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 5 460.55 5.23 2 2 10 8 443.75 4.41 3 2 73 71 32.03 0.98 4 2 127 125 27.53 0.03 5 2 128 126 27.52 0.03 6 2 131 129 27.52 0.03 7 3 6 3 479.51 2.77 8 3 7 4 474.13 5.38 9 4 7 3 476.38 4.26 10 4 8 4 476.39 4.26 11 5 8 3 484.63 0.15 12 5 9 4 474.14 5.39 13 6 9 3 485.97 0.52 14 6 10 4 476.38 4.28 15 6 124 118 52.63 1.75 16 6 127 121 53.80 1.23 17 7 10 3 485.99 0.51 18 7 11 4 481.48 1.75 19 7 73 66 54.89 0.71 20 7 74 67 54.88 0.71 21 8 11 3 481.48 1.76 22 8 12 4 481.48 1.75 23 9 12 3 481.48 1.75 24 9 13 4 474.38 1.79 25 9 120 111 72.48 1.20 26 9 121 112 72.47 1.20 27 9 124 115 72.44 1.20 28 9 125 116 72.45 1.20 29 10 13 3 481.54 0.64 30 10 14 4 473.72 1.23 31 10 70 60 72.36 1.16 32 10 73 63 72.44 1.20 33 10 124 114 72.47 1.21 34 10 125 115 72.45 1.20 35 10 128 118 72.43 1.20 36 11 14 3 479.50 1.66 37 11 15 4 478.62 1.22 38 11 70 59 72.45 1.20 39 12 15 3 483.29 0.53 40 12 16 4 478.72 1.17 41 13 16 3 487.82 2.79 42 13 17 4 478.60 1.23 43 13 116 103 82.06 1.74 44 13 121 108 77.25 0.67 45 13 125 112 73.53 1.18 46 14 17 3 481.63 0.29 47 14 18 4 473.64 3.70 48 14 63 49 76.94 0.52 49 14 67 53 73.53 1.17 50 14 70 56 73.30 1.05 51 14 125 111 76.94 0.53 52 15 18 3 481.64 0.29 53 16 19 3 484.32 1.21 54 16 20 4 472.57 2.32 55 16 113 97 94.48 1.79 56 16 116 100 94.45 1.79 57 17 20 3 482.00 2.29 58 17 21 4 466.97 0.47 59 17 24 7 417.64 13.57 60 17 63 46 88.37 1.32 61 17 109 92 91.00 0.49 62 17 113 96 96.58 0.74 63 17 125 108 90.70 0.40 64 18 21 3 466.97 0.47 65 20 23 3 486.83 2.61 66 20 24 4 467.93 3.46 67 20 112 92 128.78 0.49 68 20 113 93 129.06 0.36 69 21 24 3 478.37 4.83 70 21 25 4 467.95 3.48 71 21 63 42 127.87 11.45 72 22 25 3 475.25 1.52 73 22 26 4 473.25 2.48 74 22 56 34 142.85 6.49 75 22 60 38 135.69 7.83 76 23 26 3 478.92 0.35 77 23 27 4 473.26 2.48 78 23 56 33 143.03 6.50 79 23 112 89 141.06 2.29 80 24 27 3 483.08 1.08 81 24 28 4 476.00 1.12 82 24 63 39 140.31 5.22 83 24 105 81 139.05 4.57 84 24 108 84 139.81 2.52 85 24 109 85 138.77 1.99 86 24 112 88 140.84 2.17 87 24 113 89 140.97 2.12 88 25 28 3 483.38 1.23 89 25 29 4 477.35 1.79 90 25 59 34 141.69 5.90 91 25 63 38 140.31 5.21 92 26 29 3 479.64 0.66 93 26 30 4 477.34 1.80 94 26 55 29 145.81 5.12 95 26 56 30 145.83 5.11 96 26 59 33 145.12 5.17 97 27 30 3 476.98 1.98 98 27 31 4 474.83 0.91 99 27 108 81 142.46 2.76 100 27 112 85 142.77 2.48 101 28 31 3 477.26 1.21 102 28 32 4 474.81 0.91 103 28 101 73 142.63 2.91 104 28 104 76 142.53 2.83 105 28 105 77 142.49 2.85 106 28 108 80 142.89 2.55 107 29 32 3 475.42 0.60 108 29 33 4 475.42 0.60 109 29 55 26 147.25 4.57 110 29 58 29 146.88 4.66 111 29 59 30 146.84 4.63 112 29 101 72 142.69 2.89 113 30 33 3 477.42 1.60 114 30 34 4 469.78 1.13 115 30 55 25 148.41 5.15 116 31 34 3 485.01 2.04 117 31 35 4 466.76 0.38 118 31 104 73 143.03 2.59 119 31 107 76 143.14 2.53 120 31 108 77 143.15 2.52 121 32 35 3 485.87 1.34 122 32 36 4 463.53 1.47 123 32 39 7 370.29 14.77 124 32 100 68 143.30 2.72 125 32 101 69 143.25 2.69 126 32 104 72 143.19 2.57 127 33 36 3 488.79 2.35 128 33 37 4 459.85 0.36 129 33 39 6 375.94 11.95 130 33 40 7 305.24 1.07 131 33 43 10 296.75 5.29 132 33 48 15 167.93 14.85 133 33 55 22 157.48 9.62 134 34 37 3 496.56 0.06 135 36 39 3 494.81 2.38 136 36 100 64 143.44 2.77 137 36 104 68 143.50 2.69 138 37 40 3 495.76 6.47 139 38 41 3 502.08 3.31 140 38 97 59 143.93 2.99 141 38 100 62 143.69 2.79 142 39 42 3 500.93 3.89 143 39 43 4 482.82 0.72 144 39 97 58 143.60 2.83 145 39 100 61 143.59 2.75 146 40 43 3 484.58 1.61 147 40 48 8 186.56 23.85 148 41 44 3 488.11 1.92 149 42 91 49 144.28 3.23 150 42 93 51 144.13 3.14 151 42 94 52 144.21 3.12 152 42 97 55 144.00 2.95 153 43 46 3 480.87 8.63 154 43 48 5 375.16 9.96 155 43 58 15 177.46 19.62 156 45 54 9 204.25 32.33 157 46 54 8 178.21 19.32 158 46 55 9 204.24 32.33 159 46 58 12 178.21 19.32 160 47 52 5 204.27 32.33 161 47 54 7 204.25 32.33 162 48 55 7 204.28 32.31 163 49 52 3 479.83 3.65 164 52 55 3 477.82 0.51 165 52 56 4 453.29 5.74 166 53 56 3 467.56 1.19 167 53 57 4 465.79 0.29 168 54 57 3 483.32 0.48 169 54 58 4 460.66 2.29 170 55 58 3 476.50 2.52 171 55 59 4 461.30 2.00 172 56 59 3 480.38 0.64 173 56 60 4 475.80 2.95 174 57 60 3 479.76 4.16 175 57 61 4 476.57 2.56 176 58 61 3 480.41 2.70 177 58 62 4 475.80 2.94 178 59 62 3 477.25 2.22 179 59 63 4 477.24 2.23 180 60 63 3 484.49 4.72 181 60 64 4 468.86 0.51 182 61 64 3 483.61 1.12 183 61 65 4 470.72 1.04 184 62 65 3 470.70 1.03 185 62 66 4 467.05 0.79 186 62 101 39 144.14 2.31 187 63 66 3 473.35 0.24 188 63 67 4 471.07 1.05 189 64 67 3 486.05 6.44 190 64 68 4 472.68 1.82 191 65 68 3 472.68 1.82 192 65 69 4 472.71 1.83 193 65 80 15 150.25 4.71 194 65 83 18 145.77 2.48 195 66 69 3 473.12 2.04 196 66 70 4 472.79 1.79 197 66 105 39 166.65 8.97 198 66 125 59 166.05 9.55 199 66 128 62 165.91 9.54 200 67 70 3 476.52 0.34 201 67 71 4 472.79 1.80 202 68 71 3 481.45 2.12 203 68 72 4 472.79 1.79 204 69 72 3 472.81 1.80 205 69 73 4 451.93 1.25 206 69 76 7 243.31 36.07 207 69 80 11 185.31 7.07 208 69 128 59 183.97 18.57 209 69 132 63 158.91 6.52 210 70 73 3 461.80 3.70 211 70 128 58 184.15 18.63 212 72 75 3 469.98 3.14 213 72 76 4 431.74 15.98 214 72 79 7 281.75 6.90 215 73 76 3 480.98 2.36 216 73 128 55 184.28 18.64 217 75 78 3 485.37 1.46 218 75 79 4 475.38 1.10 219 76 79 3 481.67 2.03 220 76 80 4 468.24 4.67 221 76 128 52 185.44 19.25 222 76 131 55 185.03 19.21 223 76 132 56 184.74 19.36 224 76 135 59 184.31 19.46 225 77 80 3 482.63 1.54 226 77 81 4 460.48 0.78 227 77 135 58 184.30 19.46 228 78 81 3 481.28 2.23 229 80 83 3 477.79 1.14 230 80 84 4 468.09 5.99 231 80 132 52 191.40 22.73 232 80 135 55 190.69 23.08 233 80 136 56 190.54 23.16 234 81 84 3 477.89 1.13 235 81 85 4 468.14 6.02 236 82 85 3 492.04 1.75 237 82 86 4 473.34 3.42 238 83 86 3 477.53 5.51 239 83 87 4 473.33 3.42 240 83 136 53 190.59 23.77 241 84 87 3 482.03 3.26 242 84 88 4 473.31 3.42 243 84 135 51 191.00 23.59 244 84 136 52 190.53 23.80 245 84 138 54 190.47 23.82 246 84 139 55 190.38 23.86 247 85 88 3 476.99 5.24 248 85 89 4 457.86 4.30 249 85 90 5 445.30 1.97 250 85 139 54 190.41 23.86 251 86 90 4 426.82 7.25 252 86 91 5 408.43 0.67 253 87 91 4 388.79 6.70 254 87 92 5 388.79 6.71 255 87 93 6 311.06 6.88 256 87 98 11 274.99 0.53 257 87 140 53 190.24 23.96 258 88 92 4 339.91 7.46 259 88 139 51 190.24 23.96 260 88 140 52 190.13 24.01 261 89 92 3 482.08 4.33 262 89 139 50 190.44 23.87 263 92 140 48 189.60 24.30 264 93 97 4 482.39 6.23 265 93 98 5 469.34 0.29 266 93 140 47 189.74 24.36 267 94 97 3 488.35 3.26 268 95 98 3 497.17 1.16 269 95 99 4 478.41 1.70 270 95 137 42 190.09 24.52 271 95 140 45 188.09 25.21 272 96 99 3 488.34 3.26 273 96 100 4 476.95 0.98 274 97 100 3 473.87 2.53 275 97 101 4 472.55 1.40 276 98 101 3 477.17 0.89 277 98 102 4 472.56 1.40 278 98 133 35 191.63 23.90 279 98 136 38 191.02 24.26 280 98 137 39 190.25 24.59 281 99 102 3 475.57 0.09 282 99 103 4 472.56 1.40 283 99 133 34 191.74 23.92 284 100 103 3 480.54 1.98 285 100 104 4 472.94 1.59 286 101 104 3 476.43 0.10 287 101 105 4 472.94 1.59 288 102 105 3 476.42 0.09 289 102 106 4 468.48 3.82 290 102 129 27 192.97 23.40 291 102 133 31 191.75 23.93 292 103 106 3 473.87 1.94 293 103 107 4 468.19 3.68 294 104 107 3 478.21 0.20 295 104 108 4 473.10 1.25 296 105 108 3 473.11 1.25 297 105 109 4 473.10 1.25 298 105 129 24 193.49 23.61 299 106 109 3 475.17 1.53 300 106 110 4 475.20 2.56 301 106 117 11 233.44 4.65 302 106 122 16 207.13 16.91 303 106 125 19 193.57 23.64 304 106 126 20 193.55 23.64 305 106 129 23 193.54 23.64 306 107 110 3 476.26 2.04 307 107 111 4 475.19 2.56 308 108 111 3 476.26 2.04 309 108 112 4 456.88 2.00 310 109 112 3 474.43 1.12 311 109 113 4 450.55 4.66 312 109 117 8 241.88 0.46 313 109 125 16 210.05 15.48 314 110 114 4 396.76 3.88 315 110 117 7 244.44 1.74 316 111 114 3 483.11 1.13 317 113 116 3 478.53 0.27 318 113 117 4 450.99 5.62 319 114 117 3 483.35 3.88 320 115 118 3 519.63 0.74 321 116 121 5 448.37 3.12 322 117 121 4 448.37 3.12 323 117 122 5 448.36 3.12 324 118 121 3 477.99 1.56 325 118 122 4 449.81 2.71 326 119 122 3 470.53 1.72 327 119 123 4 458.94 1.85 328 120 123 3 470.14 1.92 329 120 124 4 454.31 0.45 330 121 124 3 476.58 2.95 331 121 125 4 462.94 3.86 332 122 125 3 474.85 2.10 333 122 126 4 462.92 3.87 334 123 126 3 484.28 1.27 335 123 127 4 462.89 3.88 336 124 127 3 476.58 5.12 337 124 128 4 458.31 1.72 338 125 128 3 467.79 3.02 339 125 129 4 458.27 1.74 340 126 129 3 473.31 4.60 341 126 130 4 462.43 3.97 342 127 130 3 475.10 2.23 343 127 131 4 469.64 0.36 344 128 131 3 475.18 2.19 345 128 132 4 469.67 3.31 346 129 132 3 469.68 3.31 347 129 133 4 468.58 2.77 348 130 133 3 477.49 0.60 349 130 134 4 467.64 3.23 350 131 134 3 467.81 3.31 351 131 135 4 472.67 0.89 352 132 135 3 485.69 1.76 353 132 136 4 472.86 0.96 354 133 136 3 478.48 1.84 355 133 137 4 472.86 0.96 356 134 137 3 479.11 2.16 357 134 138 4 463.16 3.90 358 134 141 7 406.73 2.75 359 135 138 3 476.60 1.12 360 137 140 3 494.22 0.12 361 137 141 4 475.97 1.84 362 138 141 3 484.67 2.33