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 5 434.44 2.02 2 2 73 71 30.62 0.70 3 2 76 74 25.96 0.39 4 2 127 125 23.88 0.18 5 2 128 126 23.59 0.05 6 2 131 129 22.83 0.39 7 3 6 3 473.38 1.79 8 3 7 4 462.67 5.54 9 4 7 3 474.56 0.28 10 4 8 4 474.44 0.34 11 5 8 3 474.55 0.29 12 5 9 4 474.44 0.34 13 6 9 3 484.07 1.97 14 6 10 4 474.55 0.29 15 6 124 118 48.02 0.42 16 6 127 121 48.69 0.09 17 7 10 3 474.55 0.29 18 7 11 4 472.19 1.46 19 7 73 66 49.30 0.33 20 7 74 67 49.84 0.11 21 8 11 3 476.19 0.54 22 8 12 4 469.22 2.94 23 9 12 3 477.05 0.11 24 9 13 4 469.19 2.94 25 9 121 112 63.62 0.10 26 9 124 115 63.59 0.09 27 10 13 3 486.09 2.59 28 10 14 4 460.64 7.17 29 10 70 60 63.62 0.10 30 10 124 114 63.68 0.12 31 10 125 115 63.62 0.10 32 10 128 118 63.51 0.12 33 11 14 3 477.95 1.48 34 11 15 4 460.08 7.44 35 11 70 59 63.68 0.12 36 11 71 60 63.69 0.12 37 11 73 62 63.68 0.11 38 12 15 3 462.94 5.12 39 12 16 4 460.31 6.43 40 13 16 3 474.08 0.46 41 13 17 4 454.74 4.75 42 13 113 100 77.37 1.18 43 13 121 108 66.46 1.18 44 13 125 112 64.64 0.29 45 14 17 3 464.05 0.09 46 14 18 4 454.72 4.75 47 14 21 7 408.43 6.40 48 14 63 49 66.90 1.38 49 14 66 52 64.66 0.28 50 14 67 53 64.65 0.28 51 14 70 56 64.64 0.27 52 14 109 95 72.48 1.19 53 15 18 3 462.02 1.94 54 16 116 100 87.59 3.87 55 17 20 3 484.95 0.69 56 17 21 4 424.78 1.76 57 17 24 7 416.54 2.36 58 17 109 92 85.58 1.81 59 17 113 96 92.66 2.90 60 18 21 3 493.21 3.39 61 20 23 3 485.45 3.02 62 20 24 4 445.93 6.56 63 21 24 3 463.99 0.03 64 21 25 4 447.52 5.87 65 21 63 42 98.14 1.43 66 22 25 3 464.21 1.39 67 22 26 4 452.11 3.58 68 22 60 38 100.73 2.39 69 22 63 41 100.38 0.42 70 23 26 3 464.77 0.21 71 23 27 4 463.50 2.09 72 23 56 33 124.51 0.29 73 24 27 3 479.48 5.90 74 24 28 4 463.54 0.29 75 24 108 84 125.83 0.27 76 24 109 85 126.57 0.42 77 24 112 88 131.43 1.49 78 24 113 89 131.65 1.38 79 25 28 3 473.26 0.56 80 25 29 4 468.99 2.69 81 25 59 34 124.50 0.29 82 25 63 38 117.94 0.16 83 26 29 3 474.60 0.11 84 26 30 4 465.69 1.04 85 26 55 29 130.06 0.65 86 26 56 30 131.14 1.30 87 26 59 33 124.68 0.39 88 27 30 3 474.39 3.32 89 27 31 4 465.37 1.19 90 27 108 81 132.02 1.49 91 27 112 85 132.55 1.49 92 28 31 3 470.11 1.18 93 28 32 4 465.38 1.19 94 28 101 73 131.99 1.51 95 28 104 76 131.99 1.51 96 28 105 77 131.97 1.51 97 28 108 80 132.03 1.49 98 29 32 3 468.31 0.75 99 29 33 4 463.53 0.25 100 29 55 26 132.24 1.38 101 29 58 29 132.00 1.37 102 29 59 30 131.99 1.38 103 29 101 72 132.02 1.49 104 30 33 3 485.40 0.53 105 30 34 4 465.41 1.20 106 30 50 20 132.67 1.54 107 31 34 3 480.93 1.71 108 31 35 4 464.65 1.56 109 31 104 73 132.05 1.48 110 31 107 76 132.44 1.43 111 31 108 77 132.55 1.49 112 32 35 3 474.34 0.48 113 32 36 4 456.67 1.46 114 32 39 7 307.40 2.90 115 32 43 11 295.03 3.27 116 32 101 69 132.06 1.49 117 32 104 72 132.12 1.49 118 33 36 3 474.37 5.26 119 33 37 4 415.73 6.48 120 33 39 6 307.41 2.90 121 33 40 7 295.04 3.27 122 33 43 10 295.03 3.27 123 33 48 15 132.72 1.51 124 36 39 3 490.68 5.96 125 36 100 64 132.23 1.51 126 36 103 67 132.69 1.50 127 36 104 68 132.71 1.50 128 37 40 3 475.97 0.78 129 38 41 3 482.26 0.96 130 39 42 3 487.59 1.54 131 39 97 58 132.12 1.51 132 39 100 61 132.65 1.50 133 40 43 3 489.88 4.00 134 40 48 8 194.59 25.46 135 41 44 3 494.28 1.80 136 42 92 50 132.31 1.54 137 42 93 51 132.30 1.55 138 42 94 52 132.38 1.59 139 42 97 55 132.68 1.49 140 43 46 3 477.57 1.18 141 43 48 5 415.74 4.29 142 43 58 15 136.28 0.26 143 45 54 9 198.01 26.67 144 46 54 8 197.97 26.65 145 46 55 9 197.97 26.65 146 46 58 12 197.96 26.66 147 47 52 5 276.54 12.59 148 47 54 7 198.04 26.66 149 47 55 8 198.02 26.68 150 48 52 4 354.94 12.48 151 48 55 7 198.03 26.68 152 49 52 3 471.05 0.55 153 52 55 3 469.69 2.29 154 52 56 4 461.22 7.11 155 53 56 3 471.80 1.83 156 53 57 4 471.81 1.84 157 54 57 3 480.95 2.73 158 54 58 4 471.82 1.84 159 55 58 3 471.82 1.84 160 55 59 4 472.62 1.46 161 56 59 3 474.35 1.68 162 56 60 4 472.62 1.46 163 57 60 3 485.09 3.64 164 57 61 4 472.65 1.47 165 58 61 3 475.91 0.87 166 58 62 4 472.62 1.48 167 59 62 3 481.25 1.80 168 59 63 4 472.59 1.48 169 60 63 3 484.60 0.13 170 60 64 4 466.60 0.89 171 61 64 3 471.45 1.53 172 61 65 4 468.72 1.95 173 62 65 3 483.15 0.40 174 62 66 4 473.36 0.36 175 63 66 3 475.68 1.52 176 63 67 4 464.98 1.64 177 64 67 3 469.72 1.46 178 64 68 4 460.37 3.92 179 65 68 3 472.69 4.85 180 65 69 4 455.95 2.98 181 65 83 18 141.55 2.58 182 66 69 3 468.30 7.04 183 66 70 4 457.72 2.11 184 66 105 39 195.92 3.77 185 66 129 63 180.03 4.15 186 66 132 66 152.75 2.58 187 67 70 3 461.94 4.21 188 67 71 4 461.95 4.21 189 68 71 3 475.06 1.20 190 68 72 4 461.95 4.21 191 68 80 12 161.63 1.83 192 69 72 3 475.39 1.37 193 69 73 4 457.73 2.10 194 69 76 7 272.95 1.25 195 69 80 11 165.58 0.14 196 69 128 59 212.88 8.27 197 70 73 3 470.30 1.19 198 70 128 58 228.61 0.39 199 72 75 3 472.34 0.17 200 72 76 4 426.25 3.80 201 72 79 7 297.82 1.76 202 73 76 3 481.88 0.33 203 73 128 55 229.73 0.83 204 75 78 3 483.22 0.32 205 75 79 4 448.08 0.18 206 76 79 3 469.59 1.56 207 76 80 4 441.88 2.56 208 76 128 52 231.96 0.85 209 76 131 55 231.40 0.83 210 76 132 56 229.85 0.83 211 76 135 59 229.81 0.83 212 77 80 3 471.35 0.10 213 77 81 4 447.73 0.36 214 77 135 58 229.79 0.82 215 78 81 3 460.23 5.89 216 80 83 3 480.74 0.07 217 80 84 4 478.88 1.53 218 80 132 52 232.19 0.90 219 80 135 55 231.95 0.83 220 80 136 56 232.03 0.85 221 81 84 3 478.93 1.54 222 81 85 4 478.93 1.54 223 81 139 58 231.93 0.83 224 82 85 3 485.92 1.72 225 82 86 4 483.52 0.74 226 83 86 3 485.69 1.83 227 83 87 4 483.52 0.74 228 83 136 53 232.34 0.83 229 84 87 3 485.70 1.83 230 84 88 4 483.50 0.74 231 84 135 51 232.32 0.83 232 84 136 52 232.32 0.83 233 84 138 54 232.22 0.84 234 84 139 55 232.21 0.83 235 85 88 3 489.03 0.09 236 85 89 4 475.61 4.69 237 85 139 54 232.12 0.78 238 86 89 3 483.62 0.69 239 86 90 4 460.10 2.83 240 86 91 5 438.99 2.96 241 87 91 4 438.99 2.96 242 87 92 5 377.01 28.02 243 87 93 6 302.62 5.23 244 87 98 11 290.79 2.19 245 87 136 49 232.38 0.84 246 88 92 4 391.24 20.90 247 88 139 51 232.15 0.79 248 88 140 52 231.93 0.84 249 89 92 3 490.06 1.74 250 93 97 4 482.24 0.20 251 93 98 5 480.07 1.05 252 93 140 47 232.40 0.82 253 94 97 3 487.45 0.42 254 94 98 4 484.62 0.99 255 94 140 46 232.50 0.82 256 95 98 3 482.24 0.20 257 95 99 4 482.24 0.20 258 95 137 42 232.78 0.89 259 95 140 45 232.74 0.89 260 96 99 3 492.41 5.28 261 96 100 4 481.05 0.57 262 97 100 3 479.17 1.34 263 97 101 4 476.91 0.21 264 98 101 3 479.60 1.48 265 98 102 4 476.88 0.21 266 98 133 35 233.00 0.89 267 98 136 38 233.03 0.88 268 98 137 39 233.00 0.89 269 99 102 3 474.73 0.65 270 99 103 4 474.72 0.65 271 100 103 3 474.73 0.65 272 100 104 4 474.73 0.65 273 101 104 3 476.90 0.46 274 101 105 4 465.70 3.85 275 102 105 3 469.34 3.44 276 102 106 4 463.74 0.64 277 102 129 27 233.47 0.78 278 102 133 31 233.38 0.81 279 103 106 3 475.93 1.28 280 103 107 4 463.77 0.61 281 104 107 3 461.63 0.46 282 104 108 4 461.63 0.46 283 105 108 3 469.85 3.65 284 105 109 4 466.66 2.00 285 105 129 24 234.22 0.53 286 106 109 3 484.53 0.07 287 106 110 4 469.00 0.83 288 106 117 11 244.52 4.83 289 106 122 16 234.75 0.66 290 106 125 19 234.43 0.60 291 106 126 20 234.41 0.59 292 106 129 23 234.37 0.58 293 107 110 3 476.58 2.71 294 107 111 4 472.11 2.38 295 108 111 3 474.61 3.70 296 108 112 4 466.42 1.86 297 109 112 3 466.61 1.77 298 109 113 4 451.28 1.16 299 109 125 16 235.62 0.82 300 110 113 3 479.81 1.83 301 110 117 7 244.56 4.81 302 113 116 3 477.81 0.57 303 113 117 4 444.93 10.26 304 114 117 3 473.94 1.37 305 115 118 3 526.28 0.91 306 116 121 5 463.80 3.71 307 117 121 4 463.81 3.71 308 117 122 5 412.24 6.54 309 117 125 8 412.17 6.51 310 118 121 3 468.23 1.50 311 118 122 4 452.10 2.14 312 119 122 3 468.23 1.49 313 119 123 4 457.98 0.41 314 120 123 3 464.59 2.90 315 120 124 4 458.14 0.33 316 121 124 3 458.14 0.32 317 121 125 4 457.35 0.07 318 122 125 3 474.86 1.76 319 122 126 4 474.72 1.72 320 123 126 3 474.94 1.73 321 123 127 4 474.79 1.69 322 124 127 3 474.94 1.72 323 124 128 4 475.44 2.00 324 125 128 3 482.31 2.65 325 125 129 4 475.44 2.00 326 126 129 3 497.81 0.92 327 126 130 4 465.71 2.83 328 127 130 3 481.29 0.93 329 127 131 4 465.70 2.84 330 128 131 3 464.40 1.97 331 128 132 4 463.94 1.98 332 129 132 3 475.88 3.64 333 129 133 4 462.68 1.56 334 130 133 3 474.93 2.56 335 130 134 4 465.82 2.35 336 131 134 3 465.83 2.35 337 131 135 4 468.67 0.93 338 132 135 3 479.63 2.50 339 132 136 4 468.30 0.74 340 133 136 3 480.37 2.14 341 133 137 4 467.94 1.29 342 134 137 3 480.06 1.98 343 134 138 4 463.92 1.45 344 135 138 3 479.28 2.38 345 137 140 3 489.85 1.00 346 138 141 3 521.65 0.09