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 28 27 446.65 1.36 2 1 93 92 154.23 0.53 3 1 145 144 43.29 0.33 4 1 148 147 31.63 0.59 5 1 151 150 18.07 0.86 6 2 27 25 446.66 1.36 7 2 28 26 446.65 1.36 8 2 91 89 154.16 0.49 9 2 92 90 154.27 0.51 10 2 93 91 155.04 0.12 11 2 94 92 155.18 0.14 12 2 95 93 155.12 0.11 13 2 97 95 155.79 0.10 14 2 144 142 55.78 0.39 15 2 148 146 41.18 0.48 16 3 28 25 446.66 1.36 17 3 30 27 446.66 1.36 18 3 95 92 155.23 0.11 19 3 96 93 155.21 0.10 20 3 97 94 155.79 0.10 21 4 22 18 446.75 1.34 22 4 27 23 446.74 1.34 23 4 28 24 446.73 1.34 24 4 29 25 446.67 1.36 25 4 30 26 446.67 1.36 26 4 97 93 155.81 0.10 27 4 99 95 166.93 0.70 28 4 137 133 78.12 0.52 29 4 141 137 72.56 0.80 30 5 30 25 446.67 1.36 31 5 32 27 446.64 1.36 32 5 66 61 171.31 0.14 33 5 96 91 157.62 0.78 34 5 97 92 163.19 1.93 35 5 98 93 165.12 0.96 36 5 99 94 166.94 0.70 37 6 9 3 497.83 0.54 38 6 15 9 447.12 1.21 39 6 18 12 446.87 1.32 40 6 29 23 446.76 1.33 41 6 30 24 446.73 1.34 42 6 31 25 446.66 1.36 43 6 32 26 446.66 1.36 44 6 99 93 167.41 0.72 45 6 137 131 78.16 0.52 46 7 32 25 446.68 1.35 47 7 63 56 192.31 0.67 48 7 98 91 170.44 0.60 49 7 99 92 170.44 0.60 50 7 100 93 171.00 0.32 51 7 101 94 171.55 0.48 52 7 106 99 167.44 0.72 53 7 107 100 170.60 0.77 54 7 110 103 171.00 0.58 55 8 32 24 446.72 1.34 56 8 33 25 446.66 1.36 57 8 34 26 446.64 1.36 58 8 101 93 171.57 0.48 59 8 104 96 171.91 0.48 60 9 15 6 447.87 1.42 61 9 31 22 446.80 1.32 62 9 32 23 446.79 1.32 63 9 35 26 444.19 0.71 64 9 36 27 442.46 0.02 65 9 37 28 442.45 0.03 66 9 102 93 171.69 0.53 67 10 36 26 441.14 0.61 68 10 37 27 441.16 0.61 69 10 101 91 171.66 0.53 70 10 102 92 171.72 0.54 71 10 103 93 171.78 0.55 72 10 104 94 171.94 0.50 73 11 14 3 501.54 0.69 74 11 15 4 486.15 0.55 75 11 37 26 441.12 0.61 76 11 102 91 171.70 0.54 77 12 15 3 495.93 1.89 78 12 16 4 486.15 0.55 79 12 37 25 440.03 1.15 80 12 41 29 375.17 8.30 81 12 43 31 222.98 0.38 82 12 44 32 222.36 0.07 83 13 16 3 492.47 3.62 84 13 17 4 486.14 0.54 85 13 43 30 222.91 0.34 86 14 17 3 493.92 2.89 87 14 18 4 484.50 0.29 88 14 102 88 171.59 0.56 89 14 132 118 78.47 0.51 90 14 133 119 78.46 0.50 91 14 134 120 78.44 0.51 92 15 18 3 489.73 1.79 93 15 19 4 485.75 0.91 94 15 31 16 446.86 1.29 95 15 37 22 440.03 1.15 96 15 39 24 399.19 0.70 97 15 44 29 220.60 0.80 98 16 19 3 492.65 4.36 99 16 20 4 488.48 2.27 100 16 44 28 218.14 0.42 101 16 49 33 216.68 0.41 102 17 20 3 493.22 0.10 103 17 21 4 484.88 1.93 104 17 134 117 78.36 0.47 105 18 21 3 488.16 0.29 106 18 22 4 484.89 1.93 107 18 29 11 447.12 1.31 108 18 133 115 78.45 0.50 109 18 134 116 78.31 0.45 110 18 137 119 78.29 0.45 111 19 22 3 490.88 1.06 112 19 23 4 484.88 1.93 113 19 29 10 447.12 1.32 114 19 39 20 393.81 1.01 115 19 44 25 220.40 0.72 116 19 49 30 216.68 0.41 117 19 53 34 216.14 0.29 118 19 54 35 216.12 0.29 119 19 57 38 215.75 0.33 120 20 23 3 488.57 0.09 121 20 24 4 482.60 0.79 122 20 48 28 216.83 0.35 123 20 49 29 216.67 0.42 124 20 53 33 216.14 0.29 125 21 24 3 487.66 0.55 126 21 25 4 482.94 2.74 127 21 137 116 78.22 0.48 128 21 138 117 78.08 0.51 129 21 141 120 76.58 0.63 130 21 142 121 76.44 0.57 131 22 25 3 492.81 3.60 132 22 26 4 478.62 2.72 133 22 27 5 447.20 1.35 134 22 29 7 447.16 1.33 135 23 53 30 216.10 0.29 136 25 141 116 76.33 0.51 137 25 142 117 75.38 0.04 138 25 145 120 57.54 0.69 139 27 56 29 215.66 0.37 140 27 141 114 75.06 0.17 141 27 144 117 58.19 0.98 142 27 145 118 57.53 0.69 143 28 56 28 215.63 0.36 144 29 57 28 215.64 0.36 145 29 58 29 215.64 0.36 146 30 58 28 215.62 0.36 147 30 60 30 215.62 0.37 148 30 66 36 171.16 0.21 149 30 70 40 170.20 0.08 150 30 96 66 162.25 2.39 151 31 35 4 508.58 1.30 152 31 39 8 358.75 6.57 153 31 57 26 215.84 0.28 154 31 58 27 215.74 0.33 155 31 59 28 215.62 0.37 156 31 60 29 215.62 0.37 157 32 35 3 582.20 2.21 158 32 60 28 215.62 0.37 159 32 62 30 215.25 0.46 160 32 63 31 192.49 0.58 161 32 66 34 172.16 0.20 162 32 98 66 171.41 0.53 163 33 59 26 215.77 0.33 164 33 60 27 215.64 0.36 165 33 61 28 215.62 0.38 166 35 39 4 499.74 0.24 167 35 59 24 215.84 0.32 168 37 41 4 474.50 0.52 169 37 44 7 346.72 0.58 170 38 41 3 491.67 3.80 171 39 44 5 470.71 1.10 172 39 45 6 455.03 1.50 173 39 54 15 216.70 0.38 174 39 57 18 216.39 0.35 175 39 59 20 216.03 0.26 176 40 45 5 455.03 1.50 177 41 44 3 501.32 3.17 178 41 45 4 474.23 0.65 179 42 45 3 486.10 2.42 180 42 46 4 463.26 2.62 181 43 47 4 455.01 1.49 182 44 47 3 473.83 2.16 183 44 49 5 358.00 6.88 184 44 54 10 219.17 1.60 185 45 51 6 220.05 1.21 186 45 54 9 219.19 1.60 187 49 53 4 500.24 0.37 188 49 54 5 490.42 4.51 189 50 53 3 508.55 3.79 190 50 54 4 508.54 3.78 191 51 54 3 495.15 2.63 192 54 57 3 504.93 0.52 193 58 70 12 171.53 0.01 194 60 66 6 196.76 12.54 195 60 69 9 224.84 1.50 196 60 70 10 196.78 12.55 197 62 65 3 490.31 2.76 198 62 66 4 482.55 0.09 199 63 66 3 482.56 0.09 200 63 67 4 484.10 0.86 201 63 75 12 224.97 2.54 202 63 98 35 171.97 0.39 203 63 110 47 195.60 11.89 204 64 67 3 489.49 0.74 205 64 68 4 483.69 0.46 206 65 68 3 487.64 0.54 207 65 69 4 485.24 0.32 208 66 69 3 488.80 0.04 209 66 70 4 482.37 0.19 210 66 72 6 475.69 3.14 211 66 75 9 348.62 6.54 212 66 96 30 273.53 1.18 213 67 70 3 502.38 3.75 214 67 71 4 467.86 0.78 215 67 72 5 464.06 2.54 216 67 75 8 360.56 0.58 217 68 71 3 507.60 5.46 218 70 96 26 312.04 1.43 219 72 75 3 505.53 4.38 220 72 96 24 329.36 2.94 221 73 94 21 330.23 2.66 222 74 90 16 403.78 39.43 223 74 91 17 331.10 3.08 224 74 92 18 331.17 3.00 225 74 95 21 330.24 2.66 226 74 96 22 332.11 1.73 227 74 118 44 326.35 1.32 228 75 96 21 332.11 1.73 229 75 98 23 332.21 1.69 230 75 114 39 327.25 1.13 231 75 118 43 327.00 1.07 232 76 89 13 438.28 56.55 233 76 91 15 404.06 38.02 234 76 95 19 332.40 1.79 235 76 96 20 332.24 1.71 236 76 97 21 332.23 1.70 237 76 98 22 332.23 1.69 238 76 114 38 328.94 0.76 239 76 117 41 327.24 1.14 240 76 118 42 327.01 1.08 241 76 120 44 326.35 1.32 242 77 98 21 332.23 1.69 243 77 106 29 330.53 0.69 244 77 111 34 329.57 0.46 245 77 114 37 329.53 0.48 246 77 118 41 327.25 1.13 247 77 119 42 326.94 1.05 248 77 120 43 326.37 1.33 249 78 98 20 332.41 1.62 250 78 99 21 332.39 1.61 251 78 106 28 330.73 0.77 252 78 120 42 327.13 1.12 253 78 121 43 326.36 1.33 254 78 122 44 326.36 1.33 255 78 136 58 78.42 0.49 256 78 140 62 77.96 0.46 257 79 82 3 571.09 51.20 258 79 111 32 330.57 0.70 259 79 119 40 327.55 1.15 260 79 120 41 327.24 1.13 261 79 121 42 326.97 1.04 262 80 121 41 327.24 1.13 263 81 108 27 330.97 0.67 264 82 119 37 329.04 0.70 265 82 120 38 327.76 1.08 266 82 121 39 327.58 1.16 267 83 116 33 330.38 0.62 268 83 119 36 330.21 0.60 269 83 121 38 329.62 0.42 270 84 88 4 562.19 55.66 271 84 89 5 562.19 55.66 272 84 116 32 330.42 0.60 273 84 117 33 330.38 0.61 274 84 119 35 330.26 0.61 275 84 120 36 329.92 0.49 276 84 121 37 329.89 0.51 277 85 88 3 522.29 23.36 278 85 120 35 330.25 0.60 279 85 121 36 329.92 0.50 280 85 123 38 329.56 0.41 281 86 89 3 564.05 26.55 282 86 91 5 516.24 17.57 283 86 120 34 330.25 0.61 284 86 121 35 330.24 0.60 285 86 122 36 330.00 0.51 286 86 123 37 329.75 0.39 287 86 139 53 78.23 0.48 288 86 140 54 77.97 0.46 289 86 143 57 76.19 0.73 290 87 143 56 74.98 0.20 291 87 147 60 62.06 0.15 292 89 117 28 330.38 0.57 293 89 120 31 330.29 0.58 294 89 147 58 57.61 0.69 295 90 147 57 57.23 0.67 296 91 95 4 496.62 7.11 297 91 97 6 566.23 53.86 298 91 120 29 330.32 0.56 299 91 144 53 59.91 0.48 300 91 147 56 53.84 0.42 301 91 148 57 50.90 0.30 302 92 95 3 518.03 13.60 303 92 148 56 50.12 0.51 304 97 140 43 76.58 0.67 305 97 144 47 59.14 0.12 306 98 106 8 439.47 53.79 307 98 110 12 421.91 45.05 308 99 106 7 439.38 53.72 309 99 133 34 78.45 0.49 310 99 137 38 78.16 0.52 311 99 140 41 77.66 0.65 312 100 106 6 427.84 48.01 313 100 133 33 78.46 0.50 314 101 104 3 525.05 10.99 315 101 105 4 442.39 49.14 316 102 133 31 78.48 0.51 317 106 110 4 505.00 3.50 318 106 111 5 478.58 1.83 319 107 110 3 505.01 3.50 320 107 111 4 501.61 5.20 321 108 111 3 501.67 5.17 322 108 112 4 483.06 4.07 323 109 112 3 503.73 4.15 324 109 113 4 505.02 3.50 325 110 113 3 505.01 3.48 326 110 114 4 505.00 3.49 327 111 114 3 502.06 2.02 328 111 119 8 327.25 1.13 329 114 119 5 414.19 23.61 330 115 118 3 496.09 2.71 331 115 119 4 488.37 1.94 332 116 119 3 488.37 1.94 333 120 140 20 78.15 0.53 334 122 136 14 78.42 0.49 335 122 139 17 78.42 0.49 336 122 140 18 78.42 0.49 337 124 128 4 474.07 1.68 338 124 129 5 471.85 2.79 339 125 128 3 509.88 2.79 340 131 135 4 497.34 3.75 341 131 136 5 471.66 4.53 342 132 135 3 499.10 2.88 343 132 136 4 484.01 2.92 344 133 136 3 485.78 3.79 345 133 137 4 489.45 0.20 346 134 137 3 493.45 0.05 347 134 138 4 489.45 0.20 348 135 138 3 491.63 0.94 349 135 139 4 480.07 0.47 350 136 139 3 496.44 2.37 351 136 140 4 480.13 0.40 352 137 140 3 496.50 2.35 353 137 141 4 480.43 0.48 354 138 141 3 503.16 0.41 355 138 142 4 482.23 0.42 356 139 142 3 497.10 3.44 357 139 143 4 487.47 2.04 358 140 143 3 498.00 2.17 359 140 144 4 487.47 2.05 360 141 144 3 496.82 1.21 361 141 145 4 485.59 2.99 362 142 145 3 492.05 1.18 363 142 146 4 480.37 0.38 364 142 150 8 366.21 4.32 365 143 146 3 486.99 3.70 366 143 147 4 480.44 0.43 367 144 147 3 488.79 1.28 368 144 148 4 485.07 3.14 369 145 148 3 494.66 1.65 370 145 149 4 485.05 3.15 371 145 150 5 414.79 20.91 372 145 151 6 414.79 20.91 373 145 153 8 360.64 1.48 374 146 149 3 487.24 2.06 375 146 150 4 470.61 3.66 376 148 151 3 535.30 1.37 377 150 153 3 494.25 1.27