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 5 3 520.26 0.93 2 2 6 4 507.88 1.63 3 3 6 3 520.28 0.92 4 3 7 4 510.45 0.35 5 4 7 3 521.42 1.38 6 4 8 4 509.12 0.33 7 5 8 3 514.23 2.23 8 5 9 4 514.22 2.22 9 5 44 39 138.92 0.18 10 5 47 42 141.79 1.60 11 6 9 3 516.60 1.04 12 6 10 4 516.45 0.96 13 7 10 3 516.59 1.03 14 7 11 4 516.29 0.89 15 8 11 3 517.85 0.29 16 8 12 4 515.94 0.71 17 8 32 24 152.21 0.09 18 8 34 26 152.20 0.10 19 8 36 28 152.19 0.10 20 9 12 3 516.78 0.32 21 9 13 4 516.77 0.33 22 9 44 35 150.37 0.05 23 9 47 38 150.37 0.05 24 9 48 39 150.36 0.05 25 10 13 3 518.83 0.70 26 10 14 4 516.78 0.33 27 11 14 3 516.79 0.33 28 11 15 4 516.78 0.33 29 11 32 21 152.25 0.11 30 12 15 3 525.74 4.81 31 12 16 4 516.75 0.32 32 12 28 16 152.19 0.08 33 12 32 20 152.31 0.13 34 12 36 24 152.25 0.11 35 12 41 29 152.02 0.17 36 12 44 32 151.90 0.18 37 12 48 36 151.82 0.18 38 13 16 3 527.80 3.79 39 13 17 4 504.31 3.20 40 13 48 35 151.62 0.28 41 13 52 39 151.60 0.29 42 13 70 57 151.59 0.25 43 14 17 3 515.12 1.76 44 14 18 4 513.36 1.34 45 15 18 3 514.99 2.14 46 15 19 4 506.53 2.06 47 15 28 13 152.49 0.01 48 15 31 16 152.53 0.03 49 15 32 17 152.53 0.04 50 16 19 3 528.25 0.41 51 16 23 7 153.10 0.31 52 16 28 12 152.56 0.03 53 16 45 29 152.03 0.17 54 16 61 45 151.75 0.17 55 16 68 52 151.78 0.16 56 16 69 53 151.62 0.24 57 16 70 54 151.59 0.25 58 17 70 53 151.59 0.24 59 19 23 4 454.41 15.95 60 22 67 45 152.02 0.15 61 22 68 46 152.00 0.14 62 22 69 47 151.96 0.14 63 23 27 4 512.45 3.85 64 23 28 5 502.79 7.96 65 23 67 44 152.06 0.17 66 23 68 45 151.97 0.15 67 24 27 3 520.25 0.96 68 24 28 4 515.24 2.47 69 24 66 42 152.09 0.17 70 24 67 43 152.07 0.17 71 25 28 3 521.97 0.10 72 25 29 4 514.63 2.17 73 25 36 11 158.70 2.83 74 25 37 12 158.71 2.84 75 25 38 13 158.68 2.83 76 25 41 16 152.43 0.18 77 26 29 3 523.84 1.82 78 26 30 4 514.97 2.01 79 27 30 3 517.40 1.40 80 27 31 4 514.97 2.01 81 28 31 3 534.81 0.23 82 28 32 4 507.22 1.20 83 28 41 13 158.63 2.83 84 29 32 3 532.43 0.96 85 29 33 4 501.10 4.26 86 29 34 5 446.64 17.84 87 29 36 7 193.82 1.74 88 30 33 3 523.36 3.58 89 32 36 4 547.00 1.05 90 34 40 6 503.23 1.24 91 36 40 4 513.30 1.77 92 36 41 5 483.43 0.37 93 36 44 8 482.30 0.86 94 37 40 3 508.03 2.56 95 37 41 4 506.34 1.72 96 38 41 3 517.74 1.34 97 38 42 4 515.61 2.41 98 39 42 3 518.63 1.79 99 39 43 4 506.44 1.68 100 40 43 3 525.86 4.62 101 40 44 4 506.44 1.68 102 41 44 3 526.11 4.50 103 41 45 4 511.55 2.35 104 41 68 27 169.71 5.63 105 42 45 3 511.56 2.35 106 42 46 4 510.75 0.83 107 42 63 21 169.70 5.62 108 42 68 26 169.69 5.63 109 43 46 3 513.35 1.65 110 43 47 4 514.00 0.57 111 44 47 3 518.56 2.44 112 44 48 4 516.68 1.90 113 45 48 3 516.69 1.91 114 45 49 4 514.62 2.93 115 45 61 16 169.75 5.59 116 45 68 23 169.72 5.62 117 46 49 3 524.70 3.21 118 46 50 4 514.61 2.94 119 47 50 3 514.62 2.92 120 47 51 4 503.97 2.38 121 48 51 3 514.58 2.94 122 48 52 4 511.88 1.99 123 48 61 13 169.99 5.49 124 49 52 3 515.69 3.89 125 49 53 4 513.62 1.11 126 49 60 11 169.78 5.59 127 49 61 12 169.78 5.59 128 50 53 3 520.16 1.66 129 50 54 4 513.63 1.12 130 51 54 3 517.99 1.05 131 51 55 4 511.87 2.00 132 52 55 3 530.38 2.91 133 52 56 4 509.04 3.43 134 52 57 5 431.36 2.23 135 52 59 7 209.87 9.21 136 52 60 8 175.32 3.46 137 52 61 9 198.31 14.96 138 52 70 18 170.25 5.42 139 53 56 3 512.22 1.83 140 53 60 7 207.62 10.34 141 57 60 3 625.30 2.75 142 58 72 14 170.21 5.41 143 58 73 15 170.16 5.42 144 58 76 18 169.31 5.59 145 59 70 11 171.05 5.33 146 59 71 12 170.41 5.36 147 59 72 13 170.21 5.41 148 59 73 14 170.21 5.41 149 60 70 10 171.10 5.35 150 60 71 11 170.80 5.38 151 60 73 13 170.29 5.37 152 61 68 7 176.08 3.57 153 61 69 8 173.78 4.67 154 61 70 9 171.16 5.38 155 62 67 5 425.48 4.59 156 62 68 6 176.40 3.73 157 62 69 7 174.68 4.25 158 62 71 9 171.43 5.44 159 63 67 4 314.60 50.85 160 63 68 5 183.00 0.44 161 64 67 3 522.41 1.07 162 64 69 5 305.17 32.66 163 72 80 8 191.16 1.40 164 73 76 3 532.07 0.43 165 74 77 3 509.44 5.74 166 76 79 3 522.85 4.19 167 76 80 4 511.20 1.03 168 77 80 3 513.88 0.81 169 77 81 4 508.86 2.20 170 78 81 3 510.74 2.37 171 78 82 4 509.63 1.82 172 79 82 3 514.97 0.25 173 79 83 4 506.73 0.36 174 80 83 3 510.73 2.37 175 80 84 4 500.45 2.02 176 81 84 3 519.09 2.90 177 81 85 4 498.87 1.85 178 81 86 5 498.87 1.85 179 81 90 9 487.54 0.48 180 82 86 4 480.86 7.11 181 83 86 3 531.09 0.54 182 84 89 5 509.48 1.51 183 85 89 4 509.48 1.51 184 85 90 5 501.98 2.54 185 86 89 3 529.15 3.56 186 86 90 4 507.70 2.40 187 87 90 3 518.41 5.25 188 87 91 4 507.69 2.40 189 88 91 3 521.99 1.50 190 88 92 4 507.92 2.27 191 89 92 3 521.99 1.50 192 89 93 4 507.92 2.28 193 90 93 3 514.73 2.57 194 90 94 4 505.17 0.89 195 91 94 3 520.87 3.86 196 91 95 4 505.18 0.89 197 92 95 3 532.61 2.02 198 92 96 4 502.80 0.30 199 93 96 3 529.77 0.60 200 93 97 4 510.80 1.05 201 94 97 3 518.12 3.68 202 94 98 4 508.80 2.06 203 95 98 3 525.56 0.04 204 95 99 4 508.84 2.06 205 95 118 23 373.65 0.98 206 95 123 28 373.16 0.98 207 95 125 30 373.06 0.95 208 95 128 33 373.06 0.95 209 96 99 3 521.13 1.49 210 96 100 4 508.83 2.05 211 96 125 29 373.06 0.95 212 96 128 32 373.06 0.95 213 96 129 33 373.04 0.94 214 96 132 36 372.80 1.06 215 96 134 38 372.10 1.37 216 97 100 3 509.14 1.89 217 97 101 4 498.23 3.25 218 98 101 3 511.37 3.33 219 98 102 4 502.24 1.23 220 98 118 20 373.70 0.98 221 99 102 3 506.29 1.93 222 99 103 4 500.79 0.51 223 99 114 15 373.64 0.97 224 99 118 19 373.71 0.99 225 99 125 26 373.15 0.96 226 99 126 27 373.14 0.96 227 99 129 30 373.10 0.96 228 100 103 3 508.79 0.68 229 100 104 4 496.69 2.56 230 100 129 29 373.06 0.94 231 100 134 34 372.11 1.37 232 100 135 35 372.07 1.37 233 100 152 52 354.82 0.25 234 100 156 56 281.47 10.40 235 101 104 3 522.76 7.52 236 101 105 4 516.51 7.33 237 102 105 3 534.49 1.66 238 102 106 4 501.66 0.10 239 102 114 12 373.76 0.96 240 102 117 15 373.79 0.95 241 102 118 16 373.75 0.96 242 103 106 3 534.49 1.66 243 103 107 4 499.43 1.02 244 103 109 6 426.09 5.41 245 103 114 11 373.88 0.92 246 103 135 32 372.08 1.37 247 103 150 47 362.11 0.01 248 103 151 48 355.44 0.38 249 103 152 49 355.26 0.46 250 104 107 3 536.60 2.71 251 104 152 48 355.07 0.26 252 106 109 3 545.85 0.30 253 106 117 11 373.93 0.94 254 107 138 31 371.80 1.34 255 107 150 43 363.26 0.27 256 107 151 44 359.70 0.04 257 107 152 45 360.01 0.20 258 108 138 30 371.79 1.34 259 108 149 41 363.50 0.17 260 108 150 42 363.27 0.27 261 109 113 4 500.41 0.01 262 109 114 5 495.44 1.22 263 109 149 40 363.28 0.27 264 109 150 41 363.26 0.27 265 110 113 3 516.28 0.23 266 110 114 4 508.41 4.00 267 110 141 31 363.61 0.26 268 110 147 37 363.66 0.24 269 110 148 38 363.63 0.23 270 110 149 39 363.25 0.26 271 111 114 3 521.27 0.10 272 111 115 4 507.13 4.65 273 111 126 15 373.35 0.97 274 111 150 39 363.43 0.15 275 112 115 3 526.02 2.29 276 112 116 4 509.92 3.25 277 113 116 3 518.75 1.17 278 113 117 4 509.92 3.25 279 114 117 3 512.61 0.34 280 114 118 4 501.17 0.10 281 114 126 12 373.33 0.98 282 115 118 3 518.35 3.21 283 115 119 4 499.16 0.80 284 115 120 5 458.82 0.73 285 115 122 7 377.13 2.61 286 116 119 3 514.40 3.03 287 124 127 3 513.35 5.13 288 124 128 4 502.56 1.39 289 125 128 3 518.03 0.09 290 125 129 4 502.60 1.40 291 126 129 3 521.78 1.79 292 126 130 4 502.61 1.40 293 126 135 9 374.64 0.76 294 126 150 24 361.56 0.11 295 127 130 3 524.06 0.65 296 127 131 4 502.60 1.39 297 128 131 3 520.89 2.23 298 128 132 4 502.60 1.39 299 129 132 3 519.97 2.69 300 129 133 4 497.19 1.31 301 129 134 5 461.74 17.35 302 129 135 6 376.08 0.94 303 130 133 3 503.16 1.71 304 130 135 5 402.50 12.27 305 130 136 6 375.91 0.99 306 130 150 20 363.14 0.26 307 133 153 20 355.00 0.34 308 133 155 22 348.11 1.02 309 134 152 18 355.12 0.29 310 134 153 19 354.80 0.25 311 134 156 22 271.36 15.46 312 134 159 25 243.02 1.04 313 135 150 15 362.82 0.43 314 135 151 16 358.25 1.03 315 135 152 17 355.02 0.34 316 135 153 18 355.01 0.34 317 136 150 14 363.22 0.25 318 136 151 15 362.75 0.44 319 136 153 17 355.14 0.30 320 137 148 11 363.71 0.27 321 137 149 12 363.66 0.25 322 137 150 13 363.22 0.25 323 138 149 11 363.71 0.26 324 138 150 12 363.63 0.26 325 138 151 13 363.44 0.35 326 138 152 14 363.45 0.35 327 139 148 9 363.94 0.34 328 139 149 10 363.83 0.31 329 140 146 6 364.05 0.34 330 140 147 7 363.96 0.34 331 140 148 8 363.95 0.34 332 140 149 9 363.94 0.34 333 141 146 5 364.07 0.33 334 141 147 6 364.04 0.34 335 141 149 8 363.97 0.34 336 142 146 4 492.04 2.76 337 143 146 3 516.50 1.72 338 143 147 4 518.20 0.86 339 144 147 3 591.83 0.43 340 152 156 4 493.36 5.13 341 153 156 3 500.91 1.36 342 153 157 4 493.37 5.14 343 154 157 3 509.63 1.75 344 154 158 4 499.00 2.33 345 155 158 3 514.88 0.18 346 155 159 4 499.02 2.32 347 156 159 3 506.12 4.56 348 156 160 4 499.03 2.32 349 156 162 6 493.16 5.05 350 157 160 3 513.32 3.24 351 157 161 4 494.02 4.64 352 157 162 5 464.62 8.37 353 158 161 3 512.84 0.31