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 5 8 3 485.75 5.26 2 5 9 4 471.84 2.37 3 5 34 29 181.91 0.64 4 6 9 3 491.60 2.33 5 6 10 4 476.85 0.14 6 6 34 28 181.91 0.64 7 6 36 30 181.66 0.72 8 6 40 34 178.80 0.05 9 6 44 38 176.72 0.12 10 7 10 3 480.28 1.62 11 7 11 4 477.06 0.02 12 7 44 37 176.70 0.13 13 7 47 40 176.69 0.13 14 7 48 41 176.38 0.03 15 8 11 3 480.51 1.98 16 8 12 4 480.50 1.97 17 9 12 3 487.75 1.65 18 9 13 4 475.88 4.29 19 9 29 20 182.39 0.80 20 9 32 23 182.47 0.76 21 9 34 25 182.38 0.79 22 10 13 3 483.81 0.33 23 10 14 4 475.29 4.59 24 10 25 15 182.38 0.80 25 10 29 19 182.41 0.79 26 10 44 34 177.42 0.13 27 10 48 38 176.69 0.12 28 10 50 40 176.41 0.04 29 11 14 3 492.88 4.86 30 11 15 4 475.04 4.68 31 11 48 37 176.70 0.14 32 11 64 53 163.12 0.69 33 12 15 3 481.27 1.80 34 12 16 4 456.02 1.81 35 13 16 3 483.06 0.91 36 13 17 4 475.28 4.79 37 13 19 6 418.89 5.15 38 13 25 12 182.48 0.81 39 13 28 15 182.53 0.79 40 13 29 16 182.52 0.79 41 14 17 3 485.53 4.46 42 14 19 5 324.83 36.12 43 14 25 11 198.75 7.82 44 14 50 36 176.65 0.12 45 14 62 48 167.87 0.67 46 14 63 49 167.82 0.69 47 14 64 50 167.13 0.36 48 15 64 49 167.23 0.40 49 17 28 11 210.53 1.93 50 18 24 6 465.25 1.40 51 18 55 37 168.66 0.86 52 18 61 43 168.12 0.77 53 19 24 5 462.69 2.39 54 19 25 6 455.49 1.21 55 19 28 9 424.61 8.63 56 19 61 42 168.10 0.76 57 19 62 43 167.94 0.68 58 20 24 4 469.94 0.86 59 20 52 32 176.46 0.01 60 20 59 39 168.49 0.86 61 20 60 40 168.38 0.86 62 20 61 41 168.15 0.76 63 21 24 3 481.48 0.18 64 21 25 4 474.84 3.31 65 21 62 41 168.16 0.76 66 22 25 3 474.89 3.34 67 22 26 4 474.82 3.33 68 22 38 16 184.09 1.23 69 22 41 19 183.91 1.22 70 22 42 20 183.90 1.23 71 22 45 23 183.87 1.23 72 23 26 3 481.68 0.10 73 23 27 4 474.82 3.33 74 23 38 15 184.09 1.23 75 24 27 3 477.19 2.15 76 24 28 4 482.79 0.66 77 25 28 3 487.68 3.08 78 25 29 4 482.85 0.69 79 25 41 16 183.91 1.22 80 25 45 20 183.88 1.22 81 25 50 25 176.70 0.12 82 26 29 3 486.38 1.07 83 26 30 4 482.82 0.70 84 26 36 10 211.56 1.29 85 26 38 12 184.10 1.24 86 26 41 15 183.91 1.22 87 27 30 3 486.42 2.51 88 27 31 4 481.56 1.34 89 28 31 3 485.17 3.14 90 28 32 4 481.56 1.34 91 29 32 3 486.61 2.42 92 29 33 4 481.54 1.32 93 29 34 5 428.84 1.23 94 29 36 7 326.25 50.07 95 29 41 12 192.30 3.37 96 30 33 3 481.54 1.32 97 30 34 4 440.25 4.48 98 30 35 5 428.84 1.22 99 30 36 6 328.62 48.88 100 30 37 7 421.04 2.68 101 36 40 4 472.76 4.63 102 36 41 5 462.69 0.39 103 37 40 3 480.19 1.40 104 37 41 4 474.37 4.30 105 38 41 3 486.20 1.61 106 38 42 4 473.91 4.07 107 39 42 3 482.28 0.13 108 39 43 4 478.37 1.80 109 40 43 3 488.44 0.18 110 40 44 4 472.69 4.64 111 41 44 3 482.07 0.23 112 41 45 4 475.37 1.19 113 42 45 3 488.25 0.27 114 42 46 4 476.50 1.75 115 43 46 3 480.63 0.95 116 43 47 4 471.99 0.04 117 44 47 3 476.69 2.31 118 44 48 4 470.78 0.65 119 45 48 3 487.52 1.75 120 45 49 4 454.01 1.53 121 45 50 5 435.52 3.23 122 45 62 17 168.12 0.78 123 46 49 3 460.92 4.28 124 48 65 17 164.51 0.83 125 49 65 16 164.52 0.83 126 50 62 12 168.12 0.78 127 50 63 13 168.03 0.78 128 50 64 14 167.71 0.67 129 51 62 11 168.13 0.78 130 51 63 12 168.08 0.77 131 51 64 13 168.04 0.78 132 51 65 14 167.85 0.69 133 52 60 8 168.41 0.84 134 52 61 9 168.31 0.84 135 52 62 10 168.15 0.79 136 53 60 7 168.47 0.87 137 53 61 8 168.38 0.84 138 53 63 10 168.18 0.78 139 53 67 14 167.81 0.69 140 53 69 16 162.56 0.94 141 53 70 17 152.40 0.77 142 54 59 5 168.53 0.86 143 54 60 6 168.49 0.86 144 54 69 15 166.78 0.43 145 54 70 16 163.12 1.30 146 55 59 4 193.06 8.03 147 55 61 6 168.50 0.88 148 61 69 8 198.37 5.70 149 63 67 4 433.03 4.12 150 64 67 3 483.68 2.23 151 65 75 10 34.84 6.27 152 67 70 3 505.97 1.46 153 67 75 8 330.53 18.69 154 68 108 40 71.69 1.67 155 68 112 44 60.76 3.72 156 70 75 5 484.99 0.24 157 71 74 3 485.00 0.24 158 71 75 4 480.64 2.41 159 72 75 3 487.09 4.29 160 72 76 4 474.36 0.96 161 72 112 40 80.87 0.36 162 72 113 41 80.15 0.01 163 73 76 3 482.28 1.59 164 73 77 4 473.23 1.09 165 73 113 40 81.22 0.50 166 73 115 42 81.11 0.45 167 73 148 75 45.09 0.10 168 74 77 3 480.00 0.46 169 74 78 4 478.20 1.29 170 75 78 3 486.45 1.40 171 75 79 4 478.21 1.29 172 75 109 34 81.45 0.41 173 76 79 3 484.43 0.39 174 76 80 4 475.98 0.18 175 76 106 30 81.64 0.41 176 76 109 33 81.54 0.45 177 76 110 34 81.45 0.41 178 76 113 37 81.45 0.42 179 76 145 69 52.56 1.59 180 76 148 72 44.63 0.61 181 77 80 3 487.94 1.36 182 77 81 4 478.59 0.26 183 77 148 71 44.36 0.48 184 78 81 3 495.78 3.58 185 78 82 4 478.60 0.26 186 79 82 3 490.51 6.21 187 79 83 4 478.59 0.26 188 79 106 27 175.75 47.08 189 79 109 30 175.74 47.07 190 80 83 3 479.98 1.83 191 80 84 4 457.31 2.63 192 80 96 16 301.32 0.69 193 80 106 26 238.05 15.93 194 80 145 65 56.87 0.55 195 80 148 68 45.88 0.06 196 81 148 67 49.57 0.58 197 81 149 68 45.16 0.14 198 82 99 17 352.22 2.25 199 83 98 15 351.85 2.12 200 83 99 16 352.19 2.23 201 83 102 19 351.75 2.08 202 83 106 23 350.36 1.96 203 84 87 3 638.80 6.02 204 84 96 12 352.44 2.33 205 84 97 13 352.30 2.26 206 84 146 62 62.73 1.20 207 84 149 65 46.11 0.04 208 85 97 12 352.36 2.27 209 85 98 13 352.35 2.27 210 85 99 14 352.36 2.28 211 86 96 10 352.51 2.31 212 86 97 11 352.48 2.31 213 87 94 7 352.79 2.35 214 87 95 8 352.63 2.34 215 87 96 9 352.52 2.31 216 87 142 55 66.09 1.42 217 87 145 58 66.05 1.40 218 87 146 59 65.89 1.36 219 88 94 6 352.80 2.36 220 88 95 7 352.64 2.34 221 89 93 4 352.82 2.37 222 89 94 5 352.81 2.37 223 90 93 3 483.96 2.46 224 91 135 44 276.00 4.75 225 91 138 47 274.99 5.25 226 92 131 39 352.28 2.28 227 92 132 40 352.23 2.29 228 92 134 42 338.56 1.23 229 92 135 43 275.00 5.25 230 92 138 46 267.47 8.97 231 93 129 36 352.40 2.29 232 93 130 37 352.31 2.29 233 93 131 38 352.28 2.27 234 94 128 34 352.49 2.30 235 94 129 35 352.36 2.29 236 94 130 36 352.30 2.29 237 94 132 38 352.24 2.29 238 94 138 44 243.24 3.70 239 94 141 47 195.62 1.66 240 94 142 48 68.34 1.09 241 95 127 32 352.50 2.30 242 95 128 33 352.36 2.29 243 95 129 34 352.32 2.29 244 96 106 10 352.93 2.40 245 96 127 31 352.47 2.29 246 96 128 32 352.32 2.29 247 97 126 29 352.79 2.23 248 97 127 30 352.45 2.27 249 98 102 4 437.14 1.04 250 98 103 5 353.06 2.35 251 98 106 8 353.06 2.35 252 98 126 28 353.33 2.17 253 99 102 3 490.31 3.30 254 99 126 27 370.75 9.19 255 100 126 26 371.80 8.67 256 101 125 24 372.81 8.72 257 102 105 3 484.04 2.43 258 102 106 4 482.82 0.27 259 102 125 23 373.12 8.72 260 103 106 3 491.19 3.91 261 103 107 4 478.74 2.31 262 103 123 20 373.00 8.78 263 103 124 21 373.13 8.73 264 103 125 22 373.13 8.72 265 103 126 23 373.08 8.74 266 103 127 24 373.00 8.77 267 103 128 25 372.93 8.73 268 104 107 3 491.19 3.92 269 104 108 4 482.84 0.26 270 104 123 19 373.03 8.77 271 105 108 3 482.87 0.26 272 105 109 4 482.86 0.25 273 106 109 3 482.85 0.24 274 106 110 4 482.84 0.24 275 107 110 3 482.84 0.24 276 107 111 4 482.82 0.24 277 107 121 14 373.01 8.78 278 107 123 16 373.37 8.65 279 107 128 21 373.06 8.77 280 108 111 3 482.82 0.24 281 108 112 4 482.82 0.24 282 109 112 3 480.36 1.46 283 109 113 4 477.98 2.65 284 110 113 3 485.54 4.05 285 110 114 4 485.17 3.08 286 110 118 8 373.32 8.65 287 110 121 11 373.42 8.66 288 110 128 18 373.53 8.67 289 110 130 20 373.41 8.66 290 110 145 35 212.00 5.60 291 111 114 3 490.71 0.83 292 111 121 10 373.44 8.67 293 115 118 3 483.56 0.96 294 115 141 26 284.91 14.43 295 115 144 29 269.18 8.95 296 115 148 33 266.62 7.75 297 116 133 17 373.48 8.67 298 117 132 15 373.51 8.68 299 117 133 16 373.48 8.67 300 117 137 20 351.27 16.97 301 117 140 23 325.14 30.04 302 117 141 24 284.91 14.43 303 118 121 3 556.12 1.46 304 118 130 12 373.72 8.69 305 118 131 13 373.68 8.68 306 118 132 14 373.52 8.68 307 118 141 23 269.18 8.96 308 119 131 12 373.70 8.69 309 119 132 13 373.67 8.70 310 119 133 14 373.61 8.70 311 120 130 10 373.85 8.67 312 120 131 11 373.72 8.69 313 121 128 7 374.00 8.68 314 121 129 8 373.95 8.65 315 121 130 9 373.85 8.67 316 121 131 10 373.84 8.67 317 122 128 6 374.01 8.67 318 122 129 7 373.95 8.65 319 123 127 4 472.13 0.66 320 123 128 5 373.99 8.66 321 124 127 3 472.24 0.70 322 130 145 15 220.84 8.29 323 132 137 5 437.80 7.24 324 132 138 6 321.56 18.02 325 132 141 9 268.26 8.62 326 133 137 4 466.32 0.94 327 134 137 3 466.32 0.94 328 134 138 4 466.76 0.71 329 135 138 3 466.79 0.70 330 135 139 4 476.89 3.75 331 136 139 3 481.13 1.62 332 136 140 4 476.90 3.74 333 137 140 3 487.13 1.38 334 137 141 4 474.81 2.71 335 138 141 3 477.81 4.20 336 138 142 4 472.19 1.39 337 139 142 3 474.18 0.29 338 139 143 4 465.19 2.09 339 140 143 3 480.87 2.72 340 140 144 4 464.49 5.18 341 141 144 3 480.58 2.86 342 141 145 4 462.28 4.13 343 142 145 3 483.05 1.62 344 142 146 4 475.82 2.64 345 143 146 3 482.72 1.46 346 143 147 4 474.89 3.10 347 144 147 3 481.56 1.54 348 144 148 4 476.50 0.77 349 145 148 3 483.23 0.54 350 145 149 4 482.16 2.16 351 146 149 3 493.86 3.70