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 5 456.23 3.07 2 2 74 72 30.88 0.54 3 2 77 75 25.41 0.52 4 2 128 126 22.72 0.14 5 2 129 127 22.72 0.14 6 3 6 3 472.59 5.11 7 3 7 4 470.50 3.58 8 4 7 3 482.61 0.90 9 4 8 4 471.51 3.07 10 5 8 3 484.84 3.58 11 5 9 4 474.81 1.42 12 6 9 3 477.68 0.01 13 6 10 4 473.76 0.90 14 6 125 119 49.02 0.69 15 6 128 122 49.02 0.69 16 7 10 3 475.85 1.94 17 7 11 4 473.75 0.90 18 7 74 67 49.41 0.48 19 7 75 68 49.41 0.49 20 8 11 3 478.38 0.35 21 8 12 4 465.76 1.58 22 9 12 3 472.54 2.57 23 9 13 4 465.76 1.59 24 9 125 116 53.38 2.21 25 10 13 3 480.38 1.76 26 10 14 4 466.87 2.54 27 10 71 61 53.39 2.21 28 10 74 64 53.40 2.21 29 10 125 115 53.63 2.08 30 10 126 116 53.62 2.08 31 10 129 119 53.38 2.21 32 11 14 3 474.44 1.21 33 11 15 4 468.62 1.68 34 11 74 63 53.38 2.21 35 12 15 3 489.29 0.31 36 12 16 4 474.73 1.38 37 13 16 3 478.87 3.21 38 13 17 4 467.33 2.31 39 13 117 104 81.18 0.01 40 13 122 109 55.12 1.67 41 13 126 113 54.73 1.67 42 14 17 3 474.72 1.39 43 14 18 4 464.42 3.75 44 14 21 7 416.84 17.29 45 14 67 53 54.82 1.62 46 14 68 54 54.61 1.73 47 14 71 57 54.59 1.72 48 16 19 3 524.99 0.71 49 16 117 101 94.41 0.54 50 17 20 3 503.16 2.33 51 17 24 7 449.75 1.58 52 17 110 93 94.39 0.53 53 17 114 97 95.43 0.06 54 17 117 100 95.42 0.04 55 18 21 3 469.88 0.98 56 19 114 95 123.88 1.80 57 20 23 3 475.97 0.24 58 20 24 4 463.81 0.98 59 20 114 94 123.89 1.79 60 21 24 3 474.64 4.42 61 21 25 4 463.82 0.99 62 21 64 43 101.68 0.92 63 22 25 3 474.06 4.12 64 22 26 4 474.09 4.13 65 22 61 39 109.95 3.15 66 23 26 3 477.62 2.37 67 23 27 4 477.62 2.37 68 23 113 90 132.85 0.11 69 24 27 3 482.63 1.24 70 24 28 4 474.03 4.17 71 24 64 40 124.66 1.38 72 24 106 82 124.74 1.36 73 24 109 85 127.92 0.14 74 24 110 86 130.40 0.57 75 24 113 89 132.85 0.10 76 24 114 90 132.84 0.11 77 25 28 3 479.80 3.45 78 25 29 4 471.64 5.36 79 25 60 35 124.72 1.38 80 25 64 39 124.66 1.38 81 26 29 3 479.80 3.45 82 26 30 4 474.34 4.01 83 26 56 30 132.31 0.14 84 26 57 31 132.57 0.12 85 26 60 34 127.91 0.18 86 27 30 3 473.43 0.26 87 27 31 4 471.05 1.43 88 27 109 82 132.92 0.09 89 27 113 86 134.91 0.56 90 28 31 3 489.38 2.22 91 28 32 4 476.57 4.18 92 28 102 74 132.84 0.10 93 28 105 77 132.85 0.09 94 28 106 78 132.84 0.10 95 28 109 81 133.72 0.21 96 29 32 3 484.03 5.76 97 29 33 4 476.59 4.17 98 29 56 27 134.69 0.64 99 29 59 30 134.67 0.65 100 29 60 31 133.48 0.38 101 29 63 34 133.50 0.37 102 30 33 3 491.77 1.89 103 30 34 4 471.01 1.42 104 30 51 21 134.78 0.66 105 30 56 26 134.69 0.65 106 31 34 3 474.78 3.94 107 31 35 4 470.36 1.74 108 31 105 74 134.21 0.51 109 31 108 77 134.88 0.56 110 31 109 78 134.91 0.56 111 32 35 3 482.00 1.46 112 32 36 4 462.34 5.75 113 32 39 7 360.65 3.11 114 32 43 11 338.86 2.65 115 32 101 69 134.18 0.53 116 32 102 70 134.17 0.52 117 32 105 73 134.25 0.50 118 33 36 3 492.80 3.97 119 33 37 4 456.44 2.81 120 33 39 6 345.07 4.67 121 33 40 7 305.70 13.92 122 33 43 10 305.77 13.83 123 33 49 16 135.18 0.52 124 33 56 23 135.11 0.53 125 34 37 3 482.31 1.28 126 34 51 17 135.19 0.52 127 36 39 3 499.26 2.62 128 36 101 65 134.24 0.51 129 36 104 68 134.94 0.52 130 36 105 69 134.95 0.53 131 37 40 3 493.18 1.52 132 38 41 3 516.77 1.60 133 39 42 3 504.74 1.95 134 39 43 4 492.91 1.39 135 39 98 59 134.25 0.50 136 40 43 3 497.35 1.39 137 40 44 4 483.10 3.07 138 41 44 3 487.88 0.68 139 42 45 3 549.72 2.25 140 42 94 52 132.96 0.03 141 42 95 53 134.18 0.48 142 42 98 56 134.81 0.51 143 43 46 3 496.38 1.08 144 43 49 6 135.82 0.44 145 43 59 16 135.15 0.53 146 46 49 3 492.14 2.68 147 46 55 9 136.00 0.56 148 46 56 10 137.49 0.18 149 46 59 13 136.00 0.56 150 47 55 8 199.51 30.71 151 48 53 5 288.53 10.54 152 48 55 7 272.20 5.62 153 49 53 4 340.92 13.14 154 49 56 7 266.51 2.79 155 50 53 3 478.75 2.04 156 50 56 6 328.88 7.13 157 53 56 3 488.12 0.99 158 53 57 4 467.63 2.33 159 54 57 3 479.22 3.46 160 54 58 4 467.64 2.34 161 55 58 3 489.37 1.61 162 55 59 4 467.66 2.35 163 56 59 3 480.51 0.45 164 56 60 4 471.05 3.05 165 57 60 3 488.26 1.11 166 57 61 4 486.19 2.12 167 58 61 3 493.28 0.42 168 58 62 4 486.20 2.12 169 59 62 3 486.59 1.93 170 59 63 4 486.20 2.12 171 60 63 3 486.67 1.89 172 60 64 4 486.20 2.12 173 61 64 3 486.67 1.89 174 61 65 4 471.78 3.46 175 62 65 3 471.76 3.46 176 62 66 4 471.75 3.46 177 63 66 3 475.33 1.68 178 63 67 4 475.78 1.45 179 63 102 39 204.59 1.97 180 64 67 3 481.16 4.14 181 64 68 4 469.89 1.28 182 64 106 42 206.72 1.53 183 65 68 3 486.94 2.21 184 65 69 4 474.19 0.86 185 66 69 3 477.81 0.89 186 66 70 4 474.24 0.89 187 66 84 18 204.87 2.02 188 67 70 3 480.36 2.16 189 67 71 4 479.67 1.85 190 67 106 39 211.44 0.57 191 67 129 62 219.53 3.41 192 67 130 63 207.04 1.74 193 67 133 66 206.24 2.09 194 68 71 3 480.34 2.17 195 68 72 4 479.69 1.85 196 69 72 3 480.34 2.17 197 69 73 4 479.69 1.85 198 69 80 11 234.71 15.49 199 69 81 12 233.87 15.91 200 69 83 14 233.88 15.91 201 69 84 15 233.85 15.92 202 70 73 3 479.68 1.85 203 70 74 4 446.24 2.12 204 70 77 7 286.31 2.52 205 70 81 11 233.88 15.91 206 70 129 59 240.08 2.92 207 70 133 63 206.33 2.06 208 71 74 3 475.04 0.48 209 71 129 58 240.44 2.75 210 73 76 3 486.98 3.91 211 73 77 4 438.43 8.61 212 73 80 7 287.26 2.90 213 74 77 3 484.53 4.06 214 74 129 55 250.00 1.42 215 76 79 3 494.71 1.88 216 76 80 4 467.20 2.15 217 77 80 3 469.57 1.42 218 77 81 4 467.21 2.15 219 77 129 52 252.37 1.02 220 77 132 55 251.27 1.35 221 77 133 56 251.22 1.36 222 77 136 59 251.19 1.39 223 78 81 3 500.30 0.41 224 78 82 4 467.34 0.30 225 78 136 58 251.22 1.38 226 78 139 61 251.03 1.47 227 79 82 3 487.53 0.58 228 80 83 3 560.15 0.56 229 81 84 3 488.51 1.02 230 81 85 4 472.35 0.71 231 81 133 52 253.38 1.31 232 81 136 55 253.22 1.36 233 81 137 56 253.23 1.37 234 82 85 3 487.10 0.41 235 82 86 4 472.42 0.75 236 82 140 58 253.26 1.36 237 83 86 3 483.53 1.44 238 83 87 4 472.44 0.78 239 84 87 3 481.05 2.12 240 84 88 4 475.41 0.70 241 84 137 53 253.48 1.35 242 85 88 3 487.03 0.46 243 85 89 4 472.41 0.80 244 85 136 51 253.50 1.34 245 85 137 52 253.48 1.35 246 85 139 54 253.47 1.34 247 85 140 55 253.36 1.40 248 86 89 3 488.56 0.63 249 86 90 4 472.39 0.80 250 86 140 54 253.35 1.40 251 87 90 3 490.72 1.71 252 87 91 4 436.09 10.14 253 87 92 5 403.37 2.56 254 88 92 4 397.17 5.66 255 88 93 5 374.49 16.98 256 88 94 6 290.12 5.54 257 88 99 11 256.97 1.40 258 88 141 53 253.46 1.34 259 89 93 4 347.60 26.46 260 89 140 51 253.58 1.40 261 89 141 52 253.42 1.34 262 90 93 3 466.80 6.84 263 90 140 50 253.61 1.39 264 94 141 47 253.79 1.39 265 95 98 3 492.11 0.40 266 96 99 3 504.16 4.05 267 96 141 45 253.83 1.40 268 97 100 3 519.12 3.43 269 98 101 3 491.54 2.25 270 98 102 4 468.50 0.58 271 99 102 3 484.94 3.09 272 99 103 4 468.32 0.53 273 99 134 35 254.56 1.58 274 99 137 38 254.41 1.54 275 99 141 42 254.37 1.54 276 100 103 3 471.72 1.17 277 100 104 4 463.88 2.45 278 101 104 3 481.06 0.17 279 101 105 4 471.72 1.17 280 102 105 3 484.87 3.19 281 102 106 4 468.17 1.43 282 103 106 3 476.27 1.11 283 103 107 4 475.54 1.48 284 103 130 27 254.81 1.60 285 103 134 31 254.64 1.55 286 104 107 3 474.77 1.85 287 104 108 4 474.77 1.85 288 105 108 3 484.88 3.19 289 105 109 4 465.05 3.00 290 106 109 3 484.87 3.19 291 106 110 4 462.31 5.12 292 107 110 3 476.59 3.16 293 107 111 4 467.48 7.71 294 107 118 11 257.13 1.10 295 107 126 19 255.53 1.59 296 107 127 20 255.52 1.58 297 107 130 23 255.52 1.58 298 108 111 3 475.61 2.67 299 108 112 4 460.29 5.41 300 109 112 3 470.69 0.21 301 109 113 4 460.29 5.41 302 110 113 3 475.96 2.85 303 110 114 4 450.28 2.52 304 110 118 8 266.25 2.48 305 110 126 16 256.31 1.37 306 111 115 4 365.62 2.81 307 111 118 7 266.26 2.48 308 112 115 3 493.95 1.27 309 114 117 3 493.61 1.20 310 114 118 4 386.66 8.73 311 117 122 5 464.65 2.92 312 118 122 4 464.66 2.92 313 118 123 5 451.84 3.50 314 118 126 8 420.57 2.94 315 119 122 3 468.10 1.25 316 119 123 4 468.63 0.95 317 120 123 3 480.10 4.79 318 120 124 4 481.89 2.62 319 121 124 3 483.99 2.85 320 121 125 4 481.90 2.62 321 122 125 3 485.57 3.64 322 122 126 4 477.32 3.48 323 123 126 3 489.14 1.01 324 123 127 4 468.73 0.83 325 124 127 3 481.93 5.46 326 124 128 4 458.20 4.43 327 125 128 3 487.56 1.00 328 125 129 4 455.70 5.26 329 126 129 3 473.80 1.43 330 126 130 4 471.42 2.60 331 127 130 3 471.42 2.61 332 127 131 4 468.99 3.83 333 128 131 3 477.23 4.17 334 128 132 4 463.62 3.16 335 129 132 3 469.64 0.38 336 129 133 4 463.62 3.16 337 130 133 3 469.41 0.26 338 130 134 4 464.79 2.57 339 131 134 3 471.68 0.86 340 131 135 4 464.79 2.58 341 132 135 3 471.00 8.23 342 132 136 4 478.73 4.37 343 133 136 3 479.21 4.13 344 133 137 4 478.73 4.37 345 134 137 3 478.73 4.38 346 134 138 4 476.47 5.50 347 135 138 3 472.56 0.67 348 135 139 4 462.14 3.40 349 136 139 3 479.88 1.81 350 137 141 4 493.96 3.15 351 138 141 3 492.32 3.96