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 1 132 131 19.04 0.04 2 2 128 126 29.97 0.24 3 3 7 4 457.95 0.57 4 3 8 5 458.56 0.27 5 3 74 71 32.40 0.44 6 3 77 74 32.14 0.37 7 3 128 125 29.98 0.24 8 3 129 126 29.96 0.24 9 3 132 129 28.84 0.34 10 4 7 3 460.38 0.47 11 4 8 4 475.13 5.55 12 5 8 3 475.14 5.55 13 5 9 4 475.16 5.54 14 6 9 3 475.66 5.29 15 6 10 4 475.75 5.25 16 7 10 3 488.01 0.88 17 7 11 4 475.73 5.25 18 7 125 118 53.30 0.69 19 7 128 121 52.24 0.15 20 8 11 3 478.33 3.35 21 8 12 4 471.31 3.04 22 8 74 66 54.08 0.29 23 8 75 67 55.27 0.58 24 9 12 3 485.86 1.19 25 9 13 4 480.98 2.02 26 10 13 3 484.25 0.39 27 10 14 4 477.16 0.11 28 10 121 111 68.64 0.63 29 10 122 112 68.63 0.62 30 10 125 115 68.42 0.64 31 11 14 3 494.17 2.06 32 11 15 4 468.38 4.28 33 11 71 60 68.54 0.67 34 11 125 114 68.56 0.66 35 11 126 115 68.56 0.66 36 11 129 118 68.45 0.62 37 12 15 3 480.46 1.04 38 12 16 4 467.37 1.04 39 12 71 59 68.56 0.67 40 12 74 62 68.57 0.66 41 13 16 3 480.81 1.17 42 13 17 4 472.43 2.08 43 14 17 3 487.72 1.11 44 14 18 4 485.88 2.04 45 14 114 100 76.95 0.47 46 14 122 108 69.00 0.76 47 14 126 112 68.97 0.74 48 15 18 3 485.88 2.04 49 15 19 4 485.88 2.04 50 15 22 7 418.94 1.17 51 15 64 49 73.42 0.30 52 15 67 52 68.95 0.76 53 15 68 53 68.95 0.76 54 15 71 56 68.94 0.76 55 15 110 95 76.87 0.50 56 16 19 3 477.93 4.08 57 17 114 97 77.61 0.39 58 17 117 100 80.81 2.02 59 18 21 3 490.05 2.48 60 18 22 4 429.44 1.29 61 18 25 7 418.81 1.09 62 18 110 92 77.23 0.39 63 18 114 96 82.36 1.24 64 19 22 3 491.38 1.81 65 21 24 3 483.78 2.73 66 21 25 4 474.60 1.90 67 22 25 3 482.22 1.91 68 22 26 4 474.61 1.89 69 22 64 42 88.98 4.62 70 23 26 3 477.98 0.21 71 23 27 4 478.01 0.19 72 23 61 38 97.89 0.26 73 23 64 41 97.90 0.26 74 24 27 3 486.06 0.86 75 24 28 4 481.40 1.46 76 25 28 3 481.41 1.46 77 25 29 4 481.41 1.46 78 25 109 84 127.81 1.25 79 25 110 85 124.12 0.59 80 25 113 88 137.83 1.05 81 26 29 3 485.05 3.27 82 26 30 4 481.41 1.46 83 26 60 34 123.95 0.52 84 27 30 3 485.10 3.25 85 27 31 4 481.44 1.42 86 27 56 29 134.90 0.53 87 27 57 30 132.28 1.80 88 27 60 33 125.72 1.40 89 28 31 3 480.61 0.99 90 28 32 4 482.17 1.84 91 28 109 81 138.39 0.94 92 28 113 85 138.54 0.94 93 29 32 3 482.24 1.81 94 29 33 4 474.47 1.99 95 29 102 73 138.22 0.93 96 29 105 76 138.22 0.93 97 29 106 77 138.22 0.93 98 29 109 80 138.45 0.96 99 30 33 3 477.65 2.19 100 30 34 4 477.36 0.55 101 30 56 26 138.48 0.96 102 30 59 29 138.46 0.96 103 30 60 30 138.40 0.97 104 30 102 72 138.31 0.95 105 31 34 3 480.14 1.71 106 31 35 4 476.63 0.18 107 31 51 20 138.88 0.98 108 32 35 3 490.55 1.19 109 32 36 4 476.63 0.19 110 32 105 73 138.38 0.97 111 32 108 76 138.65 0.98 112 32 109 77 138.68 0.86 113 32 112 80 138.89 0.92 114 33 36 3 477.72 0.35 115 33 37 4 455.94 4.84 116 33 40 7 334.19 12.70 117 33 102 69 138.37 0.94 118 33 105 72 138.47 0.95 119 34 38 4 453.25 6.17 120 34 40 6 339.01 10.29 121 34 41 7 226.21 24.59 122 34 44 10 226.19 24.61 123 34 49 15 139.09 0.92 124 34 56 22 139.00 0.91 125 35 38 3 487.06 1.14 126 37 40 3 500.81 2.37 127 37 101 64 138.43 0.93 128 37 104 67 138.83 0.92 129 37 105 68 138.84 0.92 130 38 41 3 491.01 0.80 131 39 42 3 491.79 0.41 132 40 43 3 506.31 3.56 133 40 44 4 487.94 0.73 134 40 98 58 138.36 0.93 135 40 101 61 138.82 0.93 136 41 44 3 487.29 1.06 137 41 45 4 486.72 1.34 138 41 49 8 205.64 32.69 139 42 45 3 497.50 1.73 140 43 46 3 647.18 2.14 141 43 94 51 138.28 0.99 142 43 95 52 138.61 1.01 143 43 98 55 138.84 0.95 144 44 47 3 485.24 1.98 145 44 49 5 409.30 8.93 146 44 59 15 140.18 1.44 147 46 55 9 143.72 1.60 148 47 55 8 143.69 1.60 149 47 56 9 143.72 1.60 150 47 59 12 143.69 1.60 151 48 53 5 276.07 2.54 152 48 55 7 143.73 1.60 153 48 56 8 143.73 1.60 154 49 56 7 201.72 30.61 155 50 53 3 480.54 6.71 156 52 57 5 442.99 5.69 157 53 56 3 481.19 1.11 158 53 57 4 469.12 1.56 159 54 57 3 475.64 4.20 160 54 58 4 469.12 1.56 161 55 58 3 482.09 0.97 162 55 59 4 469.10 1.55 163 56 59 3 485.43 0.67 164 56 60 4 470.84 2.43 165 57 60 3 485.41 0.68 166 57 61 4 474.98 0.36 167 58 61 3 487.53 0.44 168 58 62 4 475.31 0.25 169 59 62 3 477.31 1.11 170 59 63 4 475.31 0.26 171 60 63 3 483.84 2.15 172 60 64 4 471.89 1.96 173 61 64 3 481.98 3.08 174 61 65 4 471.69 2.06 175 62 65 3 487.66 0.24 176 62 66 4 472.26 1.56 177 63 66 3 477.01 0.81 178 63 67 4 472.57 1.41 179 63 102 39 155.56 2.92 180 64 67 3 479.83 4.54 181 64 68 4 469.79 0.01 182 65 68 3 472.04 6.06 183 65 69 4 461.89 3.93 184 66 69 3 474.17 5.13 185 66 70 4 468.29 8.06 186 66 81 15 156.09 2.91 187 66 84 18 155.84 3.02 188 67 70 3 470.67 0.45 189 67 71 4 462.45 3.65 190 67 106 39 200.60 8.44 191 67 130 63 176.03 3.85 192 67 133 66 156.80 3.27 193 68 71 3 474.38 1.19 194 68 72 4 467.50 1.11 195 69 72 3 473.24 1.77 196 69 73 4 467.49 1.10 197 69 80 11 177.97 3.87 198 69 81 12 166.81 1.70 199 70 73 3 474.75 1.02 200 70 74 4 453.62 0.88 201 70 77 7 270.12 3.16 202 70 81 11 177.98 3.87 203 70 129 59 228.30 3.17 204 70 133 63 186.98 7.71 205 71 74 3 478.90 1.06 206 71 129 58 228.28 3.17 207 73 76 3 477.70 2.03 208 73 77 4 440.95 1.07 209 73 80 7 273.50 2.33 210 74 77 3 487.19 1.91 211 74 129 55 251.21 2.29 212 76 79 3 496.19 1.81 213 76 80 4 474.69 3.02 214 77 80 3 474.69 3.02 215 77 81 4 458.31 4.51 216 77 129 52 260.05 6.21 217 77 132 55 259.91 6.15 218 77 133 56 252.24 2.33 219 77 136 59 251.71 2.08 220 78 82 4 474.04 3.35 221 78 136 58 251.71 2.08 222 79 82 3 478.67 5.00 223 81 84 3 492.80 1.85 224 81 85 4 463.74 0.83 225 81 133 52 261.86 5.41 226 81 136 55 261.30 5.57 227 81 137 56 261.31 5.57 228 82 85 3 477.25 5.92 229 82 86 4 474.18 0.17 230 82 140 58 261.89 5.28 231 83 86 3 483.82 2.62 232 83 87 4 475.68 0.59 233 84 87 3 481.65 3.56 234 84 88 4 474.74 0.12 235 84 137 53 262.70 5.04 236 85 88 3 499.16 2.25 237 85 89 4 475.81 0.66 238 85 136 51 262.74 5.05 239 85 137 52 262.70 5.04 240 85 139 54 262.68 5.04 241 85 140 55 262.64 5.05 242 86 89 3 481.57 0.49 243 86 90 4 477.88 0.38 244 86 91 5 474.47 2.08 245 86 140 54 262.60 5.08 246 87 90 3 496.62 3.52 247 87 91 4 457.32 6.49 248 87 92 5 457.31 6.49 249 88 92 4 434.34 0.96 250 88 93 5 422.60 6.83 251 88 94 6 422.59 6.82 252 88 99 11 305.50 4.32 253 88 137 49 262.80 5.04 254 88 141 53 262.66 5.04 255 89 93 4 434.33 0.96 256 89 140 51 262.67 5.05 257 89 141 52 262.40 5.06 258 90 93 3 503.86 0.35 259 90 140 50 262.74 5.05 260 94 98 4 482.64 1.77 261 94 99 5 477.11 0.98 262 94 141 47 262.83 5.05 263 95 98 3 497.51 1.56 264 96 99 3 497.51 1.56 265 96 138 42 263.08 5.08 266 96 141 45 263.02 5.11 267 97 100 3 497.45 2.65 268 97 101 4 482.79 1.71 269 98 101 3 483.18 0.09 270 98 102 4 480.02 0.42 271 99 102 3 483.18 0.09 272 99 103 4 478.23 2.18 273 99 134 35 263.62 5.10 274 99 137 38 263.62 5.09 275 99 138 39 263.58 5.08 276 99 141 42 263.62 5.09 277 100 103 3 478.16 2.21 278 100 104 4 474.03 1.30 279 101 104 3 477.68 0.80 280 101 105 4 474.04 1.30 281 102 105 3 475.99 0.33 282 102 106 4 470.80 2.92 283 103 106 3 481.56 1.15 284 103 107 4 470.25 2.65 285 103 130 27 263.79 5.07 286 103 134 31 263.75 5.06 287 104 107 3 482.38 1.56 288 104 108 4 468.90 3.33 289 105 108 3 480.06 2.72 290 105 109 4 470.87 4.31 291 106 109 3 477.06 1.22 292 106 110 4 477.05 1.23 293 106 130 24 264.72 5.10 294 107 110 3 477.06 1.23 295 107 111 4 467.24 6.13 296 107 118 11 266.16 5.46 297 107 123 16 265.27 5.09 298 107 126 19 265.23 5.11 299 107 127 20 265.00 5.13 300 107 130 23 264.85 5.04 301 108 111 3 472.42 3.54 302 108 112 4 467.24 6.13 303 109 112 3 477.32 1.33 304 109 113 4 475.35 2.06 305 110 113 3 478.40 0.52 306 110 114 4 458.51 2.82 307 110 126 16 265.32 5.07 308 111 114 3 477.79 1.56 309 111 118 7 266.75 5.12 310 114 117 3 480.22 0.35 311 114 118 4 340.50 19.35 312 117 122 5 420.44 12.28 313 118 123 5 418.28 14.73 314 118 126 8 446.34 0.68 315 119 122 3 476.55 1.50 316 119 123 4 471.71 3.92 317 120 123 3 481.95 2.91 318 120 124 4 471.71 3.93 319 121 124 3 481.95 1.19 320 121 125 4 479.62 0.03 321 122 125 3 481.94 1.19 322 122 126 4 476.50 1.59 323 123 126 3 479.54 2.38 324 123 127 4 479.57 0.05 325 124 127 3 481.88 1.21 326 124 128 4 477.25 1.25 327 125 128 3 484.94 0.33 328 125 129 4 477.25 1.25 329 126 129 3 480.01 0.26 330 126 130 4 479.32 0.21 331 127 130 3 479.62 0.07 332 127 131 4 479.33 0.21 333 128 131 3 479.48 0.28 334 128 132 4 471.63 3.64 335 129 132 3 483.28 1.61 336 129 133 4 471.61 3.63 337 130 133 3 485.89 0.31 338 130 134 4 470.35 0.86 339 131 134 3 471.04 1.21 340 131 135 4 472.47 1.93 341 132 135 3 472.47 1.93 342 132 136 4 471.18 2.57 343 133 136 3 472.16 2.16 344 133 137 4 471.25 2.60 345 134 137 3 477.44 5.33 346 134 138 4 472.72 3.34 347 135 138 3 484.86 2.73 348 135 139 4 463.13 4.62 349 136 139 3 480.07 0.06 350 137 141 4 504.38 1.43 351 138 141 3 479.88 0.04