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 5 8 3 543.16 1.49 2 5 9 4 530.04 1.34 3 6 9 3 548.23 0.65 4 6 10 4 543.23 1.85 5 6 159 153 18.34 0.24 6 7 10 3 549.71 1.39 7 7 11 4 531.28 1.95 8 8 11 3 532.85 1.17 9 8 12 4 533.17 1.01 10 9 12 3 542.48 1.19 11 9 13 4 534.92 0.12 12 9 152 143 29.02 3.12 13 9 159 150 22.62 0.46 14 10 13 3 542.93 3.88 15 10 14 4 534.92 0.12 16 10 156 146 30.52 2.37 17 11 14 3 545.43 2.64 18 11 15 4 539.13 0.29 19 12 15 3 539.13 0.29 20 12 16 4 534.90 0.11 21 12 148 136 47.71 0.95 22 12 149 137 47.20 0.70 23 12 152 140 42.19 1.94 24 12 153 141 42.18 1.95 25 13 16 3 541.33 1.39 26 13 17 4 530.47 0.40 27 13 27 14 252.73 60.30 28 13 153 140 42.18 1.95 29 13 156 143 42.18 1.95 30 14 17 3 533.65 0.67 31 14 18 4 532.03 0.83 32 15 18 3 539.02 0.24 33 15 19 4 530.44 1.63 34 15 147 132 52.37 0.42 35 15 148 133 49.93 0.88 36 16 19 3 534.09 0.20 37 16 22 6 479.81 3.46 38 16 27 11 379.51 2.50 39 16 45 29 122.42 1.51 40 16 49 33 122.20 1.58 41 16 148 132 49.98 0.86 42 16 150 134 49.84 0.89 43 16 153 137 49.66 0.83 44 17 21 4 514.75 3.98 45 17 22 5 451.94 17.37 46 17 27 10 367.56 2.94 47 18 21 3 535.22 1.18 48 19 145 126 66.72 0.68 49 19 148 129 54.86 0.30 50 20 49 29 122.39 1.52 51 20 52 32 122.28 1.56 52 20 145 125 66.75 0.70 53 21 52 31 122.42 1.53 54 21 66 45 121.95 1.62 55 22 26 4 519.95 0.57 56 22 27 5 518.38 1.34 57 22 49 27 122.45 1.53 58 22 52 30 122.45 1.53 59 23 26 3 533.71 1.29 60 23 27 4 521.47 1.31 61 24 27 3 522.66 0.72 62 24 28 4 521.48 1.32 63 25 28 3 552.70 3.48 64 25 29 4 521.74 1.20 65 26 29 3 547.54 6.06 66 26 30 4 521.38 1.52 67 26 89 63 124.47 2.13 68 27 30 3 553.41 3.12 69 27 31 4 531.16 2.24 70 27 45 18 231.61 53.98 71 28 31 3 535.23 0.21 72 28 32 4 531.34 2.31 73 28 157 129 49.20 1.42 74 29 32 3 547.88 2.18 75 29 33 4 531.34 2.31 76 30 33 3 533.26 1.35 77 30 34 4 531.34 2.31 78 30 45 15 231.86 53.91 79 30 48 18 230.22 54.52 80 31 34 3 535.52 1.12 81 31 35 4 540.53 3.62 82 31 41 10 351.12 5.01 83 31 45 14 231.81 53.89 84 31 157 126 49.70 1.29 85 32 35 3 545.22 1.28 86 33 36 3 556.90 0.31 87 33 91 58 128.94 2.56 88 34 37 3 554.66 0.81 89 34 41 7 351.14 5.01 90 34 44 10 237.46 51.34 91 34 45 11 237.31 51.26 92 34 48 14 237.27 51.27 93 35 41 6 351.14 5.01 94 37 44 7 417.45 10.00 95 37 47 10 391.88 2.79 96 37 48 11 362.27 0.56 97 39 43 4 538.82 2.48 98 39 44 5 525.63 1.51 99 40 43 3 541.71 1.04 100 40 44 4 541.70 1.04 101 40 141 101 79.37 1.13 102 41 44 3 541.70 1.04 103 41 45 4 541.70 1.04 104 42 45 3 547.17 3.79 105 42 46 4 541.69 1.05 106 42 150 108 52.42 0.94 107 42 154 112 51.15 1.40 108 43 46 3 535.19 2.19 109 43 47 4 530.76 4.41 110 43 141 98 74.70 1.20 111 44 47 3 536.88 1.34 112 44 48 4 536.88 1.33 113 45 48 3 543.88 2.18 114 45 49 4 536.87 1.33 115 45 150 105 52.40 0.95 116 46 49 3 543.91 2.16 117 46 144 98 72.28 0.99 118 46 145 99 72.25 1.01 119 46 148 102 61.45 1.30 120 47 50 3 555.73 0.35 121 47 51 4 535.83 1.19 122 47 138 91 82.06 1.86 123 47 139 92 74.80 1.21 124 48 51 3 538.45 2.50 125 48 52 4 530.37 1.54 126 48 91 43 324.16 3.12 127 49 52 3 545.69 0.98 128 49 55 6 489.54 0.00 129 50 55 5 483.23 3.15 130 50 56 6 473.88 0.36 131 50 123 73 225.09 3.23 132 50 139 89 74.81 1.21 133 50 144 94 72.36 1.05 134 52 55 3 539.82 0.83 135 52 56 4 540.58 0.44 136 53 56 3 545.38 2.51 137 53 57 4 545.09 2.66 138 53 73 20 335.19 0.33 139 53 80 27 325.62 2.58 140 53 85 32 326.31 2.65 141 53 87 34 326.80 2.88 142 53 88 35 326.36 2.66 143 53 90 37 326.28 2.62 144 53 91 38 326.03 2.69 145 53 92 39 326.01 2.69 146 54 57 3 545.10 2.66 147 54 58 4 537.04 1.37 148 54 69 15 335.25 0.30 149 54 70 16 335.25 0.30 150 54 73 19 335.23 0.32 151 55 58 3 545.10 2.66 152 55 59 4 528.58 2.77 153 56 59 3 536.92 1.40 154 56 60 4 529.43 2.35 155 56 98 42 324.32 3.23 156 56 124 68 283.49 0.49 157 56 135 79 280.62 1.07 158 57 60 3 545.06 2.67 159 57 61 4 536.92 1.40 160 57 62 5 491.22 1.72 161 57 63 6 459.81 6.08 162 57 69 12 335.29 0.32 163 57 72 15 335.33 0.29 164 57 73 16 335.36 0.28 165 57 78 21 329.93 0.49 166 58 63 5 425.26 3.64 167 58 64 6 412.32 10.10 168 58 65 7 367.37 2.35 169 58 69 11 335.29 0.31 170 59 119 60 284.36 0.50 171 59 121 62 283.83 0.34 172 59 124 65 283.73 0.38 173 60 117 57 284.58 0.47 174 60 120 60 284.10 0.47 175 60 124 64 283.90 0.46 176 60 126 66 283.77 0.65 177 60 133 73 283.34 0.83 178 61 113 52 291.05 1.99 179 61 114 53 290.98 1.96 180 61 117 56 284.58 0.47 181 62 72 10 349.56 2.04 182 62 100 38 324.43 3.04 183 62 110 48 291.17 1.94 184 62 113 51 291.06 1.99 185 62 114 52 291.01 1.97 186 62 126 64 283.89 0.59 187 63 68 5 401.69 3.50 188 63 69 6 370.38 3.71 189 63 72 9 362.07 3.56 190 63 113 50 291.00 1.97 191 64 68 4 501.98 4.12 192 64 112 48 291.24 1.97 193 64 113 49 291.05 1.99 194 64 116 52 290.80 1.90 195 65 68 3 532.63 0.50 196 65 69 4 508.44 0.88 197 66 69 3 515.06 0.01 198 66 70 4 499.38 6.49 199 67 71 4 528.90 2.43 200 68 71 3 536.53 3.64 201 68 72 4 529.23 2.27 202 68 109 41 291.26 1.94 203 69 72 3 552.94 0.79 204 69 73 4 530.88 1.43 205 70 73 3 552.94 0.79 206 70 74 4 530.61 1.29 207 71 74 3 551.09 1.72 208 71 75 4 531.64 1.81 209 72 75 3 533.74 2.85 210 72 76 4 531.64 1.81 211 72 77 5 496.41 1.95 212 72 78 6 484.26 4.12 213 72 107 35 297.67 0.14 214 72 109 37 291.30 1.95 215 72 110 38 291.25 1.94 216 73 76 3 535.85 1.80 217 73 85 12 327.89 3.07 218 73 86 13 327.82 3.08 219 73 87 14 327.82 3.08 220 73 88 15 327.80 3.08 221 74 86 12 327.81 3.08 222 76 84 8 328.07 3.00 223 76 86 10 327.87 3.06 224 76 101 25 325.76 2.52 225 77 99 22 326.20 2.68 226 77 100 23 326.06 2.68 227 77 101 24 325.71 2.51 228 77 104 27 318.88 1.94 229 77 107 30 299.25 0.45 230 78 83 5 448.89 13.26 231 78 84 6 374.54 10.27 232 78 85 7 346.33 4.00 233 78 98 20 326.31 2.64 234 78 99 21 326.18 2.67 235 78 100 22 326.06 2.68 236 79 82 3 522.41 2.33 237 79 83 4 391.62 12.76 238 79 84 5 380.60 7.25 239 79 97 18 326.93 2.79 240 79 98 19 326.44 2.69 241 79 99 20 326.19 2.67 242 79 100 21 326.18 2.66 243 79 101 22 326.08 2.67 244 80 83 3 519.85 3.93 245 80 85 5 380.61 7.25 246 80 92 12 327.61 3.03 247 80 96 16 326.99 2.81 248 80 97 17 326.88 2.79 249 80 98 18 326.44 2.69 250 81 96 15 326.98 2.81 251 81 97 16 326.91 2.77 252 84 101 17 326.08 2.67 253 85 90 5 415.18 18.52 254 87 90 3 538.67 1.15 255 90 96 6 536.68 0.28 256 92 96 4 532.67 1.65 257 92 98 6 466.40 5.11 258 92 135 43 280.58 1.09 259 93 96 3 552.02 1.38 260 94 135 41 280.61 1.05 261 94 138 44 275.68 0.53 262 95 135 40 282.05 0.37 263 96 135 39 282.04 0.36 264 97 132 35 283.51 0.80 265 97 133 36 283.40 0.83 266 97 134 37 282.43 0.56 267 98 132 34 283.49 0.80 268 98 133 35 283.34 0.81 269 99 131 32 283.67 0.78 270 99 132 33 283.40 0.84 271 100 104 4 527.00 5.23 272 100 105 5 478.30 8.13 273 100 110 10 375.91 6.49 274 100 131 31 283.68 0.79 275 101 104 3 527.00 5.23 276 101 105 4 527.00 5.23 277 102 105 3 540.20 0.12 278 104 107 3 543.08 0.06 279 104 110 6 490.91 10.19 280 105 111 6 506.19 2.67 281 105 131 26 283.75 0.81 282 106 111 5 506.43 2.78 283 107 110 3 538.40 1.25 284 107 111 4 524.79 6.29 285 108 111 3 536.64 0.37 286 108 112 4 524.92 6.23 287 109 112 3 546.61 1.88 288 109 113 4 535.35 0.99 289 110 113 3 538.53 0.14 290 110 114 4 525.73 5.80 291 110 131 21 283.99 0.77 292 111 114 3 542.00 1.86 293 111 131 20 284.03 0.78 294 112 115 3 550.81 0.30 295 112 116 4 540.75 1.24 296 113 116 3 542.66 0.18 297 113 117 4 531.92 5.18 298 114 117 3 543.65 0.68 299 114 126 12 284.24 0.62 300 114 131 17 283.97 0.78 301 117 120 3 593.20 3.23 302 119 143 24 162.34 1.52 303 120 124 4 521.92 7.67 304 120 126 6 370.38 3.01 305 121 124 3 547.73 1.51 306 121 143 22 162.33 1.52 307 123 135 12 283.88 1.11 308 123 136 13 283.78 1.09 309 123 137 14 283.50 1.10 310 123 138 15 283.07 1.28 311 123 139 16 281.42 0.68 312 123 143 20 168.14 4.13 313 124 134 10 284.05 1.08 314 124 135 11 283.88 1.11 315 124 136 12 283.87 1.14 316 125 133 8 284.07 1.08 317 125 134 9 284.06 1.08 318 125 136 11 283.92 1.12 319 126 132 6 284.23 1.03 320 126 133 7 284.08 1.07 321 127 131 4 380.71 8.28 322 127 132 5 284.23 1.03 323 128 131 3 430.85 2.06 324 135 138 3 601.03 0.82 325 135 139 4 573.31 1.66 326 139 144 5 478.41 0.18 327 140 143 3 556.50 0.64 328 140 144 4 514.72 7.03 329 141 144 3 524.06 9.22 330 145 148 3 548.49 1.08 331 149 152 3 574.81 0.87 332 149 153 4 549.83 3.81 333 150 153 3 529.96 0.03 334 150 154 4 511.34 3.33 335 151 154 3 523.87 2.97 336 151 155 4 535.47 2.83 337 152 156 4 535.65 2.75 338 153 156 3 542.12 2.50 339 153 157 4 544.07 1.53 340 154 157 3 558.11 0.07 341 155 158 3 535.61 2.71 342 155 159 4 533.98 1.89 343 156 159 3 546.02 0.29