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 3 79 76 29.70 0.69 2 3 80 77 28.04 0.30 3 3 135 132 32.11 0.57 4 4 7 3 498.15 2.79 5 4 8 4 498.15 2.79 6 5 8 3 490.60 0.67 7 5 9 4 480.67 0.88 8 5 132 127 33.74 0.12 9 5 135 130 33.76 0.14 10 6 9 3 487.73 0.65 11 6 10 4 480.30 0.69 12 6 79 73 33.79 0.15 13 6 80 74 37.38 1.12 14 7 10 3 485.72 1.66 15 7 11 4 480.18 0.63 16 8 11 3 487.36 2.37 17 8 12 4 482.95 0.18 18 8 129 121 52.57 0.33 19 8 132 124 52.58 0.32 20 9 12 3 489.35 0.11 21 9 13 4 486.19 1.46 22 9 76 67 52.58 0.32 23 9 79 70 52.68 0.30 24 9 132 123 52.72 0.30 25 9 133 124 52.57 0.32 26 9 136 127 52.58 0.32 27 10 13 3 489.35 0.11 28 10 14 4 490.70 0.80 29 10 76 66 52.72 0.29 30 10 79 69 52.73 0.29 31 10 80 70 52.73 0.29 32 11 14 3 491.84 0.28 33 12 15 3 516.69 0.86 34 12 16 4 494.75 0.56 35 12 121 109 57.72 1.70 36 12 129 117 56.36 1.59 37 12 133 121 56.34 1.59 38 13 16 3 498.69 0.36 39 13 17 4 479.47 0.62 40 13 69 56 57.43 1.55 41 13 72 59 56.33 1.60 42 13 73 60 56.33 1.60 43 13 76 63 56.32 1.61 44 13 117 104 57.68 1.68 45 13 133 120 56.38 1.58 46 14 17 3 491.94 5.45 47 14 18 4 483.60 2.68 48 15 121 106 68.09 3.25 49 16 19 3 499.61 0.89 50 16 20 4 471.31 3.14 51 16 23 7 183.40 1.45 52 16 69 53 67.08 2.73 53 16 116 100 68.11 3.25 54 16 117 101 68.09 3.24 55 16 120 104 68.12 3.25 56 17 20 3 487.38 2.41 57 19 22 3 494.91 0.98 58 19 23 4 486.84 2.12 59 20 23 3 493.00 0.94 60 20 24 4 480.99 0.51 61 20 66 46 88.84 0.20 62 20 69 49 87.78 0.48 63 21 24 3 491.68 0.70 64 21 25 4 481.09 0.56 65 21 62 41 93.55 1.00 66 21 65 44 89.73 0.21 67 21 66 45 88.88 0.20 68 22 25 3 487.62 3.83 69 22 26 4 482.18 0.02 70 23 26 3 487.17 2.52 71 23 27 4 482.18 0.02 72 23 69 46 102.03 0.09 73 23 116 93 106.31 0.10 74 23 120 97 119.91 1.25 75 24 27 3 482.18 0.02 76 24 28 4 481.82 0.50 77 24 65 41 102.05 0.09 78 24 69 45 102.02 0.09 79 25 28 3 490.46 3.77 80 25 29 4 481.85 0.52 81 25 56 31 120.49 1.17 82 25 65 40 111.35 3.27 83 26 29 3 489.73 1.07 84 26 30 4 481.94 0.48 85 26 115 89 120.45 1.21 86 26 116 90 120.44 1.21 87 27 30 3 488.38 0.60 88 27 31 4 481.94 0.47 89 27 72 45 120.38 1.20 90 27 109 82 120.36 1.19 91 27 112 85 120.38 1.18 92 27 113 86 120.39 1.20 93 27 116 89 120.45 1.21 94 28 31 3 486.13 1.34 95 28 32 4 482.23 0.61 96 28 42 14 155.78 10.03 97 28 61 33 120.58 1.17 98 28 64 36 120.58 1.16 99 28 65 37 120.56 1.16 100 28 68 40 120.52 1.18 101 29 32 3 492.89 0.70 102 29 33 4 491.55 1.36 103 30 33 3 498.32 2.02 104 30 34 4 491.55 1.36 105 30 112 82 120.84 0.97 106 30 115 85 121.30 0.98 107 31 34 3 492.99 0.65 108 31 35 4 466.81 0.77 109 31 38 7 428.62 8.55 110 31 108 77 120.64 1.07 111 31 109 78 120.53 1.12 112 31 112 81 121.19 0.96 113 32 35 3 477.33 2.24 114 32 36 4 431.69 7.17 115 32 38 6 399.81 8.77 116 32 39 7 388.36 3.04 117 32 42 10 388.36 3.04 118 32 52 20 122.03 1.03 119 32 55 23 122.02 1.02 120 32 61 29 121.92 0.97 121 34 108 74 121.19 0.96 122 34 111 77 121.34 0.97 123 34 112 78 121.39 0.99 124 35 38 3 519.94 2.10 125 35 105 70 121.16 0.98 126 35 108 73 121.29 0.99 127 36 39 3 516.23 0.93 128 36 40 4 519.94 2.10 129 37 40 3 526.19 0.76 130 38 41 3 510.86 2.63 131 38 42 4 510.65 3.73 132 38 105 67 121.28 0.99 133 39 42 3 514.73 1.70 134 39 49 10 124.67 0.60 135 39 50 11 124.68 0.60 136 39 51 12 124.67 0.60 137 39 52 13 124.31 0.46 138 39 55 16 124.23 0.56 139 40 43 3 516.22 0.96 140 40 48 8 125.49 0.22 141 41 99 58 121.22 0.96 142 41 100 59 121.22 0.96 143 41 101 60 121.24 0.97 144 42 49 7 132.67 1.02 145 42 61 19 124.03 0.81 146 42 64 22 124.03 0.81 147 43 47 4 211.10 7.38 148 43 48 5 140.44 1.05 149 44 47 3 494.11 2.21 150 44 49 5 449.07 4.66 151 44 58 14 124.73 0.69 152 44 60 16 124.66 0.70 153 44 61 17 124.69 0.70 154 44 64 20 124.66 0.70 155 45 60 15 124.71 0.70 156 49 54 5 448.31 5.76 157 49 55 6 363.30 11.75 158 49 58 9 165.88 10.88 159 49 61 12 144.28 1.82 160 50 54 4 494.67 1.54 161 51 54 3 496.78 0.48 162 51 55 4 494.67 1.54 163 52 55 3 508.74 1.22 164 52 56 4 494.67 1.54 165 53 56 3 499.82 1.05 166 53 57 4 492.80 0.60 167 54 57 3 503.84 0.10 168 54 58 4 487.06 3.46 169 55 58 3 490.75 1.35 170 55 61 6 422.03 6.61 171 56 61 5 437.24 1.01 172 56 62 6 421.11 6.00 173 56 65 9 400.08 4.36 174 58 61 3 488.15 0.77 175 58 62 4 485.34 0.65 176 59 62 3 485.36 0.66 177 59 63 4 475.81 5.42 178 60 63 3 491.15 1.81 179 60 64 4 490.72 2.02 180 61 64 3 490.73 2.03 181 61 65 4 490.73 2.03 182 62 65 3 486.68 4.05 183 62 66 4 486.65 4.06 184 63 66 3 486.65 4.06 185 63 67 4 480.31 0.90 186 64 67 3 483.68 0.80 187 64 68 4 479.72 1.18 188 64 96 32 121.62 1.05 189 65 68 3 483.16 0.42 190 65 69 4 476.31 0.35 191 66 69 3 487.09 3.60 192 66 70 4 476.29 0.34 193 67 70 3 488.99 2.21 194 67 71 4 480.75 1.91 195 68 71 3 489.28 1.68 196 68 72 4 484.44 0.06 197 69 72 3 485.56 0.46 198 69 73 4 484.45 0.04 199 69 116 47 173.66 4.47 200 70 73 3 484.47 0.04 201 70 74 4 484.45 0.04 202 71 74 3 481.43 3.15 203 71 75 4 479.00 2.68 204 71 88 17 158.56 0.48 205 71 89 18 140.02 0.58 206 71 92 21 140.02 0.58 207 72 75 3 488.91 2.27 208 72 76 4 478.88 2.73 209 72 113 41 173.69 4.49 210 72 133 61 181.26 0.96 211 73 76 3 493.45 0.01 212 73 77 4 464.26 4.56 213 74 77 3 492.43 1.00 214 74 78 4 467.57 6.21 215 74 85 11 173.36 3.70 216 75 78 3 469.28 5.36 217 75 79 4 464.10 4.50 218 75 82 7 329.94 7.97 219 75 85 10 176.44 2.83 220 75 136 61 181.23 0.96 221 75 140 65 167.53 1.48 222 76 79 3 479.85 6.63 223 76 133 57 207.61 2.29 224 76 136 60 183.75 2.17 225 78 81 3 483.06 4.42 226 78 82 4 450.18 6.89 227 78 84 6 208.69 2.02 228 78 85 7 196.52 4.05 229 79 82 3 521.14 1.16 230 79 136 57 228.09 6.83 231 81 84 3 516.14 1.34 232 82 136 54 293.98 2.87 233 82 139 57 291.19 4.25 234 82 140 58 289.97 3.64 235 83 86 3 499.36 5.17 236 85 88 3 492.18 2.56 237 85 89 4 491.70 2.16 238 86 89 3 492.37 2.48 239 86 90 4 491.70 2.16 240 86 143 57 300.88 0.48 241 86 146 60 300.60 0.34 242 87 90 3 491.72 2.15 243 87 91 4 487.06 0.18 244 87 146 59 305.31 1.23 245 88 91 3 491.71 2.15 246 88 92 4 486.89 0.09 247 89 92 3 486.88 0.08 248 89 93 4 479.85 3.43 249 89 140 51 308.26 0.75 250 89 143 54 307.76 0.89 251 89 144 55 307.76 0.88 252 90 93 3 496.36 8.85 253 90 94 4 477.30 2.16 254 90 143 53 307.99 0.89 255 90 144 54 307.81 0.91 256 90 146 56 307.69 0.85 257 90 147 57 307.68 0.84 258 91 94 3 480.27 3.44 259 91 95 4 481.48 0.14 260 92 95 3 496.03 1.33 261 92 96 4 481.48 0.14 262 92 144 52 308.04 0.87 263 93 96 3 489.95 4.38 264 93 97 4 477.36 2.20 265 93 144 51 308.04 0.87 266 93 147 54 307.87 0.89 267 93 148 55 307.88 0.90 268 94 97 3 491.76 3.46 269 94 98 4 477.24 2.27 270 94 147 53 307.94 0.86 271 94 149 55 307.87 0.91 272 95 98 3 486.89 2.81 273 95 99 4 477.19 2.25 274 96 99 3 486.89 2.81 275 96 100 4 476.99 2.36 276 96 101 5 460.75 3.54 277 96 106 10 311.51 0.85 278 96 144 48 308.62 0.70 279 96 148 52 308.06 0.85 280 97 100 3 482.38 5.06 281 97 101 4 465.80 1.02 282 97 147 50 308.16 0.91 283 97 148 51 308.03 0.87 284 97 149 52 308.12 0.89 285 101 105 4 492.12 2.14 286 101 106 5 482.47 2.68 287 101 148 47 308.76 0.79 288 102 105 3 501.25 1.93 289 102 106 4 500.33 1.96 290 102 148 46 308.78 0.80 291 103 106 3 511.37 3.55 292 103 141 38 309.02 0.84 293 103 145 42 308.81 0.78 294 103 148 45 308.78 0.80 295 104 107 3 500.13 0.48 296 105 108 3 496.19 2.44 297 105 109 4 489.46 0.18 298 106 109 3 486.75 1.17 299 106 110 4 486.18 1.48 300 106 137 31 309.51 0.85 301 106 141 35 309.05 0.85 302 106 144 38 309.03 0.86 303 106 148 42 308.97 0.85 304 107 110 3 487.12 1.01 305 107 111 4 486.18 1.48 306 108 111 3 487.12 1.01 307 108 112 4 486.17 1.48 308 109 112 3 489.82 1.67 309 109 113 4 481.80 0.87 310 109 137 28 309.56 0.86 311 110 113 3 489.04 0.04 312 110 114 4 481.88 0.86 313 110 137 27 309.55 0.86 314 111 114 3 490.06 2.58 315 111 115 4 481.90 0.86 316 112 115 3 490.25 2.49 317 112 116 4 482.72 1.27 318 113 116 3 495.10 3.27 319 113 117 4 482.73 1.27 320 113 133 20 310.22 1.00 321 113 137 24 309.80 0.98 322 114 117 3 488.60 0.28 323 114 118 4 482.20 1.01 324 114 125 11 311.40 0.90 325 114 130 16 310.26 1.01 326 114 133 19 310.15 0.96 327 114 134 20 310.11 0.95 328 115 118 3 488.60 0.29 329 115 119 4 477.66 3.30 330 116 119 3 487.55 0.24 331 116 120 4 477.66 3.29 332 117 120 3 490.10 2.79 333 117 121 4 477.63 3.29 334 117 125 8 311.41 0.90 335 117 133 16 310.42 0.94 336 118 121 3 493.05 1.73 337 118 122 4 460.69 5.19 338 118 125 7 311.41 0.89 339 121 124 3 494.28 2.01 340 121 125 4 412.20 17.46 341 121 129 8 322.01 1.57 342 122 125 3 506.04 0.21 343 123 126 3 524.69 3.78 344 125 129 4 475.78 6.16 345 125 130 5 476.56 5.73 346 125 133 8 434.89 12.59 347 126 129 3 487.22 0.47 348 126 130 4 480.97 3.59 349 127 130 3 487.23 0.47 350 127 131 4 476.68 5.73 351 128 131 3 486.59 1.06 352 128 132 4 487.02 0.59 353 129 132 3 494.49 2.89 354 129 133 4 488.44 0.18 355 130 133 3 494.80 0.93 356 130 134 4 482.49 3.16 357 131 134 3 490.86 1.03 358 131 135 4 482.49 3.16 359 132 135 3 490.86 1.03 360 132 136 4 490.86 1.03 361 133 136 3 495.25 1.16 362 133 137 4 483.71 2.53 363 134 137 3 495.25 1.16 364 134 138 4 489.35 1.79 365 135 138 3 495.43 1.25 366 135 139 4 489.82 1.55 367 136 139 3 484.07 1.54 368 136 140 4 482.74 1.99 369 137 140 3 483.70 2.47 370 137 141 4 482.26 1.75 371 138 141 3 487.60 0.53 372 138 142 4 482.20 1.73 373 139 142 3 487.60 0.52 374 139 143 4 476.16 1.29 375 140 143 3 497.66 4.35 376 140 144 4 478.25 3.10 377 141 144 3 487.74 1.65 378 141 145 4 472.67 0.41 379 142 145 3 498.17 0.79 380 142 146 4 493.82 1.39 381 143 146 3 504.78 0.79 382 144 147 3 502.28 2.04 383 144 148 4 497.95 1.56 384 145 148 3 499.64 0.72 385 146 149 3 485.67 0.57 386 146 150 4 471.05 0.96