 6 128 122 51.82 0.58 16 6 129 123 47.49 0.01 17 6 132 126 47.30 0.05 18 7 10 3 500.07 1.58 19 7 11 4 490.00 1.82 20 7 73 66 46.05 0.74 21 8 11 3 509.95 3.27 22 8 12 4 489.56 2.04 23 9 12 3 501.39 0.92 24 9 13 4 489.57 2.04 25 9 125 116 63.71 0.04 26 9 126 117 63.44 0.17 27 9 129 120 63.38 0.20 28 10 13 3 508.18 2.27 29 10 14 4 489.49 2.00 30 10 70 60 63.34 0.18 31 10 73 63 63.34 0.19 32 10 129 119 63.44 0.17 33 10 130 120 63.43 0.17 34 10 133 123 63.37 0.18 35 11 14 3 501.51 0.85 36 11 15 4 491.53 3.00 37 11 70 59 63.32 0.18 38 12 15 3 501.72 0.96 39 13 16 3 498.34 0.42 40 13 17 4 485.64 0.70 41 13 118 105 89.19 0.68 42 13 121 108 81.34 0.18 43 13 126 113 80.38 0.57 44 13 130 117 78.00 0.61 45 14 17 3 490.94 3.29 46 14 18 4 485.64 0.70 47 14 63 49 80.55 0.48 48 14 66 52 78.15 0.70 49 14 67 53 78.07 0.66 50 14 70 56 75.38 0.67 51 14 130 116 80.46 0.53 52 15 18 3 498.70 2.93 53 15 19 4 486.74 1.25 54 16 19 3 486.74 1.25 55 16 117 101 94.59 0.26 56 16 118 102 94.53 0.23 57 16 121 105 94.53 0.23 58 17 23 6 127.41 16.75 59 17 26 9 94.52 0.22 60 17 63 46 94.36 0.23 61 17 114 97 94.18 0.14 62 17 117 100 94.60 0.26 63 17 118 101 94.59 0.26 64 17 122 105 94.59 0.26 65 17 130 113 94.22 0.17 66 18 21 3 515.98 1.24 67 18 22 4 190.30 5.00 68 18 23 5 127.38 16.74 69 18 117 99 95.12 0.01 70 19 117 98 97.69 1.27 71 21 24 3 497.05 1.54 72 21 25 4 483.93 1.15 73 21 117 96 127.72 0.48 74 22 64 42 97.19 1.04 75 23 26 3 496.64 1.17 76 23 27 4 490.25 2.02 77 23 63 40 101.09 0.38 78 23 117 94 131.88 0.96 79 24 27 3 496.63 1.18 80 24 28 4 492.87 0.70 81 24 60 36 109.71 1.25 82 25 28 3 495.40 1.97 83 25 29 4 492.87 0.70 84 25 117 92 135.72 0.15 85 26 29 3 496.26 1.54 86 26 30 4 480.20 4.44 87 26 63 37 127.62 0.53 88 26 110 84 127.89 0.51 89 26 113 87 133.34 0.24 90 26 114 88 132.62 0.58 91 26 117 91 135.91 0.24 92 27 30 3 496.69 1.33 93 27 31 4 480.21 4.44 94 27 59 32 127.60 0.54 95 27 63 36 127.62 0.53 96 28 31 3 507.51 4.09 97 28 32 4 493.16 4.63 98 28 56 28 130.65 0.85 99 28 59 31 129.93 0.62 100 29 32 3 498.33 2.06 101 29 33 4 489.10 1.27 102 29 113 84 137.60 0.07 103 29 116 87 140.16 0.70 104 30 33 3 498.33 2.06 105 30 34 4 495.07 3.69 106 30 106 76 137.44 0.14 107 30 109 79 137.44 0.14 108 30 110 80 136.81 0.41 109 30 113 83 138.90 0.42 110 31 34 3 491.22 0.21 111 31 35 4 490.90 0.36 112 31 55 24 139.71 0.86 113 31 58 27 139.31 0.77 114 31 59 28 138.03 0.15 115 32 35 3 504.25 0.66 116 32 36 4 482.29 5.87 117 32 50 18 141.54 1.25 118 32 55 23 141.03 1.10 119 33 36 3 490.05 2.00 120 33 37 4 482.29 5.87 121 33 109 76 141.16 1.16 122 34 37 3 497.40 1.50 123 34 38 4 487.33 3.35 124 34 41 7 413.25 7.65 125 34 45 11 321.60 3.92 126 34 102 68 141.12 1.19 127 34 105 71 141.16 1.16 128 34 106 72 141.09 1.19 129 34 109 75 141.23 1.19 130 35 38 3 492.17 5.77 131 35 39 4 474.78 6.44 132 35 41 6 426.87 6.54 133 35 42 7 402.38 5.67 134 35 45 10 259.67 34.99 135 35 47 12 156.60 1.57 136 35 50 15 143.10 1.70 137 35 55 20 142.91 1.74 138 36 39 3 502.33 2.15 139 36 50 14 143.02 1.66 140 38 41 3 510.95 2.17 141 38 105 67 141.90 1.49 142 39 42 3 510.95 2.17 143 40 43 3 517.94 3.57 144 40 44 4 501.72 2.23 145 41 44 3 498.84 0.81 146 41 45 4 495.47 0.88 147 41 102 61 141.90 1.52 148 42 45 3 503.47 1.01 149 42 46 4 490.39 1.48 150 42 47 5 417.34 10.13 151 42 49 7 143.41 1.59 152 43 46 3 493.56 2.06 153 43 95 52 142.77 1.83 154 43 96 53 142.78 1.83 155 44 94 50 142.68 1.79 156 44 95 51 142.77 1.83 157 44 96 52 142.77 1.82 158 44 98 54 142.75 1.81 159 44 102 58 142.72 1.78 160 45 58 13 143.09 1.75 161 46 95 49 142.77 1.83 162 47 52 5 176.91 6.80 163 47 54 7 149.93 2.67 164 47 55 8 150.16 2.56 165 47 58 11 149.78 2.75 166 48 52 4 415.51 8.32 167 49 52 3 492.97 1.27 168 49 55 6 415.55 8.32 169 50 55 5 442.82 8.34 170 52 55 3 502.91 0.26 171 53 56 3 503.10 0.35 172 53 57 4 492.42 2.81 173 54 57 3 497.84 2.80 174 54 58 4 487.73 0.47 175 55 58 3 500.15 1.65 176 55 59 4 485.95 1.77 177 56 59 3 498.70 2.37 178 56 60 4 486.15 1.69 179 57 60 3 504.14 3.33 180 57 61 4 488.55 0.48 181 58 61 3 497.62 0.17 182 58 62 4 488.18 1.07 183 59 62 3 495.28 0.36 184 59 63 4 488.85 0.77 185 60 63 3 499.40 2.77 186 60 64 4 488.85 0.77 187 61 64 3 499.40 2.77 188 61 65 4 490.56 0.03 189 62 65 3 496.42 2.96 190 62 66 4 490.56 0.04 191 63 66 3 499.81 1.27 192 63 67 4 490.44 0.10 193 63 110 47 147.10 2.10 194 64 67 3 499.75 1.30 195 64 68 4 493.79 1.78 196 65 68 3 502.64 2.65 197 65 69 4 499.79 1.22 198 65 83 18 146.68 2.20 199 65 86 21 145.88 1.95 200 66 69 3 509.28 0.68 201 66 70 4 493.79 1.79 202 66 110 44 154.72 0.47 203 66 130 64 172.74 8.23 204 66 137 71 146.86 2.18 205 67 70 3 506.43 2.11 206 67 71 4 503.50 3.57 207 68 71 3 506.45 2.10 208 68 72 4 503.50 3.57 209 68 82 14 153.06 0.34 210 69 72 3 507.77 1.43 211 69 73 4 499.82 1.21 212 69 79 10 152.96 0.53 213 69 83 14 151.66 0.14 214 69 137 68 152.87 0.46 215 70 73 3 501.15 1.89 216 70 130 60 194.15 2.10 217 72 75 3 490.49 1.70 218 72 78 6 338.88 15.35 219 72 79 7 189.87 0.01 220 72 82 10 192.01 1.07 221 73 79 6 338.89 15.36 222 75 78 3 507.53 1.49 223 75 79 4 499.49 2.45 224 76 79 3 507.45 1.53 225 76 80 4 495.02 0.23 226 77 80 3 508.53 2.50 227 77 81 4 495.02 0.24 228 78 81 3 503.31 0.00 229 78 82 4 495.01 0.24 230 79 82 3 504.87 2.81 231 79 83 4 495.41 0.43 232 79 137 58 295.24 0.62 233 79 140 61 292.52 0.60 234 80 83 3 510.47 4.08 235 80 84 4 495.41 0.43 236 80 140 60 292.51 0.60 237 81 84 3 496.88 0.29 238 81 85 4 495.10 0.59 239 82 85 3 507.90 6.16 240 82 86 4 505.40 7.42 241 83 86 3 505.40 7.41 242 83 87 4 493.12 5.15 243 83 137 54 301.47 0.75 244 83 140 57 301.31 0.70 245 83 141 58 301.31 0.69 246 84 87 3 494.24 4.53 247 84 88 4 493.11 5.09 248 84 140 56 301.36 0.70 249 84 143 59 301.33 0.70 250 84 144 60 301.30 0.69 251 85 88 3 508.62 5.93 252 85 89 4 493.12 5.08 253 86 89 3 506.27 0.57 254 86 90 4 503.80 0.21 255 86 141 55 302.15 1.08 256 87 90 3 505.49 0.96 257 87 91 4 503.81 0.21 258 87 141 54 302.15 1.08 259 87 144 57 302.08 1.08 260 87 145 58 302.11 1.07 261 88 91 3 520.99 3.65 262 88 144 56 302.11 1.08 263 88 145 57 302.14 1.09 264 88 147 59 302.06 1.09 265 89 92 3 529.86 0.79 266 89 93 4 500.10 1.65 267 90 93 3 500.10 1.65 268 90 98 8 302.30 1.10 269 90 141 51 302.28 1.08 270 90 145 55 302.19 1.09 271 91 144 53 302.29 1.08 272 91 145 54 302.21 1.09 273 91 146 55 302.21 1.09 274 91 147 56 302.20 1.09 275 93 98 5 402.66 13.97 276 97 102 5 518.61 0.04 277 98 102 4 518.53 0.01 278 98 103 5 515.69 1.44 279 98 145 47 302.61 1.05 280 99 102 3 521.03 1.25 281 99 103 4 518.61 0.04 282 100 103 3 521.77 1.54 283 100 142 42 302.76 1.09 284 100 146 46 302.76 1.09 285 101 104 3 524.19 0.33 286 101 105 4 521.03 1.25 287 102 105 3 520.94 1.29 288 102 106 4 515.18 1.66 289 103 106 3 511.44 0.70 290 103 107 4 503.98 0.95 291 103 134 31 304.31 1.02 292 103 138 35 303.58 1.02 293 103 141 38 303.59 1.02 294 103 142 39 303.56 1.02 295 103 145 42 303.58 1.02 296 104 107 3 509.36 1.74 297 104 108 4 508.86 1.50 298 105 108 3 502.67 4.59 299 105 109 4 502.66 4.59 300 106 109 3 506.89 2.48 301 106 110 4 491.43 0.80 302 106 134 28 304.42 1.05 303 107 110 3 509.97 0.94 304 107 111 4 485.72 3.66 305 107 134 27 304.37 1.04 306 108 111 3 510.56 1.23 307 108 112 4 483.48 2.55 308 109 112 3 503.17 5.07 309 109 113 4 485.03 3.56 310 110 113 3 507.97 2.68 311 110 114 4 483.00 2.79 312 110 134 24 304.78 0.89 313 111 114 3 494.86 3.14 314 111 115 4 489.12 5.38 315 111 127 16 305.23 0.81 316 111 130 19 304.83 0.90 317 111 131 20 304.83 0.90 318 111 134 23 304.79 0.88 319 112 115 3 501.50 0.55 320 112 116 4 493.63 3.12 321 113 116 3 495.73 2.08 322 113 117 4 493.63 3.12 323 114 117 3 503.98 2.04 324 114 118 4 486.56 6.66 325 114 122 8 306.17 0.90 326 114 130 16 305.17 0.85 327 115 118 3 487.90 0.85 328 115 119 4 462.81 1.85 329 115 122 7 305.88 0.95 330 115 127 12 305.57 0.81 331 118 121 3 505.97 2.77 332 118 122 4 477.38 3.87 333 119 122 3 511.78 1.40 334 120 123 3 513.53 2.85 335 121 126 5 455.91 4.93 336 122 126 4 455.91 4.93 337 122 127 5 467.03 1.17 338 122 130 8 432.28 6.87 339 123 126 3 495.87 1.68 340 123 127 4 476.52 1.54 341 124 127 3 492.92 0.21 342 124 128 4 482.28 4.42 343 125 128 3 492.92 0.89 344 125 129 4 486.29 2.43 345 126 129 3 496.42 1.09 346 126 130 4 480.48 2.24 347 127 130 3 494.34 0.83 348 127 131 4 488.78 1.90 349 128 131 3 496.98 1.38 350 128 132 4 491.41 0.63 351 129 132 3 494.75 1.03 352 129 133 4 487.04 2.81 353 130 133 3 492.19 0.21 354 130 134 4 479.40 6.59 355 131 134 3 493.23 4.92 356 131 135 4 488.01 2.32 357 132 135 3 494.56 0.95 358 132 136 4 488.01 2.32 359 133 136 3 493.04 0.19 360 133 137 4 488.00 2.32 361 134 137 3 502.07 0.58 362 134 138 4 478.61 2.38 363 135 138 3 502.72 0.26 364 135 139 4 459.49 7.16 365 136 139 3 499.53 1.17 366 136 140 4 486.50 7.21 367 137 140 3 505.19 1.06 368 137 141 4 491.54 4.69 369 138 141 3 497.07 1.50 370 138 142 4 470.83 5.67 371 139 142 3 492.98 3.54 372 139 143 4 470.86 5.68 373 140 143 3 492.47 2.22 374 140 144 4 478.34 2.64 375 141 144 3 499.23 6.96 376 141 145 4 489.00 0.96 377 142 145 3 489.00 0.95 378 142 146 4 474.31 6.38 379 143 146 3 496.98 1.35 380 143 147 4 465.48 8.13 381 144 147 3 499.13 0.28