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 5 463.70 0.05 2 2 129 127 16.91 0.48 3 2 130 128 16.89 0.49 4 2 133 131 16.84 0.47 5 3 6 3 473.78 2.19 6 3 7 4 473.78 2.19 7 4 7 3 478.05 0.54 8 4 8 4 471.91 3.24 9 5 8 3 477.12 0.63 10 5 9 4 470.99 3.69 11 6 9 3 490.44 0.51 12 6 10 4 471.10 3.64 13 6 126 120 43.14 0.23 14 6 129 123 41.84 0.43 15 7 10 3 482.13 1.88 16 7 11 4 471.11 3.64 17 7 79 72 43.44 0.35 18 7 80 73 48.57 0.35 19 8 11 3 491.47 2.80 20 8 12 4 463.86 0.01 21 9 12 3 476.32 0.47 22 9 13 4 464.18 0.50 23 9 121 112 66.73 0.80 24 9 122 113 61.44 1.05 25 9 123 114 60.71 1.42 26 9 126 117 58.05 0.09 27 10 13 3 480.37 0.99 28 10 14 4 470.01 2.41 29 10 76 66 58.06 0.09 30 10 79 69 58.07 0.09 31 10 126 116 60.71 1.41 32 10 127 117 58.05 0.09 33 10 130 120 58.02 0.08 34 11 14 3 482.28 2.27 35 11 15 4 476.35 0.70 36 11 76 65 58.06 0.09 37 12 15 3 476.36 0.70 38 12 16 4 476.25 0.60 39 13 16 3 483.45 2.46 40 13 17 4 476.12 0.50 41 13 117 104 74.91 0.15 42 13 120 107 75.06 0.21 43 13 121 108 75.06 0.21 44 13 122 109 75.00 0.20 45 13 127 114 74.03 0.59 46 14 17 3 476.29 0.58 47 14 18 4 476.12 0.50 48 14 21 7 457.45 2.82 49 14 69 55 75.03 0.32 50 14 72 58 74.82 0.27 51 14 73 59 74.09 0.62 52 14 76 62 74.09 0.64 53 14 117 103 75.06 0.21 54 14 127 113 75.04 0.22 55 15 18 3 476.29 0.58 56 15 19 4 476.29 0.58 57 16 19 3 482.30 1.70 58 16 20 4 481.56 1.63 59 16 120 104 78.89 2.12 60 16 121 105 78.94 2.10 61 17 20 3 482.30 1.70 62 17 21 4 476.06 0.48 63 17 117 100 78.87 2.12 64 17 120 103 78.89 2.12 65 18 21 3 469.90 2.59 66 18 69 51 113.16 19.40 67 20 23 3 492.50 0.23 68 20 24 4 467.07 0.83 69 20 120 100 107.48 1.57 70 21 24 3 469.40 0.33 71 21 25 4 467.07 0.83 72 21 26 5 467.18 0.79 73 21 28 7 451.48 2.06 74 21 65 44 164.68 1.18 75 21 68 47 161.51 2.73 76 21 69 48 127.84 13.54 77 21 116 95 119.14 0.91 78 22 26 4 494.28 3.16 79 23 26 3 502.91 0.50 80 23 27 4 476.29 4.43 81 24 27 3 490.24 2.55 82 24 28 4 469.24 0.91 83 24 116 92 131.15 0.70 84 24 120 96 135.84 2.10 85 25 28 3 481.18 2.38 86 25 29 4 468.67 1.19 87 25 65 40 174.14 3.62 88 26 29 3 485.81 4.80 89 26 30 4 468.65 1.20 90 26 56 30 191.94 0.35 91 26 61 35 183.13 0.71 92 26 65 39 174.16 3.63 93 27 30 3 476.53 0.06 94 27 31 4 472.94 1.85 95 27 56 29 196.89 2.11 96 27 116 89 143.78 0.61 97 28 31 3 476.95 0.13 98 28 32 4 476.04 0.34 99 28 68 40 182.92 0.72 100 28 112 84 143.81 0.61 101 28 113 85 143.77 0.62 102 28 116 88 143.78 0.60 103 29 32 3 476.05 0.34 104 29 33 4 476.55 0.09 105 29 61 32 189.12 0.80 106 29 64 35 188.60 0.56 107 29 65 36 182.84 0.51 108 29 68 39 174.56 3.62 109 30 33 3 478.68 0.97 110 30 34 4 476.55 0.09 111 30 52 22 214.16 0.60 112 30 53 23 214.14 0.58 113 30 55 25 212.12 0.21 114 30 56 26 206.83 2.37 115 30 61 31 192.28 0.31 116 31 34 3 482.09 2.43 117 31 35 4 476.55 0.09 118 31 112 81 143.83 0.61 119 32 35 3 487.62 1.23 120 32 36 4 468.30 4.04 121 32 39 7 397.88 4.49 122 32 109 77 143.80 0.62 123 32 112 80 143.84 0.61 124 33 36 3 482.96 1.65 125 33 39 6 385.54 1.69 126 33 40 7 306.67 0.72 127 33 43 10 281.10 0.17 128 33 47 14 244.22 0.71 129 33 52 19 215.50 0.92 130 33 55 22 214.50 0.42 131 33 61 28 212.12 0.19 132 34 52 18 214.73 0.46 133 36 39 3 481.23 3.70 134 36 40 4 477.01 1.59 135 36 108 72 144.16 0.56 136 36 112 76 144.06 0.58 137 37 40 3 489.76 1.07 138 37 41 4 477.01 1.59 139 37 52 15 216.72 1.05 140 38 41 3 489.76 1.07 141 38 42 4 477.01 1.59 142 38 105 67 144.22 0.56 143 39 42 3 488.47 1.73 144 39 43 4 477.00 1.59 145 39 105 66 144.18 0.56 146 40 43 3 488.12 1.90 147 40 47 7 396.92 9.10 148 40 50 10 260.81 0.35 149 40 52 12 216.79 1.05 150 40 55 15 216.71 1.08 151 41 44 3 483.07 0.62 152 42 99 57 144.75 0.54 153 42 100 58 144.76 0.56 154 42 101 59 144.71 0.58 155 42 105 63 144.62 0.62 156 43 46 3 481.92 0.05 157 43 47 4 466.32 4.58 158 43 64 21 215.38 1.22 159 44 47 3 485.02 1.51 160 44 48 4 461.13 7.17 161 44 49 5 281.12 4.79 162 45 48 3 476.48 0.50 163 46 60 14 216.21 1.41 164 46 64 18 216.18 1.41 165 47 50 3 479.03 2.87 166 47 55 8 230.28 4.26 167 47 58 11 220.27 2.83 168 47 60 13 216.28 1.45 169 47 61 14 216.55 1.57 170 50 54 4 475.56 2.25 171 50 55 5 448.19 1.24 172 51 54 3 501.92 1.79 173 51 55 4 486.65 2.00 174 52 55 3 495.76 1.29 175 54 58 4 495.92 2.08 176 55 58 3 494.14 1.19 177 55 61 6 365.09 3.22 178 56 61 5 417.10 4.88 179 58 61 3 481.38 4.87 180 58 62 4 467.21 2.24 181 59 62 3 467.22 2.24 182 59 63 4 467.20 2.24 183 60 63 3 478.75 0.04 184 60 64 4 470.62 0.53 185 61 64 3 475.18 1.74 186 61 65 4 470.62 0.53 187 62 65 3 478.75 0.05 188 62 66 4 470.58 0.51 189 63 66 3 472.48 0.52 190 63 67 4 459.50 5.04 191 64 67 3 467.71 2.91 192 64 68 4 459.47 5.03 193 65 68 3 475.93 2.31 194 65 69 4 459.47 5.02 195 66 69 3 483.53 3.34 196 66 70 4 460.64 4.43 197 67 70 3 486.97 1.61 198 67 71 4 464.98 1.88 199 68 71 3 487.19 1.54 200 68 72 4 466.88 2.83 201 68 113 45 144.15 0.57 202 69 72 3 486.57 1.85 203 69 73 4 463.81 2.42 204 70 73 3 474.50 0.98 205 70 74 4 468.10 2.67 206 71 74 3 472.24 0.60 207 71 75 4 467.62 2.94 208 71 88 17 148.71 0.42 209 71 92 21 148.37 0.44 210 72 75 3 481.54 2.00 211 72 76 4 473.62 5.96 212 73 76 3 480.75 2.40 213 73 77 4 479.75 2.89 214 74 77 3 481.89 1.82 215 74 78 4 480.75 2.40 216 74 88 14 148.99 0.43 217 75 78 3 484.00 0.77 218 75 79 4 479.75 2.89 219 75 85 10 150.86 1.36 220 75 88 13 149.00 0.43 221 75 89 14 148.99 0.43 222 75 92 17 148.99 0.43 223 75 110 35 144.48 0.46 224 75 134 59 143.87 0.59 225 76 79 3 492.84 0.28 226 78 81 3 465.43 4.28 227 78 84 6 281.60 0.86 228 78 85 7 267.56 3.21 229 79 85 6 379.95 25.20 230 79 130 51 144.13 0.56 231 81 84 3 484.16 0.91 232 81 85 4 458.29 4.70 233 82 85 3 475.41 3.47 234 82 86 4 456.96 0.86 235 83 86 3 478.86 0.90 236 83 87 4 465.67 4.07 237 84 87 3 484.17 1.25 238 84 88 4 474.03 6.32 239 85 88 3 483.66 1.51 240 85 89 4 477.62 4.53 241 85 134 49 143.91 0.61 242 85 137 52 143.70 0.66 243 86 89 3 479.95 3.35 244 86 90 4 471.19 1.30 245 86 137 51 143.69 0.66 246 87 90 3 496.28 1.30 247 87 91 4 481.22 2.73 248 88 91 3 492.79 3.05 249 88 92 4 474.55 0.42 250 89 92 3 481.82 3.20 251 89 93 4 474.53 0.42 252 89 134 45 143.91 0.61 253 89 137 48 143.31 0.67 254 89 138 49 141.59 1.26 255 90 93 3 489.59 3.31 256 90 94 4 473.39 0.14 257 91 94 3 483.45 1.20 258 91 95 4 479.85 3.00 259 92 95 3 488.13 0.71 260 92 96 4 476.21 4.82 261 92 106 14 176.63 0.75 262 92 138 46 141.58 1.26 263 93 96 3 488.13 0.71 264 93 97 4 471.27 2.38 265 93 138 45 139.00 0.03 266 93 141 48 117.82 3.65 267 93 142 49 117.44 3.71 268 94 97 3 485.55 0.15 269 94 98 4 474.43 0.81 270 95 98 3 483.36 1.17 271 95 99 4 477.96 2.48 272 96 99 3 481.22 1.38 273 96 100 4 477.81 2.41 274 96 101 5 427.26 8.09 275 96 106 10 250.41 3.86 276 97 100 3 487.73 3.23 277 97 101 4 466.59 2.00 278 97 142 45 109.14 0.37 279 101 105 4 469.88 0.39 280 101 106 5 469.88 0.40 281 101 142 41 109.16 0.35 282 102 105 3 471.81 0.57 283 102 106 4 469.92 0.40 284 102 142 40 109.16 0.36 285 103 106 3 481.92 0.43 286 103 107 4 472.69 0.12 287 103 135 32 143.59 0.53 288 103 139 36 130.71 0.40 289 103 142 39 109.21 0.33 290 104 107 3 477.39 2.09 291 104 108 4 472.86 0.18 292 105 108 3 479.25 3.02 293 105 109 4 473.28 0.03 294 106 109 3 488.85 3.70 295 106 110 4 474.79 0.79 296 106 135 29 143.65 0.49 297 106 138 32 135.52 0.74 298 106 142 36 109.30 0.29 299 107 110 3 478.76 1.20 300 107 111 4 474.74 0.82 301 107 135 28 143.52 0.53 302 108 111 3 474.73 0.82 303 108 112 4 474.71 0.83 304 109 112 3 480.06 3.46 305 109 113 4 474.63 0.85 306 110 113 3 474.30 0.81 307 110 114 4 474.11 0.64 308 110 131 21 143.74 0.51 309 110 134 24 143.68 0.48 310 110 135 25 143.63 0.47 311 110 138 28 135.53 0.73 312 111 114 3 479.06 1.49 313 111 115 4 474.15 0.62 314 112 115 3 503.54 3.10 315 112 116 4 474.13 0.63 316 113 116 3 487.25 1.05 317 113 117 4 475.31 0.04 318 113 127 14 151.20 3.10 319 114 117 3 486.26 0.57 320 114 124 10 192.66 23.58 321 114 127 13 146.15 0.70 322 114 128 14 151.68 3.55 323 115 118 3 493.01 3.91 324 115 124 9 202.02 18.91 325 116 119 3 499.97 0.43 326 116 120 4 493.01 3.91 327 117 120 3 492.97 3.93 328 117 121 4 481.70 1.70 329 117 122 5 278.17 6.87 330 117 127 10 241.23 6.61 331 118 121 3 479.58 2.75 332 118 122 4 440.07 13.04 333 118 124 6 263.18 1.16 334 122 127 5 457.06 6.33 335 123 126 3 471.92 2.18 336 123 127 4 465.36 2.21 337 124 127 3 469.25 3.52 338 124 128 4 465.37 2.21 339 125 128 3 474.88 0.70 340 125 129 4 478.35 4.29 341 126 129 3 481.61 2.66 342 126 130 4 478.49 4.21 343 127 130 3 478.50 4.21 344 127 131 4 478.50 4.22 345 128 131 3 482.88 6.41 346 128 132 4 478.50 4.23 347 129 132 3 484.87 5.40 348 129 133 4 480.24 3.37 349 130 133 3 484.87 5.40 350 130 134 4 481.24 2.87 351 131 134 3 479.56 2.56 352 131 135 4 473.43 0.04 353 132 135 3 474.45 0.54 354 132 136 4 474.44 0.55 355 133 136 3 492.84 1.64 356 133 137 4 481.83 4.21 357 134 137 3 484.99 5.56 358 134 138 4 473.94 0.27 359 135 138 3 479.66 2.58 360 135 139 4 470.00 1.47 361 135 140 5 476.19 0.55 362 136 140 4 488.94 0.30 363 137 140 3 505.69 0.67 364 137 141 4 489.70 0.58 365 138 141 3 489.60 0.64 366 138 142 4 482.81 2.76 367 139 142 3 489.28 0.48