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 2 120 118 32.48 0.06 2 2 121 119 32.49 0.06 3 2 124 122 32.52 0.05 4 2 135 133 32.52 0.05 5 2 138 136 32.49 0.04 6 2 139 137 32.46 0.05 7 2 142 140 32.47 0.05 8 3 8 5 413.66 12.46 9 3 139 136 32.51 0.04 10 3 142 139 32.48 0.06 11 3 143 140 32.47 0.06 12 4 117 113 32.51 0.06 13 4 142 138 32.48 0.06 14 4 143 139 32.47 0.06 15 4 146 142 32.45 0.06 16 5 143 138 32.51 0.05 17 6 143 137 32.62 0.01 18 7 143 136 32.88 0.01 19 8 136 128 43.76 0.67 20 8 139 131 35.38 0.91 21 8 140 132 33.38 0.07 22 8 143 135 33.37 0.07 23 9 136 127 48.04 1.04 24 10 136 126 49.77 0.74 25 11 15 4 477.89 0.59 26 11 16 5 478.07 0.70 27 11 19 8 457.20 9.73 28 11 88 77 54.05 0.14 29 11 133 122 64.27 0.06 30 11 136 125 49.78 0.74 31 11 137 126 49.16 1.05 32 11 140 129 49.75 0.76 33 12 15 3 490.62 3.37 34 12 16 4 487.58 2.73 35 13 16 3 509.21 5.92 36 13 17 4 488.83 2.35 37 14 17 3 516.79 2.13 38 14 18 4 497.55 2.00 39 15 18 3 506.34 6.05 40 15 19 4 497.40 1.92 41 15 133 118 75.47 1.30 42 15 136 121 75.61 1.25 43 16 19 3 497.67 1.79 44 16 20 4 495.62 1.03 45 16 88 72 80.14 0.76 46 16 89 73 80.14 0.76 47 17 20 3 496.04 0.85 48 17 21 4 497.06 0.41 49 18 21 3 500.84 2.29 50 18 22 4 497.06 0.41 51 18 131 113 95.28 0.02 52 19 22 3 500.84 2.29 53 19 23 4 496.68 1.17 54 19 85 66 95.21 0.05 55 19 88 69 95.35 0.10 56 19 133 114 95.23 0.04 57 19 134 115 95.10 0.04 58 19 137 118 95.10 0.04 59 20 23 3 513.40 3.98 60 20 24 4 504.07 2.52 61 20 85 65 95.36 0.09 62 20 88 68 95.40 0.07 63 20 89 69 97.12 0.94 64 21 24 3 514.74 3.35 65 21 25 4 514.74 3.35 66 22 25 3 535.19 2.56 67 22 26 4 508.56 0.28 68 22 127 105 103.27 0.15 69 22 128 106 103.28 0.15 70 23 26 3 512.37 2.18 71 23 27 4 497.37 0.45 72 23 78 55 103.33 0.14 73 23 81 58 103.27 0.15 74 23 82 59 103.24 0.14 75 23 85 62 103.24 0.14 76 23 123 100 103.31 0.15 77 23 127 104 103.31 0.15 78 23 134 111 103.29 0.16 79 24 27 3 503.50 1.61 80 24 28 4 497.38 0.44 81 25 28 3 503.07 1.82 82 25 29 4 503.50 1.61 83 26 29 3 516.06 2.06 84 26 30 4 495.11 0.59 85 26 33 7 287.95 38.98 86 26 127 101 103.47 0.20 87 27 30 3 485.31 0.14 88 27 79 52 103.49 0.18 89 27 82 55 103.45 0.20 90 29 32 3 509.69 0.48 91 29 33 4 488.19 0.65 92 30 33 3 497.41 0.42 93 30 34 4 488.06 0.70 94 30 75 45 126.66 3.34 95 30 78 48 107.18 1.79 96 30 79 49 114.12 2.88 97 31 35 4 488.99 1.08 98 31 75 44 126.66 3.34 99 32 35 3 505.98 1.52 100 32 36 4 497.92 5.54 101 33 36 3 503.56 2.73 102 33 37 4 497.91 5.54 103 34 37 3 507.00 1.01 104 34 38 4 497.97 5.52 105 34 74 40 144.21 2.54 106 34 78 44 138.27 0.30 107 35 38 3 509.00 1.40 108 35 39 4 491.50 2.29 109 35 65 30 160.97 0.70 110 35 71 36 159.75 0.37 111 35 74 39 158.77 0.01 112 36 39 3 499.63 1.77 113 36 40 4 487.62 4.25 114 36 65 29 161.09 0.66 115 37 40 3 500.31 2.08 116 37 41 4 494.50 0.82 117 37 78 41 160.61 0.58 118 37 119 82 159.97 0.57 119 37 122 85 160.10 0.50 120 37 123 86 160.11 0.51 121 37 126 89 160.72 0.65 122 38 41 3 500.31 2.08 123 38 42 4 494.51 0.83 124 38 52 14 166.74 0.36 125 38 55 17 162.50 0.24 126 38 70 32 160.99 0.64 127 38 73 35 160.91 0.61 128 38 74 36 160.85 0.62 129 38 77 39 160.68 0.58 130 39 42 3 502.75 2.05 131 39 43 4 497.29 0.56 132 39 61 22 162.26 0.39 133 39 64 25 161.93 0.26 134 39 65 26 161.29 0.57 135 39 70 31 161.00 0.65 136 40 43 3 508.29 0.71 137 40 44 4 498.55 0.06 138 40 122 82 160.66 0.68 139 41 44 3 502.76 2.05 140 41 45 4 490.22 4.10 141 41 48 7 406.26 13.89 142 41 52 11 197.22 3.18 143 41 115 74 160.19 0.52 144 41 118 77 160.27 0.48 145 41 119 78 160.19 0.62 146 41 122 81 160.67 0.68 147 42 45 3 501.80 1.45 148 42 49 7 203.66 0.62 149 42 52 10 180.51 2.90 150 42 55 13 164.43 0.49 151 42 64 22 162.70 0.35 152 43 61 18 162.69 0.35 153 43 64 21 162.71 0.35 154 45 48 3 504.56 1.67 155 45 49 4 496.88 0.88 156 45 115 70 160.66 0.69 157 45 118 73 160.68 0.69 158 46 49 3 502.82 2.18 159 47 115 68 160.71 0.69 160 48 51 3 514.72 0.38 161 48 52 4 510.30 1.83 162 48 115 67 160.63 0.67 163 49 52 3 510.74 1.61 164 51 110 59 159.98 0.54 165 51 111 60 159.98 0.54 166 51 112 61 160.20 0.64 167 51 115 64 160.74 0.61 168 52 55 3 504.88 3.16 169 52 73 21 162.46 0.21 170 53 56 3 511.05 0.90 171 54 69 15 163.38 0.51 172 55 58 3 495.04 0.69 173 55 69 14 163.40 0.51 174 55 70 15 163.40 0.51 175 55 73 18 163.40 0.51 176 58 63 5 470.79 6.25 177 58 64 6 376.91 1.09 178 58 67 9 197.90 3.25 179 59 63 4 493.68 0.66 180 60 63 3 498.50 1.76 181 60 64 4 494.45 1.05 182 61 64 3 495.56 0.95 183 61 65 4 492.45 2.25 184 62 65 3 502.62 1.58 185 62 66 4 492.70 2.37 186 63 66 3 512.61 3.25 187 63 67 4 492.44 2.25 188 64 67 3 504.69 1.35 189 64 70 6 452.79 2.52 190 65 71 6 455.77 4.00 191 66 71 5 484.04 1.39 192 67 70 3 504.94 1.39 193 67 71 4 494.99 3.60 194 68 71 3 500.87 0.66 195 68 72 4 491.01 2.09 196 69 72 3 507.59 2.70 197 69 73 4 496.27 0.54 198 70 73 3 508.36 2.82 199 70 74 4 491.37 1.91 200 71 74 3 500.35 1.18 201 71 75 4 491.36 1.91 202 72 75 3 504.07 1.34 203 72 76 4 494.09 0.51 204 73 76 3 501.78 4.35 205 73 77 4 488.03 2.52 206 74 77 3 502.17 4.55 207 74 78 4 493.58 0.26 208 75 78 3 506.81 2.23 209 75 79 4 497.00 0.77 210 76 79 3 505.92 2.67 211 76 80 4 494.80 0.33 212 77 80 3 509.92 1.42 213 77 81 4 494.80 0.34 214 77 119 42 161.19 0.56 215 78 81 3 511.75 6.94 216 78 82 4 494.77 0.35 217 79 82 3 490.36 2.22 218 79 83 4 489.91 2.01 219 80 83 3 503.13 2.96 220 80 84 4 491.91 1.00 221 80 101 21 160.92 0.74 222 81 84 3 506.15 2.91 223 81 85 4 490.03 0.06 224 81 123 42 166.17 0.15 225 81 138 57 161.88 0.79 226 81 141 60 161.64 0.74 227 82 85 3 501.19 0.43 228 82 86 4 493.91 2.00 229 83 86 3 510.58 0.76 230 83 87 4 495.92 2.20 231 83 97 14 170.54 0.27 232 84 87 3 496.88 0.52 233 84 88 4 494.72 1.60 234 84 94 10 169.04 0.49 235 84 141 57 167.79 1.03 236 85 88 3 506.37 3.01 237 85 137 52 196.65 0.01 238 87 90 3 504.18 6.21 239 87 91 4 464.32 3.73 240 87 93 6 413.29 0.42 241 87 94 7 292.18 25.03 242 88 94 6 448.36 0.99 243 88 137 49 272.12 4.13 244 90 93 3 511.40 6.46 245 90 94 4 494.54 1.95 246 91 94 3 496.42 1.01 247 91 95 4 496.54 0.95 248 91 140 49 334.68 0.41 249 92 95 3 515.62 5.87 250 92 96 4 502.10 1.00 251 93 96 3 516.66 5.35 252 93 97 4 502.11 0.99 253 94 97 3 516.66 5.36 254 94 98 4 495.24 0.28 255 94 137 43 342.62 2.00 256 94 140 46 342.61 1.98 257 95 98 3 501.30 0.83 258 95 99 4 496.68 1.04 259 95 144 49 342.45 1.94 260 96 99 3 508.08 0.45 261 96 100 4 503.97 2.50 262 97 100 3 508.09 0.45 263 97 101 4 503.99 2.50 264 98 101 3 503.99 2.50 265 98 102 4 503.98 2.50 266 98 141 43 342.77 1.91 267 98 144 46 342.67 1.88 268 98 145 47 342.63 1.86 269 99 102 3 504.00 2.49 270 99 103 4 504.00 2.48 271 99 144 45 342.63 1.85 272 99 147 48 342.32 1.95 273 100 103 3 521.50 0.07 274 100 104 4 503.98 2.47 275 101 104 3 504.02 0.05 276 101 105 4 504.02 0.05 277 101 145 44 342.84 1.84 278 102 105 3 510.05 2.12 279 102 106 4 501.58 1.27 280 102 144 42 342.92 1.85 281 102 145 43 342.85 1.84 282 102 146 44 342.83 1.84 283 102 147 45 342.69 1.89 284 102 148 46 342.28 1.93 285 103 106 3 507.70 1.89 286 103 107 4 488.99 0.10 287 103 148 45 342.28 1.93 288 104 107 3 507.30 1.97 289 104 108 4 466.50 2.25 290 104 109 5 454.75 3.62 291 105 109 4 436.73 3.02 292 105 110 5 404.69 12.99 293 105 111 6 345.85 1.72 294 105 116 11 343.08 1.85 295 105 149 44 342.69 1.91 296 106 110 4 404.69 12.99 297 106 148 42 342.79 1.91 298 106 149 43 342.47 2.00 299 111 116 5 504.49 0.14 300 111 149 38 343.18 1.97 301 112 115 3 530.44 1.46 302 113 116 3 521.77 1.21 303 113 146 33 343.37 1.99 304 113 149 36 343.30 2.00 305 114 117 3 537.91 0.65 306 114 118 4 515.07 0.38 307 114 146 32 344.05 1.97 308 115 118 3 510.48 1.91 309 115 119 4 505.43 0.62 310 116 119 3 518.74 2.23 311 116 120 4 500.00 0.34 312 116 142 26 344.23 1.91 313 116 145 29 344.23 1.91 314 116 146 30 344.22 1.91 315 116 149 33 344.09 1.94 316 117 120 3 499.89 0.28 317 117 121 4 499.87 0.27 318 117 142 25 344.33 1.87 319 118 121 3 504.26 1.72 320 118 122 4 496.52 1.97 321 119 122 3 503.19 1.19 322 119 123 4 495.11 2.67 323 120 123 3 510.62 3.52 324 120 124 4 495.09 2.68 325 120 138 18 344.55 1.94 326 120 142 22 344.39 1.87 327 121 124 3 503.11 7.28 328 121 125 4 482.58 2.33 329 122 125 3 507.37 5.15 330 122 126 4 482.59 2.33 331 123 126 3 501.76 4.36 332 123 127 4 485.43 3.79 333 123 134 11 345.73 2.18 334 123 138 15 344.64 1.98 335 124 127 3 514.86 2.19 336 124 128 4 485.43 3.79 337 124 129 5 409.46 2.98 338 124 134 10 344.99 2.00 339 124 138 14 344.68 1.99 340 125 129 4 377.40 16.63 341 127 134 7 351.22 0.35 342 128 131 3 510.87 1.79 343 128 134 6 352.03 0.06 344 131 134 3 508.06 3.21 345 131 135 4 491.20 0.23 346 132 135 3 506.02 3.00 347 132 136 4 499.31 4.28 348 133 136 3 504.44 1.72 349 133 137 4 499.30 4.29 350 134 137 3 499.32 4.27 351 134 138 4 502.23 2.82 352 135 138 3 502.23 2.82 353 135 139 4 505.50 1.18 354 136 139 3 505.75 1.29 355 136 140 4 505.75 1.29 356 137 140 3 505.76 1.28 357 137 141 4 505.75 1.28 358 138 141 3 508.94 2.88 359 138 142 4 502.31 0.43 360 139 142 3 508.65 5.26 361 139 143 4 490.86 5.29 362 140 143 3 510.00 2.35 363 140 144 4 490.56 5.44 364 141 144 3 512.15 1.43 365 141 145 4 490.56 5.44 366 142 145 3 501.53 0.71 367 142 146 4 490.44 4.83 368 143 146 3 505.92 2.91 369 143 147 4 498.80 0.65 370 144 147 3 500.20 3.51 371 145 149 4 515.60 2.44 372 146 149 3 508.50 0.71