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 46 44 116.36 23.86 2 2 134 132 70.11 0.74 3 3 44 41 118.42 24.88 4 3 45 42 118.22 24.79 5 3 47 44 117.84 24.59 6 3 48 45 117.84 24.60 7 3 71 68 117.83 24.61 8 3 74 71 118.41 24.89 9 3 133 130 70.15 0.76 10 3 134 131 70.11 0.74 11 3 136 133 70.11 0.74 12 4 42 38 118.73 25.01 13 4 43 39 118.44 24.89 14 4 44 40 118.43 24.88 15 4 134 130 70.16 0.75 16 4 135 131 70.13 0.75 17 4 136 132 70.12 0.75 18 5 42 37 118.84 25.06 19 5 43 38 118.56 24.92 20 5 45 40 118.71 24.99 21 5 69 64 118.42 24.90 22 5 70 65 118.43 24.89 23 5 71 66 118.44 24.89 24 5 128 123 70.13 0.75 25 5 136 131 70.13 0.75 26 5 138 133 70.11 0.74 27 6 40 34 119.19 25.23 28 6 41 35 119.15 25.21 29 6 42 36 118.74 25.01 30 6 136 130 70.17 0.75 31 6 137 131 70.13 0.75 32 6 138 132 70.13 0.75 33 7 34 27 119.22 25.19 34 7 40 33 119.28 25.27 35 7 41 34 119.16 25.21 36 7 54 47 119.14 25.21 37 7 69 62 118.85 25.08 38 7 138 131 70.13 0.75 39 7 140 133 70.11 0.74 40 8 40 32 119.29 25.27 41 8 138 130 70.17 0.75 42 8 139 131 70.13 0.75 43 8 140 132 70.12 0.75 44 9 41 32 119.34 25.25 45 9 56 47 119.38 25.32 46 9 140 131 70.13 0.75 47 9 142 133 70.12 0.76 48 10 139 129 70.17 0.75 49 10 140 130 70.15 0.75 50 10 141 131 70.12 0.76 51 10 142 132 70.12 0.75 52 11 17 6 274.91 51.69 53 11 18 7 122.89 24.07 54 11 142 131 70.12 0.76 55 12 141 129 70.17 0.75 56 12 142 130 70.14 0.75 57 12 143 131 70.12 0.76 58 13 122 109 88.83 4.46 59 13 143 130 70.16 0.75 60 15 122 107 103.48 1.37 61 16 58 42 348.96 0.36 62 16 60 44 348.99 0.38 63 16 61 45 348.97 0.36 64 17 57 40 349.08 0.39 65 17 58 41 349.04 0.36 66 18 56 38 348.97 0.35 67 18 57 39 349.08 0.39 68 18 58 40 349.08 0.38 69 18 63 45 349.10 0.39 70 18 64 46 349.03 0.39 71 18 65 47 349.03 0.38 72 18 122 104 116.85 9.56 73 18 124 106 104.28 11.18 74 18 142 124 70.11 0.74 75 19 56 37 349.13 0.38 76 19 57 38 349.37 0.48 77 19 59 40 349.87 0.45 78 20 41 21 349.75 0.52 79 20 55 35 349.68 0.49 80 20 56 36 349.68 0.49 81 21 55 34 349.78 0.49 82 21 56 35 349.76 0.47 83 21 57 36 349.86 0.45 84 22 54 32 349.81 0.51 85 22 55 33 349.80 0.49 86 22 89 67 260.84 0.69 87 22 90 68 260.68 0.69 88 22 91 69 260.77 0.65 89 23 34 11 351.92 1.49 90 23 36 13 351.97 1.47 91 23 41 18 351.94 1.44 92 23 53 30 350.01 0.60 93 23 54 31 349.87 0.48 94 24 34 10 352.12 1.42 95 24 52 28 351.48 1.27 96 24 53 29 350.09 0.58 97 24 90 66 260.93 0.65 98 24 91 67 260.88 0.64 99 24 94 70 260.53 0.60 100 25 32 7 352.20 1.45 101 25 33 8 352.20 1.44 102 25 34 9 352.20 1.44 103 25 43 18 352.18 1.45 104 25 51 26 351.93 1.48 105 25 52 27 351.86 1.45 106 25 94 69 260.84 0.60 107 26 31 5 379.13 0.17 108 26 50 24 352.29 1.66 109 26 51 25 351.93 1.48 110 26 94 68 260.87 0.61 111 26 95 69 260.82 0.59 112 26 98 72 260.30 0.57 113 27 31 4 384.75 2.98 114 28 31 3 470.63 3.02 115 28 49 21 373.01 0.34 116 28 50 22 363.18 4.16 117 28 98 70 260.77 0.61 118 29 46 17 375.57 0.03 119 29 47 18 375.31 0.06 120 29 48 19 375.38 0.09 121 29 49 20 374.13 0.22 122 29 50 21 372.99 0.32 123 30 46 16 376.01 0.24 124 31 45 14 376.16 0.23 125 31 46 15 376.12 0.20 126 31 50 19 375.38 0.10 127 32 44 12 376.25 0.20 128 32 45 13 376.18 0.21 129 33 42 9 380.83 1.60 130 33 43 10 377.90 0.49 131 33 44 11 376.31 0.18 132 34 41 7 381.76 1.98 133 34 42 8 380.83 1.60 134 34 43 9 380.31 1.70 135 34 52 18 375.94 0.19 136 34 53 19 375.89 0.22 137 34 54 20 375.86 0.21 138 35 40 5 425.88 11.41 139 35 41 6 391.96 3.09 140 35 42 7 380.83 1.60 141 36 40 4 434.13 7.29 142 36 41 5 391.97 3.09 143 37 40 3 462.14 2.29 144 37 42 5 425.86 11.40 145 41 54 13 375.89 0.20 146 41 56 15 375.89 0.20 147 43 51 8 376.02 0.23 148 43 52 9 375.94 0.20 149 43 69 26 349.92 0.39 150 45 50 5 382.78 2.27 151 45 51 6 377.35 0.94 152 45 70 25 349.93 0.40 153 45 71 26 349.91 0.41 154 48 71 23 349.92 0.41 155 48 73 25 349.76 0.39 156 48 74 26 348.59 0.47 157 49 71 22 349.94 0.40 158 49 98 49 260.81 0.61 159 50 70 20 349.95 0.39 160 50 71 21 349.94 0.39 161 50 98 48 260.74 0.63 162 51 68 17 350.06 0.35 163 51 69 18 349.96 0.39 164 51 70 19 349.91 0.39 165 51 77 26 262.20 0.81 166 51 94 43 260.87 0.61 167 51 98 47 260.41 0.62 168 52 68 16 350.03 0.35 169 52 69 17 350.00 0.35 170 52 94 42 260.77 0.58 171 53 66 13 350.35 0.21 172 53 67 14 350.31 0.23 173 53 68 15 350.04 0.33 174 53 90 37 260.91 0.65 175 53 94 41 260.59 0.55 176 54 66 12 350.33 0.21 177 54 67 13 350.31 0.21 178 54 69 15 350.30 0.21 179 55 65 10 350.35 0.21 180 55 66 11 350.31 0.19 181 55 84 29 261.11 0.65 182 55 89 34 260.88 0.67 183 55 90 35 260.79 0.62 184 56 64 8 350.47 0.21 185 56 65 9 350.44 0.21 186 56 140 84 70.18 0.74 187 57 63 6 350.69 0.19 188 57 64 7 350.48 0.21 189 58 61 3 475.35 1.21 190 58 62 4 435.53 7.49 191 58 63 5 384.07 16.50 192 59 62 3 440.18 5.17 193 61 120 59 127.95 9.04 194 63 118 55 128.21 9.10 195 63 120 57 127.95 9.04 196 63 122 59 125.08 10.11 197 64 82 18 261.05 0.65 198 64 84 20 260.98 0.63 199 65 80 15 261.17 0.66 200 65 81 16 261.10 0.65 201 65 82 17 261.04 0.64 202 65 84 19 261.00 0.64 203 65 124 59 109.86 17.33 204 65 140 75 70.20 0.74 205 65 142 77 70.11 0.74 206 66 80 14 261.18 0.66 207 66 81 15 261.13 0.65 208 66 84 18 261.10 0.65 209 66 90 24 260.82 0.62 210 66 93 27 260.63 0.54 211 67 79 12 261.25 0.68 212 67 80 13 261.18 0.66 213 67 126 59 108.25 18.07 214 67 140 73 70.12 0.74 215 68 77 9 262.03 0.83 216 68 78 10 261.43 0.72 217 68 79 11 261.27 0.68 218 68 94 26 260.65 0.55 219 68 97 29 259.48 0.78 220 69 77 8 262.04 0.84 221 69 78 9 261.44 0.72 222 69 126 57 108.25 18.07 223 69 128 59 107.64 17.91 224 69 138 69 70.19 0.74 225 70 76 6 262.24 0.82 226 70 77 7 262.12 0.80 227 71 74 3 479.14 1.21 228 71 75 4 406.06 1.73 229 71 76 5 262.24 0.82 230 71 77 6 262.24 0.82 231 71 136 65 78.37 3.35 232 72 75 3 471.78 0.88 233 72 77 5 409.32 2.62 234 72 107 35 187.72 0.09 235 72 108 36 187.52 0.00 236 72 110 38 186.55 0.14 237 73 110 37 187.40 0.00 238 75 110 35 186.38 0.18 239 76 110 34 184.78 0.78 240 76 112 36 147.21 18.16 241 76 128 52 108.06 18.12 242 76 131 55 93.98 11.16 243 76 132 56 93.77 11.04 244 76 136 60 78.88 3.60 245 77 97 20 260.79 0.61 246 77 98 21 260.79 0.61 247 77 107 30 187.13 0.11 248 77 110 33 143.68 16.34 249 77 111 34 143.43 16.23 250 77 128 51 108.19 18.09 251 78 111 33 141.89 15.03 252 78 114 36 128.87 9.13 253 78 126 48 108.34 18.11 254 78 128 50 108.21 18.07 255 79 97 18 259.56 0.81 256 79 106 27 186.68 0.12 257 79 114 35 128.87 9.12 258 79 126 47 108.69 17.94 259 80 114 34 128.88 9.12 260 80 115 35 128.75 9.11 261 80 116 36 128.52 9.03 262 80 124 44 108.83 17.87 263 80 125 45 108.83 17.87 264 80 126 46 108.81 17.88 265 81 84 3 518.58 0.96 266 81 93 12 260.71 0.54 267 81 97 16 257.48 1.78 268 81 103 22 187.60 0.10 269 82 116 34 128.50 8.98 270 82 117 35 128.43 9.01 271 82 118 36 128.18 9.12 272 82 124 42 112.91 15.98 273 83 118 35 128.19 9.12 274 83 119 36 128.18 9.12 275 84 88 4 422.98 6.98 276 84 93 9 398.60 0.16 277 85 88 3 462.82 1.61 278 87 92 5 449.16 2.35 279 88 92 4 456.72 1.38 280 88 93 5 446.69 1.34 281 88 103 15 405.36 5.16 282 89 92 3 466.69 0.51 283 89 93 4 465.19 0.24 284 90 93 3 465.26 0.27 285 90 94 4 465.26 0.27 286 91 95 4 480.76 1.95 287 92 95 3 487.87 1.60 288 92 96 4 480.76 1.95 289 93 96 3 480.76 1.95 290 93 97 4 480.76 1.95 291 93 103 10 416.60 8.28 292 94 97 3 486.07 1.30 293 94 98 4 484.29 1.61 294 95 98 3 484.29 1.61 295 96 99 3 483.92 0.21 296 96 100 4 451.12 3.43 297 96 103 7 416.60 8.28 298 97 103 6 416.60 8.28 299 97 104 7 416.60 8.28 300 97 107 10 406.52 3.25 301 98 104 6 435.20 0.93 302 98 107 9 419.04 7.03 303 99 104 5 448.81 0.95 304 100 103 3 476.28 3.68 305 100 104 4 454.43 1.60 306 101 104 3 467.73 0.62 307 101 105 4 463.56 1.45 308 102 105 3 469.41 0.21 309 102 106 4 467.73 0.63 310 103 106 3 470.71 0.86 311 103 107 4 465.13 1.93 312 104 107 3 470.71 0.85 313 104 108 4 459.31 0.98 314 105 108 3 464.11 1.41 315 105 109 4 455.62 0.36 316 106 109 3 466.00 2.32 317 107 110 3 480.57 1.36 318 111 114 3 507.02 1.59 319 111 128 17 108.33 18.12 320 112 127 15 108.35 18.11 321 112 128 16 108.28 18.12 322 112 131 19 98.14 13.23 323 113 126 13 108.84 17.89 324 113 127 14 108.34 18.09 325 114 125 11 108.89 17.89 326 114 126 12 108.84 17.88 327 115 124 9 109.32 17.79 328 115 125 10 108.84 17.87 329 116 123 7 113.13 16.07 330 116 124 8 110.06 17.48 331 117 122 5 268.81 60.82 332 117 123 6 114.91 15.19 333 118 121 3 463.65 2.89 334 118 122 4 417.15 0.62 335 118 124 6 390.97 0.27 336 122 142 20 70.19 0.74 337 122 143 21 70.09 0.72 338 123 143 20 69.86 0.60 339 124 141 17 70.17 0.74 340 124 142 18 70.12 0.73 341 125 140 15 70.19 0.74 342 125 141 16 70.14 0.74 343 126 138 12 70.23 0.73 344 126 139 13 70.19 0.74 345 126 140 14 70.15 0.74 346 127 138 11 70.22 0.72 347 127 139 12 70.19 0.73 348 128 131 3 477.26 1.09 349 128 136 8 78.14 3.22 350 128 137 9 70.23 0.72 351 128 138 10 70.20 0.71 352 129 137 8 78.04 3.18 353 129 138 9 75.20 1.76 354 129 139 10 75.20 1.76 355 130 135 5 414.96 8.76 356 130 136 6 81.48 4.88 357 130 137 7 78.13 3.22 358 131 136 5 394.39 2.35 359 132 136 4 457.44 5.19 360 133 136 3 503.37 1.25