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 2 133 131 19.84 0.66 2 3 6 3 511.26 3.37 3 3 7 4 501.75 1.24 4 4 7 3 510.11 2.83 5 4 8 4 501.76 1.24 6 5 8 3 508.32 1.46 7 5 9 4 501.84 1.28 8 6 9 3 503.00 0.70 9 6 10 4 501.16 1.62 10 6 130 124 52.73 0.41 11 7 10 3 506.48 0.72 12 7 11 4 495.10 4.65 13 7 79 72 54.83 1.02 14 7 134 127 53.02 0.25 15 8 11 3 504.20 0.30 16 8 12 4 493.78 5.31 17 9 12 3 513.39 4.50 18 9 13 4 493.77 5.31 19 9 127 118 62.61 0.12 20 9 130 121 62.57 0.11 21 10 13 3 514.54 3.92 22 10 14 4 501.71 1.33 23 10 127 117 63.32 0.24 24 10 130 120 62.57 0.11 25 10 131 121 62.54 0.12 26 10 134 124 62.53 0.12 27 11 14 3 511.26 2.27 28 11 15 4 498.87 2.74 29 11 76 65 62.55 0.12 30 11 77 66 62.55 0.12 31 12 15 3 502.88 1.92 32 12 16 4 490.30 1.56 33 13 16 3 495.25 0.32 34 13 17 4 496.26 0.50 35 13 122 109 90.09 1.28 36 13 123 110 88.53 0.50 37 14 17 3 504.69 4.71 38 14 18 4 494.35 0.46 39 14 69 55 192.02 1.66 40 14 73 59 111.76 20.50 41 14 76 62 100.44 17.45 42 14 77 63 100.98 17.20 43 14 115 101 84.69 2.42 44 15 18 3 495.82 4.41 45 15 19 4 478.67 2.19 46 16 19 3 503.65 0.21 47 16 119 103 99.03 0.92 48 17 24 7 456.63 6.78 49 17 115 98 98.06 1.31 50 17 116 99 98.50 1.18 51 17 118 101 99.03 0.92 52 17 119 102 99.03 0.92 53 17 123 106 101.22 2.02 54 18 21 3 534.48 1.11 55 18 24 6 433.40 4.82 56 18 69 51 240.96 2.21 57 19 24 5 492.35 2.92 58 20 23 3 509.91 1.98 59 20 24 4 492.35 2.91 60 21 24 3 508.81 1.43 61 21 25 4 493.78 3.56 62 21 66 45 272.14 10.48 63 21 69 48 261.94 7.27 64 21 70 49 261.94 7.26 65 22 25 3 511.96 0.16 66 22 26 4 503.50 1.32 67 22 62 40 274.81 9.30 68 22 66 44 272.14 10.47 69 23 26 3 517.92 3.15 70 23 27 4 502.22 1.97 71 23 62 39 274.91 9.34 72 24 27 3 517.94 3.14 73 24 28 4 502.23 1.96 74 24 69 45 273.76 9.65 75 25 28 3 505.96 0.26 76 25 29 4 502.20 1.97 77 25 65 40 273.93 9.70 78 25 66 41 274.68 9.31 79 25 68 43 273.81 9.64 80 25 69 44 273.77 9.65 81 26 29 3 508.28 0.90 82 26 30 4 501.38 4.36 83 26 56 30 275.66 9.14 84 26 57 31 275.64 9.15 85 26 61 35 274.94 9.33 86 26 62 36 274.92 9.34 87 26 65 39 274.72 9.31 88 27 30 3 507.93 1.08 89 27 31 4 501.39 4.35 90 28 31 3 508.21 0.96 91 28 32 4 501.43 4.34 92 28 68 40 274.81 9.33 93 28 69 41 274.67 9.25 94 28 107 79 126.98 0.68 95 28 111 83 127.27 0.54 96 28 114 86 127.64 0.60 97 29 32 3 507.32 1.40 98 29 33 4 501.44 4.34 99 29 43 14 281.11 7.34 100 29 46 17 276.64 8.87 101 29 61 32 275.43 9.16 102 29 64 35 275.19 9.22 103 29 65 36 274.94 9.33 104 29 68 39 274.83 9.31 105 30 33 3 503.70 3.21 106 30 34 4 501.43 4.33 107 30 55 25 275.75 9.19 108 30 56 26 275.78 9.18 109 30 61 31 275.44 9.15 110 31 34 3 502.65 0.75 111 31 35 4 481.14 1.33 112 31 110 79 127.94 0.38 113 31 113 82 128.19 0.43 114 31 114 83 128.19 0.41 115 32 35 3 496.64 1.62 116 32 36 4 473.06 2.69 117 32 39 7 384.59 5.99 118 32 107 75 127.27 0.54 119 33 36 3 503.69 1.17 120 33 37 4 444.78 16.12 121 33 39 6 384.59 5.99 122 33 40 7 384.58 6.00 123 33 43 10 299.08 1.31 124 33 46 13 277.07 8.87 125 33 55 22 275.94 9.21 126 33 61 28 275.58 9.22 127 34 37 3 487.36 3.91 128 34 55 21 275.94 9.20 129 36 39 3 509.13 0.50 130 36 106 70 127.99 0.38 131 37 40 3 496.77 0.81 132 37 41 4 496.78 0.81 133 38 41 3 496.78 0.81 134 38 42 4 492.39 3.00 135 38 103 65 127.99 0.39 136 39 42 3 501.31 2.29 137 39 43 4 491.56 2.59 138 40 43 3 509.87 1.10 139 40 47 7 277.39 8.72 140 40 50 10 276.41 9.18 141 42 98 56 124.09 0.35 142 42 100 58 127.42 0.60 143 42 103 61 128.03 0.39 144 43 46 3 522.46 3.12 145 43 47 4 485.27 2.00 146 45 64 19 276.00 9.26 147 46 49 3 535.05 1.28 148 46 60 14 276.04 9.26 149 46 61 15 276.03 9.26 150 47 50 3 526.74 2.10 151 49 54 5 410.18 6.77 152 49 55 6 396.52 13.60 153 49 58 9 292.68 2.69 154 50 54 4 493.17 0.18 155 51 54 3 502.55 4.51 156 51 55 4 493.17 0.18 157 52 55 3 509.00 1.28 158 52 56 4 481.47 6.03 159 53 56 3 493.16 0.19 160 53 57 4 481.47 6.03 161 54 58 4 437.89 15.27 162 55 61 6 339.11 2.00 163 57 62 5 487.98 4.14 164 58 61 3 499.09 1.44 165 58 62 4 494.95 0.69 166 59 62 3 506.77 0.48 167 59 63 4 499.68 3.05 168 60 63 3 515.78 6.98 169 60 64 4 499.68 3.05 170 61 64 3 516.38 1.14 171 61 65 4 496.76 0.22 172 62 65 3 496.76 0.23 173 62 66 4 499.09 1.39 174 63 66 3 513.22 2.73 175 63 67 4 499.35 1.26 176 64 67 3 501.79 0.04 177 64 68 4 496.58 0.30 178 65 68 3 497.99 0.68 179 65 69 4 495.30 0.77 180 66 69 3 498.12 0.19 181 66 70 4 494.62 0.44 182 67 70 3 500.50 2.50 183 67 71 4 491.63 1.94 184 68 71 3 518.61 2.90 185 68 72 4 505.78 1.76 186 69 72 3 516.34 1.46 187 69 73 4 510.70 0.70 188 70 73 3 511.30 1.00 189 71 74 3 515.75 0.17 190 71 75 4 510.71 0.70 191 72 75 3 512.83 1.29 192 72 76 4 510.70 0.70 193 72 135 63 127.41 0.57 194 73 76 3 515.69 1.12 195 73 77 4 496.25 4.21 196 74 77 3 501.50 1.58 197 74 78 4 496.24 4.20 198 74 82 8 164.31 1.97 199 75 82 7 163.06 2.59 200 75 138 63 127.08 0.42 201 76 79 3 511.74 0.74 202 76 82 6 285.06 12.15 203 76 134 58 127.54 0.62 204 76 135 59 127.59 0.62 205 78 81 3 482.00 3.77 206 78 82 4 315.75 3.15 207 78 83 5 334.00 5.98 208 78 84 6 297.73 5.86 209 81 84 3 543.81 3.85 210 82 86 4 480.38 6.92 211 82 137 55 128.34 0.56 212 82 141 59 128.30 0.55 213 83 86 3 495.14 0.47 214 85 88 3 506.38 2.15 215 85 89 4 505.95 0.96 216 86 89 3 507.42 0.23 217 86 90 4 500.58 1.10 218 86 138 52 129.68 1.08 219 86 142 56 129.57 1.10 220 87 90 3 503.41 0.32 221 87 91 4 498.48 2.16 222 87 145 58 129.47 1.07 223 88 91 3 505.58 1.40 224 88 92 4 497.74 0.65 225 89 92 3 497.75 0.65 226 89 93 4 497.76 0.64 227 90 93 3 497.76 0.64 228 90 94 4 488.93 3.77 229 90 145 55 129.58 1.11 230 90 146 56 129.57 1.11 231 91 94 3 499.38 1.45 232 91 95 4 497.43 0.47 233 92 95 3 500.05 1.78 234 92 96 4 497.41 0.47 235 92 97 5 480.17 1.58 236 93 96 3 496.71 0.83 237 93 97 4 462.38 1.99 238 93 98 5 345.14 17.09 239 93 146 53 129.69 1.12 240 94 98 4 350.94 8.36 241 94 146 52 129.67 1.11 242 94 151 57 98.31 16.18 243 98 146 48 129.99 1.07 244 99 104 5 444.06 7.49 245 99 142 43 130.09 1.06 246 99 143 44 130.05 1.07 247 99 146 47 129.98 1.04 248 100 103 3 504.37 4.68 249 100 104 4 499.11 2.06 250 101 104 3 537.17 1.57 251 102 105 3 506.55 1.67 252 102 106 4 484.92 2.91 253 103 106 3 514.46 2.29 254 103 107 4 490.12 2.25 255 104 107 3 496.73 0.72 256 104 108 4 495.13 0.24 257 104 139 35 131.03 0.80 258 104 142 38 131.05 0.79 259 105 108 3 498.29 0.91 260 105 109 4 496.04 0.21 261 105 139 34 131.12 0.83 262 106 109 3 502.30 3.33 263 106 110 4 488.11 3.29 264 107 110 3 506.93 3.39 265 107 111 4 497.54 0.95 266 108 111 3 509.31 0.90 267 108 112 4 494.59 2.46 268 108 135 27 131.31 0.83 269 108 139 31 131.25 0.82 270 109 112 3 498.38 1.37 271 109 113 4 495.39 2.87 272 110 113 3 504.78 3.17 273 110 114 4 491.80 4.66 274 111 114 3 496.75 3.29 275 111 115 4 490.78 4.90 276 112 115 3 510.76 0.17 277 112 116 4 494.63 2.98 278 112 128 16 132.85 0.81 279 112 131 19 132.65 0.91 280 112 132 20 132.53 0.95 281 112 135 23 132.53 0.94 282 113 116 3 509.84 0.29 283 113 117 4 491.06 4.86 284 114 117 3 508.78 3.82 285 114 118 4 497.09 1.84 286 115 118 3 504.44 1.68 287 115 119 4 504.28 1.76 288 116 119 3 521.42 1.05 289 116 120 4 490.10 4.79 290 116 123 7 141.97 3.50 291 116 131 15 133.25 0.88 292 117 120 3 521.42 1.05 293 123 127 4 485.64 0.42 294 123 128 5 476.41 1.31 295 123 131 8 457.52 2.67 296 124 127 3 503.97 2.45 297 124 128 4 494.28 4.55 298 125 128 3 502.19 0.59 299 125 129 4 500.32 1.53 300 126 129 3 502.19 0.60 301 126 130 4 501.84 0.78 302 127 130 3 506.48 1.54 303 127 131 4 502.11 0.64 304 128 131 3 516.62 2.23 305 128 132 4 502.08 0.61 306 129 132 3 503.05 0.14 307 129 133 4 502.08 0.61 308 130 133 3 502.08 0.61 309 130 134 4 481.88 1.67 310 131 134 3 504.44 0.58 311 131 135 4 501.90 0.70 312 132 135 3 507.49 0.95 313 132 136 4 491.69 0.81 314 133 136 3 497.04 1.04 315 133 137 4 497.14 1.91 316 134 137 3 497.95 1.51 317 134 138 4 497.15 1.92 318 135 138 3 508.07 6.55 319 135 139 4 497.15 1.92 320 136 139 3 507.06 3.85 321 136 140 4 497.15 1.92 322 137 140 3 502.98 1.00 323 137 141 4 492.64 1.91 324 138 141 3 504.72 2.12 325 138 142 4 499.81 1.68 326 139 142 3 504.65 2.38 327 139 143 4 486.57 1.13 328 140 143 3 508.41 2.62 329 140 144 4 486.64 1.17 330 141 144 3 497.25 1.33 331 141 145 4 493.91 2.46 332 142 145 3 503.22 1.88 333 142 146 4 495.50 1.67 334 143 146 3 491.18 0.48 335 143 147 4 489.06 0.56 336 144 147 3 508.05 0.01 337 144 148 4 489.06 0.57 338 145 148 3 507.60 0.24 339 145 149 4 486.55 0.64 340 145 150 5 469.46 7.12 341 146 149 3 508.44 0.66 342 146 150 4 418.25 5.86 343 146 151 5 425.38 2.29 344 147 151 4 425.38 2.29 345 147 152 5 348.81 5.44 346 148 152 4 410.49 5.16