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 1 103 102 21.27 0.01 2 3 102 99 21.73 0.24 3 3 103 100 21.28 0.01 4 4 10 6 364.08 20.10 5 5 103 98 50.63 11.88 6 5 106 101 50.66 11.89 7 6 9 3 474.99 0.12 8 6 10 4 463.24 5.75 9 6 106 100 91.72 1.80 10 7 10 3 474.99 0.12 11 7 11 4 463.24 5.75 12 7 47 40 277.48 8.54 13 8 11 3 474.99 0.12 14 8 12 4 451.76 0.71 15 8 47 39 277.44 8.56 16 8 48 40 277.22 8.68 17 8 53 45 276.24 8.80 18 8 71 63 208.66 0.30 19 9 12 3 466.63 4.28 20 9 13 4 455.31 1.06 21 9 71 62 208.63 0.29 22 9 75 66 206.81 0.84 23 9 106 97 126.09 1.11 24 10 13 3 466.62 1.79 25 10 14 4 456.95 0.24 26 10 34 24 281.00 8.80 27 10 105 95 128.13 1.11 28 10 106 96 126.09 1.12 29 11 14 3 461.91 1.80 30 11 15 4 459.79 1.63 31 11 30 19 281.36 8.46 32 11 34 23 281.02 8.81 33 11 36 25 280.92 8.77 34 11 41 30 278.08 8.29 35 11 44 33 278.06 8.29 36 11 45 34 278.06 8.29 37 11 48 37 277.97 8.31 38 12 15 3 466.61 0.69 39 12 16 4 458.95 1.19 40 12 48 36 277.98 8.32 41 12 53 41 276.37 8.77 42 12 54 42 276.22 8.81 43 12 64 52 260.49 5.21 44 12 68 56 210.00 0.35 45 12 71 59 208.86 0.20 46 12 72 60 208.60 0.28 47 13 16 3 459.06 1.13 48 13 17 4 458.94 1.19 49 13 75 62 208.29 0.43 50 13 76 63 208.21 0.47 51 13 79 66 207.68 0.18 52 13 98 85 130.65 0.99 53 13 102 89 129.34 1.25 54 13 105 92 129.46 1.13 55 14 17 3 465.32 4.38 56 14 18 4 451.75 0.38 57 14 30 16 281.96 8.23 58 14 33 19 281.60 8.56 59 14 34 20 281.56 8.55 60 15 18 3 463.91 5.08 61 15 19 4 451.69 0.41 62 15 25 10 282.47 8.38 63 15 30 15 282.14 8.31 64 15 54 39 276.37 8.79 65 15 62 47 263.10 6.37 66 15 64 49 262.30 6.02 67 16 19 3 458.03 2.75 68 16 20 4 451.67 0.42 69 16 72 56 208.96 0.17 70 16 73 57 208.96 0.16 71 16 76 60 208.77 0.20 72 16 133 117 54.78 0.80 73 17 20 3 451.63 0.44 74 17 21 4 451.62 0.44 75 17 33 16 282.32 8.31 76 17 76 59 208.87 0.14 77 18 21 3 468.05 0.47 78 18 22 4 450.84 0.82 79 18 23 5 437.10 1.93 80 18 25 7 290.18 4.83 81 18 29 11 282.50 8.37 82 18 30 12 282.50 8.37 83 18 33 15 282.48 8.38 84 19 22 3 451.39 1.49 85 20 80 60 208.94 0.15 86 20 131 111 61.85 0.48 87 21 33 12 300.71 2.53 88 23 29 6 444.54 2.28 89 24 29 5 448.23 1.47 90 24 61 37 263.32 6.36 91 25 61 36 263.25 6.34 92 25 62 37 263.18 6.36 93 26 29 3 471.63 5.03 94 26 30 4 457.44 2.07 95 27 30 3 459.36 1.11 96 27 31 4 457.44 2.06 97 27 41 14 280.90 8.89 98 27 42 15 280.88 8.88 99 27 45 18 280.83 8.87 100 27 56 29 276.16 8.73 101 27 60 33 263.30 6.34 102 27 62 35 263.07 6.36 103 28 31 3 468.35 1.45 104 28 32 4 457.44 2.06 105 29 32 3 472.50 0.59 106 29 33 4 457.43 2.06 107 30 33 3 474.31 2.56 108 30 34 4 445.81 2.86 109 30 62 32 263.08 6.37 110 31 34 3 466.04 2.63 111 31 35 4 442.88 4.32 112 31 36 5 377.51 25.04 113 31 38 7 295.06 2.89 114 31 41 10 282.42 8.20 115 32 35 3 455.38 2.22 116 36 41 5 416.22 4.94 117 37 40 3 471.84 1.55 118 37 41 4 448.85 1.39 119 38 41 3 456.37 2.45 120 38 42 4 448.85 1.39 121 39 43 4 442.37 3.95 122 40 43 3 443.60 8.30 123 40 44 4 446.39 2.00 124 41 44 3 466.81 0.48 125 41 45 4 448.25 1.33 126 42 45 3 452.11 0.09 127 42 46 4 448.19 1.31 128 43 46 3 466.88 4.87 129 43 47 4 452.78 0.94 130 44 47 3 457.66 3.06 131 44 48 4 452.76 0.94 132 45 48 3 466.07 5.27 133 45 49 4 448.20 1.34 134 45 54 9 354.99 15.59 135 45 56 11 293.74 0.03 136 45 62 17 263.08 6.36 137 46 49 3 447.93 1.48 138 46 50 4 455.05 2.13 139 47 50 3 455.10 2.11 140 47 51 4 455.04 2.14 141 48 51 3 454.93 2.10 142 48 52 4 454.84 2.14 143 48 53 5 423.72 1.15 144 48 54 6 397.81 5.82 145 49 52 3 466.02 0.65 146 49 54 5 417.72 4.14 147 49 56 7 341.94 15.05 148 52 65 13 261.29 5.60 149 52 67 15 258.67 5.56 150 53 64 11 261.31 5.60 151 53 65 12 261.28 5.61 152 53 67 14 252.12 4.49 153 53 68 15 220.78 5.75 154 54 62 8 263.14 6.36 155 54 63 9 262.88 6.26 156 54 64 10 261.42 5.66 157 54 65 11 261.28 5.60 158 55 62 7 263.14 6.36 159 55 63 8 262.91 6.25 160 55 64 9 262.89 6.26 161 55 65 10 262.72 6.23 162 56 60 4 360.00 30.02 163 56 62 6 263.16 6.36 164 57 60 3 430.64 5.97 165 57 63 6 263.17 6.37 166 64 68 4 412.47 3.50 167 64 69 5 399.68 9.88 168 64 72 8 353.43 13.25 169 65 68 3 441.62 1.44 170 65 69 4 433.99 2.79 171 66 70 4 436.38 3.99 172 67 70 3 459.50 2.41 173 67 71 4 446.55 1.06 174 68 71 3 462.48 4.24 175 68 72 4 450.01 0.67 176 69 72 3 462.30 0.18 177 69 73 4 446.55 1.05 178 70 73 3 462.55 1.04 179 70 74 4 454.29 1.45 180 71 75 4 450.03 0.69 181 72 75 3 467.24 1.32 182 72 76 4 458.79 5.54 183 73 76 3 467.21 1.34 184 73 77 4 448.02 0.16 185 73 133 60 54.66 0.81 186 73 134 61 54.45 0.90 187 73 137 64 47.06 0.48 188 74 77 3 456.47 4.38 189 74 78 4 456.45 4.39 190 75 78 3 458.80 3.23 191 75 79 4 452.00 6.62 192 75 105 30 129.58 1.19 193 76 79 3 456.62 4.30 194 76 80 4 450.38 0.96 195 76 133 57 55.16 0.80 196 77 80 3 464.27 0.80 197 77 81 4 463.51 0.42 198 77 110 33 128.96 1.28 199 77 113 36 126.22 0.54 200 77 132 55 55.27 0.80 201 77 133 56 55.17 0.80 202 77 134 57 54.72 0.83 203 77 135 58 54.45 0.90 204 77 137 60 52.11 0.20 205 77 138 61 46.30 0.10 206 78 81 3 463.55 0.40 207 78 82 4 463.51 0.42 208 78 105 27 130.04 1.26 209 78 108 30 129.37 1.26 210 78 109 31 129.50 1.20 211 78 110 32 129.09 1.22 212 78 113 35 126.22 0.54 213 79 82 3 471.44 2.71 214 79 83 4 463.51 0.42 215 79 98 19 131.44 1.28 216 79 101 22 130.17 1.21 217 79 102 23 130.18 1.21 218 79 105 26 130.06 1.24 219 80 83 3 464.90 0.28 220 80 84 4 464.84 0.24 221 80 126 46 73.67 1.15 222 80 130 50 68.84 0.73 223 80 131 51 67.59 0.10 224 80 132 52 56.87 0.30 225 80 133 53 58.73 0.12 226 81 84 3 473.81 0.81 227 81 85 4 464.89 0.27 228 81 108 27 129.88 1.31 229 81 113 32 127.12 0.98 230 81 116 35 123.24 0.62 231 81 117 36 123.16 0.67 232 81 120 39 108.57 0.58 233 81 123 42 77.95 2.54 234 81 132 51 59.70 0.11 235 81 138 57 51.73 0.15 236 82 85 3 464.40 0.53 237 82 86 4 454.94 5.19 238 82 101 19 131.19 1.28 239 82 104 22 131.15 1.28 240 82 108 26 129.63 1.19 241 83 86 3 466.63 0.64 242 83 87 4 454.94 5.19 243 83 97 14 131.78 1.39 244 83 98 15 131.81 1.39 245 83 101 18 131.16 1.28 246 83 126 43 73.74 1.16 247 83 127 44 73.73 1.15 248 84 87 3 465.31 1.30 249 84 88 4 429.10 3.43 250 84 120 36 108.92 0.72 251 84 122 38 103.66 0.46 252 84 125 41 73.87 1.21 253 84 126 42 73.76 1.17 254 84 127 43 73.75 1.15 255 84 132 48 71.92 1.24 256 85 89 4 400.28 9.19 257 85 90 5 396.01 7.87 258 85 104 19 131.78 1.38 259 85 108 23 130.27 1.12 260 85 116 31 123.35 0.62 261 85 120 35 108.94 0.71 262 86 90 4 382.55 9.22 263 86 91 5 337.17 13.46 264 86 92 6 217.65 32.27 265 86 97 11 132.31 1.36 266 86 100 14 132.25 1.38 267 86 101 15 132.12 1.32 268 86 104 18 131.81 1.39 269 87 91 4 337.17 13.47 270 87 94 7 215.19 33.54 271 87 97 10 139.88 1.47 272 87 127 40 73.80 1.16 273 88 120 32 117.43 0.19 274 89 120 31 118.00 0.07 275 90 104 14 147.85 1.95 276 92 96 4 462.98 1.66 277 92 97 5 382.07 21.09 278 92 100 8 375.12 21.64 279 93 96 3 470.07 1.90 280 93 97 4 447.78 0.09 281 94 97 3 471.48 2.60 282 94 127 33 73.79 1.17 283 94 128 34 73.78 1.16 284 96 99 3 480.13 0.66 285 96 100 4 459.00 0.15 286 97 100 3 464.59 0.34 287 97 101 4 459.53 0.42 288 97 128 31 73.75 1.15 289 98 101 3 477.66 0.58 290 98 102 4 469.29 1.40 291 99 102 3 471.56 2.54 292 99 103 4 470.86 0.62 293 100 103 3 470.86 0.62 294 100 104 4 470.86 0.62 295 101 104 3 474.75 2.56 296 101 105 4 467.60 0.48 297 102 105 3 479.34 0.27 298 102 106 4 470.93 0.65 299 103 106 3 480.12 3.13 300 103 107 4 469.03 0.18 301 104 107 3 467.75 0.47 302 104 108 4 467.68 0.46 303 108 112 4 447.86 3.77 304 108 113 5 438.54 8.40 305 108 116 8 422.81 5.65 306 109 112 3 464.69 4.14 307 109 113 4 443.75 6.85 308 110 113 3 462.61 5.19 309 110 114 4 462.61 5.19 310 110 138 28 42.84 0.36 311 111 114 3 472.13 1.59 312 111 115 4 454.85 1.31 313 112 115 3 460.11 3.92 314 112 116 4 454.72 1.38 315 113 116 3 467.30 0.83 316 113 117 4 454.42 1.21 317 113 138 25 48.97 1.23 318 114 117 3 459.88 3.94 319 114 118 4 454.41 1.21 320 114 138 24 52.21 0.14 321 115 118 3 468.35 0.30 322 115 119 4 451.60 0.20 323 116 119 3 461.18 0.58 324 116 120 4 414.35 11.85 325 116 123 7 219.51 28.37 326 117 123 6 116.65 11.01 327 117 135 18 56.74 0.21 328 117 138 21 52.68 0.29 329 117 140 23 42.48 0.55 330 120 123 3 483.19 0.77 331 123 132 9 102.89 14.22 332 123 135 12 65.08 0.74 333 124 131 7 137.03 2.79 334 124 132 8 102.91 14.23 335 125 129 4 306.11 5.31 336 125 130 5 306.10 5.31 337 125 131 6 137.00 2.81 338 125 132 7 137.00 2.81 339 126 129 3 464.49 1.13 340 126 130 4 314.31 9.41 341 126 132 6 147.59 2.49 342 132 135 3 493.05 0.17 343 134 137 3 462.00 2.63 344 134 138 4 414.70 15.50 345 135 138 3 462.62 3.26 346 135 139 4 450.22 2.94 347 135 140 5 408.11 17.48 348 136 139 3 484.12 1.08