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 5 449.13 1.31 2 2 73 71 31.74 0.14 3 2 76 74 26.70 0.01 4 2 127 125 22.31 0.13 5 2 128 126 22.24 0.16 6 3 6 3 474.34 0.29 7 3 7 4 469.11 2.32 8 4 7 3 473.99 0.12 9 4 8 4 469.46 2.15 10 5 8 3 481.84 0.84 11 5 9 4 474.45 0.33 12 6 9 3 477.72 1.21 13 6 10 4 474.47 0.33 14 6 124 118 47.24 0.79 15 6 127 121 47.27 0.80 16 7 10 3 477.05 1.54 17 7 11 4 474.48 0.33 18 7 73 66 48.61 0.67 19 7 74 67 48.88 0.78 20 8 11 3 476.19 0.54 21 8 12 4 474.45 0.33 22 9 12 3 477.05 0.10 23 9 13 4 471.76 1.65 24 9 121 112 59.30 0.28 25 9 124 115 59.30 0.28 26 10 13 3 486.09 2.59 27 10 14 4 458.88 8.06 28 10 70 60 59.30 0.29 29 10 124 114 59.31 0.28 30 10 125 115 59.30 0.28 31 10 128 118 59.29 0.29 32 11 15 4 442.80 1.20 33 11 70 59 59.32 0.29 34 11 71 60 59.55 0.40 35 11 73 62 59.47 0.36 36 12 15 3 469.56 1.80 37 12 16 4 470.87 1.15 38 13 16 3 477.82 1.42 39 13 17 4 467.19 0.97 40 13 113 100 78.59 0.58 41 13 121 108 60.13 0.50 42 13 125 112 60.13 0.50 43 14 17 3 479.48 5.18 44 14 18 4 466.62 1.25 45 14 21 7 407.20 4.54 46 14 63 49 75.48 0.91 47 14 66 52 60.14 0.50 48 14 67 53 66.39 3.62 49 14 70 56 60.13 0.50 50 15 18 3 476.02 1.74 51 16 113 97 95.53 1.52 52 16 116 100 90.96 0.75 53 17 20 3 485.44 0.44 54 17 21 4 422.73 8.38 55 17 24 7 415.31 12.06 56 17 109 92 89.39 0.04 57 17 113 96 95.61 1.56 58 18 21 3 495.86 2.06 59 20 23 3 470.12 0.65 60 20 24 4 466.43 1.20 61 21 24 3 469.04 0.10 62 21 25 4 464.25 2.50 63 21 63 42 97.09 0.82 64 22 25 3 468.12 0.57 65 22 26 4 470.69 1.85 66 22 60 38 101.50 0.19 67 22 63 41 98.88 1.05 68 23 26 3 482.83 4.22 69 23 27 4 466.84 3.77 70 24 27 3 482.82 4.22 71 24 28 4 468.69 2.85 72 24 108 84 117.54 0.42 73 24 109 85 120.84 0.16 74 24 112 88 130.50 0.05 75 25 28 3 473.26 0.56 76 25 29 4 469.00 2.69 77 25 59 34 116.62 0.84 78 25 63 38 113.84 0.52 79 26 29 3 474.60 0.11 80 26 30 4 465.69 1.03 81 26 55 29 125.89 1.21 82 26 56 30 125.58 1.58 83 26 59 33 117.21 0.52 84 27 30 3 465.68 1.03 85 27 31 4 465.50 3.17 86 27 108 81 130.96 0.23 87 27 112 85 132.32 0.18 88 28 31 3 467.73 2.06 89 28 32 4 465.32 1.21 90 28 101 73 130.75 0.15 91 28 104 76 130.92 0.23 92 28 105 77 130.78 0.15 93 28 108 80 131.09 0.29 94 29 32 3 475.07 1.22 95 29 33 4 463.62 2.08 96 29 55 26 131.57 0.06 97 29 58 29 131.16 0.12 98 29 59 30 131.16 0.12 99 29 101 72 130.94 0.23 100 30 33 3 479.87 1.18 101 30 34 4 466.03 3.31 102 30 50 20 132.54 0.32 103 31 34 3 478.25 0.38 104 31 35 4 465.75 3.45 105 31 104 73 132.03 0.30 106 31 107 76 132.46 0.26 107 31 108 77 132.57 0.30 108 31 111 80 132.79 0.32 109 32 35 3 473.98 0.66 110 32 36 4 456.29 1.27 111 32 39 7 322.43 4.40 112 32 100 68 132.02 0.32 113 32 101 69 132.05 0.34 114 32 104 72 132.22 0.36 115 33 37 4 436.83 3.60 116 33 39 6 323.17 4.75 117 33 40 7 238.16 37.73 118 33 43 10 238.18 37.73 119 33 48 15 132.87 0.29 120 33 55 22 132.71 0.33 121 36 39 3 485.89 2.97 122 36 100 64 132.09 0.32 123 36 103 67 132.68 0.30 124 36 104 68 132.69 0.31 125 37 40 3 480.07 0.06 126 38 41 3 487.44 1.63 127 39 42 3 486.45 0.97 128 39 43 4 489.88 4.00 129 39 97 58 132.06 0.34 130 39 100 61 132.63 0.29 131 40 43 3 494.28 1.80 132 40 48 8 141.84 4.34 133 41 44 3 498.08 0.10 134 42 45 3 646.64 0.14 135 42 93 51 131.94 0.29 136 42 94 52 132.43 0.24 137 42 97 55 132.72 0.33 138 43 46 3 472.86 3.54 139 43 48 5 423.64 6.67 140 43 58 15 132.88 0.38 141 45 54 9 152.93 1.09 142 46 54 8 142.14 4.30 143 46 55 9 142.16 4.29 144 46 58 12 142.12 4.30 145 47 52 5 166.50 3.56 146 47 54 7 142.18 4.29 147 47 55 8 142.18 4.29 148 48 52 4 432.15 0.33 149 48 55 7 162.18 5.73 150 49 52 3 475.97 0.88 151 51 56 5 452.98 11.20 152 52 55 3 468.34 3.52 153 52 56 4 468.36 3.53 154 53 56 3 472.49 1.47 155 53 57 4 472.50 1.47 156 54 57 3 472.50 1.47 157 54 58 4 472.51 1.47 158 55 58 3 472.58 1.44 159 55 59 4 472.59 1.47 160 56 59 3 474.35 1.68 161 56 60 4 472.62 1.48 162 57 60 3 483.98 4.19 163 57 61 4 472.63 1.48 164 58 61 3 474.88 0.35 165 58 62 4 472.62 1.47 166 59 62 3 474.86 0.35 167 59 63 4 472.59 1.48 168 60 63 3 471.31 1.49 169 60 64 4 463.54 2.40 170 61 64 3 471.53 1.00 171 61 65 4 465.69 3.46 172 62 65 3 483.15 0.40 173 62 66 4 467.17 2.73 174 62 101 39 144.53 2.65 175 63 66 3 478.30 2.83 176 63 67 4 467.17 2.73 177 64 67 3 478.30 2.83 178 64 68 4 468.14 0.03 179 65 68 3 470.36 1.14 180 65 69 4 466.49 0.82 181 65 80 15 153.87 2.10 182 65 83 18 144.02 2.24 183 66 69 3 481.63 0.38 184 66 70 4 466.60 0.77 185 66 105 39 162.62 2.35 186 66 129 63 157.61 0.29 187 66 132 66 154.16 1.95 188 67 70 3 475.33 1.32 189 67 71 4 475.09 1.19 190 68 71 3 475.09 1.19 191 68 72 4 475.08 1.19 192 68 79 11 155.94 1.18 193 69 72 3 475.42 1.36 194 69 73 4 463.61 0.74 195 69 76 7 231.87 24.37 196 69 80 11 154.28 2.01 197 69 128 59 186.08 1.48 198 69 132 63 165.00 3.38 199 70 73 3 470.31 1.20 200 70 128 58 186.11 1.48 201 72 75 3 471.40 0.30 202 72 76 4 421.93 3.45 203 72 79 7 279.75 0.57 204 73 76 3 479.60 1.58 205 75 78 3 479.88 1.34 206 75 79 4 451.59 7.42 207 76 79 3 468.80 1.18 208 76 80 4 442.07 10.08 209 76 128 52 274.19 0.79 210 76 131 55 271.31 0.01 211 76 132 56 271.25 0.02 212 76 135 59 271.22 0.04 213 77 80 3 476.75 2.60 214 77 81 4 442.70 9.76 215 77 135 58 271.22 0.04 216 78 81 3 469.18 1.42 217 80 83 3 480.17 0.21 218 80 84 4 478.89 1.52 219 80 132 52 275.64 0.89 220 80 135 55 275.47 0.85 221 80 136 56 275.44 0.83 222 81 84 3 478.92 1.51 223 81 85 4 478.89 1.51 224 81 139 58 275.61 0.78 225 82 85 3 480.11 0.91 226 82 86 4 478.89 1.52 227 83 86 3 478.89 1.52 228 83 87 4 478.88 1.52 229 83 136 53 275.97 0.77 230 84 88 4 454.47 0.89 231 84 135 51 275.97 0.78 232 84 136 52 275.96 0.77 233 84 138 54 275.95 0.77 234 84 139 55 275.94 0.76 235 85 88 3 470.24 2.79 236 85 89 4 450.57 2.83 237 85 139 54 275.88 0.78 238 86 89 3 483.52 0.73 239 86 90 4 439.69 2.62 240 86 91 5 419.30 12.80 241 87 91 4 385.03 21.01 242 87 92 5 381.51 20.36 243 87 93 6 374.62 23.80 244 87 98 11 290.97 2.10 245 87 136 49 276.06 0.77 246 87 140 53 275.92 0.77 247 88 92 4 381.50 20.36 248 88 139 51 275.95 0.77 249 88 140 52 275.88 0.79 250 89 92 3 492.91 3.16 251 92 140 48 276.02 0.78 252 93 97 4 480.25 0.90 253 93 98 5 471.75 2.24 254 93 140 47 276.19 0.80 255 94 97 3 494.35 3.02 256 95 98 3 482.74 0.31 257 95 140 45 276.47 0.77 258 96 99 3 491.43 5.77 259 96 100 4 480.01 1.01 260 97 100 3 480.00 0.99 261 97 101 4 479.98 1.00 262 98 101 3 485.39 1.42 263 98 102 4 474.42 0.79 264 98 133 35 277.01 0.90 265 98 136 38 277.03 0.90 266 98 137 39 277.01 0.90 267 98 140 42 277.01 0.90 268 99 102 3 474.57 0.71 269 99 103 4 474.42 0.79 270 100 103 3 474.42 0.80 271 100 104 4 473.29 1.35 272 101 104 3 476.09 0.06 273 101 105 4 466.01 0.78 274 102 105 3 471.24 1.19 275 102 106 4 466.08 0.81 276 102 129 27 277.36 0.81 277 102 133 31 277.13 0.92 278 103 106 3 481.62 4.00 279 103 107 4 466.08 0.81 280 104 107 3 467.94 1.74 281 104 108 4 463.53 0.46 282 105 108 3 471.50 2.82 283 105 109 4 462.59 0.01 284 105 129 24 277.98 0.60 285 106 109 3 471.69 2.91 286 106 110 4 464.06 0.73 287 106 117 11 279.13 0.70 288 106 122 16 278.62 0.78 289 106 125 19 278.56 0.75 290 106 126 20 278.53 0.75 291 106 129 23 278.44 0.79 292 107 110 3 472.11 2.38 293 107 111 4 462.50 0.02 294 108 111 3 474.81 1.81 295 108 112 4 458.74 0.96 296 109 112 3 472.11 0.47 297 109 113 4 453.81 1.06 298 109 125 16 278.62 0.78 299 110 117 7 279.14 0.70 300 113 116 3 478.36 0.81 301 113 117 4 456.62 0.14 302 114 117 3 480.09 1.67 303 115 118 3 526.28 0.91 304 116 121 5 451.13 1.07 305 117 121 4 455.91 1.31 306 117 122 5 448.92 0.03 307 117 125 8 425.31 0.09 308 118 121 3 461.92 1.69 309 118 122 4 458.86 0.16 310 119 122 3 465.07 0.10 311 119 123 4 458.87 0.17 312 120 123 3 473.31 1.42 313 120 124 4 459.32 0.40 314 121 124 3 471.25 3.44 315 121 125 4 460.95 0.07 316 122 125 3 476.53 2.62 317 122 126 4 469.63 4.27 318 123 126 3 474.83 1.78 319 123 127 4 469.63 4.27 320 124 127 3 474.83 1.67 321 124 128 4 471.71 3.22 322 125 128 3 474.24 2.60 323 125 129 4 467.89 0.73 324 126 129 3 482.05 1.31 325 126 130 4 467.89 0.73 326 127 130 3 481.29 0.93 327 127 131 4 467.26 0.42 328 128 131 3 475.13 4.01 329 128 132 4 465.65 2.06 330 129 132 3 475.88 3.64 331 129 133 4 464.81 1.64 332 130 133 3 468.29 0.74 333 130 134 4 463.59 1.02 334 131 134 3 468.29 0.74 335 131 135 4 466.99 0.09 336 132 135 3 475.73 4.46 337 132 136 4 466.22 0.29 338 133 136 3 476.43 4.11 339 133 137 4 462.59 0.51 340 134 137 3 481.12 1.46 341 134 138 4 461.69 0.06 342 135 138 3 481.12 1.46 343 136 140 4 489.82 1.20 344 137 140 3 485.50 0.97