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 7 5 463.84 1.70 2 2 73 71 24.12 0.50 3 2 129 127 28.41 0.45 4 2 132 130 24.63 1.04 5 2 133 131 22.83 0.15 6 2 136 134 22.82 0.15 7 3 6 3 501.07 2.77 8 3 7 4 484.16 11.22 9 4 7 3 499.97 3.32 10 4 8 4 492.60 3.20 11 5 8 3 499.88 3.36 12 5 9 4 496.07 1.46 13 6 9 3 500.38 2.97 14 6 10 4 496.06 1.46 15 6 128 122 53.24 1.52 16 6 129 123 48.55 0.81 17 6 132 126 48.47 0.77 18 7 10 3 496.29 1.52 19 7 11 4 496.06 1.46 20 7 73 66 48.34 0.80 21 7 74 67 48.48 0.73 22 8 11 3 505.45 5.15 23 8 12 4 494.08 2.44 24 9 12 3 495.97 1.50 25 9 13 4 483.62 2.79 26 9 126 117 61.26 0.67 27 9 129 120 60.20 0.14 28 10 13 3 505.34 5.45 29 10 14 4 483.61 2.79 30 10 70 60 61.52 1.16 31 10 73 63 61.87 0.97 32 10 129 119 60.48 0.28 33 10 130 120 60.20 0.14 34 10 133 123 59.80 0.29 35 11 14 3 510.75 2.74 36 11 15 4 500.68 3.89 37 11 70 59 59.56 0.18 38 12 15 3 515.61 0.38 39 13 16 3 510.78 2.79 40 13 17 4 487.03 2.94 41 13 118 105 89.64 0.58 42 13 121 108 89.64 0.58 43 13 126 113 78.48 0.79 44 13 130 117 75.24 0.10 45 14 17 3 500.11 0.22 46 14 18 4 484.54 4.17 47 14 63 49 81.76 0.58 48 14 66 52 75.34 0.78 49 14 67 53 75.31 0.77 50 14 70 56 75.11 0.90 51 14 130 116 80.11 0.26 52 15 18 3 496.25 1.69 53 15 19 4 490.60 4.51 54 16 19 3 491.94 2.13 55 16 118 102 90.34 0.85 56 16 121 105 90.38 0.86 57 17 23 6 89.81 0.74 58 17 26 9 90.09 0.74 59 17 114 97 89.84 0.71 60 17 117 100 90.35 0.85 61 17 118 101 90.38 0.86 62 17 122 105 90.38 0.86 63 17 130 113 89.97 0.74 64 18 21 3 520.55 1.61 65 18 22 4 256.93 39.57 66 18 23 5 130.07 20.89 67 18 117 99 93.28 0.50 68 19 117 98 96.34 2.02 69 21 24 3 508.41 0.83 70 21 25 4 500.89 4.58 71 21 117 96 128.74 0.48 72 22 63 41 100.59 0.07 73 22 64 42 96.20 2.02 74 23 26 3 497.28 1.24 75 23 27 4 480.31 0.82 76 23 63 40 100.64 0.10 77 23 117 94 129.22 0.67 78 24 27 3 499.81 2.08 79 24 28 4 484.47 1.26 80 24 60 36 105.53 0.15 81 25 28 3 496.12 0.23 82 25 29 4 489.32 3.68 83 25 117 92 140.65 1.05 84 26 29 3 491.81 2.44 85 26 30 4 491.72 2.48 86 26 63 37 128.49 0.36 87 26 110 84 128.78 0.46 88 26 113 87 128.81 0.45 89 26 114 88 134.15 2.21 90 26 117 91 140.95 1.11 91 27 30 3 493.83 3.54 92 27 31 4 493.84 3.53 93 27 59 32 128.56 0.39 94 27 63 36 128.48 0.36 95 28 31 3 500.79 0.07 96 28 32 4 491.38 2.25 97 28 56 28 133.62 0.20 98 28 59 31 131.88 0.67 99 29 32 3 499.73 0.59 100 29 33 4 485.88 0.50 101 29 113 84 141.90 0.83 102 29 116 87 142.38 0.86 103 30 33 3 502.37 0.73 104 30 34 4 493.68 3.20 105 30 106 76 141.84 0.81 106 30 109 79 141.84 0.82 107 30 110 80 141.76 0.80 108 30 113 83 142.00 0.79 109 31 34 3 504.60 2.26 110 31 35 4 489.73 1.21 111 31 45 14 173.52 0.27 112 31 55 24 142.25 0.81 113 31 59 28 142.09 0.75 114 31 62 31 142.09 0.74 115 31 106 75 141.91 0.83 116 32 35 3 509.90 0.39 117 32 36 4 489.73 1.21 118 32 50 18 142.68 0.96 119 32 55 23 142.62 0.99 120 33 36 3 500.61 4.25 121 33 37 4 489.07 1.52 122 33 109 76 142.43 1.08 123 33 112 79 142.85 1.10 124 33 113 80 142.87 1.11 125 34 37 3 498.90 3.21 126 34 38 4 486.01 0.01 127 34 41 7 432.31 6.38 128 34 45 11 385.81 19.07 129 34 105 71 142.43 1.08 130 34 106 72 142.35 1.05 131 34 109 75 142.64 1.10 132 35 38 3 495.69 4.82 133 35 39 4 474.67 5.66 134 35 41 6 432.34 6.40 135 35 42 7 424.98 10.03 136 35 45 10 414.50 4.73 137 35 47 12 160.75 0.43 138 35 50 15 143.15 1.11 139 35 55 20 143.05 1.14 140 36 39 3 513.26 1.53 141 36 50 14 143.10 1.12 142 38 41 3 516.59 0.43 143 38 105 67 142.66 1.09 144 39 42 3 516.59 0.43 145 40 43 3 527.10 3.81 146 40 44 4 509.66 0.64 147 41 44 3 508.21 1.36 148 41 45 4 508.21 1.36 149 41 102 61 142.54 1.15 150 42 45 3 508.21 1.36 151 42 46 4 489.57 0.71 152 42 47 5 381.00 18.16 153 42 49 7 143.31 1.09 154 43 46 3 489.77 0.61 155 43 95 52 142.00 1.45 156 44 94 50 141.97 1.43 157 44 95 51 141.97 1.43 158 44 98 54 142.02 1.41 159 44 102 58 142.69 1.21 160 45 58 13 143.21 1.12 161 45 94 49 141.50 1.66 162 47 52 5 352.23 9.69 163 47 54 7 154.00 3.89 164 47 55 8 159.29 2.37 165 47 58 11 150.37 2.09 166 48 52 4 371.64 0.00 167 49 52 3 512.73 1.48 168 49 55 6 397.44 12.89 169 50 55 5 446.86 11.83 170 52 55 3 510.76 1.12 171 53 56 3 513.85 0.42 172 53 57 4 491.63 0.39 173 54 57 3 497.38 3.26 174 54 58 4 489.32 0.44 175 55 58 3 495.60 2.21 176 55 59 4 489.34 0.43 177 56 59 3 490.45 0.21 178 56 60 4 494.97 2.46 179 57 60 3 501.73 2.19 180 57 61 4 494.99 2.46 181 58 61 3 496.98 1.47 182 58 62 4 495.00 2.46 183 59 62 3 509.49 0.36 184 59 63 4 495.00 2.47 185 60 63 3 504.75 2.40 186 60 64 4 494.12 2.90 187 61 64 3 494.74 2.60 188 61 65 4 493.35 3.25 189 62 65 3 491.80 1.61 190 62 66 4 486.73 0.06 191 63 66 3 489.04 1.10 192 63 67 4 486.73 0.06 193 63 110 47 156.23 0.45 194 64 67 3 489.02 1.11 195 64 68 4 489.00 1.12 196 65 68 3 491.58 0.16 197 65 69 4 488.42 1.41 198 65 83 18 155.10 0.04 199 65 86 21 149.94 2.61 200 66 69 3 490.76 0.23 201 66 70 4 484.09 0.75 202 66 110 44 164.88 3.49 203 66 130 64 168.75 1.77 204 67 70 3 490.79 0.24 205 67 71 4 486.16 0.30 206 68 71 3 491.64 0.35 207 68 72 4 489.56 1.40 208 68 82 14 157.13 0.12 209 69 72 3 496.89 0.98 210 69 73 4 491.64 0.36 211 69 79 10 157.10 0.10 212 69 82 13 157.13 0.12 213 69 83 14 156.40 0.46 214 69 137 68 156.42 0.47 215 70 73 3 497.59 2.14 216 70 130 60 169.13 1.96 217 72 75 3 508.06 1.32 218 72 78 6 360.81 7.47 219 72 79 7 168.38 1.57 220 72 82 10 241.16 33.69 221 73 79 6 379.92 36.32 222 75 78 3 495.07 1.93 223 75 79 4 480.91 0.99 224 76 79 3 492.90 3.01 225 76 80 4 478.12 2.41 226 77 80 3 490.09 1.61 227 77 81 4 481.32 4.00 228 78 81 3 501.85 5.48 229 78 82 4 484.88 2.25 230 79 82 3 507.53 3.72 231 79 83 4 484.87 2.25 232 79 136 57 301.49 1.18 233 79 137 58 301.47 1.19 234 80 83 3 489.05 0.34 235 80 84 4 481.34 4.03 236 80 140 60 296.71 0.75 237 81 84 3 494.48 2.54 238 81 85 4 491.69 6.08 239 82 85 3 501.73 1.07 240 82 86 4 491.70 6.08 241 83 86 3 501.98 0.95 242 83 87 4 501.75 1.06 243 83 137 54 301.85 1.27 244 83 140 57 301.76 1.24 245 83 141 58 301.76 1.24 246 84 87 3 501.75 1.06 247 84 88 4 501.75 1.05 248 84 140 56 301.77 1.24 249 84 143 59 301.76 1.24 250 84 144 60 301.73 1.26 251 85 88 3 504.79 2.58 252 85 89 4 501.60 0.98 253 86 89 3 501.99 0.93 254 86 90 4 501.61 0.97 255 86 141 55 301.86 1.26 256 87 90 3 506.77 1.61 257 87 91 4 504.52 0.48 258 87 141 54 301.86 1.26 259 87 144 57 301.74 1.27 260 87 145 58 301.77 1.25 261 88 91 3 513.99 2.12 262 88 144 56 301.81 1.24 263 88 145 57 301.85 1.26 264 88 147 59 301.62 1.19 265 89 92 3 520.28 0.27 266 89 93 4 499.53 1.13 267 90 93 3 494.06 0.37 268 90 98 8 302.17 1.20 269 90 141 51 302.05 1.26 270 90 145 55 301.89 1.26 271 91 96 5 304.81 2.05 272 91 144 53 302.04 1.26 273 91 145 54 301.94 1.27 274 91 147 56 301.93 1.27 275 92 96 4 329.73 14.50 276 93 96 3 482.24 3.60 277 93 98 5 383.38 12.32 278 97 102 5 519.13 2.61 279 98 102 4 519.13 2.60 280 98 103 5 519.12 2.60 281 98 145 47 302.18 1.25 282 99 102 3 519.13 2.61 283 99 103 4 519.14 2.61 284 100 103 3 524.61 0.12 285 100 142 42 302.49 1.12 286 100 146 46 302.41 1.16 287 101 104 3 528.45 1.48 288 101 105 4 520.44 1.96 289 102 105 3 524.23 0.63 290 102 106 4 510.35 3.62 291 103 106 3 501.64 0.02 292 103 107 4 494.25 0.95 293 103 134 31 303.39 1.38 294 103 138 35 302.99 1.31 295 103 141 38 303.00 1.31 296 103 142 39 302.98 1.31 297 103 145 42 302.99 1.31 298 104 107 3 499.83 0.93 299 104 108 4 496.66 0.13 300 105 108 3 503.94 0.74 301 105 109 4 494.34 1.03 302 106 109 3 506.92 3.68 303 106 110 4 488.42 2.35 304 106 134 28 303.45 1.40 305 107 110 3 491.64 3.96 306 107 111 4 499.06 4.69 307 107 134 27 303.44 1.39 308 108 111 3 515.24 3.40 309 108 112 4 483.25 3.22 310 109 112 3 505.66 8.19 311 109 113 4 481.87 1.14 312 110 113 3 495.26 3.21 313 110 114 4 478.00 0.80 314 110 134 24 303.63 1.36 315 111 114 3 495.26 3.21 316 111 115 4 490.64 5.52 317 111 127 16 303.82 1.28 318 111 130 19 303.88 1.27 319 111 131 20 303.93 1.24 320 112 115 3 492.10 4.80 321 112 116 4 489.12 6.29 322 113 116 3 488.23 0.55 323 113 117 4 485.92 1.71 324 114 117 3 502.25 0.70 325 114 118 4 477.53 0.93 326 114 122 8 305.22 1.43 327 114 130 16 304.15 1.13 328 115 118 3 497.11 1.88 329 115 119 4 462.73 3.04 330 115 122 7 305.06 1.51 331 115 127 12 305.04 1.51 332 118 121 3 502.32 0.68 333 118 122 4 493.98 2.31 334 119 122 3 508.40 1.80 335 120 123 3 518.23 3.11 336 121 126 5 459.44 1.91 337 122 126 4 459.44 1.91 338 122 127 5 460.56 1.34 339 122 130 8 406.22 1.07 340 123 126 3 502.54 3.18 341 123 127 4 489.34 5.79 342 124 127 3 504.91 1.99 343 124 128 4 489.33 5.79 344 125 128 3 504.70 1.86 345 125 129 4 487.87 6.53 346 126 129 3 496.19 2.37 347 126 130 4 487.87 6.54 348 127 130 3 494.62 3.16 349 127 131 4 490.92 5.01 350 128 131 3 494.18 4.72 351 128 132 4 490.62 4.86 352 129 132 3 499.17 0.89 353 129 133 4 477.94 0.10 354 130 133 3 498.86 0.74 355 130 134 4 477.94 0.10 356 131 134 3 499.12 0.61 357 131 135 4 487.83 5.04 358 132 135 3 498.12 0.09 359 132 136 4 487.83 5.04 360 133 136 3 499.22 0.64 361 133 137 4 477.69 4.69 362 134 137 3 508.49 5.13 363 134 138 4 470.56 1.39 364 135 138 3 512.63 0.28 365 135 139 4 460.84 4.63 366 136 139 3 503.75 1.88 367 136 140 4 480.24 6.92 368 137 140 3 503.75 1.88 369 137 141 4 488.26 2.91 370 138 141 3 488.28 2.91 371 138 142 4 484.07 0.81 372 139 142 3 496.85 0.44 373 139 143 4 484.89 0.40 374 140 143 3 487.69 1.01 375 140 144 4 484.89 0.40 376 141 144 3 493.95 2.23 377 141 145 4 481.28 0.60 378 142 145 3 481.62 0.43 379 142 146 4 481.22 0.64 380 143 146 3 486.69 2.10 381 143 147 4 461.61 4.60 382 144 147 3 484.05 1.69