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 2 144 142 16.85 0.20 2 3 6 3 498.23 1.33 3 3 7 4 487.54 1.64 4 3 91 88 20.44 0.39 5 3 94 91 19.89 0.39 6 3 95 92 20.04 0.49 7 3 141 138 17.17 0.06 8 3 144 141 17.00 0.12 9 3 145 142 16.98 0.12 10 4 7 3 504.22 1.67 11 4 8 4 490.42 1.27 12 4 91 87 23.36 1.22 13 5 8 3 507.79 1.20 14 5 9 4 505.69 3.56 15 6 9 3 514.64 0.27 16 6 141 135 21.22 1.02 17 6 144 138 21.22 1.02 18 7 10 3 517.13 1.51 19 7 91 84 32.08 3.12 20 7 141 134 24.57 0.61 21 9 14 5 486.96 0.44 22 9 137 128 37.13 0.58 23 10 14 4 486.95 0.45 24 10 15 5 474.74 6.54 25 10 84 74 50.91 0.04 26 10 90 80 46.73 0.46 27 10 137 127 40.20 1.80 28 10 138 128 41.95 0.92 29 10 141 131 40.19 1.80 30 11 14 3 499.90 0.10 31 11 15 4 502.19 1.07 32 12 15 3 502.20 1.07 33 12 16 4 502.19 1.07 34 13 16 3 502.19 1.07 35 13 17 4 502.19 1.07 36 14 17 3 515.16 1.42 37 14 18 4 497.66 3.33 38 14 134 120 73.75 0.44 39 14 137 123 73.80 0.46 40 15 18 3 506.17 3.08 41 15 19 4 498.00 3.15 42 15 84 69 78.67 1.57 43 15 85 70 85.47 1.38 44 16 19 3 510.84 0.75 45 16 20 4 498.00 3.15 46 17 20 3 502.14 1.07 47 17 21 4 497.77 3.25 48 17 130 113 91.64 0.74 49 17 131 114 91.46 0.79 50 17 134 117 91.45 0.79 51 18 21 3 513.23 0.53 52 18 22 4 494.68 1.67 53 18 81 63 91.61 0.72 54 18 84 66 91.66 0.70 55 18 134 116 91.48 0.79 56 18 135 117 91.45 0.79 57 18 138 120 91.45 0.79 58 19 22 3 505.17 0.25 59 19 23 4 498.51 3.58 60 19 81 62 91.67 0.70 61 19 84 65 91.68 0.70 62 19 85 66 97.14 1.36 63 20 23 3 498.68 3.65 64 21 24 3 508.07 2.76 65 21 25 4 498.45 3.62 66 21 122 101 98.02 1.45 67 21 127 106 98.05 1.44 68 21 131 110 97.66 1.29 69 21 135 114 97.63 1.29 70 22 25 3 498.45 3.62 71 22 26 4 468.42 3.71 72 22 29 7 448.41 6.28 73 22 74 52 191.25 1.34 74 22 77 55 97.71 1.29 75 22 78 56 97.69 1.32 76 22 81 59 97.65 1.31 77 22 135 113 97.69 1.28 78 23 27 4 476.24 0.20 79 24 27 3 512.14 0.03 80 24 125 101 117.88 1.88 81 24 127 103 108.84 2.58 82 25 28 3 523.19 1.81 83 25 32 7 321.06 3.10 84 25 74 49 204.81 5.09 85 25 122 97 108.86 2.58 86 25 125 100 117.88 1.88 87 25 135 110 106.39 2.47 88 26 29 3 516.75 3.30 89 28 31 3 501.71 0.04 90 28 32 4 455.53 2.52 91 29 33 4 483.06 2.93 92 29 74 45 208.38 3.31 93 29 75 46 208.38 3.31 94 29 78 49 208.33 3.27 95 30 33 3 498.51 0.61 96 30 34 4 493.11 0.58 97 30 61 31 226.44 6.17 98 30 67 37 225.21 6.54 99 30 71 41 222.90 5.69 100 31 34 3 509.32 0.49 101 31 35 4 493.12 0.57 102 31 61 30 226.47 6.19 103 32 35 3 493.26 0.61 104 32 36 4 493.12 0.57 105 32 74 42 224.65 6.45 106 32 125 93 170.59 0.87 107 33 36 3 503.00 5.25 108 33 37 4 493.66 0.29 109 33 70 37 225.24 6.53 110 33 74 41 224.64 6.45 111 34 37 3 497.57 2.12 112 34 38 4 488.05 2.65 113 34 60 26 226.59 6.18 114 34 61 27 226.50 6.20 115 34 67 33 225.49 6.44 116 34 70 36 225.19 6.36 117 35 38 3 505.38 1.54 118 35 39 4 489.79 6.25 119 35 121 86 174.42 0.17 120 36 39 3 503.19 0.45 121 36 40 4 499.37 1.46 122 36 73 37 225.63 6.44 123 36 74 38 225.63 6.43 124 36 77 41 225.58 6.42 125 36 117 81 175.22 0.57 126 36 118 82 175.21 0.57 127 36 121 85 174.57 0.23 128 37 40 3 503.81 0.76 129 37 41 4 499.38 1.46 130 37 51 14 261.20 0.82 131 37 66 29 226.53 6.15 132 37 69 32 226.06 6.36 133 37 70 33 225.81 6.40 134 37 73 36 225.69 6.45 135 38 41 3 499.38 1.46 136 38 42 4 493.72 4.28 137 38 60 22 226.77 6.25 138 38 66 28 226.56 6.16 139 39 42 3 495.28 0.51 140 39 43 4 488.75 1.79 141 39 117 78 175.26 0.57 142 39 120 81 175.31 0.54 143 40 43 3 513.01 5.56 144 40 44 4 488.74 1.78 145 40 47 7 415.39 6.44 146 40 51 11 303.60 3.78 147 40 113 73 175.56 0.71 148 40 114 74 175.43 0.67 149 40 117 77 175.30 0.55 150 41 44 3 498.38 1.30 151 41 45 4 484.29 3.92 152 41 48 7 325.75 11.20 153 41 51 10 293.63 0.58 154 41 57 16 227.21 6.12 155 41 66 25 227.11 6.11 156 42 45 3 520.59 0.96 157 43 120 77 175.75 0.49 158 44 47 3 510.20 0.72 159 44 113 69 175.96 0.54 160 45 48 3 507.80 1.85 161 46 113 67 176.49 0.71 162 47 50 3 510.31 2.91 163 47 51 4 510.12 3.00 164 47 110 63 176.65 0.79 165 47 113 66 176.42 0.69 166 48 51 3 522.45 3.16 167 48 57 9 233.56 4.69 168 49 52 3 516.34 0.10 169 50 104 54 177.08 0.80 170 50 106 56 176.91 0.76 171 50 110 60 176.88 0.76 172 51 54 3 511.88 1.17 173 51 69 18 228.95 5.36 174 52 55 3 519.22 1.90 175 53 65 12 243.21 4.15 176 54 57 3 536.11 2.22 177 54 63 9 262.29 0.92 178 54 65 11 235.34 2.46 179 54 66 12 235.31 2.48 180 54 69 15 235.31 2.46 181 56 59 3 520.49 2.98 182 56 63 7 288.83 9.92 183 57 60 3 506.79 1.99 184 57 63 6 306.78 7.57 185 57 66 9 272.69 5.97 186 59 62 3 505.86 1.17 187 59 63 4 424.18 12.29 188 60 63 3 508.19 1.70 189 60 66 6 398.79 20.32 190 61 67 6 329.74 0.54 191 63 66 3 499.90 1.89 192 63 67 4 490.29 3.27 193 64 67 3 496.50 0.17 194 64 68 4 493.41 0.79 195 65 68 3 499.74 1.57 196 65 69 4 491.34 0.24 197 66 69 3 501.53 3.27 198 66 70 4 499.46 4.30 199 67 70 3 507.23 0.42 200 67 71 4 501.25 3.41 201 68 71 3 516.40 4.19 202 68 72 4 505.64 1.20 203 69 72 3 505.66 1.20 204 69 73 4 505.65 1.19 205 70 73 3 516.38 4.19 206 70 74 4 505.63 1.18 207 71 74 3 506.91 0.54 208 71 75 4 505.62 1.18 209 72 75 3 505.61 1.19 210 72 76 4 505.58 1.18 211 73 76 3 505.21 0.99 212 73 77 4 499.74 1.73 213 74 77 3 507.65 1.95 214 74 78 4 495.92 0.19 215 75 78 3 495.04 0.25 216 75 79 4 493.32 1.48 217 76 79 3 497.05 3.34 218 76 80 4 500.41 0.12 219 76 97 21 179.88 0.34 220 77 80 3 511.42 3.95 221 77 81 4 502.12 0.73 222 77 135 58 174.71 0.06 223 78 81 3 502.13 0.73 224 78 82 4 501.41 1.08 225 79 82 3 505.23 2.29 226 79 83 4 501.41 1.08 227 79 93 14 209.34 13.75 228 79 97 18 209.22 13.79 229 80 83 3 515.13 2.67 230 80 84 4 501.43 1.09 231 80 90 10 209.37 13.75 232 80 93 13 209.34 13.75 233 80 94 14 209.32 13.76 234 80 97 17 209.31 13.76 235 80 138 58 174.68 0.08 236 80 142 62 172.69 0.61 237 81 84 3 505.03 2.89 238 81 135 54 174.76 0.07 239 81 138 57 174.70 0.09 240 83 86 3 499.68 0.43 241 83 89 6 340.18 9.38 242 83 90 7 279.27 5.51 243 83 93 10 279.28 5.51 244 84 90 6 352.41 1.36 245 84 138 54 174.75 0.07 246 86 89 3 505.88 1.20 247 86 90 4 496.12 3.69 248 87 90 3 496.13 3.68 249 87 91 4 499.41 2.05 250 88 91 3 508.74 2.59 251 88 92 4 499.51 2.04 252 89 92 3 501.41 1.25 253 89 93 4 499.51 2.04 254 90 93 3 513.83 4.65 255 90 94 4 499.52 2.05 256 90 138 48 174.76 0.07 257 91 94 3 501.31 1.16 258 91 95 4 501.30 1.16 259 92 95 3 506.28 1.30 260 92 96 4 501.34 1.17 261 93 96 3 507.77 2.04 262 93 97 4 501.32 1.18 263 94 97 3 507.76 2.05 264 94 98 4 500.61 1.52 265 94 141 47 172.85 0.59 266 94 142 48 168.19 1.70 267 94 145 51 162.40 0.65 268 95 98 3 496.32 0.62 269 95 99 4 495.37 1.10 270 95 145 50 162.38 0.66 271 96 99 3 501.74 1.40 272 96 100 4 495.38 1.10 273 97 100 3 500.63 1.54 274 97 101 4 500.63 1.54 275 98 101 3 506.94 1.61 276 98 102 4 496.13 3.79 277 98 145 47 162.38 0.66 278 98 146 48 162.29 0.69 279 99 102 3 501.38 1.17 280 99 103 4 489.03 0.24 281 100 103 3 507.44 1.66 282 100 104 4 500.80 3.56 283 101 104 3 499.61 2.25 284 101 105 4 488.89 0.17 285 101 106 5 384.56 11.71 286 101 111 10 266.54 3.21 287 101 146 45 162.28 0.70 288 102 105 3 494.12 2.44 289 102 145 43 162.41 0.64 290 102 146 44 162.06 0.71 291 106 110 4 484.53 1.95 292 106 111 5 470.86 2.37 293 106 146 40 161.90 0.79 294 107 110 3 502.29 2.20 295 107 111 4 493.86 2.02 296 107 146 39 161.66 0.68 297 108 111 3 502.30 2.20 298 108 112 4 496.77 0.56 299 108 143 35 162.38 0.63 300 108 146 38 160.46 1.06 301 109 112 3 505.39 0.67 302 109 113 4 505.39 0.66 303 110 113 3 507.23 0.99 304 111 114 3 514.79 1.21 305 111 139 28 175.50 0.51 306 111 142 31 163.66 1.25 307 111 143 32 162.41 0.65 308 111 146 35 161.58 0.72 309 112 115 3 508.99 0.32 310 112 139 27 175.43 0.55 311 112 143 31 162.40 0.65 312 113 116 3 524.88 1.49 313 113 117 4 509.19 0.97 314 114 117 3 509.19 0.97 315 114 118 4 504.11 0.75 316 114 139 25 175.68 0.66 317 115 118 3 509.06 1.04 318 115 119 4 506.29 0.35 319 115 136 21 175.72 0.68 320 115 139 24 175.93 0.79 321 116 119 3 515.11 4.05 322 116 120 4 506.18 0.41 323 117 120 3 506.70 0.14 324 117 121 4 504.29 1.35 325 118 121 3 510.00 0.48 326 118 122 4 499.07 3.95 327 118 135 17 176.17 0.85 328 118 139 21 175.97 0.81 329 119 122 3 516.47 2.77 330 119 123 4 492.46 0.68 331 119 129 10 213.82 9.75 332 119 132 13 176.55 1.02 333 119 133 14 176.86 1.12 334 120 123 3 497.42 0.61 335 120 124 4 487.35 3.23 336 121 124 3 500.06 2.29 337 121 125 4 496.23 1.22 338 122 125 3 500.06 2.29 339 122 126 4 485.73 4.03 340 122 127 5 445.94 0.49 341 122 131 9 268.17 10.89 342 122 132 10 214.03 9.84 343 122 135 13 207.70 12.73 344 123 126 3 496.25 1.20 345 123 127 4 461.00 7.00 346 127 131 4 479.94 2.40 347 128 131 3 506.82 0.49 348 128 132 4 483.30 0.77 349 129 132 3 486.94 1.06 350 129 133 4 483.98 0.51 351 130 133 3 509.84 1.89 352 130 134 4 487.79 2.34 353 131 134 3 501.85 2.00 354 131 135 4 496.91 2.22 355 132 135 3 515.21 3.83 356 132 136 4 496.90 2.23 357 133 136 3 515.21 3.84 358 133 137 4 496.90 2.23 359 134 137 3 515.22 3.83 360 134 138 4 504.43 1.54 361 135 138 3 498.11 1.61 362 135 139 4 498.11 1.61 363 136 139 3 498.43 4.05 364 136 140 4 496.79 3.23 365 137 140 3 501.94 0.66 366 137 141 4 499.76 1.75 367 138 141 3 512.69 4.71 368 138 142 4 504.50 0.62 369 139 142 3 511.59 4.17 370 139 143 4 502.04 0.59 371 140 143 3 502.01 0.58 372 140 144 4 497.90 1.48 373 141 144 3 506.81 0.49 374 141 145 4 501.80 0.48 375 142 145 3 505.00 0.90 376 142 146 4 501.76 0.49 377 143 146 3 504.76 1.02