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 1 131 130 20.32 0.43 2 2 6 4 469.10 0.29 3 2 7 5 457.00 6.30 4 2 73 71 32.52 0.21 5 2 127 125 24.30 0.04 6 2 128 126 22.86 0.76 7 2 131 129 21.54 0.10 8 3 6 3 470.89 1.19 9 3 7 4 469.09 0.29 10 4 7 3 479.97 0.68 11 4 8 4 469.10 0.29 12 5 8 3 486.81 0.88 13 5 9 4 476.79 4.13 14 6 9 3 486.81 0.88 15 6 10 4 475.25 4.90 16 6 124 118 52.63 0.25 17 7 10 3 485.99 2.25 18 7 11 4 475.25 4.90 19 7 73 66 53.84 0.35 20 7 74 67 53.85 0.34 21 8 11 3 483.28 0.90 22 8 12 4 477.60 3.73 23 9 12 3 478.21 4.03 24 9 13 4 470.40 0.12 25 9 121 112 68.62 1.52 26 9 124 115 68.54 1.54 27 10 13 3 485.81 1.49 28 10 14 4 475.26 2.54 29 10 70 60 68.59 1.51 30 10 73 63 68.59 1.51 31 10 124 114 68.59 1.51 32 10 125 115 68.59 1.51 33 10 128 118 68.50 1.55 34 11 14 3 484.55 0.85 35 11 15 4 478.56 0.90 36 11 70 59 68.59 1.51 37 11 73 62 68.59 1.51 38 12 15 3 483.30 1.48 39 12 16 4 478.56 0.90 40 13 16 3 482.62 2.93 41 13 17 4 475.30 2.54 42 13 121 108 68.77 1.55 43 13 125 112 68.73 1.56 44 14 17 3 479.23 4.77 45 14 18 4 467.73 1.40 46 14 21 7 442.74 2.88 47 14 66 52 68.75 1.55 48 14 67 53 68.77 1.55 49 14 70 56 68.75 1.56 50 14 109 95 89.83 0.70 51 15 18 3 476.95 4.67 52 16 113 97 98.58 1.02 53 16 116 100 95.49 0.50 54 17 20 3 488.16 2.68 55 17 21 4 448.25 1.57 56 17 24 7 421.93 7.51 57 17 109 92 97.08 0.27 58 17 113 96 100.10 0.52 59 18 21 3 506.32 0.89 60 20 23 3 471.28 0.70 61 20 24 4 461.81 1.51 62 21 24 3 478.88 0.84 63 21 25 4 469.14 1.81 64 21 63 42 106.78 0.03 65 21 67 46 106.75 0.01 66 22 25 3 480.67 1.73 67 22 26 4 471.72 0.62 68 22 56 34 128.38 0.58 69 22 59 37 120.39 1.23 70 22 60 38 110.85 1.85 71 22 63 41 107.08 0.03 72 23 26 3 486.62 4.71 73 23 27 4 469.27 1.85 74 23 56 33 128.44 0.56 75 24 27 3 483.09 3.37 76 24 28 4 469.25 1.84 77 24 108 84 131.74 1.09 78 24 109 85 131.75 1.10 79 24 112 88 139.56 1.58 80 25 28 3 481.69 4.07 81 25 29 4 470.87 1.03 82 25 59 34 128.45 0.56 83 25 62 37 128.41 0.58 84 26 29 3 484.30 1.85 85 26 30 4 470.85 1.02 86 26 55 29 137.29 1.64 87 26 56 30 137.30 1.63 88 26 59 33 131.77 1.10 89 27 30 3 474.55 0.85 90 27 31 4 470.79 0.98 91 27 108 81 140.27 1.36 92 27 112 85 140.62 1.51 93 28 31 3 479.13 2.02 94 28 32 4 470.76 0.98 95 28 101 73 139.88 1.46 96 28 104 76 139.88 1.47 97 28 105 77 139.89 1.46 98 28 108 80 140.29 1.36 99 29 32 3 482.37 3.04 100 29 33 4 474.47 0.91 101 29 55 26 140.54 1.48 102 29 58 29 140.33 1.38 103 29 59 30 140.32 1.38 104 29 62 33 140.15 1.46 105 29 101 72 139.99 1.49 106 30 33 3 489.77 0.54 107 30 34 4 473.51 0.43 108 30 50 20 141.12 1.49 109 31 34 3 489.79 0.53 110 31 35 4 466.12 4.13 111 31 104 73 140.54 1.47 112 31 107 76 140.66 1.47 113 31 108 77 140.68 1.48 114 31 111 80 141.03 1.45 115 32 35 3 482.51 3.08 116 32 36 4 465.18 4.61 117 32 39 7 317.38 6.16 118 32 100 68 140.53 1.47 119 32 101 69 140.50 1.48 120 32 104 72 140.59 1.48 121 33 37 4 440.85 0.46 122 33 39 6 316.35 6.69 123 33 40 7 269.60 1.71 124 33 43 10 267.58 0.70 125 33 48 15 141.28 1.45 126 33 55 22 141.15 1.48 127 34 37 3 484.60 1.95 128 36 39 3 492.68 0.32 129 36 100 64 140.52 1.48 130 36 103 67 140.98 1.46 131 36 104 68 141.00 1.46 132 37 40 3 489.37 2.03 133 38 41 3 500.75 2.07 134 39 42 3 507.08 0.85 135 39 43 4 494.99 4.28 136 39 97 58 140.52 1.49 137 39 100 61 140.85 1.41 138 40 43 3 487.67 0.61 139 40 48 8 260.36 2.12 140 41 44 3 501.06 1.24 141 42 93 51 140.46 1.49 142 42 94 52 140.72 1.42 143 42 97 55 140.89 1.41 144 43 46 3 474.18 3.93 145 43 48 5 420.69 14.50 146 43 58 15 257.20 2.72 147 45 54 9 261.76 1.69 148 46 54 8 261.74 1.68 149 46 55 9 261.70 1.68 150 46 58 12 261.68 1.69 151 47 52 5 291.91 13.35 152 47 54 7 261.81 1.67 153 47 55 8 261.81 1.67 154 48 52 4 444.39 3.85 155 48 55 7 261.77 1.64 156 49 52 3 469.98 3.81 157 52 55 3 487.63 1.00 158 52 56 4 463.49 1.22 159 53 56 3 472.00 0.57 160 53 57 4 463.49 1.22 161 54 57 3 479.37 0.98 162 54 58 4 461.39 1.08 163 55 58 3 474.24 3.54 164 55 59 4 467.47 0.17 165 56 59 3 476.43 4.64 166 56 60 4 471.81 2.33 167 57 60 3 481.12 0.87 168 57 61 4 474.18 3.51 169 58 61 3 483.24 0.19 170 58 62 4 474.18 3.51 171 59 62 3 478.12 5.48 172 59 63 4 474.16 3.56 173 60 63 3 479.62 0.83 174 60 64 4 474.97 3.98 175 61 64 3 472.19 5.37 176 61 65 4 471.52 5.70 177 62 65 3 481.41 0.76 178 62 66 4 473.48 4.73 179 63 66 3 481.98 0.53 180 63 67 4 473.44 4.74 181 64 67 3 481.40 0.76 182 64 68 4 474.81 4.05 183 65 68 3 479.11 0.90 184 65 69 4 472.05 2.67 185 65 83 18 172.21 1.88 186 66 69 3 478.63 0.63 187 66 70 4 472.06 2.68 188 66 105 39 188.27 0.26 189 66 128 62 189.00 0.13 190 66 129 63 188.27 0.19 191 66 132 66 173.22 1.57 192 67 70 3 481.09 2.81 193 67 71 4 473.10 2.16 194 68 71 3 477.75 4.48 195 68 72 4 473.10 2.16 196 68 79 11 228.34 25.80 197 68 80 12 173.31 1.51 198 69 72 3 473.17 2.12 199 69 73 4 467.88 4.75 200 69 76 7 293.62 1.35 201 69 80 11 207.61 15.63 202 69 128 59 202.91 1.02 203 69 132 63 182.84 3.19 204 70 73 3 485.37 3.67 205 70 128 58 204.30 1.63 206 72 75 3 482.34 1.24 207 72 76 4 464.75 2.08 208 72 79 7 305.97 3.77 209 73 76 3 495.12 4.39 210 73 128 55 208.88 0.04 211 75 78 3 487.25 1.26 212 75 79 4 469.50 3.98 213 76 79 3 481.83 1.57 214 76 80 4 468.39 4.54 215 76 131 55 216.93 3.75 216 76 132 56 209.24 0.08 217 76 135 59 209.22 0.09 218 77 80 3 482.33 1.32 219 77 81 4 463.28 7.08 220 77 135 58 209.24 0.09 221 78 81 3 478.18 0.35 222 80 83 3 488.70 1.91 223 80 84 4 481.41 1.75 224 80 132 52 220.74 4.94 225 80 135 55 220.75 4.96 226 80 136 56 220.76 4.95 227 81 84 3 486.79 0.94 228 81 85 4 481.41 1.75 229 82 85 3 484.76 0.09 230 82 86 4 481.41 1.75 231 83 86 3 481.79 1.57 232 83 87 4 476.99 3.95 233 83 136 53 222.05 5.51 234 84 88 4 465.95 0.04 235 84 135 51 222.04 5.52 236 84 136 52 222.03 5.51 237 84 138 54 222.09 5.55 238 84 139 55 222.06 5.56 239 85 88 3 483.47 0.65 240 85 89 4 432.40 12.66 241 85 90 5 375.14 8.45 242 85 139 54 222.03 5.54 243 86 90 4 357.97 13.78 244 86 91 5 314.86 7.78 245 87 91 4 314.86 7.79 246 87 92 5 314.83 7.78 247 87 93 6 292.13 0.95 248 87 98 11 267.05 7.27 249 87 136 49 222.46 5.61 250 88 92 4 314.81 7.78 251 88 136 48 222.49 5.62 252 88 137 49 222.38 5.67 253 88 139 51 222.22 5.62 254 88 140 52 222.21 5.63 255 89 139 50 222.22 5.64 256 92 140 48 222.50 5.62 257 93 97 4 482.15 0.28 258 93 98 5 473.62 0.21 259 93 140 47 222.71 5.71 260 94 97 3 490.55 2.02 261 95 98 3 491.82 1.21 262 95 137 42 222.90 5.69 263 95 140 45 222.88 5.70 264 96 99 3 487.60 3.20 265 96 100 4 479.80 1.97 266 97 100 3 484.93 4.54 267 97 101 4 478.70 1.43 268 98 101 3 489.31 2.35 269 98 102 4 478.31 1.24 270 98 133 35 223.50 5.47 271 98 136 38 223.55 5.45 272 98 137 39 223.50 5.47 273 99 102 3 482.70 0.95 274 99 103 4 478.31 1.24 275 100 103 3 479.99 0.41 276 100 104 4 478.31 1.25 277 101 104 3 478.31 1.25 278 101 105 4 478.30 1.25 279 102 105 3 479.59 0.41 280 102 106 4 478.09 1.15 281 102 129 27 223.69 5.45 282 103 106 3 485.10 0.86 283 103 107 4 478.06 1.15 284 104 107 3 486.76 3.20 285 104 108 4 478.04 1.16 286 105 108 3 480.27 0.76 287 105 109 4 473.79 0.96 288 105 129 24 224.99 5.23 289 106 109 3 479.57 1.93 290 106 110 4 472.62 0.46 291 106 117 11 230.55 5.80 292 106 122 16 226.11 4.86 293 106 125 19 225.32 5.09 294 106 126 20 225.19 5.17 295 106 129 23 225.14 5.16 296 107 110 3 474.88 0.66 297 107 111 4 475.20 1.76 298 108 111 3 480.10 0.70 299 108 112 4 475.19 1.76 300 109 112 3 485.35 0.34 301 109 113 4 455.02 6.42 302 109 117 8 280.33 12.95 303 109 125 16 226.33 4.98 304 110 114 4 429.57 8.20 305 110 117 7 242.28 6.56 306 111 114 3 497.34 0.65 307 113 116 3 481.87 1.35 308 113 117 4 469.42 1.28 309 114 117 3 488.89 2.16 310 115 118 3 518.63 0.46 311 116 121 5 453.88 2.44 312 117 121 4 456.82 3.92 313 117 122 5 427.03 1.62 314 117 125 8 425.67 1.02 315 118 121 3 479.57 0.35 316 118 122 4 465.56 8.28 317 119 122 3 481.20 0.46 318 119 123 4 465.61 8.26 319 120 123 3 481.46 0.34 320 120 124 4 478.84 1.65 321 121 124 3 481.45 0.34 322 121 125 4 474.56 3.78 323 122 125 3 476.56 0.51 324 122 126 4 470.82 1.92 325 123 126 3 475.37 0.34 326 123 127 4 471.89 1.42 327 124 127 3 477.15 0.56 328 124 128 4 472.42 1.15 329 125 128 3 481.28 1.51 330 125 129 4 472.42 1.15 331 126 129 3 482.06 1.90 332 126 130 4 474.19 2.04 333 127 130 3 481.42 2.88 334 127 131 4 472.88 1.38 335 128 131 3 483.37 1.91 336 128 132 4 467.60 3.39 337 129 132 3 483.37 1.91 338 129 133 4 473.88 0.26 339 130 133 3 489.03 3.91 340 130 134 4 479.06 2.33 341 131 134 3 491.92 2.46 342 131 135 4 487.41 4.75 343 132 135 3 487.41 4.75 344 132 136 4 472.85 1.79 345 133 136 3 481.26 1.53 346 133 137 4 474.42 0.20 347 134 137 3 488.11 1.96 348 134 138 4 456.24 5.53 349 134 141 7 390.93 4.90 350 135 138 3 479.50 2.33 351 137 140 3 493.49 0.75 352 137 141 4 484.88 5.04 353 138 141 3 477.23 1.22