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 2 144 142 16.18 0.21 2 3 6 3 496.13 0.28 3 3 7 4 491.56 0.56 4 3 91 88 23.69 0.06 5 3 94 91 22.09 0.66 6 3 95 92 20.63 0.07 7 3 141 138 17.79 0.48 8 3 144 141 16.29 0.23 9 3 145 142 16.23 0.24 10 4 7 3 493.00 1.14 11 4 8 4 491.70 0.48 12 4 91 87 27.82 0.48 13 5 8 3 504.96 1.72 14 5 9 4 491.70 0.48 15 6 9 3 509.66 0.26 16 6 141 135 23.55 1.41 17 6 144 138 23.87 1.19 18 7 10 3 511.62 1.25 19 7 90 83 37.03 0.42 20 7 91 84 33.70 0.57 21 7 141 134 25.51 0.81 22 9 137 128 38.54 0.21 23 10 14 4 483.38 3.94 24 10 15 5 459.36 1.18 25 10 18 8 453.50 1.57 26 10 84 74 51.18 1.76 27 10 90 80 47.31 0.72 28 10 137 127 39.49 0.25 29 10 138 128 39.49 0.26 30 10 141 131 39.77 0.39 31 11 14 3 497.71 1.24 32 11 15 4 495.66 2.20 33 12 15 3 500.12 0.03 34 12 16 4 495.66 2.20 35 13 16 3 500.12 0.03 36 13 17 4 503.68 1.81 37 14 17 3 512.65 2.68 38 14 18 4 503.67 1.80 39 14 134 120 67.86 2.38 40 14 137 123 67.82 2.36 41 15 18 3 504.43 1.44 42 15 19 4 496.73 5.29 43 15 84 69 73.49 0.20 44 16 19 3 508.32 0.51 45 16 20 4 496.80 5.25 46 17 20 3 498.81 4.24 47 17 21 4 496.80 5.24 48 17 130 113 92.20 0.30 49 17 131 114 92.01 0.39 50 17 134 117 91.95 0.37 51 18 21 3 512.03 1.52 52 18 22 4 488.56 1.11 53 18 81 63 92.19 0.30 54 18 84 66 92.22 0.30 55 18 134 116 92.16 0.32 56 18 135 117 91.95 0.36 57 18 138 120 91.94 0.37 58 19 22 3 501.79 0.39 59 19 23 4 495.38 2.30 60 19 81 62 92.21 0.33 61 19 84 65 92.25 0.31 62 19 85 66 98.48 0.70 63 20 23 3 504.53 0.98 64 21 24 3 504.53 0.98 65 21 25 4 496.65 2.96 66 21 122 101 100.04 0.96 67 21 127 106 103.58 0.81 68 21 131 110 100.00 0.96 69 21 135 114 99.82 0.89 70 22 25 3 500.95 0.81 71 22 26 4 474.61 8.03 72 22 29 7 456.11 1.23 73 22 74 52 150.73 20.30 74 22 77 55 103.56 0.82 75 22 78 56 103.55 0.81 76 22 81 59 103.47 0.85 77 22 135 113 100.02 0.95 78 23 27 4 488.19 0.17 79 24 27 3 510.44 0.88 80 24 125 101 110.37 2.27 81 24 127 103 110.30 2.27 82 25 28 3 521.74 4.04 83 25 32 7 313.37 1.03 84 25 74 49 155.71 20.43 85 25 121 96 110.34 2.27 86 25 122 97 110.32 2.27 87 25 125 100 110.38 2.27 88 25 135 110 110.20 2.33 89 26 29 3 510.25 0.98 90 26 74 48 154.85 20.00 91 28 31 3 498.37 3.21 92 28 32 4 482.74 4.61 93 29 33 4 489.03 1.47 94 29 74 45 168.87 22.98 95 29 75 46 171.08 21.89 96 29 78 49 171.08 21.88 97 30 33 3 495.31 2.19 98 30 34 4 493.34 1.21 99 30 61 31 196.69 16.66 100 30 67 37 189.38 19.81 101 30 71 41 183.78 22.32 102 31 34 3 505.40 1.46 103 31 35 4 496.07 0.16 104 31 61 30 196.69 16.66 105 32 35 3 496.09 0.15 106 32 36 4 496.09 0.15 107 32 74 42 189.16 19.71 108 32 121 89 149.41 0.18 109 33 36 3 506.15 5.18 110 33 37 4 496.09 0.15 111 33 70 37 191.43 18.74 112 33 74 41 189.16 19.71 113 34 37 3 497.61 0.91 114 34 38 4 489.06 1.46 115 34 60 26 196.85 16.64 116 34 61 27 196.81 16.62 117 34 67 33 196.32 16.49 118 34 70 36 196.06 16.43 119 35 38 3 497.62 0.91 120 35 39 4 489.16 1.51 121 35 121 86 165.96 1.31 122 36 39 3 500.85 0.71 123 36 40 4 495.26 3.51 124 36 73 37 196.44 16.50 125 36 74 38 196.40 16.48 126 36 77 41 196.38 16.48 127 36 117 81 165.99 1.34 128 36 118 82 165.97 1.33 129 36 121 85 165.98 1.30 130 37 40 3 500.85 0.71 131 37 41 4 495.26 3.51 132 37 51 14 254.84 3.73 133 37 66 29 196.86 16.64 134 37 69 32 196.74 16.59 135 37 70 33 196.55 16.50 136 37 73 36 196.50 16.50 137 37 114 77 166.25 1.64 138 38 41 3 500.87 0.71 139 38 42 4 490.32 1.04 140 38 60 22 196.93 16.68 141 38 66 28 196.86 16.64 142 39 42 3 490.62 1.19 143 39 43 4 490.28 1.02 144 39 117 78 165.81 1.43 145 39 120 81 166.03 1.31 146 40 43 3 501.29 0.91 147 40 44 4 487.79 0.14 148 40 47 7 357.77 23.87 149 40 51 11 283.23 7.36 150 40 113 73 166.28 1.65 151 40 114 74 166.20 1.61 152 40 117 77 166.00 1.33 153 41 45 4 433.62 1.76 154 41 48 7 269.39 0.43 155 41 51 10 266.50 1.02 156 41 57 16 197.03 16.70 157 41 66 25 197.02 16.69 158 43 120 77 166.20 1.33 159 44 47 3 507.80 1.84 160 44 113 69 166.47 1.61 161 45 48 3 509.29 1.09 162 46 113 67 167.30 1.94 163 47 50 3 512.26 1.94 164 47 51 4 500.15 2.24 165 47 110 63 167.46 2.21 166 47 113 66 167.22 1.91 167 48 51 3 510.66 2.74 168 48 57 9 246.31 0.54 169 49 52 3 513.17 1.48 170 50 106 56 167.50 2.30 171 50 110 60 167.59 2.24 172 51 54 3 500.92 0.74 173 51 57 6 309.89 7.54 174 51 69 18 232.84 1.83 175 52 55 3 510.07 6.47 176 53 65 12 251.34 1.93 177 54 57 3 532.90 0.58 178 54 63 9 275.92 5.89 179 54 65 11 244.27 5.46 180 54 66 12 242.32 6.42 181 54 69 15 240.47 5.50 182 56 59 3 521.98 2.23 183 56 63 7 296.42 1.83 184 57 60 3 508.17 2.79 185 57 63 6 299.07 0.51 186 57 66 9 266.85 1.35 187 59 62 3 514.51 2.51 188 59 63 4 443.97 16.85 189 60 63 3 508.12 0.23 190 60 66 6 339.12 2.68 191 61 67 6 374.46 3.76 192 63 66 3 493.91 2.07 193 63 67 4 498.05 0.90 194 64 67 3 498.06 0.89 195 64 68 4 489.44 3.41 196 65 68 3 505.05 1.08 197 65 69 4 489.44 3.41 198 66 69 3 498.06 0.89 199 66 70 4 483.08 0.23 200 67 70 3 495.50 0.85 201 67 71 4 493.72 1.75 202 68 71 3 515.71 6.04 203 68 72 4 501.68 2.23 204 69 72 3 501.70 2.23 205 69 73 4 501.68 2.23 206 70 73 3 517.83 4.97 207 70 74 4 507.03 0.42 208 71 74 3 507.03 0.42 209 71 75 4 501.81 2.18 210 72 75 3 502.66 1.76 211 72 76 4 501.82 2.18 212 73 76 3 506.69 0.26 213 73 77 4 501.81 2.18 214 73 114 41 171.74 1.09 215 74 77 3 501.81 2.18 216 74 78 4 491.36 0.89 217 75 78 3 492.49 3.02 218 75 79 4 492.00 3.27 219 76 79 3 493.06 3.31 220 76 80 4 494.56 4.55 221 76 97 21 184.60 5.06 222 77 80 3 500.70 1.48 223 77 81 4 503.62 0.02 224 77 135 58 183.01 7.27 225 78 81 3 503.63 0.01 226 78 82 4 497.92 2.83 227 79 82 3 506.77 3.58 228 79 83 4 500.68 1.45 229 79 93 14 195.78 9.56 230 79 97 18 195.78 9.57 231 80 83 3 502.91 0.34 232 80 84 4 502.91 0.34 233 80 90 10 254.68 7.50 234 80 93 13 196.06 9.44 235 80 94 14 195.82 9.56 236 80 97 17 195.78 9.58 237 80 138 58 183.14 7.37 238 80 142 62 181.46 8.05 239 81 84 3 512.89 5.33 240 81 135 54 183.27 7.37 241 81 138 57 183.18 7.38 242 83 86 3 502.40 1.79 243 83 89 6 303.64 1.00 244 83 90 7 270.67 0.35 245 83 93 10 280.83 4.74 246 84 90 6 358.81 10.88 247 86 89 3 503.49 1.49 248 86 90 4 497.36 1.18 249 87 90 3 492.11 3.88 250 87 91 4 493.84 2.96 251 88 91 3 502.30 2.06 252 88 92 4 500.61 2.92 253 89 92 3 502.69 1.89 254 89 93 4 497.19 4.63 255 90 93 3 507.69 0.07 256 90 94 4 497.19 4.62 257 90 138 48 186.20 8.89 258 91 94 3 500.69 2.88 259 91 95 4 500.04 3.20 260 92 95 3 501.16 0.65 261 92 96 4 496.74 1.55 262 93 96 3 502.30 1.22 263 93 97 4 500.62 0.82 264 94 97 3 507.06 2.40 265 94 98 4 493.32 0.35 266 94 141 47 185.84 9.06 267 94 142 48 184.33 9.82 268 94 145 51 183.72 10.10 269 95 98 3 500.62 0.82 270 95 99 4 495.80 1.59 271 95 145 50 183.72 10.10 272 96 99 3 503.26 2.14 273 96 100 4 495.80 1.59 274 97 100 3 493.78 0.61 275 97 101 4 493.78 0.60 276 98 101 3 508.23 0.96 277 98 102 4 490.68 0.93 278 98 145 47 183.73 10.10 279 98 146 48 183.70 10.11 280 99 102 3 495.12 1.61 281 99 103 4 495.55 1.52 282 100 103 3 508.93 1.00 283 100 104 4 504.75 3.08 284 101 104 3 498.47 0.04 285 101 105 4 491.92 3.19 286 101 106 5 379.88 14.04 287 101 111 10 278.50 5.84 288 101 146 45 183.79 10.20 289 102 105 3 498.69 0.15 290 102 145 43 185.25 10.84 291 102 146 44 183.79 10.20 292 106 110 4 477.92 3.31 293 106 111 5 476.15 4.19 294 106 146 40 185.25 10.96 295 107 110 3 494.10 0.94 296 107 111 4 477.92 3.31 297 107 146 39 185.23 10.97 298 108 111 3 503.79 2.95 299 108 112 4 489.75 1.54 300 108 143 35 186.28 11.37 301 108 146 38 185.71 11.41 302 109 112 3 507.27 1.22 303 109 113 4 506.89 1.41 304 110 113 3 506.90 1.41 305 111 114 3 522.12 0.45 306 111 139 28 189.00 10.39 307 111 142 31 187.88 10.87 308 111 143 32 186.64 11.48 309 111 146 35 186.04 11.57 310 112 115 3 510.27 0.96 311 112 139 27 189.00 10.39 312 112 143 31 186.66 11.48 313 113 116 3 518.09 1.91 314 113 117 4 510.69 0.22 315 114 117 3 510.69 0.22 316 114 118 4 505.49 0.07 317 115 118 3 505.84 0.26 318 115 119 4 501.58 4.19 319 115 136 21 189.41 10.46 320 115 139 24 189.27 10.53 321 116 119 3 507.59 1.19 322 116 120 4 507.59 1.19 323 117 120 3 500.57 4.70 324 117 121 4 486.26 2.44 325 118 121 3 505.78 2.10 326 118 122 4 492.77 0.82 327 118 135 17 190.81 11.16 328 118 139 21 190.65 11.23 329 119 122 3 509.08 2.43 330 119 123 4 497.65 1.61 331 119 129 10 237.65 0.72 332 119 132 13 190.81 11.16 333 120 123 3 500.66 1.99 334 120 124 4 497.67 1.62 335 121 124 3 501.56 1.54 336 121 125 4 498.81 1.06 337 122 125 3 503.93 0.35 338 122 126 4 497.69 1.61 339 122 127 5 400.03 7.88 340 122 131 9 250.83 5.46 341 122 132 10 241.75 2.75 342 122 135 13 238.50 1.17 343 123 126 3 497.69 1.61 344 123 127 4 483.62 8.63 345 127 131 4 478.55 3.29 346 128 131 3 504.09 0.27 347 128 132 4 484.88 1.11 348 129 132 3 490.43 1.66 349 129 133 4 483.94 1.58 350 130 133 3 501.47 1.59 351 130 134 4 496.13 1.19 352 131 134 3 503.35 1.25 353 131 135 4 496.14 1.18 354 132 135 3 510.69 6.09 355 132 136 4 493.88 0.05 356 133 136 3 497.64 1.83 357 133 137 4 489.20 2.39 358 134 137 3 510.38 6.25 359 134 138 4 499.59 0.85 360 135 138 3 495.31 1.28 361 135 139 4 489.50 2.54 362 136 139 3 489.49 2.55 363 136 140 4 497.45 1.43 364 137 140 3 498.84 0.74 365 137 141 4 497.81 1.44 366 138 141 3 507.26 0.62 367 138 142 4 500.72 2.52 368 139 142 3 512.83 3.54 369 139 143 4 497.63 1.35 370 140 143 3 497.88 1.47 371 140 144 4 492.97 1.36 372 141 144 3 506.03 0.10 373 141 145 4 503.50 1.35 374 142 145 3 508.68 0.94 375 142 146 4 503.50 1.35 376 143 146 3 502.04 2.38