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 26.52 0.18 2 1 81 80 24.38 0.12 3 1 84 83 24.35 0.12 4 1 132 131 24.48 0.07 5 1 136 135 23.75 0.20 6 2 6 4 461.20 3.84 7 2 7 5 461.15 3.81 8 2 78 76 26.73 0.28 9 2 79 77 26.74 0.28 10 2 129 127 27.18 0.01 11 2 132 130 24.48 0.07 12 2 133 131 24.48 0.07 13 2 136 134 24.49 0.07 14 3 6 3 476.10 4.48 15 3 7 4 469.28 7.79 16 3 79 76 32.34 0.34 17 4 7 3 488.70 1.82 18 4 8 4 480.16 2.35 19 4 79 75 36.93 0.47 20 5 8 3 500.71 2.90 21 5 9 4 485.19 4.87 22 6 9 3 501.86 6.84 23 6 10 4 491.47 5.27 24 6 129 123 45.73 1.18 25 6 132 126 49.52 0.71 26 7 10 3 491.48 5.27 27 7 11 4 491.48 5.26 28 7 78 71 49.68 3.15 29 7 79 72 53.26 1.39 30 8 11 3 491.49 5.26 31 8 12 4 491.48 5.26 32 9 12 3 489.82 2.37 33 9 13 4 487.95 3.30 34 9 124 115 72.30 2.16 35 9 125 116 66.58 1.97 36 9 126 117 60.10 0.05 37 9 129 120 60.11 0.05 38 10 13 3 489.25 2.66 39 10 14 4 498.30 1.88 40 10 75 65 60.10 0.06 41 10 129 119 60.23 0.10 42 10 130 120 60.11 0.04 43 11 14 3 499.73 1.17 44 11 15 4 498.35 1.86 45 11 75 64 60.22 0.11 46 12 15 3 507.34 1.34 47 12 16 4 505.56 0.46 48 12 123 111 85.29 0.79 49 13 16 3 524.67 0.00 50 13 17 4 502.65 1.92 51 13 116 103 85.24 0.80 52 13 122 109 85.28 0.78 53 13 123 110 85.73 1.00 54 13 126 113 85.25 0.80 55 13 130 117 85.19 0.78 56 14 17 3 499.86 1.11 57 14 18 4 496.15 0.74 58 14 68 54 85.78 0.97 59 14 71 57 85.34 0.82 60 14 72 58 85.34 0.82 61 14 75 61 85.32 0.81 62 14 112 98 85.28 0.79 63 14 130 116 85.26 0.80 64 15 18 3 493.24 2.20 65 15 19 4 484.19 0.26 66 16 19 3 492.84 4.07 67 16 119 103 86.30 1.05 68 16 120 104 86.30 1.05 69 17 20 3 515.37 4.53 70 17 24 7 285.44 6.32 71 17 68 51 86.20 1.04 72 17 115 98 86.26 1.04 73 17 116 99 86.16 1.02 74 17 119 102 86.29 1.04 75 18 21 3 486.39 1.35 76 18 68 50 86.15 1.02 77 18 72 54 86.13 1.02 78 20 23 3 506.64 0.95 79 20 24 4 464.13 2.25 80 21 24 3 486.37 1.34 81 21 25 4 467.84 0.39 82 21 68 47 101.23 3.29 83 22 25 3 496.81 3.91 84 22 26 4 471.13 2.04 85 22 61 39 129.75 0.04 86 23 26 3 499.86 2.39 87 23 27 4 482.07 3.44 88 24 27 3 484.12 2.44 89 24 28 4 476.18 0.48 90 24 68 44 129.91 0.05 91 24 115 91 130.01 0.04 92 24 119 95 143.85 0.00 93 25 28 3 500.14 0.42 94 25 29 4 479.92 1.38 95 25 64 39 136.34 3.18 96 25 68 43 129.81 0.01 97 26 29 3 500.23 0.03 98 26 30 4 486.94 0.71 99 26 60 34 144.16 0.15 100 26 61 35 144.18 0.14 101 26 64 38 143.59 0.23 102 27 30 3 494.31 2.98 103 27 31 4 486.95 0.70 104 27 115 88 144.02 0.07 105 28 31 3 498.10 1.57 106 28 32 4 486.95 0.70 107 28 67 39 144.22 0.12 108 28 68 40 144.22 0.12 109 28 108 80 143.79 0.04 110 28 111 83 144.01 0.07 111 28 112 84 144.00 0.07 112 28 115 87 144.02 0.07 113 29 32 3 498.71 1.26 114 29 33 4 481.45 2.05 115 29 43 14 261.46 1.41 116 29 46 17 189.88 22.54 117 29 60 31 144.55 0.04 118 29 63 34 144.30 0.09 119 29 64 35 144.24 0.11 120 29 67 38 144.23 0.12 121 30 33 3 500.49 2.16 122 30 34 4 481.43 2.05 123 30 51 21 144.96 0.17 124 30 55 25 144.62 0.07 125 30 60 30 144.57 0.06 126 31 34 3 500.49 2.16 127 31 35 4 488.74 1.65 128 31 111 80 144.01 0.07 129 32 35 3 499.50 4.62 130 32 36 4 472.42 0.28 131 32 39 7 423.50 16.36 132 32 108 76 143.99 0.06 133 32 111 79 144.01 0.07 134 33 36 3 499.33 2.44 135 33 37 4 463.85 3.67 136 33 39 6 423.53 16.34 137 33 40 7 354.27 1.75 138 33 43 10 326.08 1.00 139 33 46 13 190.14 22.42 140 33 51 18 145.24 0.18 141 33 54 21 145.22 0.15 142 34 37 3 503.55 2.15 143 34 51 17 145.24 0.18 144 35 111 76 144.17 0.07 145 36 39 3 506.23 1.35 146 36 107 71 143.99 0.06 147 36 110 74 144.31 0.07 148 36 111 75 144.34 0.07 149 37 40 3 506.30 1.32 150 38 41 3 505.73 1.10 151 38 42 4 505.44 1.25 152 39 42 3 507.01 0.85 153 39 43 4 505.44 1.25 154 40 43 3 501.75 0.59 155 40 46 6 255.84 3.25 156 40 47 7 196.47 25.47 157 40 54 14 189.89 22.48 158 41 47 6 196.36 25.43 159 42 99 57 143.25 0.24 160 42 100 58 143.24 0.25 161 42 104 62 143.96 0.12 162 43 46 3 483.71 5.38 163 43 47 4 413.62 15.71 164 43 63 20 145.21 0.32 165 45 49 4 516.29 1.34 166 45 59 14 145.63 0.35 167 46 49 3 496.88 1.33 168 46 54 8 274.15 0.11 169 46 59 13 145.63 0.35 170 46 60 14 145.60 0.37 171 46 63 17 145.50 0.39 172 49 53 4 457.31 8.54 173 49 54 5 456.41 8.10 174 50 53 3 488.57 2.79 175 50 54 4 465.06 8.96 176 51 54 3 493.18 0.48 177 51 55 4 465.06 8.96 178 52 55 3 491.47 0.60 179 52 56 4 479.40 1.79 180 53 56 3 491.44 0.61 181 53 57 4 466.84 2.91 182 54 57 3 491.44 0.61 183 54 60 6 361.31 26.59 184 55 60 5 361.56 26.71 185 57 60 3 482.49 4.27 186 59 62 3 497.90 2.12 187 59 63 4 489.28 0.20 188 60 63 3 506.14 1.92 189 60 64 4 482.28 0.84 190 61 64 3 493.68 0.00 191 61 65 4 485.69 0.86 192 62 65 3 496.72 2.76 193 62 66 4 489.32 0.94 194 63 66 3 504.15 0.88 195 63 67 4 489.32 0.94 196 64 67 3 492.98 0.89 197 64 68 4 489.31 0.95 198 65 68 3 499.11 2.19 199 65 69 4 485.22 0.83 200 66 69 3 497.44 3.62 201 66 70 4 488.54 0.83 202 67 70 3 497.10 1.34 203 67 71 4 488.54 0.85 204 68 71 3 493.21 3.28 205 68 72 4 488.45 0.89 206 68 115 47 203.32 3.00 207 69 72 3 496.15 4.16 208 69 73 4 488.49 0.89 209 70 73 3 490.06 0.10 210 70 74 4 490.09 0.09 211 70 91 21 200.37 4.45 212 71 74 3 490.05 0.06 213 71 75 4 490.05 0.06 214 71 112 41 203.40 3.05 215 71 130 59 203.69 2.90 216 71 134 63 203.36 3.06 217 72 75 3 488.75 0.58 218 72 76 4 479.78 5.08 219 73 76 3 493.78 1.91 220 73 77 4 479.38 5.29 221 74 77 3 491.76 0.91 222 74 78 4 471.29 1.25 223 74 84 10 262.43 4.71 224 74 87 13 203.83 3.04 225 74 88 14 203.82 3.03 226 74 91 17 203.81 3.03 227 74 133 59 203.86 3.00 228 74 137 63 203.82 3.02 229 75 78 3 488.89 0.53 230 75 130 55 203.97 2.95 231 75 133 58 203.97 2.96 232 77 80 3 492.44 1.49 233 77 83 6 310.75 3.88 234 77 84 7 310.72 3.89 235 77 87 10 289.16 3.50 236 78 84 6 313.97 2.27 237 78 133 55 203.99 2.96 238 80 83 3 504.43 1.83 239 80 84 4 488.03 0.53 240 81 84 3 497.54 5.28 241 81 85 4 488.04 0.53 242 82 85 3 497.54 5.28 243 82 86 4 502.81 2.65 244 83 86 3 496.65 0.43 245 83 87 4 491.38 2.21 246 84 87 3 496.65 0.43 247 84 88 4 487.97 0.54 248 84 133 49 235.08 6.75 249 84 136 52 234.83 6.65 250 85 88 3 497.29 0.76 251 85 89 4 487.95 0.54 252 86 89 3 503.03 2.10 253 86 90 4 492.38 3.21 254 87 90 3 496.27 2.65 255 87 91 4 485.16 1.51 256 88 91 3 498.66 1.45 257 88 92 4 488.57 0.20 258 88 136 48 235.08 6.75 259 88 137 49 234.99 6.71 260 88 140 52 234.74 6.61 261 89 92 3 493.97 0.57 262 89 93 4 484.44 1.14 263 90 93 3 492.84 3.18 264 90 94 4 484.44 1.14 265 91 94 3 502.27 1.54 266 91 95 4 484.44 1.12 267 91 105 14 251.62 0.91 268 91 137 46 235.10 6.75 269 92 95 3 496.25 1.34 270 92 96 4 484.42 1.12 271 92 140 48 235.01 6.73 272 92 141 49 234.83 6.65 273 92 144 52 233.47 6.15 274 93 96 3 493.47 0.08 275 93 97 4 486.93 0.33 276 94 97 3 501.55 0.12 277 94 98 4 486.93 0.34 278 95 98 3 486.70 0.23 279 95 99 4 486.22 0.02 280 95 100 5 435.75 11.84 281 95 105 10 360.81 3.82 282 95 141 46 235.09 6.75 283 96 99 3 482.66 3.39 284 96 100 4 467.63 4.12 285 96 141 45 235.21 6.70 286 96 144 48 235.00 6.72 287 96 146 50 233.62 6.08 288 100 104 4 490.67 2.89 289 100 105 5 485.62 0.37 290 100 141 41 236.16 6.69 291 101 104 3 506.42 0.65 292 101 105 4 496.68 1.28 293 101 141 40 236.16 6.69 294 101 146 45 233.71 6.13 295 102 105 3 495.29 0.58 296 102 106 4 484.88 0.74 297 102 138 36 236.18 6.70 298 102 141 39 236.17 6.69 299 102 142 40 236.16 6.69 300 102 146 44 233.91 6.13 301 103 106 3 496.93 0.24 302 103 107 4 484.09 1.13 303 104 107 3 496.76 1.23 304 104 108 4 495.35 4.50 305 105 108 3 495.24 4.55 306 105 109 4 482.89 1.63 307 105 137 32 236.27 6.71 308 105 138 33 236.26 6.71 309 105 141 36 236.25 6.71 310 106 109 3 495.11 2.27 311 106 110 4 492.32 0.83 312 106 138 32 236.27 6.71 313 107 110 3 494.02 1.68 314 107 111 4 492.69 1.01 315 108 111 3 505.23 0.04 316 108 112 4 488.43 1.11 317 108 134 26 237.27 6.67 318 109 112 3 507.10 0.90 319 109 113 4 507.10 0.90 320 109 131 22 237.29 6.67 321 109 134 25 237.24 6.66 322 109 135 26 237.27 6.67 323 109 138 29 237.23 6.66 324 110 113 3 551.82 0.19 325 111 114 3 503.83 0.10 326 111 115 4 498.37 0.49 327 112 115 3 501.91 0.71 328 112 116 4 491.89 2.73 329 112 130 18 237.60 6.65 330 112 134 22 237.45 6.58 331 113 116 3 495.83 0.89 332 113 117 4 489.62 3.84 333 113 127 14 237.90 6.61 334 113 131 18 237.80 6.56 335 114 117 3 495.69 0.81 336 114 118 4 489.62 3.84 337 115 118 3 495.69 0.81 338 115 119 4 495.69 0.81 339 116 119 3 497.19 0.04 340 116 120 4 487.23 2.64 341 116 122 6 353.35 0.70 342 116 130 14 238.15 6.50 343 117 120 3 494.81 1.15 344 117 122 5 393.43 11.57 345 122 126 4 454.17 15.22 346 122 127 5 432.77 12.93 347 123 126 3 506.50 0.39 348 125 128 3 505.41 0.02 349 125 129 4 484.95 1.75 350 126 129 3 492.53 2.04 351 126 130 4 483.23 2.62 352 127 130 3 493.12 0.10 353 127 131 4 483.25 2.62 354 128 131 3 502.60 5.03 355 128 132 4 483.22 2.63 356 129 132 3 490.56 0.17 357 129 133 4 484.05 3.08 358 130 133 3 490.81 0.29 359 130 134 4 484.05 3.08 360 131 134 3 490.85 0.31 361 131 135 4 482.81 3.70 362 132 135 3 486.33 0.67 363 132 136 4 487.20 4.41 364 133 136 3 492.49 1.82 365 133 137 4 489.39 3.31 366 134 137 3 493.80 1.16 367 134 138 4 489.38 3.31 368 135 138 3 490.59 2.77 369 135 139 4 487.71 2.48 370 136 139 3 493.25 1.45 371 136 140 4 489.43 3.35 372 137 140 3 492.84 1.65 373 137 141 4 489.39 3.37 374 138 141 3 495.48 0.32 375 138 142 4 487.39 2.38 376 139 142 3 493.58 0.62 377 139 143 4 487.40 2.38 378 140 143 3 497.20 0.24 379 140 144 4 487.40 2.38 380 141 144 3 493.20 1.74 381 141 145 4 490.82 0.67 382 141 146 5 420.25 10.51 383 142 145 3 493.11 1.81 384 142 146 4 440.91 20.84