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 7 5 463.26 1.99 2 2 129 127 30.62 0.66 3 2 132 130 22.62 0.07 4 2 133 131 22.48 0.02 5 2 136 134 22.48 0.02 6 3 6 3 501.07 2.77 7 3 7 4 487.61 9.50 8 4 7 3 496.41 5.09 9 4 8 4 480.99 2.61 10 5 8 3 498.34 4.13 11 5 9 4 491.95 0.59 12 6 9 3 499.73 3.29 13 6 10 4 491.95 0.59 14 6 128 122 49.26 0.05 15 6 129 123 46.97 0.36 16 6 132 126 46.97 0.36 17 7 10 3 506.45 0.07 18 7 11 4 485.59 3.77 19 7 73 66 46.95 0.36 20 7 74 67 48.18 0.15 21 8 11 3 509.19 3.46 22 8 12 4 485.63 3.80 23 9 12 3 504.47 5.66 24 9 13 4 485.16 2.02 25 9 125 116 67.72 0.12 26 9 126 117 66.20 0.85 27 9 129 120 61.87 0.39 28 10 13 3 499.56 3.03 29 10 14 4 483.61 2.79 30 10 73 63 65.28 1.32 31 10 129 119 65.29 1.31 32 10 130 120 61.86 0.40 33 10 133 123 61.77 0.39 34 11 14 3 505.34 5.45 35 11 70 59 61.91 0.38 36 12 15 3 508.51 3.92 37 13 16 3 504.82 5.76 38 13 17 4 482.30 5.49 39 13 118 105 93.83 1.52 40 13 121 108 89.64 0.58 41 13 126 113 80.73 0.51 42 13 130 117 80.70 0.52 43 14 17 3 495.73 2.41 44 14 18 4 495.95 1.85 45 14 22 8 253.53 37.41 46 14 63 49 81.42 0.38 47 14 66 52 80.69 0.53 48 14 67 53 76.86 0.45 49 14 70 56 78.69 0.51 50 14 130 116 81.16 0.30 51 15 18 3 507.07 0.71 52 15 19 4 495.94 1.84 53 16 19 3 497.93 0.86 54 16 117 101 94.70 1.28 55 16 118 102 94.70 1.28 56 16 121 105 94.70 1.29 57 17 23 6 252.25 38.02 58 17 26 9 94.62 1.28 59 17 63 46 94.58 1.27 60 17 114 97 94.59 1.27 61 17 117 100 94.72 1.28 62 17 118 101 94.77 1.29 63 17 122 105 94.71 1.29 64 17 130 113 94.59 1.27 65 18 21 3 525.50 0.86 66 18 22 4 256.31 36.02 67 18 23 5 134.06 21.07 68 18 117 99 97.62 0.46 69 19 117 98 98.47 0.81 70 21 24 3 508.41 0.83 71 21 25 4 497.99 6.03 72 21 117 96 127.39 1.15 73 22 63 41 98.77 0.85 74 22 64 42 97.70 0.35 75 23 26 3 499.34 3.02 76 23 27 4 489.24 3.67 77 23 63 40 99.06 0.71 78 23 117 94 130.88 0.21 79 24 27 3 499.81 2.08 80 24 28 4 489.23 3.68 81 24 60 36 107.62 2.60 82 25 28 3 496.12 0.24 83 25 29 4 489.29 3.71 84 25 117 92 138.85 0.15 85 26 29 3 490.19 3.27 86 26 30 4 486.78 4.96 87 26 63 37 126.52 1.10 88 26 110 84 127.92 0.90 89 26 113 87 127.97 0.91 90 26 114 88 127.98 0.91 91 26 117 91 138.94 0.11 92 27 30 3 492.68 4.11 93 27 31 4 492.63 4.13 94 27 59 32 126.95 1.21 95 27 63 36 126.55 1.10 96 28 31 3 501.75 0.55 97 28 32 4 490.56 3.05 98 28 56 28 129.62 0.46 99 28 59 31 127.97 0.90 100 29 32 3 499.72 0.59 101 29 33 4 490.56 3.04 102 29 113 84 139.38 0.14 103 29 116 87 139.59 0.15 104 30 33 3 512.29 1.58 105 30 34 4 489.73 1.21 106 30 106 76 139.32 0.15 107 30 109 79 139.35 0.14 108 30 110 80 139.34 0.14 109 30 113 83 139.47 0.17 110 31 34 3 509.90 0.40 111 31 35 4 498.99 5.84 112 31 45 14 152.76 6.40 113 31 55 24 139.57 0.14 114 31 58 27 139.52 0.13 115 31 59 28 139.44 0.17 116 31 62 31 139.44 0.17 117 31 106 75 139.44 0.17 118 32 35 3 509.91 0.39 119 32 36 4 498.99 5.84 120 32 50 18 140.68 0.61 121 32 55 23 140.59 0.62 122 33 36 3 505.65 2.52 123 33 37 4 489.70 1.20 124 33 112 79 140.78 0.69 125 33 113 80 140.78 0.70 126 34 37 3 498.89 3.22 127 34 38 4 480.35 2.75 128 34 41 7 437.11 3.95 129 34 45 11 182.67 1.61 130 34 105 71 140.65 0.66 131 34 106 72 140.54 0.66 132 34 109 75 140.72 0.69 133 35 38 3 496.30 4.51 134 35 39 4 476.93 3.84 135 35 41 6 437.11 3.96 136 35 42 7 374.01 2.11 137 35 45 10 169.78 8.05 138 35 47 12 157.22 1.82 139 35 50 15 140.97 0.74 140 35 55 20 140.94 0.74 141 36 39 3 514.94 2.37 142 36 50 14 141.03 0.71 143 38 41 3 507.06 1.81 144 39 42 3 510.05 0.03 145 41 44 3 494.01 3.21 146 41 45 4 479.81 2.96 147 41 102 61 140.74 0.70 148 42 45 3 505.69 2.62 149 42 46 4 466.25 3.81 150 42 47 5 250.21 32.26 151 42 49 7 141.45 0.65 152 43 46 3 489.43 0.44 153 43 95 52 140.70 0.81 154 44 94 50 140.60 0.85 155 44 95 51 140.69 0.81 156 44 98 54 140.70 0.80 157 44 102 58 140.89 0.71 158 45 58 13 141.12 0.70 159 45 94 49 140.55 0.85 160 46 94 48 140.56 0.86 161 47 52 5 176.00 7.05 162 47 54 7 152.34 4.74 163 47 55 8 152.41 4.71 164 47 58 11 152.34 4.75 165 48 52 4 401.66 21.40 166 49 52 3 512.77 1.46 167 49 55 6 395.19 2.85 168 50 55 5 423.01 2.83 169 52 55 3 510.76 1.12 170 53 56 3 512.73 0.14 171 53 57 4 491.80 2.48 172 54 57 3 491.97 1.22 173 54 58 4 487.51 0.34 174 55 58 3 506.97 1.53 175 55 59 4 484.41 1.86 176 56 59 3 501.91 1.00 177 56 60 4 494.90 2.43 178 57 60 3 507.34 0.61 179 57 61 4 496.98 1.47 180 58 61 3 501.35 2.29 181 58 62 4 494.97 2.47 182 59 62 3 507.35 0.71 183 59 63 4 493.26 3.33 184 60 63 3 509.88 0.16 185 60 64 4 492.82 3.51 186 61 64 3 499.89 5.17 187 61 65 4 492.82 3.50 188 62 65 3 501.36 4.43 189 62 66 4 492.63 3.58 190 63 66 3 498.21 6.00 191 63 67 4 486.57 0.49 192 63 110 47 162.51 2.15 193 63 114 51 165.28 3.39 194 64 67 3 489.62 0.81 195 64 68 4 486.58 0.49 196 65 68 3 489.73 1.08 197 65 69 4 486.17 0.29 198 65 83 18 160.09 2.22 199 65 86 21 160.02 2.24 200 66 69 3 488.52 0.90 201 66 70 4 487.75 2.33 202 66 110 44 165.33 3.43 203 66 130 64 174.74 7.49 204 67 70 3 487.22 2.59 205 67 71 4 487.20 2.60 206 68 71 3 490.05 1.64 207 68 72 4 488.12 0.69 208 68 82 14 165.15 3.54 209 69 72 3 502.55 3.81 210 69 73 4 471.78 2.79 211 69 79 10 162.52 2.25 212 69 82 13 164.56 3.27 213 69 83 14 162.25 2.39 214 69 137 68 165.10 3.53 215 70 73 3 501.75 4.21 216 70 130 60 192.18 0.76 217 72 75 3 508.06 1.32 218 72 78 6 308.15 0.20 219 72 79 7 238.25 35.13 220 72 82 10 170.35 1.16 221 73 79 6 308.91 0.18 222 75 78 3 503.69 6.23 223 75 79 4 482.55 0.14 224 76 79 3 492.90 3.01 225 76 80 4 482.57 0.13 226 77 80 3 492.45 1.11 227 77 81 4 482.57 0.12 228 78 81 3 504.66 4.07 229 78 82 4 491.51 4.08 230 79 82 3 510.20 2.39 231 79 83 4 494.44 2.62 232 79 136 57 304.04 0.10 233 79 137 58 304.03 0.10 234 80 83 3 494.70 2.49 235 80 84 4 481.23 3.99 236 80 140 60 296.98 0.88 237 81 84 3 496.96 1.36 238 81 85 4 497.61 3.13 239 82 85 3 501.73 1.07 240 82 86 4 497.61 3.13 241 83 86 3 497.61 3.13 242 83 87 4 494.42 2.62 243 83 137 54 304.68 0.17 244 83 140 57 304.55 0.15 245 83 141 58 304.53 0.14 246 84 87 3 501.75 1.05 247 84 88 4 496.07 1.79 248 84 140 56 304.57 0.17 249 84 143 59 304.53 0.14 250 84 144 60 304.53 0.14 251 85 88 3 504.81 2.58 252 85 89 4 503.92 0.20 253 86 89 3 505.49 0.96 254 86 90 4 503.91 0.20 255 86 141 55 304.69 0.15 256 87 90 3 506.76 1.61 257 87 91 4 504.51 0.49 258 87 141 54 304.69 0.15 259 87 144 57 304.55 0.15 260 87 145 58 304.56 0.14 261 88 91 3 513.60 2.31 262 88 144 56 304.59 0.16 263 88 145 57 304.60 0.15 264 88 147 59 304.45 0.18 265 89 92 3 514.76 2.50 266 89 93 4 498.12 0.44 267 90 93 3 493.75 2.62 268 90 98 8 306.13 0.77 269 90 141 51 304.85 0.14 270 90 145 55 304.73 0.12 271 91 96 5 324.25 6.65 272 91 144 53 304.85 0.14 273 91 145 54 304.80 0.15 274 91 147 56 304.80 0.15 275 92 96 4 403.94 2.05 276 93 96 3 503.26 0.26 277 93 98 5 480.75 11.52 278 95 98 3 539.04 0.85 279 97 102 5 519.49 2.43 280 98 102 4 519.12 2.61 281 98 103 5 519.12 2.60 282 98 145 47 304.94 0.14 283 99 102 3 524.60 0.12 284 99 103 4 519.49 2.43 285 100 103 3 524.60 0.12 286 100 142 42 305.06 0.17 287 100 146 46 305.06 0.17 288 101 104 3 527.88 1.76 289 101 105 4 520.42 1.96 290 102 105 3 524.23 0.63 291 102 106 4 510.69 3.44 292 103 106 3 511.68 2.98 293 103 107 4 501.92 0.61 294 103 134 31 305.81 0.07 295 103 138 35 305.63 0.02 296 103 141 38 305.63 0.02 297 103 142 39 305.58 0.03 298 103 145 42 305.62 0.02 299 104 107 3 510.22 2.39 300 104 108 4 500.69 2.38 301 105 108 3 505.17 0.14 302 105 109 4 499.22 3.12 303 106 109 3 510.47 1.91 304 106 110 4 486.74 1.50 305 106 134 28 306.16 0.18 306 107 110 3 502.16 3.15 307 107 111 4 499.08 4.68 308 107 134 27 305.91 0.08 309 108 111 3 502.15 3.15 310 108 112 4 484.86 2.41 311 109 112 3 498.80 7.83 312 109 113 4 480.89 0.42 313 110 113 3 491.31 3.79 314 110 114 4 480.50 1.60 315 110 134 24 306.31 0.14 316 111 114 3 498.24 3.20 317 111 115 4 479.51 1.12 318 111 130 19 306.44 0.10 319 111 131 20 306.44 0.11 320 112 115 3 498.50 3.06 321 112 116 4 482.51 1.50 322 113 116 3 495.08 4.79 323 113 117 4 482.48 1.52 324 114 117 3 493.35 3.76 325 114 118 4 482.48 1.52 326 114 122 8 308.13 0.04 327 114 130 16 306.57 0.09 328 115 118 3 493.35 3.76 329 115 119 4 450.32 3.09 330 115 122 7 308.13 0.04 331 115 127 12 307.42 0.32 332 118 121 3 493.29 1.59 333 118 122 4 484.97 2.58 334 119 122 3 508.40 1.80 335 120 123 3 505.97 3.02 336 121 126 5 467.25 0.85 337 122 126 4 450.76 7.39 338 122 127 5 455.36 9.69 339 122 130 8 405.60 2.36 340 123 126 3 499.83 1.82 341 123 127 4 480.07 4.98 342 124 127 3 498.66 1.24 343 124 128 4 495.48 2.71 344 125 128 3 504.71 1.86 345 125 129 4 495.47 2.71 346 126 129 3 501.04 0.05 347 126 130 4 495.47 2.73 348 127 130 3 495.41 2.77 349 127 131 4 492.85 4.04 350 128 131 3 498.71 1.11 351 128 132 4 495.41 2.77 352 129 132 3 499.17 0.89 353 129 133 4 481.23 1.76 354 130 133 3 490.62 4.86 355 130 134 4 477.00 0.58 356 131 134 3 497.66 0.14 357 131 135 4 472.74 2.73 358 132 135 3 498.12 0.09 359 132 136 4 479.60 0.70 360 133 136 3 499.50 0.79 361 133 137 4 478.41 0.11 362 134 137 3 493.78 3.35 363 134 138 4 478.10 0.26 364 135 138 3 506.04 3.02 365 135 139 4 478.10 0.26 366 136 139 3 503.75 1.88 367 136 140 4 496.00 0.96 368 137 140 3 503.75 1.88 369 137 141 4 499.22 0.70 370 138 141 3 498.31 1.17 371 138 142 4 493.16 3.73 372 139 142 3 498.31 1.17 373 139 143 4 493.16 3.74 374 140 143 3 499.43 0.61 375 140 144 4 493.16 3.74 376 141 144 3 495.06 2.79 377 141 145 4 490.30 5.17 378 142 145 3 482.77 1.01 379 142 146 4 481.23 0.64 380 143 146 3 482.79 0.99 381 143 147 4 472.59 2.09 382 144 147 3 485.06 2.29