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 5 454.93 3.62 2 2 73 71 26.96 0.52 3 2 76 74 26.87 0.51 4 2 127 125 25.01 0.12 5 2 128 126 24.67 0.29 6 3 6 3 471.79 1.92 7 3 7 4 476.12 4.09 8 4 7 3 487.45 1.57 9 4 8 4 475.56 4.38 10 5 8 3 481.18 1.86 11 5 9 4 475.56 4.38 12 6 9 3 482.66 0.83 13 6 10 4 475.56 4.38 14 6 124 118 47.04 1.23 15 6 127 121 47.05 1.23 16 7 10 3 483.81 0.55 17 7 11 4 468.82 1.01 18 7 73 66 47.06 1.22 19 7 74 67 53.38 1.93 20 8 11 3 482.88 1.02 21 8 12 4 468.74 1.05 22 9 12 3 482.88 1.02 23 9 13 4 472.62 4.24 24 9 120 111 62.43 1.03 25 9 121 112 62.23 1.08 26 9 124 115 62.16 1.07 27 10 13 3 480.96 0.07 28 10 14 4 468.90 2.39 29 10 70 60 62.16 1.07 30 10 124 114 62.21 1.08 31 10 125 115 62.18 1.09 32 10 128 118 62.05 1.02 33 11 14 3 485.63 0.65 34 11 15 4 477.23 1.77 35 11 70 59 62.08 1.04 36 11 73 62 62.08 1.04 37 12 15 3 486.67 1.16 38 12 16 4 482.59 0.89 39 13 16 3 486.68 1.15 40 13 17 4 482.60 0.89 41 13 121 108 62.74 1.17 42 13 125 112 62.64 1.21 43 14 17 3 483.64 1.43 44 14 63 49 62.74 1.19 45 14 66 52 62.63 1.25 46 14 67 53 62.63 1.24 47 14 70 56 62.59 1.24 48 14 109 95 74.53 1.09 49 15 18 3 481.13 0.27 50 16 113 97 85.15 0.09 51 16 116 100 84.98 0.04 52 17 20 3 482.09 2.23 53 17 21 4 429.02 1.77 54 17 24 7 351.85 5.89 55 17 109 92 85.06 0.12 56 18 21 3 492.67 0.96 57 20 23 3 471.93 0.32 58 20 24 4 462.67 2.60 59 21 24 3 473.97 1.76 60 21 25 4 462.67 2.60 61 21 63 42 101.91 0.86 62 21 64 43 101.94 0.88 63 22 25 3 480.28 0.78 64 22 26 4 462.69 2.60 65 22 59 37 104.95 0.39 66 22 60 38 104.89 0.42 67 22 63 41 104.89 0.41 68 23 26 3 483.37 0.76 69 23 27 4 467.82 0.68 70 23 112 89 135.61 0.30 71 24 27 3 471.31 1.06 72 24 28 4 467.20 0.33 73 24 108 84 129.31 0.10 74 24 109 85 132.31 1.61 75 24 112 88 135.61 0.30 76 24 113 89 135.61 0.30 77 25 28 3 476.45 2.70 78 25 29 4 474.64 3.39 79 25 59 34 122.22 0.73 80 25 63 38 121.11 0.21 81 26 29 3 474.88 3.27 82 26 30 4 474.88 3.27 83 26 55 29 134.39 0.49 84 26 56 30 134.38 0.49 85 26 59 33 125.44 0.67 86 27 30 3 475.31 3.06 87 27 31 4 467.14 0.32 88 27 108 81 136.13 0.39 89 27 112 85 137.03 0.29 90 28 31 3 477.01 2.23 91 28 32 4 474.60 3.43 92 28 101 73 135.98 0.39 93 28 104 76 135.99 0.39 94 28 105 77 135.91 0.42 95 28 108 80 136.17 0.39 96 29 32 3 477.01 2.23 97 29 33 4 475.31 3.08 98 29 55 26 137.02 0.29 99 29 58 29 136.59 0.43 100 29 59 30 136.31 0.52 101 29 62 33 136.12 0.43 102 29 101 72 136.12 0.38 103 30 33 3 485.13 0.47 104 30 34 4 475.30 3.08 105 30 50 20 137.43 0.32 106 31 34 3 483.77 1.16 107 31 35 4 464.74 1.33 108 31 104 73 137.13 0.32 109 31 107 76 137.25 0.36 110 31 108 77 137.25 0.38 111 31 111 80 137.50 0.35 112 32 35 3 482.62 0.49 113 32 36 4 464.31 1.12 114 32 39 7 314.42 2.46 115 32 100 68 137.13 0.32 116 32 101 69 137.13 0.33 117 32 104 72 137.15 0.33 118 33 36 3 480.80 1.83 119 33 37 4 462.78 1.76 120 33 39 6 377.24 25.25 121 33 40 7 308.83 5.25 122 33 43 10 290.41 1.52 123 33 48 15 137.60 0.29 124 34 37 3 489.78 2.79 125 36 39 3 488.69 2.06 126 36 100 64 137.22 0.35 127 36 103 67 137.44 0.36 128 36 104 68 137.45 0.36 129 37 40 3 488.69 2.06 130 38 41 3 492.24 0.72 131 39 42 3 497.67 3.44 132 39 97 58 137.18 0.35 133 39 100 61 137.40 0.35 134 40 43 3 491.54 3.23 135 40 44 4 480.78 0.26 136 40 48 8 191.75 26.21 137 41 44 3 496.31 0.84 138 42 93 51 137.19 0.35 139 42 94 52 137.31 0.34 140 42 97 55 137.41 0.35 141 43 46 3 482.35 0.59 142 43 48 5 457.69 8.60 143 43 58 15 177.41 19.63 144 46 54 8 244.29 2.36 145 46 58 12 243.97 2.52 146 47 52 5 291.46 0.62 147 47 54 7 246.51 1.27 148 47 55 8 244.36 2.34 149 48 52 4 363.62 17.88 150 48 55 7 247.66 0.69 151 49 52 3 463.06 4.00 152 52 55 3 473.95 4.30 153 52 56 4 471.59 5.26 154 53 56 3 475.91 3.11 155 53 57 4 471.59 5.26 156 54 57 3 474.62 3.75 157 54 58 4 471.59 5.26 158 55 58 3 481.05 0.54 159 55 59 4 471.54 5.28 160 56 59 3 481.03 0.53 161 56 60 4 471.51 5.28 162 57 60 3 480.75 0.66 163 57 61 4 476.47 1.79 164 58 61 3 480.32 0.52 165 58 62 4 476.19 2.02 166 59 62 3 480.19 0.58 167 59 63 4 476.12 1.97 168 60 63 3 481.57 0.77 169 60 64 4 466.27 2.94 170 61 64 3 476.06 3.24 171 61 65 4 465.97 3.09 172 62 65 3 473.05 0.13 173 62 66 4 467.29 0.92 174 62 101 39 175.90 2.46 175 63 66 3 476.45 1.52 176 63 67 4 473.27 0.04 177 64 67 3 473.30 0.05 178 64 68 4 473.31 0.06 179 65 68 3 473.30 0.06 180 65 69 4 473.30 0.06 181 65 83 18 163.45 1.10 182 66 69 3 473.30 0.05 183 66 70 4 475.10 0.85 184 66 105 39 184.29 0.46 185 66 128 62 186.46 0.65 186 66 129 63 183.76 0.08 187 66 132 66 180.52 1.24 188 67 70 3 479.79 0.17 189 67 71 4 468.15 4.33 190 68 71 3 481.61 0.75 191 68 72 4 470.42 3.20 192 69 72 3 474.74 1.02 193 69 73 4 462.38 7.19 194 69 76 7 283.12 2.69 195 69 80 11 179.44 0.70 196 69 128 59 201.92 7.04 197 69 132 63 183.46 0.24 198 70 73 3 463.45 6.65 199 70 128 58 201.94 7.04 200 72 75 3 478.30 1.02 201 72 76 4 440.21 1.21 202 72 79 7 296.84 4.11 203 73 76 3 481.72 0.69 204 75 78 3 486.29 1.00 205 75 79 4 462.43 3.29 206 76 79 3 466.77 2.16 207 76 80 4 454.05 7.48 208 76 128 52 217.53 4.65 209 76 131 55 217.28 4.59 210 76 132 56 216.69 4.30 211 76 135 59 216.68 4.30 212 77 80 3 480.91 3.69 213 77 81 4 451.17 8.92 214 77 135 58 216.68 4.30 215 77 140 63 192.19 3.44 216 78 81 3 475.10 0.78 217 80 83 3 472.67 2.12 218 80 84 4 456.22 6.12 219 80 132 52 218.81 4.26 220 80 135 55 218.04 4.65 221 80 136 56 218.04 4.65 222 80 140 60 214.22 4.29 223 81 84 3 480.76 1.93 224 81 85 4 472.68 2.10 225 81 140 59 211.43 5.67 226 82 85 3 477.04 2.19 227 82 86 4 461.92 5.37 228 83 86 3 473.89 5.37 229 83 87 4 458.29 7.17 230 83 136 53 219.03 4.28 231 84 87 3 470.51 1.69 232 84 88 4 447.66 4.35 233 84 135 51 219.03 4.28 234 84 136 52 219.03 4.28 235 84 138 54 219.03 4.28 236 84 140 56 218.53 4.34 237 85 89 4 415.00 11.49 238 85 90 5 379.16 11.00 239 86 90 4 353.56 23.79 240 86 91 5 353.56 23.79 241 87 91 4 290.01 7.99 242 87 92 5 275.38 0.68 243 87 93 6 274.19 1.23 244 87 98 11 261.37 3.41 245 87 136 49 219.17 4.28 246 88 92 4 344.88 35.43 247 88 136 48 219.21 4.28 248 88 137 49 219.11 4.29 249 88 138 50 219.09 4.28 250 88 139 51 219.06 4.28 251 89 92 3 480.75 2.50 252 89 139 50 219.06 4.28 253 93 97 4 474.38 0.30 254 93 98 5 463.30 0.82 255 94 97 3 490.84 1.98 256 95 98 3 482.34 2.27 257 95 99 4 480.32 3.27 258 95 137 42 219.84 4.20 259 96 99 3 475.77 0.99 260 96 100 4 474.62 0.43 261 97 100 3 472.81 1.34 262 97 101 4 469.37 3.06 263 98 101 3 478.19 0.62 264 98 102 4 468.63 3.43 265 98 133 35 219.97 4.17 266 98 136 38 219.99 4.19 267 98 137 39 219.99 4.18 268 99 102 3 473.55 1.71 269 99 103 4 465.74 4.86 270 100 103 3 474.66 1.15 271 100 104 4 469.27 3.04 272 101 104 3 476.06 5.53 273 101 105 4 463.99 0.40 274 102 105 3 470.56 2.77 275 102 106 4 464.75 0.14 276 102 129 27 220.18 4.17 277 102 133 31 220.17 4.17 278 103 106 3 478.23 2.84 279 103 107 4 468.80 1.89 280 104 107 3 471.39 0.59 281 104 108 4 463.94 4.32 282 105 108 3 473.48 0.59 283 105 109 4 463.99 4.29 284 105 129 24 222.43 4.23 285 106 109 3 482.54 3.09 286 106 110 4 464.12 0.12 287 106 117 11 226.74 3.15 288 106 122 16 223.49 4.41 289 106 125 19 222.59 4.20 290 106 126 20 222.51 4.23 291 106 129 23 222.48 4.24 292 107 110 3 469.24 2.45 293 107 111 4 468.30 1.99 294 108 111 3 469.18 2.48 295 108 112 4 468.25 2.02 296 109 112 3 459.75 2.39 297 109 113 4 453.07 5.41 298 109 117 8 263.43 0.59 299 109 125 16 223.28 4.50 300 110 114 4 448.70 3.34 301 110 117 7 226.41 3.31 302 113 116 3 479.81 1.05 303 113 117 4 438.31 0.78 304 114 117 3 475.94 0.89 305 115 118 3 510.81 1.66 306 116 121 5 446.09 3.08 307 117 121 4 458.84 1.85 308 117 122 5 442.72 4.79 309 117 125 8 431.56 0.74 310 118 121 3 470.66 2.24 311 118 122 4 452.90 4.83 312 119 122 3 469.49 3.18 313 119 123 4 460.60 7.27 314 120 123 3 473.75 6.29 315 120 124 4 454.31 4.13 316 121 124 3 469.81 0.97 317 121 125 4 453.98 4.30 318 122 125 3 473.10 0.66 319 122 126 4 459.98 2.21 320 123 126 3 473.11 0.66 321 123 127 4 464.00 3.68 322 124 127 3 474.42 1.53 323 124 128 4 464.00 3.68 324 125 128 3 464.08 3.65 325 125 129 4 463.12 4.12 326 126 129 3 474.22 1.43 327 126 130 4 463.12 4.12 328 127 130 3 474.46 1.55 329 127 131 4 463.92 3.71 330 128 131 3 466.39 3.85 331 128 132 4 457.61 0.54 332 129 132 3 468.60 1.35 333 129 133 4 463.43 3.35 334 130 133 3 472.42 0.83 335 130 134 4 465.79 2.18 336 131 134 3 473.77 1.23 337 131 135 4 455.42 3.00 338 132 135 3 472.11 0.98 339 132 136 4 457.07 0.18 340 133 136 3 469.88 2.42 341 133 137 4 460.25 1.78 342 134 137 3 469.26 2.73 343 134 138 4 457.01 3.40 344 135 138 3 461.41 1.82 345 135 140 5 462.73 0.54