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 5 438.29 1.41 2 2 73 71 30.46 0.29 3 2 76 74 28.17 1.25 4 2 127 125 22.73 0.58 5 2 128 126 22.72 0.59 6 3 6 3 468.49 2.32 7 3 7 4 469.92 1.62 8 4 7 3 473.43 0.10 9 4 8 4 470.88 1.15 10 5 8 3 477.97 2.17 11 5 9 4 470.91 1.16 12 6 9 3 473.49 0.07 13 6 10 4 471.55 0.89 14 6 124 118 46.26 0.01 15 6 127 121 46.34 0.03 16 7 10 3 479.72 2.38 17 7 11 4 471.56 0.90 18 7 73 66 47.67 0.33 19 7 74 67 48.23 0.06 20 8 11 3 477.74 1.09 21 8 12 4 471.57 0.90 22 9 12 3 477.13 0.79 23 9 13 4 471.57 0.91 24 9 121 112 64.02 0.24 25 9 124 115 63.94 0.21 26 10 13 3 478.41 0.89 27 10 14 4 462.69 5.72 28 10 70 60 63.98 0.23 29 10 124 114 64.02 0.24 30 10 125 115 64.00 0.24 31 10 128 118 63.95 0.21 32 11 14 3 475.54 2.30 33 11 15 4 463.47 4.95 34 11 70 59 64.03 0.23 35 11 71 60 64.05 0.23 36 11 73 62 64.03 0.23 37 12 15 3 478.36 0.86 38 12 16 4 474.80 2.66 39 13 16 3 478.38 0.87 40 13 17 4 474.81 2.66 41 13 113 100 83.86 0.54 42 13 121 108 67.70 1.07 43 13 125 112 65.18 0.18 44 14 17 3 478.37 0.86 45 14 18 4 474.81 2.65 46 14 21 7 400.64 7.00 47 14 63 49 67.80 1.09 48 14 66 52 65.15 0.18 49 14 67 53 65.19 0.17 50 14 70 56 65.14 0.18 51 15 18 3 478.46 0.82 52 16 113 97 93.50 1.44 53 16 116 100 93.08 1.64 54 17 20 3 482.47 6.19 55 17 21 4 451.38 5.38 56 17 24 7 408.31 9.83 57 17 109 92 88.23 0.63 58 17 113 96 98.98 0.68 59 18 21 3 503.83 0.94 60 20 23 3 478.51 1.43 61 20 24 4 462.81 0.33 62 21 24 3 472.04 2.37 63 21 25 4 468.51 2.50 64 21 63 42 99.39 0.78 65 22 25 3 477.72 1.94 66 22 26 4 473.68 0.07 67 22 59 37 108.87 0.20 68 22 60 38 101.84 0.34 69 22 63 41 101.81 0.34 70 23 26 3 473.69 0.08 71 23 27 4 468.53 2.50 72 23 56 33 117.19 0.57 73 24 27 3 469.86 3.16 74 24 28 4 468.53 2.50 75 24 108 84 123.01 1.82 76 24 109 85 124.08 1.86 77 24 112 88 129.09 0.94 78 24 113 89 130.46 1.37 79 25 28 3 466.24 1.35 80 25 29 4 462.16 1.49 81 25 59 34 117.19 0.58 82 25 63 38 116.13 0.13 83 26 29 3 478.38 0.12 84 26 30 4 462.20 1.59 85 26 55 29 123.36 1.96 86 26 56 30 123.58 1.84 87 26 59 33 117.83 0.26 88 27 30 3 473.23 2.69 89 27 31 4 462.17 1.62 90 27 108 81 130.30 0.60 91 27 112 85 131.62 1.21 92 28 31 3 468.04 3.88 93 28 32 4 462.29 1.70 94 28 101 73 129.56 0.94 95 28 104 76 129.58 0.93 96 28 105 77 129.59 0.93 97 28 108 80 131.18 1.01 98 29 32 3 473.26 4.01 99 29 33 4 465.47 0.12 100 29 55 26 131.29 1.07 101 29 58 29 131.24 1.09 102 29 59 30 130.29 0.61 103 29 101 72 130.24 0.60 104 30 33 3 477.07 2.11 105 30 34 4 465.46 0.11 106 30 50 20 131.50 1.12 107 31 34 3 479.40 0.95 108 31 35 4 465.45 0.11 109 31 104 73 131.33 1.12 110 31 107 76 131.56 1.20 111 31 108 77 131.57 1.19 112 31 111 80 131.67 1.20 113 32 35 3 469.29 2.03 114 32 36 4 457.57 3.89 115 32 39 7 389.09 8.98 116 32 100 68 131.34 1.11 117 32 101 69 131.31 1.10 118 32 104 72 131.46 1.15 119 33 37 4 436.05 2.03 120 33 39 6 360.92 23.07 121 33 40 7 298.79 8.00 122 33 43 10 280.67 1.06 123 33 48 15 131.65 1.19 124 34 37 3 485.55 0.65 125 36 39 3 501.90 2.67 126 36 100 64 131.35 1.12 127 36 103 67 131.61 1.18 128 36 104 68 131.61 1.19 129 37 40 3 489.13 0.78 130 38 41 3 494.04 0.22 131 39 42 3 496.54 1.48 132 39 43 4 487.59 1.07 133 39 97 58 131.33 1.11 134 39 100 61 131.57 1.20 135 40 43 3 488.76 0.49 136 40 48 8 201.85 29.64 137 41 44 3 495.09 2.68 138 42 93 51 131.16 1.09 139 42 94 52 131.44 1.16 140 42 97 55 131.57 1.22 141 43 46 3 481.12 0.21 142 43 48 5 430.45 11.83 143 43 58 15 194.14 29.85 144 45 54 9 203.11 29.86 145 46 54 8 203.09 29.86 146 46 55 9 203.11 29.87 147 46 58 12 203.09 29.86 148 47 52 5 257.61 2.73 149 47 54 7 257.47 2.69 150 47 55 8 257.49 2.68 151 48 52 4 391.51 17.61 152 48 55 7 257.51 2.67 153 49 52 3 452.84 0.06 154 52 55 3 467.01 3.77 155 52 56 4 467.12 0.79 156 53 56 3 470.05 2.25 157 53 57 4 464.20 2.25 158 54 57 3 473.44 0.33 159 54 58 4 464.23 2.27 160 55 58 3 474.31 2.77 161 55 59 4 461.02 0.67 162 56 59 3 473.86 0.49 163 56 60 4 473.84 0.49 164 57 60 3 482.62 2.90 165 57 61 4 470.30 2.26 166 58 61 3 473.19 0.82 167 58 62 4 474.01 0.29 168 59 62 3 480.99 3.08 169 59 63 4 468.47 3.06 170 60 63 3 470.48 2.06 171 60 64 4 473.81 0.39 172 61 64 3 476.14 1.56 173 61 65 4 473.84 0.37 174 62 65 3 478.10 3.01 175 62 66 4 469.04 2.03 176 62 101 39 141.62 2.05 177 63 66 3 469.07 2.01 178 63 67 4 469.01 2.04 179 64 67 3 469.01 2.04 180 64 68 4 469.00 2.04 181 65 68 3 478.73 2.68 182 65 69 4 466.76 0.64 183 65 80 15 143.41 3.12 184 65 83 18 136.93 0.04 185 66 69 3 477.93 3.09 186 66 70 4 466.76 0.64 187 66 105 39 182.19 3.01 188 66 128 62 179.97 4.20 189 66 129 63 168.47 1.16 190 66 132 66 154.39 2.33 191 67 70 3 477.93 3.09 192 67 71 4 469.89 0.93 193 68 71 3 468.79 7.66 194 68 72 4 460.99 3.52 195 68 79 11 247.37 4.46 196 69 72 3 478.05 1.43 197 69 73 4 449.46 0.86 198 69 76 7 266.00 7.94 199 69 80 11 158.94 3.17 200 69 128 59 183.66 2.38 201 69 132 63 165.12 2.21 202 70 73 3 473.17 3.60 203 70 128 58 191.05 1.32 204 72 75 3 464.81 7.78 205 72 76 4 431.96 1.53 206 72 79 7 314.16 21.05 207 73 76 3 476.03 1.18 208 75 78 3 491.87 2.23 209 75 79 4 445.27 8.84 210 76 79 3 468.57 2.81 211 76 80 4 432.42 19.23 212 76 128 52 236.27 2.85 213 76 131 55 235.44 2.89 214 76 132 56 232.22 1.83 215 76 135 59 231.96 1.94 216 77 81 4 413.32 7.32 217 77 135 58 231.94 1.93 218 78 81 3 471.34 4.20 219 80 83 3 476.00 1.12 220 80 84 4 457.66 4.28 221 80 132 52 237.83 2.50 222 80 135 55 237.67 2.46 223 80 136 56 237.70 2.47 224 81 84 3 471.75 3.62 225 81 85 4 462.24 4.28 226 81 139 58 237.72 2.48 227 82 85 3 475.36 1.80 228 82 86 4 470.98 4.00 229 83 86 3 476.48 1.26 230 83 87 4 466.09 6.44 231 83 136 53 238.16 2.43 232 84 87 3 471.78 3.61 233 84 88 4 464.06 5.37 234 84 135 51 238.22 2.41 235 84 136 52 238.14 2.42 236 84 139 55 238.12 2.43 237 85 88 3 471.77 3.62 238 85 89 4 457.73 2.27 239 85 139 54 238.12 2.43 240 86 89 3 482.39 0.28 241 86 90 4 456.28 2.98 242 86 91 5 427.78 5.33 243 87 91 4 387.29 3.21 244 87 92 5 330.23 1.40 245 87 98 11 275.20 1.18 246 87 136 49 238.37 2.40 247 87 140 53 238.12 2.43 248 88 92 4 371.49 16.64 249 88 139 51 238.15 2.43 250 88 140 52 238.11 2.43 251 89 92 3 483.61 0.33 252 92 140 48 238.38 2.41 253 93 97 4 480.89 1.28 254 93 98 5 472.13 0.87 255 93 140 47 238.49 2.42 256 94 97 3 489.69 3.10 257 95 98 3 489.70 3.10 258 95 137 42 239.12 2.25 259 95 140 45 239.05 2.21 260 96 99 3 488.53 2.51 261 96 100 4 477.19 0.57 262 97 100 3 478.68 2.42 263 97 101 4 474.95 0.55 264 98 101 3 481.06 3.60 265 98 102 4 474.94 0.55 266 98 133 35 239.88 2.48 267 98 136 38 239.89 2.46 268 98 137 39 239.90 2.48 269 98 140 42 239.80 2.46 270 99 102 3 481.06 3.60 271 99 103 4 474.93 0.54 272 100 103 3 481.13 3.56 273 100 104 4 474.92 0.54 274 101 104 3 471.75 0.81 275 101 105 4 466.09 1.80 276 102 105 3 476.38 3.34 277 102 106 4 466.10 1.80 278 102 129 27 240.24 2.54 279 102 133 31 240.21 2.54 280 103 106 3 476.37 3.33 281 103 107 4 466.24 1.73 282 104 107 3 471.26 0.10 283 104 108 4 466.93 2.06 284 105 108 3 482.91 2.66 285 105 109 4 466.22 2.42 286 105 129 24 241.22 2.59 287 106 109 3 479.56 5.00 288 106 110 4 461.54 0.08 289 106 117 11 243.19 2.71 290 106 122 16 241.96 2.42 291 106 125 19 241.81 2.37 292 106 126 20 241.72 2.38 293 106 129 23 241.30 2.58 294 107 110 3 469.75 3.33 295 107 111 4 468.87 3.77 296 108 111 3 477.28 0.43 297 108 112 4 464.65 5.88 298 109 112 3 470.82 6.27 299 109 113 4 456.87 2.14 300 109 125 16 242.27 2.27 301 110 117 7 243.19 2.72 302 113 116 3 479.14 0.52 303 113 117 4 458.68 0.46 304 114 117 3 479.15 0.51 305 115 118 3 516.98 2.60 306 116 121 5 449.99 4.01 307 117 121 4 456.25 0.90 308 117 122 5 449.99 4.01 309 117 125 8 449.99 4.01 310 118 121 3 472.78 0.78 311 118 122 4 456.29 0.90 312 119 122 3 474.17 1.47 313 119 123 4 466.06 5.54 314 120 123 3 474.21 1.49 315 120 124 4 474.19 1.49 316 121 124 3 473.81 1.68 317 121 125 4 471.49 2.84 318 122 125 3 477.57 0.20 319 122 126 4 471.56 2.79 320 123 126 3 471.78 2.69 321 123 127 4 466.12 0.07 322 124 127 3 472.88 2.40 323 124 128 4 471.83 2.92 324 125 128 3 471.83 2.93 325 125 129 4 463.17 1.41 326 126 129 3 484.19 3.39 327 126 130 4 463.27 1.32 328 127 130 3 474.17 1.45 329 127 131 4 464.95 1.73 330 128 131 3 474.11 1.78 331 128 132 4 464.95 1.73 332 129 132 3 473.03 2.31 333 129 133 4 464.94 1.73 334 130 133 3 465.32 1.54 335 130 134 4 465.31 1.54 336 131 134 3 467.56 0.39 337 131 135 4 464.54 1.90 338 132 135 3 465.53 0.80 339 132 136 4 462.33 0.81 340 133 136 3 470.75 3.40 341 133 137 4 461.75 1.04 342 134 137 3 474.17 1.83 343 134 138 4 458.14 0.76 344 135 138 3 474.56 1.15 345 136 140 4 490.22 1.10 346 137 140 3 487.37 0.33