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 27.62 0.83 2 1 81 80 25.70 0.71 3 1 84 83 25.66 0.73 4 1 132 131 25.66 0.72 5 1 136 135 25.52 0.71 6 2 6 4 460.53 3.38 7 2 7 5 460.43 3.36 8 2 10 8 460.25 3.45 9 2 78 76 27.78 0.81 10 2 79 77 27.79 0.81 11 2 129 127 28.73 0.73 12 2 132 130 27.12 0.00 13 2 133 131 25.66 0.72 14 2 136 134 25.66 0.72 15 3 6 3 474.84 2.04 16 3 7 4 469.06 0.86 17 3 79 76 33.58 0.96 18 4 7 3 473.03 1.12 19 4 8 4 469.39 0.70 20 4 79 75 35.75 0.12 21 5 8 3 497.51 4.50 22 5 9 4 487.32 0.42 23 6 9 3 492.57 2.20 24 6 10 4 496.34 4.08 25 6 129 123 44.07 0.57 26 6 132 126 44.51 0.68 27 7 10 3 496.34 4.08 28 7 11 4 487.77 8.37 29 7 78 71 50.65 2.69 30 7 79 72 50.68 2.69 31 8 11 3 500.36 2.07 32 8 12 4 475.23 2.00 33 9 12 3 491.44 2.31 34 9 13 4 486.84 0.20 35 9 123 114 72.69 2.01 36 9 124 115 73.34 1.68 37 9 125 116 68.31 1.21 38 9 126 117 66.47 2.05 39 9 129 120 66.34 2.10 40 10 13 3 491.76 2.15 41 10 14 4 490.49 2.02 42 10 75 65 66.50 2.06 43 10 129 119 66.51 2.02 44 10 130 120 66.34 2.09 45 11 14 3 490.49 2.02 46 11 15 4 495.85 0.65 47 11 75 64 66.47 2.04 48 12 15 3 502.41 1.12 49 12 16 4 502.31 1.14 50 12 123 111 87.64 0.74 51 13 16 3 524.16 0.25 52 13 17 4 501.69 1.44 53 13 116 103 87.61 0.73 54 13 122 109 87.66 0.73 55 13 123 110 87.67 0.73 56 13 126 113 87.45 0.69 57 13 130 117 87.33 0.71 58 14 17 3 501.11 1.73 59 14 18 4 497.40 0.12 60 14 68 54 87.94 0.81 61 14 71 57 87.58 0.71 62 14 72 58 87.59 0.72 63 14 75 61 87.50 0.73 64 14 112 98 87.61 0.73 65 14 130 116 87.61 0.74 66 15 18 3 497.42 0.12 67 15 19 4 485.35 0.93 68 16 19 3 482.16 2.98 69 16 119 103 88.19 0.74 70 16 120 104 88.19 0.75 71 17 20 3 503.47 0.73 72 17 24 7 283.60 9.51 73 17 68 51 88.08 0.76 74 17 115 98 88.11 0.74 75 17 116 99 88.09 0.74 76 17 119 102 88.17 0.73 77 18 21 3 473.61 1.78 78 18 68 50 88.09 0.76 79 18 72 54 87.95 0.81 80 20 23 3 507.89 0.32 81 20 24 4 468.53 1.74 82 21 24 3 489.73 0.92 83 21 25 4 467.86 1.41 84 21 65 44 120.03 1.42 85 21 68 47 108.97 0.67 86 21 69 48 104.44 3.48 87 22 25 3 487.59 0.21 88 22 26 4 479.95 3.96 89 22 61 39 130.08 1.10 90 23 26 3 498.04 3.29 91 23 27 4 478.50 1.72 92 24 27 3 482.71 1.72 93 24 28 4 481.49 3.21 94 24 68 44 130.16 1.08 95 24 115 91 132.65 0.08 96 24 119 95 143.56 0.25 97 25 28 3 501.52 0.97 98 25 29 4 485.35 1.34 99 25 64 39 130.95 0.69 100 25 68 43 130.11 1.10 101 26 29 3 492.74 2.41 102 26 30 4 482.23 3.64 103 26 60 34 143.61 0.03 104 26 61 35 143.56 0.00 105 26 64 38 140.19 0.06 106 27 30 3 495.56 3.60 107 27 31 4 481.48 3.27 108 27 115 88 144.10 0.07 109 28 31 3 492.91 2.27 110 28 32 4 482.68 2.64 111 28 67 39 144.13 0.08 112 28 68 40 144.08 0.06 113 28 108 80 143.99 0.07 114 28 111 83 144.05 0.09 115 28 112 84 144.03 0.07 116 28 115 87 144.11 0.07 117 29 32 3 499.96 0.64 118 29 33 4 489.76 0.90 119 29 60 31 144.24 0.05 120 29 63 34 144.21 0.05 121 29 64 35 144.15 0.07 122 29 67 38 144.14 0.07 123 30 33 3 496.37 4.21 124 30 34 4 486.87 0.55 125 30 51 21 144.97 0.21 126 30 54 24 144.90 0.21 127 30 55 25 144.90 0.21 128 30 60 30 144.41 0.01 129 31 34 3 495.29 4.75 130 31 35 4 474.84 1.48 131 31 111 80 144.12 0.07 132 32 35 3 499.30 4.73 133 32 36 4 474.81 1.48 134 32 39 7 381.39 6.89 135 32 108 76 144.03 0.08 136 32 111 79 144.13 0.07 137 33 36 3 490.87 1.97 138 33 37 4 441.35 0.83 139 33 39 6 394.47 8.30 140 33 40 7 334.89 16.36 141 33 43 10 323.47 22.06 142 33 46 13 250.91 0.12 143 33 54 21 145.13 0.19 144 34 37 3 495.87 1.42 145 34 51 17 145.14 0.18 146 34 55 21 145.18 0.19 147 35 111 76 144.12 0.09 148 36 39 3 507.48 0.73 149 36 107 71 144.03 0.08 150 36 110 74 144.28 0.05 151 36 111 75 144.30 0.04 152 37 40 3 507.50 0.72 153 38 41 3 506.61 0.27 154 39 42 3 507.41 0.66 155 39 43 4 502.37 1.44 156 39 104 65 143.98 0.04 157 40 43 3 502.37 1.44 158 40 46 6 265.56 1.43 159 40 47 7 260.12 4.14 160 40 54 14 188.06 21.57 161 41 47 6 261.14 3.64 162 42 99 57 143.93 0.01 163 42 100 58 143.93 0.01 164 42 104 62 144.28 0.01 165 43 46 3 486.28 0.55 166 43 47 4 463.27 7.87 167 43 63 20 145.00 0.23 168 44 47 3 495.58 0.57 169 45 49 4 486.26 1.00 170 45 57 12 188.27 21.46 171 45 59 14 145.44 0.15 172 46 49 3 490.47 3.10 173 46 54 8 265.48 4.24 174 46 57 11 251.69 1.08 175 46 59 13 145.59 0.22 176 46 60 14 145.41 0.16 177 46 63 17 145.37 0.14 178 49 53 4 456.89 13.05 179 49 54 5 451.20 10.18 180 50 53 3 489.82 3.41 181 50 54 4 471.31 5.84 182 51 54 3 489.87 3.39 183 51 55 4 473.69 4.65 184 52 55 3 492.72 0.03 185 52 56 4 473.26 4.87 186 53 56 3 496.35 1.39 187 53 57 4 482.38 5.17 188 54 57 3 492.69 0.01 189 54 60 6 367.54 23.71 190 55 60 5 387.86 13.55 191 57 60 3 478.54 6.25 192 59 62 3 499.15 2.75 193 59 63 4 480.29 1.83 194 60 63 3 494.92 0.62 195 60 64 4 479.92 1.65 196 61 64 3 494.93 0.62 197 61 65 4 490.57 0.34 198 62 65 3 497.99 3.37 199 62 66 4 494.25 1.50 200 63 66 3 506.72 0.99 201 63 67 4 494.25 1.50 202 64 67 3 502.90 2.83 203 64 68 4 494.25 1.49 204 65 68 3 494.25 1.50 205 65 69 4 485.03 3.12 206 66 69 3 496.27 4.21 207 66 70 4 481.79 2.08 208 67 70 3 499.87 2.73 209 67 71 4 485.88 0.05 210 68 71 3 495.05 3.62 211 68 72 4 480.17 2.91 212 68 115 47 204.60 2.37 213 69 72 3 492.26 2.22 214 69 73 4 480.16 2.91 215 70 73 3 487.94 0.98 216 70 74 4 487.93 0.97 217 70 87 17 204.91 2.42 218 70 91 21 204.40 2.57 219 70 94 24 204.65 2.48 220 71 74 3 487.90 0.99 221 71 75 4 482.47 3.71 222 71 112 41 204.78 2.36 223 71 130 59 204.90 2.31 224 71 134 63 204.78 2.36 225 72 75 3 489.04 1.16 226 72 76 4 483.21 4.07 227 73 76 3 489.04 1.16 228 73 77 4 483.24 4.05 229 73 87 14 205.06 2.41 230 74 77 3 493.72 1.18 231 74 78 4 474.66 0.23 232 74 84 10 285.61 11.04 233 74 87 13 205.07 2.41 234 74 88 14 251.32 2.91 235 74 91 17 205.05 2.41 236 74 133 59 205.00 2.38 237 74 137 63 205.00 2.38 238 75 78 3 489.58 0.88 239 75 130 55 205.03 2.35 240 77 80 3 493.92 2.00 241 77 83 6 305.07 1.35 242 77 84 7 299.25 4.26 243 77 87 10 293.19 7.25 244 78 84 6 317.48 6.09 245 78 133 55 205.09 2.38 246 80 83 3 500.45 3.83 247 80 84 4 472.57 8.25 248 81 84 3 487.28 0.91 249 81 85 4 483.20 2.94 250 82 85 3 496.79 5.66 251 82 86 4 497.89 1.05 252 83 86 3 497.90 1.05 253 83 87 4 485.56 1.75 254 84 87 3 488.95 3.41 255 84 88 4 481.53 2.06 256 84 133 49 227.83 2.17 257 84 136 52 227.50 2.18 258 85 88 3 497.88 1.06 259 85 89 4 485.69 1.78 260 86 89 3 504.28 1.48 261 86 90 4 485.69 1.78 262 87 90 3 496.15 2.58 263 87 91 4 480.28 0.93 264 88 91 3 493.22 1.27 265 88 92 4 485.65 1.76 266 88 136 48 227.68 2.19 267 88 137 49 227.67 2.19 268 88 140 52 227.37 2.33 269 89 92 3 491.69 1.26 270 89 93 4 485.69 1.74 271 90 93 3 493.23 2.02 272 90 94 4 485.69 1.74 273 91 94 3 489.28 0.04 274 91 95 4 485.68 1.75 275 91 105 14 244.97 2.07 276 91 137 46 227.94 2.20 277 92 95 3 491.37 1.10 278 92 96 4 477.35 2.19 279 92 140 48 227.77 2.19 280 92 141 49 227.66 2.19 281 92 144 52 227.61 2.21 282 93 97 4 485.99 0.80 283 94 97 3 498.57 1.61 284 94 98 4 488.16 0.28 285 95 98 3 491.03 3.92 286 95 99 4 485.23 1.74 287 95 100 5 423.07 16.86 288 95 105 10 334.72 5.43 289 95 141 46 227.99 2.17 290 96 99 3 478.30 0.72 291 96 100 4 448.44 6.58 292 96 141 45 228.05 2.19 293 96 144 48 227.88 2.21 294 96 146 50 227.75 2.22 295 100 104 4 484.33 2.26 296 100 105 5 484.33 2.26 297 100 141 41 230.07 2.64 298 101 104 3 507.67 0.03 299 101 105 4 490.30 4.33 300 101 141 40 230.07 2.64 301 101 146 45 227.74 2.18 302 102 105 3 490.38 4.29 303 102 106 4 484.33 2.26 304 102 138 36 230.07 2.64 305 102 141 39 230.07 2.64 306 102 142 40 230.07 2.64 307 102 146 44 227.81 2.18 308 103 106 3 496.62 1.16 309 103 107 4 484.32 2.26 310 104 107 3 498.01 1.85 311 104 108 4 484.27 2.25 312 105 108 3 490.18 7.08 313 105 109 4 482.06 1.21 314 105 137 32 231.12 2.87 315 105 138 33 230.99 2.83 316 105 141 36 230.89 2.77 317 106 109 3 483.12 1.74 318 106 110 4 489.44 0.57 319 106 138 32 231.36 2.98 320 106 142 36 231.36 2.98 321 107 110 3 493.55 1.45 322 107 111 4 489.66 0.50 323 108 111 3 505.83 0.26 324 108 112 4 489.62 0.48 325 108 134 26 232.50 3.08 326 109 112 3 508.35 1.52 327 109 113 4 500.37 2.47 328 109 131 22 232.56 3.04 329 109 134 25 232.51 3.07 330 109 135 26 232.54 3.06 331 109 138 29 232.50 3.08 332 110 113 3 552.18 1.26 333 111 114 3 499.73 0.18 334 111 115 4 484.83 1.91 335 112 115 3 497.69 2.82 336 112 116 4 485.25 1.65 337 112 130 18 232.89 3.08 338 112 134 22 232.75 3.14 339 113 116 3 492.13 1.79 340 113 117 4 481.73 0.11 341 113 127 14 232.94 3.07 342 113 131 18 232.91 3.08 343 114 117 3 484.19 1.23 344 114 118 4 487.73 3.16 345 115 118 3 494.54 0.24 346 115 119 4 494.54 0.24 347 116 119 3 494.54 0.24 348 116 120 4 488.47 3.27 349 116 122 6 382.47 1.47 350 117 120 3 496.06 0.53 351 117 122 5 382.48 1.47 352 122 126 4 455.42 14.60 353 122 127 5 420.39 2.92 354 123 126 3 495.60 2.42 355 125 128 3 494.55 5.46 356 125 129 4 480.11 1.77 357 126 129 3 483.61 0.01 358 126 130 4 480.04 2.23 359 127 130 3 489.10 0.34 360 127 131 4 482.75 1.03 361 128 131 3 503.85 4.41 362 128 132 4 476.11 4.36 363 129 132 3 501.43 5.62 364 129 133 4 485.48 2.37 365 130 133 3 485.48 2.37 366 130 134 4 485.48 2.37 367 131 134 3 492.07 0.92 368 131 135 4 487.01 1.60 369 132 135 3 494.45 2.12 370 132 136 4 487.03 1.59 371 133 136 3 498.35 0.17 372 133 137 4 491.88 3.41 373 134 137 3 491.88 3.41 374 134 138 4 491.88 3.40 375 135 138 3 496.77 0.96 376 135 139 4 490.68 3.98 377 136 139 3 494.51 2.08 378 136 140 4 491.87 3.38 379 137 140 3 494.08 2.27 380 137 141 4 491.93 3.35 381 138 141 3 496.73 0.95 382 138 142 4 490.00 2.33 383 139 142 3 494.75 0.04 384 139 143 4 490.00 2.33 385 140 143 3 496.75 0.47 386 140 144 4 490.01 2.33 387 141 144 3 501.15 0.98 388 141 145 4 490.01 2.33 389 141 146 5 402.54 3.16 390 142 145 3 494.16 0.82 391 142 146 4 437.73 1.77