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 5 457.95 0.14 2 2 79 77 25.52 0.38 3 2 129 127 17.78 0.10 4 2 130 128 17.86 0.28 5 3 6 3 466.26 1.39 6 3 7 4 469.03 2.78 7 4 7 3 479.07 3.16 8 4 8 4 471.04 3.79 9 5 8 3 471.67 4.09 10 5 9 4 468.97 4.83 11 6 9 3 476.30 1.78 12 6 10 4 471.62 4.10 13 6 126 120 41.55 0.10 14 6 129 123 41.59 0.09 15 7 10 3 481.64 0.97 16 7 11 4 471.63 4.10 17 7 79 72 44.52 0.74 18 7 80 73 47.28 1.33 19 8 11 3 474.42 5.50 20 8 12 4 473.20 3.32 21 9 12 3 485.72 1.12 22 9 13 4 472.94 3.04 23 9 121 112 70.64 1.05 24 9 122 113 60.95 0.35 25 9 123 114 60.97 0.35 26 9 126 117 60.95 0.35 27 10 13 3 478.63 5.05 28 10 14 4 473.41 3.22 29 10 76 66 60.96 0.34 30 10 79 69 60.97 0.34 31 10 126 116 60.96 0.35 32 10 127 117 60.94 0.35 33 10 130 120 60.94 0.34 34 11 14 3 475.88 1.58 35 11 15 4 473.05 3.00 36 11 76 65 60.97 0.33 37 12 15 3 473.84 2.66 38 12 16 4 475.87 4.41 39 13 16 3 481.00 1.84 40 13 17 4 473.11 3.02 41 13 117 104 73.81 0.83 42 13 120 107 74.00 0.83 43 13 121 108 74.00 0.83 44 13 122 109 73.30 0.96 45 13 127 114 73.08 0.86 46 14 17 3 487.58 4.21 47 14 18 4 473.09 3.03 48 14 21 7 454.89 5.95 49 14 69 55 73.71 0.89 50 14 72 58 73.06 0.85 51 14 73 59 73.32 0.98 52 14 76 62 72.77 0.99 53 14 113 99 73.91 0.81 54 14 117 103 73.95 0.82 55 14 127 113 73.52 0.98 56 15 18 3 481.13 0.88 57 15 19 4 472.98 3.08 58 16 19 3 492.02 2.23 59 16 20 4 473.85 2.64 60 16 120 104 74.00 0.83 61 17 20 3 474.55 2.99 62 17 21 4 468.70 2.25 63 17 117 100 74.00 0.83 64 17 120 103 74.07 0.84 65 18 21 3 475.76 2.44 66 18 69 51 114.92 19.68 67 20 23 3 493.34 0.80 68 20 24 4 464.93 3.52 69 20 120 100 113.61 0.73 70 21 24 3 477.35 1.62 71 21 25 4 469.24 5.68 72 21 26 5 476.78 1.92 73 21 28 7 464.92 3.50 74 21 65 44 179.52 1.27 75 21 68 47 174.97 3.57 76 21 69 48 157.80 0.89 77 21 116 95 118.45 1.67 78 22 26 4 488.16 0.18 79 23 26 3 501.43 0.97 80 23 27 4 487.82 0.03 81 24 27 3 487.83 0.02 82 24 28 4 482.38 2.73 83 24 116 92 126.25 1.30 84 24 120 96 131.68 1.41 85 25 28 3 483.51 2.18 86 25 29 4 482.39 2.73 87 25 65 40 180.97 0.84 88 26 29 3 481.86 2.47 89 26 30 4 481.85 2.46 90 26 56 30 195.83 1.12 91 26 61 35 188.48 3.67 92 26 65 39 180.96 0.84 93 27 30 3 481.86 2.47 94 27 31 4 480.72 3.03 95 27 56 29 196.18 1.19 96 27 116 89 142.34 0.10 97 28 31 3 480.72 3.04 98 28 32 4 477.03 1.20 99 28 68 40 181.06 0.90 100 28 112 84 142.72 0.07 101 28 113 85 142.69 0.07 102 28 116 88 142.34 0.10 103 29 32 3 476.29 1.56 104 29 33 4 470.91 1.12 105 29 43 14 253.89 2.54 106 29 61 32 195.86 1.03 107 29 64 35 190.05 1.65 108 29 65 36 184.69 1.02 109 29 68 39 182.80 1.77 110 30 33 3 475.60 1.62 111 30 34 4 470.89 1.14 112 30 52 22 212.68 1.02 113 30 55 25 210.73 1.61 114 30 56 26 200.95 1.81 115 30 61 31 196.27 1.20 116 31 34 3 482.07 0.94 117 31 35 4 469.10 0.24 118 31 112 81 142.72 0.07 119 32 35 3 480.10 3.75 120 32 36 4 465.79 1.40 121 32 39 7 425.72 1.79 122 32 109 77 142.90 0.15 123 32 112 80 142.74 0.07 124 33 36 3 467.62 0.24 125 33 37 4 461.60 3.23 126 33 39 6 397.90 11.87 127 33 40 7 345.10 27.66 128 33 43 10 351.86 22.33 129 33 47 14 273.25 0.29 130 33 52 19 217.08 2.35 131 33 55 22 215.78 2.34 132 33 61 28 212.16 1.14 133 34 52 18 222.99 3.98 134 35 112 77 143.08 0.06 135 36 39 3 483.32 3.71 136 36 40 4 473.52 2.51 137 36 108 72 143.40 0.13 138 36 112 76 143.33 0.14 139 37 40 3 477.54 4.52 140 37 41 4 473.53 2.51 141 37 52 15 227.97 1.99 142 38 41 3 479.97 0.70 143 38 42 4 476.64 3.55 144 38 105 67 143.74 0.17 145 39 42 3 489.12 0.08 146 39 43 4 489.12 0.07 147 39 105 66 143.56 0.09 148 40 43 3 489.79 0.41 149 40 47 7 439.80 9.69 150 40 50 10 256.67 0.46 151 40 51 11 239.59 0.61 152 40 52 12 227.97 1.98 153 40 55 15 227.91 1.96 154 41 44 3 491.03 1.51 155 42 99 57 144.60 0.20 156 42 100 58 144.53 0.16 157 42 101 59 144.48 0.15 158 43 46 3 476.91 1.35 159 43 47 4 445.44 6.88 160 43 64 21 214.06 0.36 161 44 47 3 487.90 0.34 162 44 48 4 445.44 6.88 163 44 49 5 333.94 23.87 164 45 48 3 485.50 1.54 165 46 60 14 217.58 1.71 166 46 64 18 217.56 1.71 167 47 50 3 494.07 3.21 168 47 55 8 239.53 0.64 169 47 58 11 223.69 4.36 170 47 60 13 217.56 1.70 171 47 61 14 217.72 1.68 172 50 54 4 475.66 0.29 173 50 55 5 443.05 2.95 174 51 54 3 488.10 0.42 175 51 55 4 479.97 1.16 176 52 55 3 501.83 2.27 177 54 58 4 486.74 1.09 178 55 58 3 482.18 0.96 179 55 61 6 346.70 2.41 180 56 61 5 380.35 4.67 181 58 61 3 467.06 1.29 182 58 62 4 466.67 4.08 183 59 62 3 481.12 1.67 184 59 63 4 469.51 2.65 185 60 63 3 480.88 1.54 186 60 64 4 469.50 2.65 187 61 64 3 479.37 2.28 188 61 65 4 466.04 0.79 189 62 65 3 478.05 2.94 190 62 66 4 471.11 1.75 191 63 66 3 478.62 2.01 192 63 67 4 466.00 0.77 193 64 67 3 479.41 2.41 194 64 68 4 465.84 0.69 195 65 68 3 475.88 1.79 196 65 69 4 474.01 0.99 197 66 69 3 482.59 0.77 198 66 70 4 474.03 0.99 199 67 70 3 485.51 2.08 200 67 71 4 474.07 0.97 201 68 71 3 492.01 1.19 202 68 72 4 472.55 0.21 203 68 113 45 143.10 0.04 204 69 72 3 484.12 2.77 205 69 73 4 471.14 0.48 206 70 73 3 486.88 1.38 207 70 74 4 473.47 0.68 208 71 74 3 484.32 2.66 209 71 75 4 479.10 1.52 210 71 88 17 152.38 0.57 211 71 92 21 148.84 1.26 212 72 75 3 479.10 1.52 213 72 76 4 479.10 1.52 214 73 76 3 479.10 1.52 215 73 77 4 479.10 1.52 216 74 77 3 482.59 3.26 217 74 78 4 479.11 1.52 218 74 88 14 152.68 0.49 219 75 78 3 487.09 1.01 220 75 79 4 475.55 3.31 221 75 85 10 157.37 0.79 222 75 88 13 152.69 0.49 223 75 89 14 152.66 0.49 224 75 92 17 152.66 0.49 225 75 110 35 143.91 0.12 226 75 134 59 142.19 0.09 227 76 79 3 484.35 0.36 228 76 127 51 142.72 0.14 229 78 81 3 474.66 1.76 230 78 84 6 333.53 27.03 231 78 85 7 250.69 1.81 232 79 85 6 411.77 14.47 233 79 130 51 142.64 0.11 234 81 84 3 487.85 2.35 235 81 85 4 472.97 5.91 236 82 85 3 480.11 4.49 237 82 86 4 483.95 0.42 238 83 86 3 489.79 2.50 239 83 87 4 480.37 1.76 240 84 87 3 493.43 0.68 241 84 88 4 479.99 1.56 242 85 88 3 490.60 0.70 243 85 89 4 477.39 2.85 244 85 134 49 142.25 0.10 245 85 137 52 141.57 0.18 246 86 89 3 483.23 0.07 247 86 90 4 478.84 2.12 248 86 137 51 141.57 0.18 249 87 90 3 482.71 1.78 250 87 91 4 473.49 1.82 251 88 91 3 482.85 0.70 252 88 92 4 472.37 1.27 253 89 92 3 479.38 2.44 254 89 93 4 474.24 0.12 255 89 134 45 142.22 0.10 256 89 137 48 141.18 0.31 257 89 138 49 140.63 0.35 258 90 93 3 482.75 4.12 259 90 94 4 477.76 1.90 260 91 94 3 481.88 0.17 261 91 95 4 478.26 1.67 262 92 95 3 487.94 2.87 263 92 96 4 478.28 1.67 264 92 106 14 207.00 7.11 265 92 138 46 140.28 0.18 266 93 96 3 488.09 2.79 267 93 97 4 478.58 1.55 268 93 138 45 138.94 0.35 269 93 141 48 112.06 0.46 270 93 142 49 106.63 1.86 271 94 97 3 483.06 0.26 272 94 98 4 478.61 1.54 273 95 98 3 482.87 0.50 274 95 99 4 482.12 0.20 275 96 99 3 486.71 1.69 276 96 100 4 482.12 0.20 277 96 101 5 450.29 1.63 278 96 106 10 273.51 4.91 279 97 100 3 482.53 0.41 280 97 101 4 461.07 7.03 281 97 102 5 450.29 1.64 282 97 142 45 106.46 1.94 283 101 105 4 467.23 0.77 284 101 106 5 463.25 1.20 285 101 142 41 106.49 1.92 286 102 105 3 467.24 0.78 287 102 106 4 475.28 3.25 288 102 142 40 106.49 1.92 289 103 106 3 484.26 1.24 290 103 107 4 475.28 3.25 291 103 135 32 141.90 0.23 292 103 139 36 133.03 0.42 293 103 142 39 104.66 1.04 294 104 107 3 483.65 0.94 295 104 108 4 475.27 3.25 296 105 108 3 483.66 0.94 297 105 109 4 480.32 0.42 298 106 109 3 483.36 1.09 299 106 110 4 483.36 1.09 300 106 135 29 141.91 0.24 301 106 138 32 135.05 0.01 302 106 142 36 104.69 1.02 303 107 110 3 483.36 1.09 304 107 111 4 476.48 4.54 305 107 135 28 141.56 0.40 306 108 111 3 483.35 1.10 307 108 112 4 473.45 3.03 308 109 112 3 481.55 5.08 309 109 113 4 470.03 3.04 310 110 113 3 475.07 5.68 311 110 114 4 466.33 2.52 312 110 131 21 142.15 0.14 313 110 134 24 142.27 0.22 314 110 135 25 142.07 0.17 315 110 138 28 136.61 0.79 316 111 114 3 481.64 2.40 317 111 115 4 473.87 6.29 318 112 115 3 478.17 4.13 319 112 116 4 472.09 5.40 320 113 116 3 476.24 3.33 321 113 117 4 472.07 5.41 322 113 127 14 142.56 0.18 323 114 117 3 486.96 4.22 324 114 124 10 146.13 0.62 325 114 127 13 142.56 0.18 326 114 128 14 142.72 0.28 327 115 118 3 502.11 0.04 328 115 124 9 149.56 1.69 329 116 119 3 502.41 0.10 330 116 120 4 497.93 2.12 331 117 120 3 490.40 2.42 332 117 121 4 482.59 1.48 333 117 122 5 273.92 3.20 334 117 127 10 208.03 6.88 335 118 121 3 482.86 1.34 336 118 122 4 398.81 7.75 337 118 124 6 279.20 0.57 338 122 127 5 449.20 2.33 339 123 126 3 474.66 3.43 340 123 127 4 464.81 0.48 341 124 127 3 472.12 4.12 342 124 128 4 468.28 1.26 343 125 128 3 484.67 3.37 344 125 129 4 468.56 1.12 345 126 129 3 485.50 2.96 346 126 130 4 468.56 1.12 347 127 130 3 478.06 1.61 348 127 131 4 462.73 1.63 349 128 131 3 468.43 1.22 350 128 132 4 462.74 1.63 351 129 132 3 478.98 0.30 352 129 133 4 466.56 3.54 353 130 133 3 480.96 0.69 354 130 134 4 466.57 3.54 355 131 134 3 479.61 1.37 356 131 135 4 464.57 4.53 357 132 135 3 479.48 1.43 358 132 136 4 468.43 2.60 359 133 136 3 480.95 0.70 360 133 137 4 472.80 4.77 361 134 137 3 479.08 1.63 362 134 138 4 476.43 2.95 363 135 138 3 468.02 2.39 364 135 139 4 460.71 2.79 365 136 140 4 494.67 5.50 366 137 140 3 513.51 1.94 367 137 141 4 498.81 3.43 368 138 141 3 502.86 0.67 369 138 142 4 478.66 0.57 370 139 142 3 478.66 0.57