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 4 467.10 1.27 2 2 7 5 461.75 1.40 3 2 10 8 458.27 3.15 4 2 73 71 32.79 0.35 5 2 127 125 26.13 0.85 6 2 128 126 24.96 0.35 7 3 6 3 474.16 0.44 8 3 7 4 469.08 0.29 9 4 7 3 480.50 0.41 10 4 8 4 473.26 1.80 11 5 8 3 482.73 1.53 12 5 9 4 473.29 1.81 13 6 9 3 480.99 2.04 14 6 10 4 480.99 2.04 15 6 124 118 47.48 0.07 16 6 127 121 47.41 0.09 17 7 10 3 491.13 2.68 18 7 11 4 476.04 0.42 19 7 73 66 49.32 1.00 20 7 74 67 53.40 0.56 21 8 11 3 491.14 2.68 22 8 12 4 477.77 1.29 23 9 12 3 477.79 1.30 24 9 13 4 473.31 1.77 25 9 121 112 63.96 0.24 26 9 124 115 63.86 0.21 27 10 13 3 484.54 0.85 28 10 14 4 476.12 5.06 29 10 70 60 63.88 0.21 30 10 73 63 63.95 0.21 31 10 124 114 63.91 0.21 32 10 125 115 63.88 0.21 33 10 128 118 63.83 0.19 34 11 14 3 484.54 0.85 35 11 15 4 473.17 3.56 36 11 70 59 63.90 0.21 37 11 73 62 63.94 0.20 38 12 15 3 481.52 2.38 39 12 16 4 476.23 5.01 40 13 16 3 479.23 4.77 41 13 17 4 473.26 3.52 42 13 121 108 64.53 0.24 43 13 125 112 64.52 0.24 44 14 17 3 475.00 2.66 45 14 18 4 464.16 0.95 46 14 21 7 405.76 5.48 47 14 66 52 64.50 0.24 48 14 67 53 64.51 0.24 49 14 70 56 64.50 0.24 50 14 109 95 83.09 0.21 51 15 18 3 476.17 5.06 52 16 113 97 95.64 0.64 53 16 116 100 90.84 1.73 54 17 20 3 485.47 1.41 55 17 21 4 445.43 2.95 56 17 24 7 444.18 3.58 57 17 109 92 90.89 1.73 58 17 113 96 96.23 0.62 59 20 23 3 476.30 3.21 60 20 24 4 458.97 0.29 61 21 24 3 479.96 1.38 62 21 25 4 462.62 1.54 63 21 63 42 96.83 0.54 64 21 67 46 96.79 0.56 65 22 25 3 470.06 5.25 66 22 26 4 459.41 0.49 67 22 59 37 108.02 3.25 68 22 60 38 100.43 0.53 69 22 63 41 99.80 0.84 70 23 26 3 487.06 4.49 71 23 27 4 477.30 0.39 72 24 27 3 477.30 0.39 73 24 28 4 475.53 1.27 74 24 105 81 124.95 2.02 75 24 108 84 128.69 0.18 76 24 109 85 128.69 0.18 77 24 112 88 137.62 0.38 78 24 113 89 137.40 0.49 79 25 28 3 477.14 0.04 80 25 29 4 470.95 1.02 81 25 59 34 124.67 1.96 82 25 105 80 128.69 0.18 83 26 29 3 479.50 1.22 84 26 30 4 470.95 1.03 85 26 55 29 135.46 0.82 86 26 56 30 131.65 2.73 87 26 59 33 127.31 0.59 88 27 30 3 479.15 1.40 89 27 31 4 470.93 1.04 90 27 108 81 137.87 0.43 91 27 112 85 138.50 0.47 92 28 31 3 479.22 4.62 93 28 32 4 471.48 0.79 94 28 101 73 137.83 0.44 95 28 104 76 137.83 0.44 96 28 105 77 137.78 0.42 97 28 108 80 138.13 0.30 98 29 32 3 481.62 5.84 99 29 33 4 473.70 0.35 100 29 55 26 138.20 0.61 101 29 58 29 138.19 0.61 102 29 59 30 137.81 0.42 103 29 101 72 137.87 0.43 104 30 33 3 483.85 4.73 105 30 34 4 473.70 0.35 106 30 50 20 138.75 0.35 107 31 34 3 477.44 2.31 108 31 35 4 473.56 0.42 109 31 104 73 138.56 0.47 110 31 107 76 138.69 0.46 111 31 108 77 138.70 0.47 112 31 111 80 138.99 0.45 113 32 35 3 474.84 1.11 114 32 36 4 473.47 0.46 115 32 39 7 350.36 22.25 116 32 100 68 138.54 0.46 117 32 101 69 138.58 0.46 118 32 104 72 138.65 0.45 119 33 37 4 456.72 7.91 120 33 39 6 348.83 23.02 121 33 40 7 291.82 7.50 122 33 43 10 266.26 0.35 123 33 48 15 139.01 0.43 124 33 55 22 138.98 0.42 125 34 37 3 481.18 0.48 126 36 39 3 490.88 0.59 127 36 100 64 138.68 0.45 128 36 103 67 138.91 0.45 129 36 104 68 138.93 0.45 130 37 40 3 488.17 2.56 131 38 41 3 496.77 1.67 132 39 42 3 498.44 2.55 133 39 97 58 138.64 0.46 134 39 100 61 138.84 0.42 135 40 43 3 489.46 0.60 136 40 48 8 248.69 2.77 137 41 44 3 507.65 1.35 138 42 92 50 138.55 0.49 139 42 93 51 138.59 0.48 140 42 94 52 138.77 0.46 141 42 97 55 138.84 0.46 142 43 46 3 481.60 0.55 143 43 48 5 419.99 3.56 144 43 58 15 245.76 3.38 145 45 54 9 251.03 2.79 146 46 54 8 251.00 2.79 147 46 55 9 250.96 2.77 148 46 58 12 250.96 2.77 149 47 52 5 260.25 1.80 150 47 54 7 251.04 2.79 151 47 55 8 257.05 0.20 152 48 52 4 424.91 0.10 153 48 55 7 257.06 0.19 154 49 52 3 469.59 1.60 155 52 55 3 487.09 0.22 156 52 56 4 465.21 0.92 157 53 56 3 476.47 5.09 158 53 57 4 468.26 2.44 159 54 57 3 468.26 2.44 160 54 58 4 468.26 2.44 161 55 58 3 477.45 2.16 162 55 59 4 474.78 0.82 163 56 59 3 474.78 0.82 164 56 60 4 475.50 1.18 165 57 60 3 477.45 2.16 166 57 61 4 477.16 2.02 167 58 61 3 475.80 2.71 168 58 62 4 474.88 3.17 169 59 62 3 477.55 2.23 170 59 63 4 472.41 1.97 171 60 63 3 480.92 0.14 172 60 64 4 474.10 3.54 173 61 64 3 489.24 0.09 174 61 65 4 476.64 2.00 175 62 65 3 479.31 0.68 176 62 66 4 476.68 2.00 177 63 66 3 480.95 0.14 178 63 67 4 476.70 1.99 179 64 67 3 479.31 0.68 180 64 68 4 469.73 1.50 181 65 68 3 469.74 1.50 182 65 69 4 470.53 1.10 183 65 83 18 163.23 2.56 184 66 69 3 470.56 1.10 185 66 70 4 470.57 1.12 186 66 105 39 169.53 1.14 187 66 128 62 196.95 4.11 188 66 129 63 168.38 0.78 189 66 132 66 163.99 2.60 190 67 70 3 470.57 1.11 191 67 71 4 470.58 1.12 192 68 71 3 474.86 3.04 193 68 72 4 472.87 2.26 194 68 79 11 258.62 10.65 195 68 80 12 196.05 13.95 196 69 72 3 476.48 2.23 197 69 73 4 473.14 2.12 198 69 76 7 291.28 3.71 199 69 80 11 186.68 13.88 200 69 128 59 198.41 4.59 201 69 132 63 168.11 0.92 202 70 73 3 486.98 2.89 203 70 128 58 198.84 4.79 204 72 75 3 480.44 1.28 205 72 76 4 430.40 0.21 206 72 79 7 270.82 4.58 207 73 76 3 478.44 3.20 208 73 128 55 205.81 2.46 209 75 78 3 492.05 0.26 210 75 79 4 476.97 3.88 211 76 79 3 481.71 1.52 212 76 80 4 454.44 3.07 213 76 131 55 206.03 2.37 214 76 132 56 209.11 0.83 215 76 135 59 205.97 2.38 216 77 81 4 417.32 18.21 217 77 135 58 206.04 2.37 218 78 81 3 464.60 2.01 219 80 83 3 483.35 0.28 220 80 84 4 476.71 0.35 221 80 132 52 211.37 0.23 222 80 135 55 211.28 0.20 223 80 136 56 211.28 0.20 224 81 84 3 485.94 0.91 225 81 85 4 484.44 0.17 226 81 139 58 211.32 0.24 227 82 85 3 491.08 3.25 228 82 86 4 484.44 0.17 229 83 86 3 484.44 0.17 230 83 87 4 481.47 1.66 231 83 136 53 211.50 0.29 232 84 87 3 489.21 0.27 233 84 88 4 466.16 0.01 234 84 135 51 211.71 0.30 235 84 136 52 211.50 0.29 236 84 138 54 211.49 0.29 237 84 139 55 211.44 0.29 238 85 88 3 483.89 0.44 239 85 89 4 458.34 1.04 240 85 90 5 448.27 5.21 241 85 139 54 211.44 0.29 242 86 90 4 427.55 3.74 243 86 91 5 406.73 14.17 244 87 91 4 355.97 11.21 245 87 92 5 332.33 4.76 246 87 93 6 297.20 1.87 247 87 98 11 284.84 0.21 248 87 136 49 211.75 0.30 249 88 92 4 318.29 2.25 250 88 139 51 211.62 0.34 251 88 140 52 211.46 0.29 252 89 92 3 479.67 2.62 253 89 139 50 211.68 0.30 254 92 140 48 211.74 0.29 255 93 97 4 482.13 0.29 256 93 98 5 478.62 1.46 257 93 140 47 211.78 0.30 258 94 97 3 494.55 0.02 259 95 98 3 494.38 0.07 260 95 137 42 211.92 0.29 261 95 140 45 211.92 0.29 262 96 99 3 493.47 0.56 263 96 100 4 484.31 0.29 264 97 100 3 489.16 2.71 265 97 101 4 480.66 1.54 266 98 101 3 481.16 1.29 267 98 102 4 477.00 1.68 268 98 133 35 212.34 0.18 269 98 136 38 212.34 0.18 270 98 137 39 212.34 0.18 271 99 102 3 482.51 1.04 272 99 103 4 477.04 1.69 273 100 103 3 482.53 1.05 274 100 104 4 477.04 1.69 275 101 104 3 485.42 2.50 276 101 105 4 477.04 1.69 277 102 105 3 485.59 2.41 278 102 106 4 476.97 1.70 279 102 129 27 212.96 0.03 280 103 106 3 485.59 2.41 281 103 107 4 472.69 0.42 282 104 107 3 484.57 2.92 283 104 108 4 472.51 0.33 284 105 108 3 478.30 2.56 285 105 109 4 472.51 0.33 286 105 129 24 214.70 0.18 287 106 109 3 478.30 2.56 288 106 110 4 472.44 0.37 289 106 117 11 226.90 1.21 290 106 122 16 215.56 0.15 291 106 125 19 215.08 0.09 292 106 126 20 215.06 0.09 293 106 129 23 215.01 0.07 294 107 110 3 475.20 1.75 295 107 111 4 475.20 1.75 296 108 111 3 475.26 1.73 297 108 112 4 471.61 3.56 298 109 112 3 480.44 0.86 299 109 113 4 466.15 0.83 300 109 117 8 258.91 2.06 301 109 125 16 216.15 0.01 302 110 114 4 426.25 0.84 303 110 117 7 250.62 6.20 304 111 114 3 495.54 1.09 305 113 116 3 494.70 0.15 306 113 117 4 462.25 2.73 307 114 117 3 487.39 3.80 308 115 118 3 514.75 0.82 309 116 121 5 449.84 12.33 310 117 121 4 449.85 12.33 311 117 122 5 426.13 0.48 312 117 125 8 426.12 0.48 313 118 121 3 474.85 3.64 314 118 122 4 468.67 2.94 315 119 122 3 476.39 2.86 316 119 123 4 472.33 1.14 317 120 123 3 487.44 2.67 318 120 124 4 473.10 0.76 319 121 124 3 482.67 0.60 320 121 125 4 472.37 1.12 321 122 125 3 477.43 2.92 322 122 126 4 472.38 1.12 323 123 126 3 480.71 1.28 324 123 127 4 474.20 2.04 325 124 127 3 477.15 0.56 326 124 128 4 474.20 2.04 327 125 128 3 474.91 1.68 328 125 129 4 469.05 4.61 329 126 129 3 480.09 0.62 330 126 130 4 464.64 2.40 331 127 130 3 478.50 1.42 332 127 131 4 461.06 0.85 333 128 131 3 475.52 2.02 334 128 132 4 461.79 0.49 335 129 132 3 476.47 1.55 336 129 133 4 470.19 4.69 337 130 133 3 473.88 2.85 338 130 134 4 469.44 5.06 339 131 134 3 481.95 1.19 340 131 135 4 480.17 2.08 341 132 135 3 489.54 3.69 342 132 136 4 473.19 1.42 343 133 136 3 483.24 0.54 344 133 137 4 477.74 2.21 345 134 137 3 478.62 1.78 346 134 138 4 456.37 1.95 347 135 138 3 481.09 0.53 348 137 140 3 496.61 0.82 349 137 141 4 489.13 4.55 350 138 141 3 496.57 0.83