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 73 71 26.39 0.37 2 2 76 74 25.41 0.11 3 2 127 125 20.07 0.64 4 2 128 126 19.93 0.57 5 2 131 129 19.91 0.57 6 3 6 3 464.50 1.23 7 3 7 4 466.69 1.96 8 4 7 3 472.29 2.67 9 4 8 4 468.44 1.08 10 5 8 3 468.44 1.08 11 5 9 4 468.44 1.08 12 6 9 3 472.25 0.83 13 6 10 4 468.44 1.07 14 6 124 118 44.84 0.45 15 6 127 121 44.84 0.45 16 7 10 3 474.81 2.25 17 7 11 4 470.98 0.35 18 7 73 66 45.27 0.23 19 7 74 67 46.64 0.07 20 8 11 3 476.73 1.28 21 8 12 4 468.25 0.97 22 9 12 3 472.05 0.92 23 9 13 4 472.05 0.92 24 9 121 112 58.75 1.69 25 9 124 115 58.72 1.69 26 10 13 3 475.53 0.82 27 10 14 4 467.86 3.01 28 10 70 60 59.16 1.94 29 10 124 114 58.73 1.70 30 10 125 115 58.72 1.69 31 10 128 118 58.64 1.72 32 11 14 3 474.75 0.43 33 11 15 4 467.83 3.02 34 11 70 59 59.12 1.96 35 11 73 62 59.12 1.96 36 12 15 3 472.06 0.91 37 12 16 4 476.95 0.15 38 13 16 3 477.56 0.15 39 13 17 4 477.56 0.15 40 13 113 100 75.21 1.10 41 13 116 103 68.43 0.90 42 13 121 108 60.25 1.60 43 13 125 112 59.92 1.74 44 14 17 3 483.56 2.84 45 14 21 7 389.38 5.53 46 14 63 49 59.98 1.74 47 14 66 52 59.95 1.75 48 14 67 53 59.95 1.76 49 14 70 56 59.95 1.76 50 15 18 3 490.12 0.44 51 16 113 97 83.58 1.92 52 16 116 100 78.36 0.34 53 17 20 3 474.14 1.53 54 17 21 4 428.20 4.78 55 17 24 7 367.78 9.58 56 17 109 92 82.55 1.39 57 17 113 96 86.38 1.60 58 18 21 3 482.91 1.41 59 20 23 3 472.81 3.64 60 20 24 4 462.23 2.89 61 21 24 3 480.26 5.91 62 21 25 4 460.82 0.35 63 21 63 42 157.60 2.81 64 22 25 3 473.74 3.18 65 22 26 4 459.64 0.24 66 22 59 37 157.84 2.75 67 22 60 38 157.69 2.81 68 22 63 41 157.63 2.79 69 23 26 3 470.03 0.68 70 23 27 4 460.34 0.28 71 24 27 3 461.57 0.12 72 24 28 4 465.30 1.76 73 24 108 84 132.92 7.59 74 24 109 85 141.16 3.48 75 24 112 88 142.62 2.45 76 25 28 3 478.69 3.62 77 25 29 4 465.31 1.76 78 25 59 34 157.94 2.72 79 26 29 3 468.57 1.20 80 26 30 4 468.97 0.07 81 26 55 29 158.63 2.58 82 26 56 30 158.60 2.59 83 26 59 33 158.47 2.62 84 27 30 3 470.41 0.79 85 27 31 4 468.97 0.07 86 27 108 81 148.00 0.06 87 27 112 85 147.80 0.05 88 28 31 3 469.47 0.60 89 28 32 4 469.47 0.60 90 28 101 73 148.71 0.11 91 28 104 76 148.54 0.10 92 28 105 77 148.37 0.03 93 28 108 80 148.27 0.07 94 29 32 3 475.88 0.33 95 29 33 4 473.36 2.56 96 29 55 26 160.33 1.92 97 29 58 29 158.89 2.64 98 29 59 30 158.78 2.58 99 29 62 33 158.74 2.60 100 29 101 72 148.71 0.11 101 30 33 3 480.00 1.48 102 30 34 4 472.72 2.88 103 30 50 20 180.38 1.36 104 31 34 3 477.28 1.01 105 31 35 4 471.74 3.37 106 31 104 73 148.58 0.09 107 31 107 76 148.57 0.09 108 31 108 77 148.58 0.08 109 31 111 80 148.52 0.07 110 32 35 3 477.76 0.36 111 32 36 4 464.07 0.46 112 32 39 7 280.62 3.79 113 32 100 68 148.83 0.10 114 32 101 69 148.84 0.12 115 32 104 72 148.59 0.10 116 33 37 4 387.29 2.21 117 33 39 6 307.57 9.69 118 33 40 7 255.62 0.77 119 33 43 10 258.77 2.33 120 33 48 15 188.12 0.57 121 33 55 22 180.52 1.48 122 36 39 3 486.66 0.17 123 36 100 64 149.32 0.15 124 36 103 67 149.32 0.15 125 36 104 68 149.31 0.15 126 37 40 3 486.66 0.17 127 38 41 3 488.89 0.95 128 39 42 3 495.28 0.90 129 39 97 58 149.41 0.12 130 39 100 61 149.39 0.12 131 40 43 3 483.25 1.18 132 40 48 8 235.44 5.62 133 41 44 3 480.64 2.48 134 42 92 50 149.95 0.19 135 42 93 51 149.88 0.21 136 42 94 52 149.90 0.20 137 42 97 55 149.60 0.12 138 43 46 3 476.39 1.86 139 43 48 5 399.05 12.04 140 43 58 15 216.92 0.14 141 45 54 9 247.26 0.13 142 46 54 8 247.25 0.12 143 46 58 12 247.18 0.10 144 47 52 5 257.24 2.46 145 47 54 7 249.96 1.19 146 47 55 8 249.97 1.18 147 48 55 7 249.93 1.20 148 49 52 3 471.42 0.49 149 51 56 5 453.62 6.79 150 52 55 3 468.57 0.93 151 52 56 4 466.19 0.53 152 53 56 3 481.19 7.23 153 53 57 4 466.35 0.44 154 54 57 3 482.11 6.76 155 54 58 4 482.08 6.78 156 55 58 3 482.09 6.78 157 55 59 4 482.10 6.77 158 56 59 3 468.82 0.12 159 56 60 4 468.82 0.12 160 57 60 3 473.44 2.19 161 57 61 4 473.44 2.19 162 58 61 3 473.67 2.08 163 58 62 4 474.68 1.57 164 59 62 3 474.69 1.57 165 59 63 4 474.68 1.57 166 60 63 3 474.69 1.57 167 60 64 4 470.00 0.77 168 61 64 3 470.10 0.72 169 61 65 4 469.97 0.79 170 62 65 3 477.26 2.85 171 62 66 4 467.25 2.15 172 62 101 39 148.79 0.15 173 63 66 3 470.11 0.72 174 63 67 4 460.31 1.31 175 64 67 3 473.09 3.99 176 64 68 4 456.60 0.55 177 65 68 3 476.30 2.39 178 65 69 4 456.63 0.56 179 65 80 15 184.12 1.91 180 65 83 18 178.31 0.54 181 66 69 3 460.04 1.14 182 66 70 4 465.00 4.74 183 66 105 39 148.60 0.18 184 66 128 62 143.52 1.10 185 66 129 63 143.28 1.20 186 66 132 66 143.12 1.28 187 67 70 3 472.19 1.15 188 67 71 4 464.98 4.75 189 68 71 3 472.19 1.16 190 68 72 4 472.19 1.16 191 68 79 11 231.38 2.80 192 68 80 12 226.72 5.12 193 69 72 3 472.19 1.16 194 69 73 4 444.97 6.26 195 69 76 7 287.56 0.76 196 69 80 11 225.25 5.87 197 69 128 59 143.73 1.07 198 69 132 63 143.19 1.28 199 70 73 3 465.05 4.71 200 70 128 58 143.64 1.13 201 72 75 3 467.87 1.81 202 72 76 4 431.31 0.71 203 72 79 7 289.46 1.43 204 73 76 3 471.31 0.28 205 73 128 55 143.84 1.12 206 75 78 3 473.98 1.04 207 75 79 4 460.50 2.60 208 76 79 3 467.45 2.73 209 76 80 4 460.50 2.60 210 76 128 52 143.85 1.11 211 76 131 55 143.67 1.05 212 76 132 56 143.28 1.25 213 76 135 59 142.77 1.35 214 77 80 3 473.39 0.74 215 77 81 4 456.71 0.70 216 77 135 58 141.88 1.66 217 78 81 3 465.61 2.29 218 80 83 3 458.60 6.10 219 80 84 4 461.39 3.18 220 80 132 52 143.20 1.24 221 80 135 55 140.59 1.04 222 80 136 56 139.41 0.46 223 81 84 3 463.99 4.46 224 81 85 4 461.50 3.18 225 81 139 58 137.38 0.34 226 82 85 3 472.25 0.70 227 82 86 4 467.22 0.33 228 83 86 3 470.43 0.22 229 83 87 4 470.43 0.20 230 83 136 53 137.76 0.35 231 84 87 3 482.82 4.75 232 84 88 4 470.44 0.20 233 84 135 51 137.87 0.31 234 84 136 52 137.44 0.36 235 84 139 55 135.09 0.72 236 85 88 3 478.77 2.12 237 85 89 4 461.38 3.12 238 85 90 5 461.26 3.18 239 85 139 54 135.19 0.69 240 86 90 4 429.23 0.89 241 86 91 5 417.57 2.27 242 87 91 4 397.51 0.16 243 87 92 5 391.39 2.90 244 87 93 6 337.38 10.50 245 87 98 11 272.95 0.67 246 88 92 4 372.01 6.79 247 88 139 51 134.00 1.23 248 88 140 52 133.83 1.19 249 89 92 3 481.86 4.02 250 89 139 50 136.94 0.20 251 89 141 52 133.85 1.22 252 93 97 4 483.11 1.94 253 93 98 5 474.49 3.50 254 93 140 47 133.75 1.30 255 94 97 3 485.41 0.80 256 95 98 3 488.22 0.60 257 95 137 42 135.14 0.69 258 95 140 45 133.59 1.29 259 96 99 3 488.24 0.62 260 96 100 4 487.63 0.33 261 97 100 3 483.44 2.43 262 97 101 4 469.47 3.36 263 98 101 3 476.81 5.81 264 98 102 4 464.71 5.72 265 98 133 35 138.27 0.11 266 98 136 38 135.59 0.52 267 98 137 39 135.15 0.69 268 99 102 3 470.88 2.85 269 99 103 4 461.17 7.49 270 100 103 3 475.00 0.80 271 100 104 4 461.19 7.46 272 101 104 3 465.12 5.51 273 101 105 4 461.19 7.46 274 102 105 3 475.10 0.52 275 102 106 4 461.24 3.45 276 102 129 27 139.56 0.14 277 102 133 31 138.88 0.20 278 103 106 3 482.02 3.98 279 103 107 4 456.31 5.04 280 104 107 3 465.63 0.38 281 104 108 4 457.93 4.23 282 105 108 3 476.03 1.24 283 105 109 4 470.94 1.29 284 105 129 24 149.35 4.96 285 106 109 3 473.68 0.06 286 106 110 4 456.95 8.46 287 106 117 11 233.87 1.90 288 106 122 16 153.15 3.90 289 106 125 19 149.44 4.93 290 106 126 20 149.44 4.95 291 106 129 23 149.37 4.96 292 107 110 3 473.80 0.12 293 107 111 4 456.93 8.46 294 108 111 3 473.71 0.08 295 108 112 4 467.93 2.97 296 109 112 3 468.75 4.30 297 109 113 4 453.00 10.42 298 109 125 16 189.34 2.30 299 110 114 4 400.54 2.18 300 110 117 7 234.11 1.80 301 113 116 3 477.37 6.02 302 113 117 4 449.39 6.20 303 114 117 3 475.29 0.79 304 115 118 3 511.62 3.62 305 116 121 5 424.17 6.27 306 117 122 5 433.47 3.90 307 117 125 8 411.03 7.32 308 118 121 3 458.47 2.01 309 118 122 4 446.19 3.44 310 119 122 3 464.07 2.24 311 119 123 4 457.26 1.17 312 120 123 3 472.81 4.12 313 120 124 4 471.93 3.68 314 121 124 3 471.93 3.68 315 121 125 4 459.40 9.95 316 122 125 3 471.93 3.68 317 122 126 4 451.59 5.95 318 123 126 3 466.77 6.26 319 123 127 4 451.60 5.95 320 124 127 3 468.27 4.79 321 124 128 4 451.60 5.93 322 125 128 3 461.09 1.20 323 125 129 4 451.61 5.94 324 126 129 3 482.66 2.60 325 126 130 4 455.91 0.56 326 127 130 3 469.83 3.81 327 127 131 4 455.39 0.82 328 128 131 3 474.29 1.58 329 128 132 4 455.64 0.68 330 129 132 3 457.56 0.27 331 129 133 4 446.00 4.15 332 130 133 3 452.28 1.19 333 130 134 4 445.99 4.16 334 131 134 3 467.48 3.91 335 131 135 4 456.57 1.15 336 132 135 3 479.55 0.03 337 132 136 4 447.21 3.53 338 133 136 3 474.43 2.46 339 133 137 4 445.68 4.16 340 134 137 3 480.81 0.40 341 134 138 4 445.81 4.22 342 135 138 3 475.88 1.79 343 137 140 3 504.83 4.98