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 5 447.66 4.83 2 2 73 71 27.08 0.58 3 2 76 74 26.20 0.34 4 2 127 125 21.74 0.99 5 2 128 126 21.48 0.86 6 3 6 3 469.02 0.36 7 3 7 4 469.02 0.36 8 4 7 3 479.72 1.04 9 4 8 4 464.06 2.85 10 5 8 3 472.96 2.33 11 5 9 4 464.07 2.85 12 6 9 3 479.92 0.54 13 6 10 4 474.30 2.27 14 6 124 118 46.74 0.10 15 6 127 121 44.59 1.18 16 7 10 3 483.17 2.16 17 7 11 4 463.89 2.88 18 7 73 66 47.19 0.34 19 7 74 67 49.17 0.58 20 8 11 3 477.81 0.52 21 8 12 4 470.38 0.37 22 9 12 3 475.35 2.79 23 9 13 4 458.17 0.01 24 9 120 111 60.98 0.74 25 9 121 112 60.68 0.62 26 9 124 115 60.50 0.68 27 10 13 3 474.08 2.22 28 10 14 4 458.18 0.01 29 10 124 114 60.68 0.62 30 10 125 115 60.64 0.61 31 10 128 118 60.57 0.64 32 11 14 3 479.22 0.35 33 11 15 4 465.43 2.93 34 11 70 59 60.59 0.65 35 11 73 62 60.60 0.65 36 12 15 3 479.64 2.40 37 12 16 4 465.43 2.94 38 13 16 3 477.53 0.56 39 13 17 4 477.47 0.53 40 13 113 100 78.27 0.48 41 13 121 108 68.69 3.08 42 13 125 112 61.02 0.76 43 14 17 3 477.54 0.56 44 14 18 4 477.46 0.53 45 14 21 7 393.75 1.24 46 14 63 49 76.47 0.35 47 14 66 52 60.98 0.77 48 14 67 53 61.48 1.03 49 14 70 56 60.96 0.78 50 14 109 95 78.27 0.48 51 15 18 3 480.63 2.11 52 16 113 97 90.44 0.70 53 16 116 100 89.25 0.12 54 17 20 3 489.17 0.70 55 17 21 4 456.88 2.58 56 17 24 7 390.03 14.69 57 17 109 92 87.60 0.96 58 17 113 96 95.14 1.46 59 18 21 3 491.21 2.33 60 19 23 4 488.72 0.93 61 20 23 3 481.31 1.82 62 20 24 4 463.75 3.55 63 21 24 3 470.09 0.34 64 21 25 4 467.01 1.86 65 21 63 42 102.51 0.56 66 22 25 3 472.84 0.29 67 22 26 4 470.13 0.30 68 22 60 38 102.58 0.56 69 22 63 41 102.56 0.56 70 23 26 3 489.08 1.27 71 23 27 4 468.33 0.38 72 24 27 3 468.62 0.24 73 24 28 4 468.03 0.06 74 24 108 84 120.69 1.03 75 24 109 85 125.17 1.18 76 24 112 88 131.69 0.14 77 25 28 3 484.94 0.01 78 25 29 4 467.74 0.09 79 25 59 34 118.63 1.76 80 25 63 38 118.48 1.72 81 25 105 80 119.59 1.57 82 26 29 3 479.57 2.67 83 26 30 4 468.73 2.74 84 26 55 29 128.53 0.20 85 26 56 30 129.40 1.01 86 26 59 33 119.20 1.52 87 27 30 3 479.57 2.68 88 27 31 4 467.27 3.47 89 27 108 81 132.38 0.02 90 27 112 85 133.00 0.09 91 28 31 3 474.37 4.62 92 28 32 4 467.27 3.47 93 28 101 73 132.17 0.05 94 28 104 76 132.19 0.06 95 28 105 77 132.17 0.05 96 28 108 80 132.38 0.02 97 29 32 3 472.04 1.08 98 29 33 4 464.00 2.04 99 29 55 26 132.56 0.07 100 29 58 29 132.55 0.07 101 29 59 30 132.55 0.07 102 29 101 72 132.28 0.04 103 30 33 3 479.55 2.68 104 30 34 4 463.76 1.94 105 30 50 20 133.13 0.23 106 31 34 3 480.25 1.12 107 31 35 4 468.09 0.96 108 31 104 73 132.57 0.16 109 31 107 76 133.01 0.07 110 31 108 77 133.02 0.07 111 32 35 3 482.99 0.24 112 32 36 4 458.85 0.84 113 32 39 7 336.86 22.29 114 32 101 69 132.56 0.17 115 32 104 72 132.92 0.07 116 33 37 4 447.16 6.71 117 33 39 6 337.33 22.05 118 33 40 7 331.01 25.21 119 33 43 10 330.74 25.34 120 33 48 15 133.45 0.12 121 33 55 22 133.32 0.11 122 34 37 3 488.48 1.59 123 36 39 3 489.20 0.74 124 36 100 64 132.85 0.10 125 36 103 67 133.05 0.06 126 36 104 68 133.06 0.06 127 37 40 3 487.16 1.77 128 38 41 3 486.79 0.16 129 39 42 3 491.45 1.32 130 39 43 4 486.81 0.15 131 39 97 58 132.62 0.20 132 39 100 61 133.04 0.06 133 40 43 3 488.35 0.62 134 40 44 4 481.50 2.80 135 40 48 8 255.34 2.29 136 41 44 3 498.69 0.85 137 42 92 50 132.60 0.24 138 42 93 51 132.60 0.24 139 42 94 52 132.83 0.17 140 42 97 55 133.05 0.07 141 43 46 3 486.31 1.65 142 43 48 5 436.31 11.26 143 43 58 15 133.53 0.10 144 45 54 9 255.50 2.60 145 46 54 8 255.48 2.61 146 46 55 9 255.49 2.60 147 46 58 12 255.43 2.60 148 47 52 5 285.58 3.65 149 47 54 7 255.50 2.60 150 47 55 8 264.29 6.99 151 48 55 7 264.30 6.99 152 49 52 3 476.04 4.20 153 51 56 5 456.84 0.42 154 52 55 3 470.25 3.22 155 52 56 4 470.57 4.28 156 53 56 3 470.57 4.28 157 53 57 4 470.56 4.28 158 54 57 3 477.23 2.56 159 54 58 4 465.88 1.92 160 55 58 3 480.59 0.72 161 55 59 4 473.37 1.74 162 56 59 3 475.97 3.04 163 56 60 4 473.37 1.74 164 57 60 3 476.75 2.65 165 57 61 4 474.14 1.35 166 58 61 3 483.14 5.84 167 58 62 4 483.13 5.85 168 59 62 3 482.53 6.16 169 59 63 4 468.66 4.08 170 60 63 3 482.35 6.25 171 60 64 4 468.66 4.07 172 61 64 3 471.55 1.29 173 61 65 4 463.18 1.33 174 62 65 3 477.89 0.59 175 62 66 4 463.28 1.40 176 62 101 39 158.00 2.67 177 63 66 3 477.12 5.52 178 63 67 4 463.19 1.42 179 64 67 3 473.06 3.49 180 64 68 4 463.12 1.45 181 65 68 3 472.22 3.06 182 65 69 4 462.97 1.52 183 65 80 15 157.95 2.62 184 65 83 18 157.94 2.62 185 66 69 3 470.66 3.84 186 66 70 4 463.81 0.42 187 66 105 39 162.44 3.88 188 66 128 62 162.59 3.79 189 66 129 63 162.25 3.79 190 66 132 66 159.04 2.50 191 67 70 3 482.54 2.89 192 67 71 4 478.43 0.84 193 68 71 3 478.43 0.84 194 68 72 4 478.46 0.86 195 68 79 11 199.65 22.80 196 68 80 12 161.90 3.94 197 69 72 3 478.49 0.86 198 69 73 4 463.04 0.81 199 69 76 7 285.55 4.71 200 69 80 11 161.91 3.94 201 69 128 59 173.53 1.65 202 69 132 63 162.25 3.79 203 70 73 3 471.37 4.39 204 70 128 58 195.18 6.66 205 72 75 3 487.89 1.11 206 72 76 4 447.12 4.49 207 72 79 7 272.12 2.10 208 73 76 3 482.13 2.94 209 75 78 3 487.14 0.46 210 75 79 4 450.34 2.90 211 76 79 3 466.54 5.20 212 76 80 4 436.72 5.41 213 76 128 52 226.42 0.13 214 76 131 55 225.00 0.62 215 76 132 56 224.90 0.68 216 76 135 59 224.50 0.52 217 77 81 4 428.85 1.48 218 77 135 58 224.50 0.52 219 78 81 3 469.89 1.06 220 80 83 3 475.22 0.84 221 80 84 4 454.18 2.00 222 80 132 52 226.53 0.24 223 80 135 55 225.64 0.60 224 80 136 56 226.42 0.22 225 81 84 3 467.54 4.68 226 81 85 4 460.37 1.09 227 82 85 3 472.50 3.67 228 82 86 4 460.53 1.01 229 83 86 3 468.61 4.15 230 83 87 4 460.55 1.01 231 83 136 53 226.59 0.28 232 84 87 3 481.20 3.67 233 84 88 4 458.91 0.20 234 84 135 51 226.69 0.23 235 84 136 52 226.59 0.28 236 84 139 55 226.53 0.30 237 85 88 3 465.76 3.60 238 85 89 4 453.38 2.96 239 85 139 54 226.53 0.30 240 86 89 3 477.02 1.48 241 86 90 4 440.76 3.35 242 86 91 5 433.18 6.02 243 87 91 4 418.10 13.55 244 87 92 5 355.45 7.79 245 87 93 6 338.44 0.72 246 87 98 11 269.18 3.68 247 87 136 49 226.88 0.23 248 87 140 53 226.57 0.29 249 88 92 4 396.30 2.65 250 88 139 51 226.65 0.33 251 88 140 52 226.33 0.21 252 89 92 3 480.32 1.40 253 89 139 50 226.87 0.23 254 93 97 4 489.26 0.82 255 93 98 5 475.37 0.16 256 93 140 47 226.93 0.21 257 94 97 3 489.77 0.56 258 95 98 3 489.27 0.81 259 95 99 4 485.59 1.03 260 95 137 42 227.08 0.15 261 95 140 45 226.99 0.20 262 96 99 3 491.85 2.10 263 96 100 4 485.25 1.20 264 97 100 3 474.75 0.47 265 97 101 4 473.84 0.58 266 98 101 3 476.37 1.84 267 98 102 4 473.95 0.70 268 98 133 35 227.75 0.23 269 98 136 38 227.65 0.28 270 98 137 39 227.56 0.26 271 98 140 42 227.57 0.24 272 99 102 3 472.32 3.87 273 99 103 4 470.00 2.71 274 99 133 34 227.83 0.24 275 100 103 3 473.51 3.27 276 100 104 4 468.43 3.54 277 101 104 3 469.94 2.79 278 101 105 4 467.72 3.91 279 102 105 3 469.94 2.79 280 102 106 4 470.34 2.60 281 102 129 27 227.84 0.24 282 102 133 31 227.86 0.23 283 103 106 3 477.48 0.80 284 103 107 4 466.65 4.44 285 104 107 3 464.95 3.58 286 104 108 4 467.91 2.20 287 105 108 3 472.23 0.05 288 105 109 4 467.91 2.20 289 105 129 24 228.76 0.02 290 106 109 3 467.92 2.21 291 106 110 4 467.91 2.21 292 106 117 11 231.21 0.39 293 106 122 16 228.91 0.07 294 106 125 19 228.88 0.06 295 106 126 20 228.85 0.06 296 106 129 23 228.83 0.05 297 107 110 3 469.81 1.45 298 107 111 4 468.10 2.30 299 108 111 3 476.85 1.45 300 108 112 4 468.09 2.30 301 109 112 3 468.23 2.25 302 109 113 4 436.41 0.12 303 109 117 8 235.22 1.21 304 109 125 16 228.96 0.04 305 110 117 7 232.47 0.17 306 113 116 3 471.34 2.24 307 113 117 4 400.05 13.70 308 114 117 3 473.13 3.29 309 116 121 5 427.06 7.74 310 117 122 5 419.11 1.76 311 117 125 8 420.49 4.45 312 118 121 3 442.20 0.62 313 118 122 4 442.20 0.63 314 119 122 3 461.36 5.69 315 119 123 4 470.43 2.12 316 120 123 3 472.41 1.14 317 120 124 4 470.45 2.12 318 121 124 3 470.45 2.12 319 121 125 4 469.59 1.58 320 122 125 3 472.92 0.89 321 122 126 4 464.34 2.89 322 123 126 3 472.38 1.13 323 123 127 4 461.88 4.12 324 124 127 3 472.38 1.14 325 124 128 4 461.77 4.17 326 125 128 3 467.03 1.54 327 125 129 4 461.78 4.17 328 126 129 3 485.17 5.38 329 126 130 4 467.02 1.54 330 127 130 3 471.20 0.56 331 127 131 4 472.12 1.02 332 128 131 3 472.13 1.02 333 128 132 4 472.12 1.02 334 129 132 3 465.47 4.42 335 129 133 4 457.38 8.39 336 130 133 3 470.49 1.91 337 130 134 4 470.49 1.91 338 131 134 3 470.41 1.86 339 131 135 4 476.66 1.26 340 132 135 3 476.60 1.30 341 132 136 4 476.10 1.54 342 133 136 3 476.60 1.30 343 133 137 4 476.73 1.23 344 134 137 3 488.86 3.51 345 134 138 4 448.09 0.92 346 135 138 3 473.43 0.55 347 136 140 4 490.12 3.00 348 137 140 3 480.53 1.49