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 6 4 471.67 6.12 2 2 7 5 461.86 0.28 3 2 10 8 458.61 1.08 4 2 73 71 31.00 1.41 5 2 132 130 20.92 1.67 6 2 133 131 20.91 1.67 7 3 6 3 499.44 4.97 8 3 7 4 491.93 3.11 9 4 7 3 493.82 2.17 10 4 8 4 491.93 3.10 11 5 8 3 491.98 3.12 12 5 9 4 491.97 3.12 13 6 9 3 498.73 1.02 14 6 10 4 492.28 2.96 15 6 128 122 52.01 0.48 16 6 129 123 47.69 0.48 17 6 132 126 47.49 0.40 18 7 10 3 509.87 3.31 19 7 11 4 489.91 1.78 20 7 73 66 47.81 0.57 21 8 11 3 509.95 3.27 22 8 12 4 489.55 1.96 23 9 12 3 496.77 3.23 24 9 13 4 489.63 2.00 25 9 125 116 65.05 0.52 26 9 126 117 64.88 0.47 27 9 129 120 63.41 0.18 28 10 13 3 507.98 2.38 29 10 14 4 489.62 2.02 30 10 70 60 63.40 0.21 31 10 73 63 63.57 0.26 32 10 129 119 63.54 0.22 33 10 130 120 63.48 0.20 34 10 133 123 63.41 0.23 35 11 14 3 499.91 1.66 36 11 15 4 490.12 2.28 37 11 70 59 63.48 0.26 38 12 15 3 501.73 0.95 39 13 16 3 497.25 1.28 40 13 17 4 487.13 1.02 41 13 118 105 87.33 0.26 42 13 121 108 81.76 0.39 43 13 126 113 80.38 0.57 44 13 130 117 75.36 0.42 45 14 17 3 496.88 3.85 46 14 18 4 487.13 1.03 47 14 63 49 80.70 0.52 48 14 66 52 75.28 0.46 49 14 67 53 77.77 0.81 50 14 70 56 74.47 0.84 51 14 130 116 80.46 0.53 52 15 18 3 496.89 3.85 53 15 19 4 482.94 1.07 54 16 19 3 489.74 1.42 55 16 117 101 88.94 0.35 56 16 118 102 88.88 0.38 57 16 121 105 88.88 0.38 58 17 23 6 124.27 17.36 59 17 26 9 88.83 0.37 60 17 63 46 88.44 0.19 61 17 114 97 88.36 0.15 62 17 117 100 88.94 0.34 63 17 118 101 88.94 0.34 64 17 130 113 88.37 0.14 65 18 21 3 515.98 1.24 66 18 22 4 253.78 33.20 67 18 23 5 123.84 17.57 68 18 117 99 89.13 0.39 69 19 117 98 91.58 0.84 70 21 24 3 497.04 1.54 71 21 25 4 485.03 0.59 72 21 117 96 127.73 0.49 73 22 64 42 89.16 0.38 74 23 26 3 496.61 1.19 75 23 27 4 496.62 1.18 76 23 63 40 101.14 2.70 77 23 117 94 132.39 0.70 78 24 27 3 496.63 1.18 79 24 28 4 490.25 2.01 80 24 60 36 109.20 0.99 81 25 28 3 496.25 1.54 82 25 29 4 490.26 2.02 83 25 117 92 139.65 1.29 84 26 29 3 496.28 1.54 85 26 30 4 482.92 5.71 86 26 63 37 126.05 0.28 87 26 110 84 127.84 0.49 88 26 113 87 131.27 1.17 89 26 114 88 130.34 0.56 90 26 117 91 139.68 1.30 91 27 30 3 500.89 0.77 92 27 31 4 485.45 6.95 93 27 59 32 127.69 0.49 94 27 63 36 126.05 0.28 95 28 31 3 510.10 2.79 96 28 32 4 495.14 3.65 97 28 56 28 134.85 1.25 98 28 59 31 129.38 0.26 99 29 32 3 498.33 2.06 100 29 33 4 485.88 0.92 101 29 113 84 140.50 1.37 102 29 116 87 141.72 0.85 103 30 33 3 503.48 0.52 104 30 34 4 485.86 0.90 105 30 106 76 140.05 1.15 106 30 109 79 140.05 1.15 107 30 110 80 140.03 1.15 108 30 113 83 140.53 1.38 109 31 34 3 492.82 0.60 110 31 35 4 487.10 1.53 111 31 45 14 161.56 2.57 112 31 55 24 141.70 0.84 113 31 58 27 141.50 0.93 114 31 59 28 140.46 1.34 115 32 35 3 504.25 0.66 116 32 36 4 482.04 6.00 117 32 50 18 142.09 0.96 118 32 55 23 141.75 0.85 119 33 36 3 491.18 2.56 120 33 37 4 482.04 6.00 121 33 109 76 142.00 0.90 122 34 37 3 497.40 1.50 123 34 38 4 480.12 5.03 124 34 41 7 423.44 4.86 125 34 45 11 291.95 53.47 126 34 102 68 141.93 0.84 127 34 105 71 141.94 0.85 128 34 106 72 141.92 0.85 129 34 109 75 142.03 0.92 130 35 38 3 487.07 8.32 131 35 39 4 474.66 6.41 132 35 41 6 406.31 3.71 133 35 42 7 292.56 53.15 134 35 45 10 291.94 53.48 135 35 47 12 159.55 2.27 136 35 50 15 142.65 0.80 137 35 55 20 142.47 0.85 138 36 39 3 501.23 1.59 139 36 50 14 142.69 0.83 140 38 41 3 500.73 2.94 141 38 105 67 142.26 0.89 142 39 42 3 510.95 2.17 143 40 43 3 520.25 2.42 144 41 44 3 498.84 0.81 145 41 45 4 488.95 2.55 146 41 102 61 142.19 0.86 147 42 45 3 501.10 0.18 148 42 46 4 482.39 2.33 149 42 47 5 244.38 35.10 150 42 49 7 148.23 3.42 151 43 46 3 477.35 3.77 152 43 95 52 142.41 0.88 153 43 96 53 142.43 0.88 154 44 94 50 142.40 0.88 155 44 95 51 142.42 0.88 156 44 96 52 142.43 0.88 157 44 98 54 142.41 0.89 158 44 102 58 142.43 0.83 159 45 58 13 142.66 0.85 160 46 95 49 142.30 0.83 161 47 52 5 171.21 1.76 162 47 54 7 159.16 2.12 163 47 55 8 152.66 1.13 164 47 58 11 151.02 0.32 165 48 52 4 417.57 0.20 166 49 52 3 492.19 1.65 167 49 55 6 434.05 18.16 168 50 55 5 411.79 7.03 169 52 55 3 502.91 0.26 170 53 56 3 499.75 1.83 171 53 57 4 484.61 1.14 172 54 57 3 492.70 2.91 173 54 58 4 484.60 1.13 174 55 58 3 500.15 1.65 175 55 59 4 488.31 0.75 176 56 59 3 503.68 0.12 177 56 60 4 488.37 0.77 178 57 60 3 507.36 1.72 179 57 61 4 490.95 1.80 180 58 61 3 497.55 0.13 181 58 62 4 488.61 0.66 182 59 62 3 497.88 3.52 183 59 63 4 490.95 1.80 184 60 63 3 491.06 1.75 185 60 64 4 488.50 0.60 186 61 64 3 489.42 1.05 187 61 65 4 488.50 0.59 188 62 65 3 490.48 0.07 189 62 66 4 490.10 0.26 190 63 66 3 493.95 1.67 191 63 67 4 490.30 0.17 192 63 110 47 156.21 1.44 193 64 67 3 493.90 1.62 194 64 68 4 493.66 1.84 195 65 68 3 497.69 0.18 196 65 69 4 493.79 1.78 197 65 83 18 148.25 0.77 198 65 86 21 148.16 0.81 199 66 69 3 499.77 1.21 200 66 70 4 493.80 1.79 201 66 110 44 156.55 1.39 202 66 130 64 175.16 7.00 203 66 137 71 152.41 1.30 204 67 70 3 506.43 2.12 205 67 71 4 503.50 3.58 206 68 71 3 506.43 2.12 207 68 72 4 503.50 3.57 208 68 82 14 156.16 1.20 209 69 72 3 507.79 1.44 210 69 73 4 503.50 3.58 211 69 79 10 154.21 1.56 212 69 83 14 154.24 1.52 213 69 137 68 155.76 1.01 214 70 73 3 507.78 1.43 215 70 130 60 193.75 2.29 216 72 75 3 498.21 3.62 217 72 78 6 327.83 11.09 218 72 79 7 189.50 0.18 219 72 82 10 249.06 29.59 220 73 79 6 413.73 5.92 221 75 78 3 507.69 1.42 222 75 79 4 507.47 1.52 223 76 79 3 507.69 1.41 224 76 80 4 504.02 0.21 225 77 80 3 512.00 0.75 226 77 81 4 499.57 2.04 227 78 81 3 503.48 0.08 228 78 82 4 499.56 2.04 229 79 82 3 506.90 1.79 230 79 83 4 499.95 1.84 231 79 137 58 294.30 1.06 232 79 140 61 292.93 0.40 233 80 83 3 511.14 3.75 234 80 84 4 495.41 0.44 235 80 140 60 292.56 0.58 236 81 84 3 496.88 0.29 237 81 85 4 499.85 1.78 238 82 85 3 508.25 5.98 239 82 86 4 499.47 10.38 240 83 86 3 499.53 10.35 241 83 87 4 491.14 6.13 242 83 137 54 302.49 0.70 243 83 140 57 302.01 0.94 244 83 141 58 301.96 0.96 245 84 87 3 507.27 1.52 246 84 88 4 493.09 5.18 247 84 140 56 302.44 0.72 248 84 143 59 301.95 0.96 249 84 144 60 301.95 0.96 250 85 88 3 512.37 4.06 251 85 89 4 503.85 0.20 252 86 89 3 506.27 0.57 253 86 90 4 503.85 0.20 254 86 141 55 302.80 0.58 255 87 90 3 513.82 3.21 256 87 91 4 512.30 3.97 257 87 141 54 302.80 0.58 258 87 144 57 302.78 0.59 259 87 145 58 302.78 0.59 260 88 91 3 524.30 1.99 261 88 144 56 302.81 0.56 262 88 145 57 302.83 0.57 263 88 147 59 302.75 0.59 264 89 92 3 529.86 0.79 265 89 93 4 508.53 5.86 266 90 93 3 508.53 5.86 267 90 98 8 303.00 0.63 268 90 141 51 303.01 0.62 269 90 145 55 302.96 0.62 270 91 144 53 303.01 0.62 271 91 145 54 302.99 0.62 272 91 147 56 302.98 0.62 273 93 98 5 368.15 30.80 274 97 102 5 515.51 1.34 275 98 102 4 515.51 1.34 276 98 103 5 515.51 1.34 277 98 145 47 303.25 0.66 278 99 102 3 524.20 0.33 279 99 103 4 518.36 0.08 280 100 103 3 521.52 1.66 281 100 142 42 303.33 0.64 282 100 146 46 303.33 0.64 283 101 104 3 524.19 0.33 284 101 105 4 521.02 1.26 285 102 105 3 520.94 1.29 286 102 106 4 508.81 1.47 287 103 106 3 509.55 1.65 288 103 107 4 501.34 2.25 289 103 134 31 304.03 0.73 290 103 138 35 303.78 0.71 291 103 141 38 303.76 0.70 292 103 142 39 303.73 0.72 293 103 145 42 303.75 0.71 294 104 107 3 509.35 1.75 295 104 108 4 501.35 2.25 296 105 108 3 499.65 1.42 297 105 109 4 488.76 2.34 298 106 109 3 495.80 3.06 299 106 110 4 482.57 0.76 300 106 134 28 304.19 0.72 301 107 110 3 493.01 4.46 302 107 111 4 488.55 2.23 303 107 134 27 304.11 0.73 304 108 111 3 488.56 2.23 305 108 112 4 485.19 3.49 306 109 112 3 496.69 2.25 307 109 113 4 488.67 1.75 308 110 113 3 507.97 2.68 309 110 114 4 486.28 0.56 310 110 134 24 304.94 0.58 311 111 114 3 493.80 0.81 312 111 115 4 487.75 0.18 313 111 122 11 305.73 0.53 314 111 127 16 305.27 0.56 315 111 130 19 305.13 0.53 316 111 131 20 305.10 0.54 317 111 134 23 304.90 0.60 318 112 115 3 490.31 0.64 319 112 116 4 478.47 3.70 320 113 116 3 490.31 0.64 321 113 117 4 480.16 0.55 322 114 117 3 503.71 1.94 323 114 118 4 474.39 1.66 324 114 130 16 305.37 0.59 325 115 118 3 494.58 2.49 326 115 119 4 444.25 0.66 327 115 122 7 306.00 0.66 328 115 127 12 305.99 0.66 329 118 121 3 505.97 2.77 330 118 122 4 487.05 6.38 331 119 122 3 511.78 1.40 332 120 123 3 515.83 1.71 333 121 126 5 461.95 7.62 334 122 126 4 461.95 7.62 335 122 127 5 461.94 7.62 336 122 130 8 445.77 0.21 337 123 126 3 495.43 1.90 338 123 127 4 473.51 2.06 339 124 127 3 495.36 2.12 340 124 128 4 475.23 1.21 341 125 128 3 497.34 3.10 342 125 129 4 484.38 3.38 343 126 129 3 493.00 0.61 344 126 130 4 479.26 2.88 345 127 130 3 494.62 0.97 346 127 131 4 488.80 1.89 347 128 131 3 496.98 1.38 348 128 132 4 491.00 0.79 349 129 132 3 494.74 1.03 350 129 133 4 479.60 2.69 351 130 133 3 491.41 0.64 352 130 134 4 486.88 2.88 353 131 134 3 494.56 4.26 354 131 135 4 488.01 2.32 355 132 135 3 499.76 1.66 356 132 136 4 488.00 2.31 357 133 136 3 488.01 2.32 358 133 137 4 488.00 2.32 359 134 137 3 493.78 4.73 360 134 138 4 478.65 2.35 361 135 138 3 502.06 0.58 362 135 139 4 475.43 0.71 363 136 139 3 499.94 0.48 364 136 140 4 477.92 1.95 365 137 140 3 505.19 1.06 366 137 141 4 499.05 0.93 367 138 141 3 496.55 1.23 368 138 142 4 488.22 2.93 369 139 142 3 497.07 1.49 370 139 143 4 477.93 1.95 371 140 143 3 492.92 3.50 372 140 144 4 486.98 6.47 373 141 144 3 506.54 3.31 374 141 145 4 495.41 2.25 375 142 145 3 495.41 2.25 376 142 146 4 484.17 7.87 377 143 146 3 497.10 1.41 378 143 147 4 484.17 7.87 379 144 147 3 482.13 1.64