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 1 135 134 14.91 0.01 2 2 6 4 462.56 1.05 3 2 7 5 462.56 1.06 4 2 79 77 30.07 0.31 5 2 131 129 24.37 1.64 6 2 132 130 18.32 0.80 7 2 135 133 18.24 0.82 8 3 6 3 478.49 4.20 9 3 7 4 465.88 2.69 10 4 7 3 479.51 5.07 11 4 8 4 465.88 2.69 12 5 8 3 486.54 0.95 13 5 9 4 465.81 2.68 14 6 9 3 480.41 2.10 15 6 10 4 470.32 0.48 16 6 128 122 45.48 1.02 17 6 131 125 45.44 1.04 18 7 10 3 486.62 0.99 19 7 11 4 476.81 0.91 20 7 79 72 91.16 21.82 21 7 80 73 91.17 21.82 22 8 11 3 482.83 0.75 23 8 12 4 478.61 0.01 24 9 12 3 497.84 1.32 25 9 13 4 478.62 0.01 26 9 124 115 64.50 1.23 27 9 125 116 64.42 1.22 28 9 128 119 64.38 1.25 29 10 13 3 488.13 3.40 30 10 14 4 478.63 0.01 31 10 76 66 139.40 1.60 32 10 79 69 139.80 1.46 33 10 125 115 64.50 1.23 34 10 128 118 64.44 1.23 35 10 129 119 64.38 1.25 36 10 132 122 64.38 1.25 37 11 14 3 487.17 1.31 38 11 15 4 478.63 0.01 39 11 76 65 139.12 1.74 40 11 79 68 139.75 1.49 41 12 15 3 481.58 1.46 42 12 16 4 476.88 0.86 43 13 16 3 477.93 1.38 44 13 17 4 476.49 0.67 45 13 18 5 476.41 0.62 46 13 115 102 88.59 0.54 47 13 119 106 88.86 0.42 48 13 120 107 88.86 0.42 49 13 121 108 88.13 0.76 50 13 125 112 83.42 2.39 51 14 17 3 490.22 0.21 52 14 18 4 444.82 6.04 53 14 19 5 443.53 5.41 54 14 22 8 387.31 8.00 55 14 69 55 188.35 0.18 56 14 73 59 146.03 1.49 57 14 76 62 145.68 1.42 58 14 115 101 88.84 0.43 59 14 129 115 86.14 1.15 60 15 19 4 430.13 1.14 61 17 21 4 482.45 3.28 62 17 119 102 88.94 0.46 63 17 120 103 88.97 0.47 64 18 21 3 488.53 2.41 65 18 22 4 452.16 3.93 66 18 25 7 327.31 1.57 67 18 69 51 194.34 2.86 68 18 115 97 89.02 0.49 69 18 119 101 89.03 0.48 70 19 22 3 482.04 0.83 71 19 73 54 166.03 5.90 72 21 24 3 494.48 1.93 73 21 25 4 479.63 0.78 74 22 25 3 492.14 1.80 75 22 26 4 476.43 0.82 76 22 66 44 196.08 2.06 77 22 69 47 195.49 2.30 78 23 26 3 479.76 0.84 79 23 27 4 479.75 0.83 80 23 62 39 196.32 2.09 81 23 65 42 196.28 2.08 82 23 66 43 196.08 2.06 83 24 27 3 483.97 2.73 84 24 28 4 479.97 0.72 85 24 119 95 123.55 2.60 86 25 28 3 492.14 1.35 87 25 29 4 479.97 0.72 88 25 69 44 195.83 2.13 89 25 119 94 123.56 2.60 90 26 29 3 485.34 0.70 91 26 30 4 476.24 3.86 92 26 65 39 196.37 2.12 93 26 66 40 196.36 2.12 94 26 69 43 195.67 2.21 95 27 30 3 494.29 5.17 96 27 31 4 465.86 1.34 97 27 56 29 204.34 0.57 98 27 61 34 204.21 0.64 99 27 62 35 200.22 2.63 100 27 65 38 196.58 2.02 101 28 31 3 476.01 5.55 102 28 32 4 466.74 0.91 103 28 56 28 219.34 1.41 104 28 114 86 123.78 2.71 105 28 118 90 123.56 2.60 106 28 119 91 123.69 2.66 107 29 32 3 495.25 2.28 108 29 33 4 474.19 1.64 109 29 69 40 196.74 2.10 110 29 107 78 125.56 2.88 111 29 111 82 124.20 2.69 112 29 114 85 123.78 2.71 113 29 115 86 123.93 2.78 114 30 33 3 475.92 0.78 115 30 34 4 469.64 2.35 116 30 44 14 244.90 2.50 117 30 61 31 214.43 3.87 118 30 65 35 197.07 1.95 119 30 68 38 196.75 2.10 120 30 107 77 125.56 2.88 121 31 34 3 476.88 0.29 122 31 35 4 468.51 1.63 123 31 52 21 229.13 0.67 124 31 55 24 221.83 1.16 125 31 56 25 221.93 0.14 126 31 61 30 220.80 0.68 127 32 35 3 491.43 1.44 128 32 36 4 467.81 1.99 129 32 110 78 125.48 2.89 130 32 114 82 124.36 2.71 131 33 36 3 487.24 3.53 132 33 37 4 468.50 1.64 133 33 40 7 424.48 5.48 134 33 103 70 126.42 2.69 135 33 106 73 125.86 2.82 136 33 107 74 125.58 2.88 137 33 110 77 125.48 2.89 138 34 37 3 471.97 3.35 139 34 38 4 446.73 5.65 140 34 41 7 323.63 0.47 141 34 44 10 324.60 0.04 142 34 47 13 255.97 8.02 143 34 52 18 229.68 0.85 144 34 55 21 229.28 0.66 145 34 61 27 225.43 1.85 146 35 38 3 481.88 1.34 147 35 52 17 229.30 0.67 148 37 40 3 493.46 0.72 149 37 106 69 126.45 2.71 150 38 41 3 496.77 1.22 151 39 42 3 503.76 0.83 152 40 43 3 495.23 2.00 153 40 44 4 495.23 2.00 154 40 103 63 138.61 1.95 155 41 44 3 496.75 1.25 156 41 47 6 443.49 7.62 157 41 48 7 264.77 3.33 158 41 50 9 254.34 1.88 159 41 52 11 236.83 0.83 160 41 55 14 236.45 0.62 161 42 45 3 512.70 4.17 162 42 48 6 297.49 11.44 163 43 97 54 139.41 1.63 164 43 99 56 139.00 1.77 165 43 103 60 138.71 1.92 166 44 47 3 491.32 0.58 167 44 48 4 405.02 5.84 168 44 64 20 232.11 0.68 169 45 48 3 476.19 0.34 170 46 60 14 234.05 0.82 171 46 64 18 233.16 0.38 172 47 50 3 483.05 5.02 173 47 55 8 251.83 1.37 174 47 58 11 235.74 1.25 175 47 60 13 234.04 0.82 176 47 61 14 233.15 0.37 177 47 64 17 233.13 0.38 178 50 54 4 447.47 14.00 179 50 55 5 367.45 21.19 180 50 58 8 287.14 4.73 181 51 54 3 494.71 1.76 182 51 55 4 480.76 0.92 183 52 55 3 494.72 1.76 184 54 57 3 494.40 0.48 185 54 58 4 456.88 6.11 186 55 58 3 469.31 2.31 187 55 61 6 364.76 16.72 188 56 61 5 459.19 2.51 189 56 62 6 444.10 2.99 190 58 61 3 488.25 2.19 191 58 62 4 476.75 0.03 192 59 62 3 484.87 4.03 193 59 63 4 477.26 0.28 194 60 63 3 498.18 2.79 195 60 64 4 477.26 0.28 196 61 64 3 484.23 1.80 197 61 65 4 477.26 0.28 198 62 65 3 481.16 2.22 199 62 66 4 477.22 0.30 200 63 66 3 496.25 3.75 201 63 67 4 475.95 0.92 202 64 67 3 487.18 0.80 203 64 68 4 476.04 0.96 204 65 68 3 484.03 2.35 205 65 69 4 476.04 0.96 206 66 69 3 478.13 0.59 207 66 70 4 471.99 2.77 208 67 70 3 483.81 2.93 209 67 71 4 475.61 0.96 210 68 71 3 483.61 3.04 211 68 72 4 472.12 0.83 212 69 72 3 475.00 2.27 213 69 73 4 478.87 2.54 214 70 73 3 481.77 1.10 215 70 74 4 481.78 1.10 216 71 74 3 486.18 1.10 217 71 75 4 481.77 1.10 218 71 86 15 152.49 0.27 219 71 87 16 152.50 0.27 220 71 89 18 152.36 0.24 221 71 90 19 152.31 0.23 222 72 75 3 481.76 1.10 223 72 76 4 480.62 0.53 224 72 87 15 152.52 0.28 225 72 108 36 125.51 2.85 226 73 76 3 483.49 0.91 227 73 77 4 482.18 1.34 228 74 77 3 485.09 0.10 229 74 78 4 482.19 1.34 230 75 78 3 485.09 0.10 231 75 79 4 479.63 2.62 232 75 83 8 240.58 0.67 233 75 86 11 152.51 0.28 234 75 87 12 152.53 0.29 235 75 136 61 121.97 2.92 236 76 79 3 479.85 2.52 237 76 129 53 123.17 2.56 238 78 81 3 470.75 2.09 239 78 82 4 389.37 21.16 240 78 83 5 282.07 7.14 241 78 86 8 290.14 6.33 242 79 83 4 310.69 13.29 243 79 136 57 121.98 2.91 244 82 85 3 474.06 0.59 245 82 86 4 474.05 0.59 246 83 86 3 474.87 0.99 247 83 87 4 474.07 0.60 248 83 136 53 121.97 2.92 249 84 87 3 481.18 4.16 250 84 88 4 480.38 2.56 251 84 139 55 120.36 3.42 252 85 88 3 484.24 0.63 253 85 89 4 479.89 2.79 254 86 89 3 487.76 1.13 255 86 90 4 488.10 2.55 256 87 90 3 492.31 0.72 257 87 136 49 121.95 2.92 258 87 140 53 120.27 3.44 259 88 91 3 488.17 1.34 260 88 92 4 494.81 0.53 261 88 139 51 120.96 3.12 262 88 140 52 120.27 3.44 263 88 141 53 120.28 3.43 264 90 93 3 503.72 0.18 265 90 94 4 479.99 0.06 266 90 104 14 144.66 4.82 267 91 94 3 486.06 1.56 268 91 95 4 476.20 1.83 269 91 101 10 180.85 12.83 270 91 140 49 120.31 3.42 271 92 95 3 480.44 0.29 272 92 96 4 480.29 0.21 273 93 96 3 484.53 0.75 274 93 97 4 482.39 0.84 275 94 97 3 490.50 3.21 276 94 98 4 482.39 0.84 277 94 99 5 415.30 4.41 278 94 104 10 341.89 19.43 279 95 98 3 483.55 0.27 280 95 99 4 450.01 0.51 281 99 103 4 467.20 0.24 282 99 104 5 469.51 0.91 283 100 103 3 489.13 2.52 284 100 104 4 474.19 2.98 285 101 104 3 474.17 0.73 286 101 105 4 474.25 0.67 287 101 140 39 120.30 3.41 288 102 105 3 484.74 0.62 289 102 106 4 474.59 0.51 290 103 106 3 490.38 3.26 291 103 107 4 482.28 2.04 292 104 107 3 485.12 0.64 293 104 108 4 473.16 0.04 294 104 140 36 120.27 3.44 295 105 108 3 482.31 2.06 296 105 109 4 475.03 5.68 297 105 137 32 121.82 2.96 298 106 109 3 485.44 1.84 299 106 110 4 482.29 2.06 300 107 110 3 492.78 3.37 301 107 111 4 484.20 0.92 302 108 111 3 492.78 3.37 303 108 133 25 121.98 2.94 304 108 136 28 122.05 2.97 305 108 137 29 121.96 2.93 306 109 130 21 123.05 2.59 307 109 133 24 122.60 2.71 308 110 113 3 484.68 0.68 309 110 114 4 470.43 0.63 310 111 114 3 483.03 0.15 311 111 115 4 476.25 3.54 312 111 129 18 123.17 2.60 313 112 115 3 476.25 3.54 314 112 116 4 475.31 4.00 315 112 126 14 123.40 2.52 316 112 129 17 123.08 2.64 317 113 116 3 476.72 3.32 318 113 117 4 475.31 4.00 319 114 117 3 479.43 2.04 320 114 118 4 470.19 1.45 321 114 119 5 469.51 1.11 322 115 119 4 446.66 0.35 323 115 120 5 446.66 0.35 324 115 121 6 272.37 5.13 325 115 129 14 143.83 7.73 326 116 121 5 267.98 7.26 327 116 126 10 152.20 6.67 328 121 125 4 462.06 1.87 329 121 126 5 454.50 5.60 330 122 125 3 483.69 2.50 331 122 126 4 467.10 2.21 332 123 126 3 472.22 0.35 333 123 127 4 467.09 2.21 334 124 127 3 469.80 2.01 335 124 128 4 472.17 0.83 336 125 128 3 472.17 0.83 337 125 129 4 472.17 0.83 338 126 129 3 473.79 0.01 339 126 130 4 472.94 0.45 340 127 130 3 486.55 4.03 341 127 131 4 476.11 2.03 342 128 131 3 496.01 0.70 343 128 132 4 472.81 0.45 344 129 132 3 476.28 1.95 345 129 133 4 474.54 1.25 346 130 133 3 483.62 0.50 347 130 134 4 483.52 0.45 348 131 134 3 486.63 1.11 349 131 135 4 483.52 0.45 350 132 135 3 488.25 1.15 351 132 136 4 485.16 0.39 352 133 136 3 488.25 1.15 353 133 137 4 485.87 0.03 354 134 137 3 485.88 0.03 355 134 138 4 479.66 3.12 356 135 138 3 485.88 0.03 357 135 139 4 485.87 0.03 358 136 139 3 485.87 0.03 359 136 140 4 479.97 2.97 360 137 140 3 475.86 0.92