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 6 4 464.79 3.09 2 2 7 5 453.30 7.25 3 2 73 71 26.89 0.59 4 2 127 125 26.48 0.47 5 2 128 126 24.67 0.42 6 2 131 129 21.68 1.08 7 3 6 3 476.39 4.22 8 3 7 4 469.47 0.77 9 4 7 3 487.72 1.44 10 4 8 4 465.22 2.90 11 5 8 3 470.56 1.31 12 5 9 4 469.85 0.58 13 6 9 3 476.72 0.56 14 6 10 4 469.85 0.58 15 6 124 118 46.23 0.23 16 6 127 121 46.04 0.13 17 7 10 3 480.54 1.05 18 7 11 4 467.44 1.69 19 7 73 66 47.79 0.12 20 7 74 67 49.33 0.90 21 8 11 3 480.55 1.05 22 8 12 4 467.05 1.48 23 9 12 3 479.37 1.64 24 9 13 4 463.19 0.46 25 9 121 112 62.87 0.43 26 9 124 115 62.79 0.47 27 10 13 3 481.69 0.48 28 10 14 4 467.20 1.54 29 10 70 60 62.80 0.46 30 10 73 63 62.80 0.46 31 10 124 114 62.87 0.43 32 10 125 115 62.81 0.46 33 10 128 118 62.77 0.47 34 11 14 3 478.59 1.08 35 11 15 4 468.79 2.33 36 11 70 59 62.80 0.46 37 11 73 62 62.80 0.46 38 12 15 3 484.59 4.41 39 12 16 4 474.56 3.25 40 13 16 3 484.92 4.24 41 13 17 4 473.53 2.73 42 13 121 108 62.99 0.47 43 13 125 112 62.88 0.45 44 14 17 3 479.00 1.02 45 14 18 4 473.90 2.54 46 14 21 7 376.76 3.47 47 14 63 49 65.83 1.87 48 14 66 52 62.88 0.43 49 14 67 53 62.84 0.45 50 14 70 56 62.88 0.46 51 15 18 3 472.64 2.29 52 16 113 97 87.05 2.02 53 16 116 100 87.05 2.03 54 17 20 3 479.21 0.98 55 17 21 4 458.97 0.52 56 17 24 7 396.22 10.42 57 17 109 92 86.92 1.96 58 17 113 96 87.08 2.04 59 18 21 3 492.67 0.96 60 20 23 3 478.95 6.79 61 20 24 4 463.20 1.26 62 21 24 3 469.30 0.97 63 21 25 4 463.25 1.23 64 21 63 42 88.31 2.67 65 22 25 3 474.99 1.87 66 22 26 4 468.48 1.39 67 22 60 38 102.73 2.08 68 22 63 41 100.45 3.22 69 23 26 3 476.94 2.85 70 23 27 4 468.48 1.39 71 24 27 3 467.18 1.32 72 24 28 4 460.56 3.46 73 24 108 84 121.76 0.48 74 24 109 85 121.77 0.47 75 24 112 88 131.34 0.43 76 25 28 3 477.58 1.92 77 25 29 4 464.38 1.55 78 25 59 34 117.75 1.50 79 25 63 38 115.00 0.06 80 26 29 3 478.54 0.10 81 26 30 4 468.25 0.39 82 26 55 29 124.46 0.89 83 26 56 30 128.54 0.46 84 26 59 33 121.01 0.10 85 27 30 3 468.35 0.34 86 27 31 4 468.70 0.23 87 27 108 81 131.57 0.36 88 27 112 85 132.18 0.41 89 28 31 3 476.59 1.80 90 28 32 4 468.72 0.24 91 28 101 73 131.40 0.41 92 28 104 76 131.41 0.41 93 28 105 77 131.43 0.40 94 28 108 80 131.84 0.40 95 29 32 3 474.21 2.98 96 29 33 4 468.66 0.27 97 29 55 26 131.78 0.45 98 29 58 29 131.64 0.40 99 29 59 30 131.63 0.40 100 29 62 33 131.62 0.38 101 29 101 72 131.55 0.35 102 30 33 3 473.33 0.44 103 30 34 4 468.66 0.26 104 30 50 20 132.16 0.38 105 31 34 3 486.32 1.37 106 31 35 4 468.64 0.26 107 31 104 73 131.75 0.27 108 31 107 76 132.09 0.38 109 31 108 77 132.13 0.40 110 32 35 3 486.12 1.48 111 32 36 4 461.75 2.83 112 32 39 7 345.30 1.05 113 32 100 68 131.75 0.26 114 32 101 69 131.75 0.27 115 32 104 72 132.02 0.37 116 33 36 3 486.12 1.48 117 33 37 4 451.50 2.25 118 33 39 6 350.81 1.71 119 33 40 7 307.88 14.88 120 33 43 10 282.52 2.21 121 33 48 15 132.27 0.41 122 34 37 3 495.33 0.67 123 36 39 3 484.87 0.14 124 36 100 64 131.96 0.36 125 36 103 67 132.20 0.39 126 37 40 3 479.59 2.21 127 38 41 3 489.73 2.87 128 39 42 3 492.97 1.25 129 39 43 4 481.87 1.29 130 39 97 58 131.76 0.26 131 39 100 61 132.12 0.39 132 40 43 3 479.08 2.69 133 40 48 8 134.72 0.83 134 41 44 3 481.12 1.99 135 42 93 51 131.60 0.26 136 42 94 52 132.05 0.38 137 42 97 55 132.15 0.35 138 43 46 3 473.24 0.93 139 43 48 5 443.98 1.67 140 43 58 15 132.44 0.41 141 45 54 9 135.31 0.70 142 46 54 8 135.27 0.71 143 46 58 12 135.23 0.69 144 47 52 5 198.49 30.88 145 47 54 7 135.32 0.70 146 47 55 8 135.33 0.69 147 48 55 7 135.32 0.69 148 49 52 3 477.62 6.08 149 51 56 5 459.80 1.03 150 52 55 3 471.25 0.82 151 52 56 4 461.51 0.18 152 53 56 3 469.99 1.44 153 53 57 4 461.51 0.18 154 54 57 3 477.34 3.73 155 54 58 4 463.53 1.18 156 55 58 3 475.97 3.04 157 55 59 4 467.21 0.67 158 56 59 3 475.62 3.21 159 56 60 4 475.62 3.21 160 57 60 3 475.63 3.21 161 57 61 4 475.62 3.22 162 58 61 3 475.62 3.23 163 58 62 4 475.61 3.23 164 59 62 3 475.86 3.12 165 59 63 4 468.08 0.51 166 60 63 3 475.59 3.25 167 60 64 4 468.10 0.49 168 61 64 3 474.03 2.48 169 61 65 4 469.09 0.02 170 62 65 3 469.06 0.04 171 62 66 4 469.06 0.04 172 63 66 3 472.88 1.96 173 63 67 4 469.04 0.04 174 64 67 3 469.03 0.04 175 64 68 4 466.29 0.46 176 65 68 3 472.59 2.14 177 65 69 4 466.28 0.46 178 65 83 18 134.20 0.65 179 66 69 3 471.11 2.85 180 66 70 4 466.25 0.46 181 66 105 39 191.88 3.88 182 66 128 62 196.96 1.31 183 66 129 63 183.50 0.15 184 66 132 66 154.82 0.96 185 67 70 3 478.90 0.60 186 67 71 4 471.06 2.88 187 68 71 3 482.55 1.58 188 68 72 4 463.98 0.66 189 68 79 11 168.22 7.67 190 69 72 3 471.39 4.36 191 69 73 4 456.61 3.02 192 69 76 7 235.00 17.75 193 69 80 11 154.82 0.97 194 69 128 59 220.63 2.71 195 69 132 63 191.62 3.95 196 70 73 3 473.72 0.93 197 70 128 58 220.66 2.70 198 72 75 3 465.61 0.98 199 72 76 4 463.10 0.30 200 72 79 7 290.60 5.53 201 73 76 3 490.39 0.18 202 73 128 55 238.17 6.45 203 75 78 3 485.62 1.33 204 75 79 4 451.60 0.35 205 76 79 3 458.57 7.29 206 76 80 4 443.47 3.95 207 76 131 55 258.69 3.62 208 76 132 56 253.46 5.78 209 76 135 59 246.59 2.32 210 77 80 3 481.91 1.91 211 77 81 4 413.56 3.38 212 77 135 58 238.23 6.47 213 80 83 3 462.00 3.45 214 80 84 4 452.22 2.02 215 80 132 52 260.24 3.77 216 80 135 55 259.77 3.96 217 80 136 56 259.76 3.96 218 81 84 3 478.40 0.81 219 81 85 4 459.14 3.91 220 81 139 58 259.21 3.71 221 82 85 3 472.00 1.79 222 82 86 4 459.14 3.91 223 83 86 3 458.01 0.83 224 83 87 4 453.84 1.26 225 83 136 53 260.37 3.79 226 84 87 3 465.73 0.61 227 84 88 4 452.18 2.07 228 84 89 5 452.18 2.07 229 84 135 51 260.40 3.79 230 84 136 52 260.37 3.79 231 84 138 54 260.35 3.79 232 84 139 55 260.25 3.79 233 85 89 4 411.70 12.03 234 85 90 5 411.70 12.03 235 85 139 54 260.25 3.79 236 86 90 4 398.07 18.84 237 86 91 5 398.06 18.84 238 87 91 4 365.26 2.46 239 87 92 5 351.61 9.28 240 87 93 6 333.39 18.38 241 87 98 11 275.44 0.57 242 87 136 49 260.60 3.85 243 88 92 4 357.29 6.44 244 88 136 48 260.62 3.84 245 88 137 49 260.48 3.81 246 88 139 51 260.37 3.78 247 88 140 52 260.25 3.78 248 89 92 3 477.39 2.75 249 89 139 50 260.37 3.78 250 89 141 52 260.11 3.85 251 92 140 48 260.50 3.81 252 92 141 49 260.50 3.81 253 93 97 4 468.45 0.98 254 93 98 5 464.49 2.96 255 93 140 47 260.52 3.81 256 94 97 3 488.50 3.18 257 95 98 3 489.44 1.28 258 95 137 42 260.76 3.83 259 95 140 45 260.73 3.81 260 96 99 3 477.19 1.11 261 96 100 4 472.95 3.23 262 97 100 3 473.75 0.60 263 97 101 4 464.98 3.10 264 98 101 3 473.68 2.32 265 98 102 4 464.81 3.17 266 98 133 35 261.13 3.91 267 98 136 38 261.16 3.91 268 98 137 39 261.13 3.90 269 99 102 3 474.51 0.40 270 99 103 4 464.81 3.17 271 100 103 3 473.64 1.24 272 100 104 4 473.63 1.27 273 101 104 3 473.66 1.28 274 101 105 4 473.62 1.27 275 102 105 3 469.03 3.58 276 102 106 4 468.16 4.00 277 102 129 27 261.53 3.81 278 103 106 3 476.45 0.14 279 103 107 4 468.17 4.00 280 104 107 3 467.96 1.81 281 104 108 4 462.24 1.04 282 105 108 3 474.55 1.83 283 105 109 4 469.17 4.53 284 105 129 24 262.29 3.60 285 106 109 3 475.43 2.45 286 106 110 4 469.13 4.54 287 106 117 11 265.31 3.02 288 106 122 16 262.94 3.50 289 106 125 19 262.92 3.48 290 106 126 20 262.48 3.62 291 106 129 23 262.44 3.62 292 107 110 3 475.43 2.45 293 107 111 4 463.76 0.26 294 108 111 3 474.07 1.59 295 108 112 4 463.06 0.10 296 109 112 3 472.38 3.08 297 109 113 4 450.30 5.03 298 109 117 8 268.32 3.00 299 109 125 16 262.98 3.45 300 110 114 4 432.54 1.90 301 110 117 7 265.74 3.23 302 111 114 3 497.87 3.90 303 113 116 3 488.00 1.50 304 113 117 4 442.51 0.80 305 114 117 3 491.37 0.19 306 115 118 3 517.01 0.76 307 116 121 5 453.39 0.37 308 117 121 4 453.11 0.52 309 117 122 5 435.12 8.49 310 117 125 8 407.26 2.31 311 118 121 3 454.55 0.20 312 118 122 4 453.98 0.09 313 119 122 3 464.65 0.76 314 119 123 4 455.36 0.60 315 120 123 3 468.55 2.71 316 120 124 4 458.03 1.50 317 121 124 3 468.31 2.17 318 121 125 4 452.29 1.38 319 122 125 3 470.30 4.38 320 122 126 4 450.64 2.19 321 123 126 3 472.19 3.54 322 123 127 4 459.65 2.31 323 124 127 3 460.87 3.00 324 124 128 4 462.19 2.33 325 125 128 3 462.20 2.34 326 125 129 4 463.08 4.13 327 126 129 3 473.56 0.42 328 126 130 4 463.37 4.00 329 127 130 3 467.15 2.10 330 127 131 4 463.37 4.00 331 128 131 3 470.14 0.61 332 128 132 4 470.12 0.61 333 129 132 3 470.14 0.61 334 129 133 4 470.12 0.61 335 130 133 3 472.69 0.70 336 130 134 4 455.67 0.13 337 131 134 3 472.61 0.74 338 131 135 4 463.43 4.01 339 132 135 3 480.77 4.22 340 132 136 4 455.10 0.42 341 133 136 3 467.18 2.58 342 133 137 4 446.82 3.71 343 134 137 3 474.76 1.22 344 134 138 4 443.94 4.51 345 135 138 3 465.88 1.04 346 137 140 3 496.03 0.71