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 2 134 132 66.30 1.39 2 3 44 41 118.77 27.57 3 3 45 42 118.67 27.54 4 3 47 44 118.25 27.32 5 3 48 45 118.61 27.50 6 3 71 68 118.56 27.50 7 3 74 71 118.89 27.64 8 3 133 130 66.31 1.39 9 3 134 131 66.29 1.39 10 3 136 133 66.28 1.38 11 4 42 38 119.20 27.63 12 4 43 39 118.89 27.63 13 4 44 40 118.86 27.62 14 4 134 130 66.33 1.39 15 4 135 131 66.31 1.39 16 4 136 132 66.30 1.39 17 5 41 36 125.06 25.26 18 5 42 37 121.47 26.94 19 5 43 38 119.13 27.60 20 5 45 40 119.16 27.62 21 5 69 64 118.85 27.65 22 5 70 65 118.89 27.64 23 5 71 66 118.89 27.64 24 5 128 123 66.31 1.39 25 5 136 131 66.31 1.39 26 6 40 34 125.28 25.19 27 6 41 35 125.06 25.26 28 6 42 36 121.50 26.94 29 6 136 130 66.35 1.39 30 6 137 131 66.31 1.39 31 6 138 132 66.30 1.39 32 7 34 27 125.39 25.13 33 7 40 33 125.29 25.20 34 7 41 34 125.23 25.21 35 7 54 47 125.23 25.17 36 7 69 62 119.55 27.91 37 7 138 131 66.31 1.39 38 7 140 133 66.25 1.38 39 8 40 32 125.51 25.30 40 8 138 130 66.34 1.39 41 8 139 131 66.29 1.39 42 8 140 132 66.28 1.39 43 9 41 32 125.65 25.23 44 9 56 47 125.87 25.12 45 9 140 131 66.29 1.39 46 9 142 133 66.28 1.39 47 10 139 129 66.36 1.39 48 10 140 130 66.32 1.38 49 10 141 131 66.28 1.39 50 10 142 132 66.28 1.39 51 11 17 6 132.13 22.74 52 11 18 7 126.98 25.29 53 11 142 131 66.30 1.38 54 12 141 129 66.36 1.39 55 12 142 130 66.31 1.38 56 12 143 131 66.30 1.39 57 13 122 109 100.98 3.46 58 13 143 130 66.31 1.39 59 15 122 107 109.79 0.73 60 16 58 42 348.26 0.88 61 16 60 44 348.18 0.82 62 16 61 45 348.24 0.78 63 16 122 106 111.36 0.09 64 17 57 40 349.90 0.09 65 17 58 41 348.29 0.88 66 18 56 38 348.28 0.88 67 18 57 39 348.84 0.61 68 18 58 40 348.37 0.84 69 18 63 45 348.92 1.04 70 18 64 46 348.37 0.84 71 18 65 47 348.28 0.88 72 18 122 104 120.71 4.82 73 18 124 106 108.59 10.81 74 18 142 124 66.30 1.38 75 19 56 37 350.88 0.06 76 19 57 38 351.22 0.34 77 19 59 40 352.19 0.34 78 20 41 21 351.30 0.15 79 20 55 35 352.19 0.17 80 20 56 36 352.12 0.21 81 21 55 34 352.49 0.29 82 21 56 35 352.48 0.29 83 21 57 36 352.43 0.28 84 22 54 32 352.52 0.29 85 22 55 33 352.50 0.30 86 22 89 67 260.91 0.18 87 22 90 68 260.83 0.20 88 22 91 69 260.83 0.20 89 23 34 11 353.17 0.04 90 23 36 13 353.44 0.04 91 23 41 18 353.02 0.12 92 23 53 30 352.56 0.28 93 23 54 31 352.53 0.29 94 24 34 10 353.49 0.00 95 24 52 28 352.94 0.09 96 24 53 29 352.80 0.17 97 24 90 66 260.92 0.18 98 24 91 67 260.89 0.17 99 24 94 70 260.66 0.19 100 25 32 7 353.48 0.02 101 25 33 8 353.50 0.01 102 25 34 9 353.51 0.01 103 25 43 18 353.48 0.01 104 25 51 26 353.38 0.04 105 25 52 27 353.01 0.06 106 25 94 69 260.85 0.20 107 26 31 5 389.52 4.44 108 26 50 24 353.50 0.13 109 26 51 25 353.38 0.04 110 26 94 68 260.85 0.20 111 26 95 69 260.82 0.20 112 26 98 72 260.45 0.18 113 27 31 4 375.16 2.75 114 28 31 3 465.59 0.48 115 28 49 21 366.08 1.36 116 28 50 22 363.17 0.69 117 28 98 70 260.79 0.18 118 29 46 17 368.92 1.84 119 29 47 18 368.69 1.73 120 29 48 19 368.68 1.73 121 29 49 20 368.65 1.73 122 29 50 21 366.77 1.78 123 30 46 16 368.98 1.85 124 31 45 14 369.19 1.83 125 31 46 15 369.17 1.83 126 31 50 19 368.69 1.73 127 32 44 12 369.31 1.82 128 32 45 13 369.18 1.82 129 33 43 10 370.32 1.79 130 33 44 11 369.37 1.83 131 34 41 7 371.12 1.89 132 34 42 8 370.91 1.97 133 34 43 9 370.33 1.79 134 34 52 18 368.87 1.73 135 34 53 19 368.86 1.73 136 34 54 20 368.81 1.71 137 34 69 35 352.81 0.59 138 35 41 6 371.14 1.89 139 35 42 7 370.94 1.96 140 36 40 4 424.50 6.03 141 36 41 5 371.15 1.89 142 37 40 3 466.85 0.13 143 37 42 5 390.80 7.73 144 41 54 13 368.85 1.72 145 41 56 15 368.85 1.72 146 43 51 8 369.00 1.77 147 43 52 9 368.87 1.74 148 43 69 26 352.81 0.59 149 45 50 5 377.44 0.61 150 45 51 6 370.52 2.54 151 45 70 25 352.56 0.47 152 45 71 26 352.54 0.47 153 48 71 23 352.52 0.48 154 48 73 25 352.32 0.43 155 48 74 26 349.70 0.10 156 49 71 22 352.50 0.47 157 49 98 49 260.77 0.21 158 50 70 20 352.51 0.48 159 50 71 21 352.50 0.48 160 50 98 48 260.65 0.23 161 51 68 17 352.80 0.58 162 51 69 18 352.70 0.56 163 51 70 19 352.38 0.51 164 51 77 26 262.01 0.38 165 51 94 43 260.88 0.21 166 51 98 47 260.45 0.18 167 52 68 16 352.79 0.60 168 52 69 17 352.75 0.60 169 52 94 42 260.77 0.21 170 53 66 13 353.00 0.70 171 53 67 14 352.85 0.64 172 53 68 15 352.75 0.62 173 53 90 37 260.90 0.20 174 53 94 41 260.61 0.19 175 54 66 12 353.00 0.70 176 54 67 13 352.94 0.69 177 54 69 15 352.82 0.66 178 55 65 10 353.02 0.71 179 55 66 11 352.92 0.74 180 55 84 29 261.06 0.16 181 55 88 33 260.95 0.18 182 55 89 34 260.88 0.18 183 55 90 35 260.81 0.19 184 56 64 8 353.08 0.73 185 56 65 9 353.06 0.75 186 56 140 84 66.35 1.38 187 57 63 6 353.16 0.76 188 57 64 7 353.10 0.74 189 58 61 3 484.81 2.04 190 58 62 4 437.68 1.75 191 58 63 5 374.63 0.81 192 59 62 3 444.02 2.93 193 61 120 59 132.44 8.60 194 62 120 58 132.44 8.60 195 63 118 55 132.50 8.62 196 63 120 57 131.97 8.84 197 63 122 59 130.02 9.46 198 64 82 18 261.05 0.17 199 64 84 20 260.94 0.17 200 65 80 15 261.23 0.14 201 65 81 16 261.13 0.15 202 65 82 17 261.07 0.15 203 65 84 19 261.00 0.17 204 65 124 59 112.55 17.81 205 65 140 75 66.36 1.38 206 65 142 77 66.28 1.38 207 66 80 14 261.26 0.14 208 66 81 15 261.19 0.14 209 66 84 18 261.07 0.15 210 66 90 24 260.76 0.16 211 66 93 27 260.64 0.21 212 67 79 12 261.32 0.14 213 67 80 13 261.26 0.14 214 67 126 59 109.73 18.99 215 67 140 73 66.30 1.39 216 68 77 9 319.08 28.91 217 68 78 10 261.42 0.14 218 68 79 11 261.32 0.15 219 68 94 26 260.66 0.21 220 68 97 29 259.56 0.21 221 68 126 58 109.91 19.08 222 69 77 8 319.08 28.91 223 69 78 9 261.42 0.14 224 69 126 57 109.91 19.08 225 69 128 59 108.75 19.11 226 69 138 69 66.34 1.39 227 70 76 6 374.47 1.34 228 70 77 7 319.12 28.93 229 71 74 3 481.94 0.09 230 71 75 4 407.30 1.86 231 71 76 5 374.48 1.34 232 71 77 6 374.47 1.34 233 71 136 65 75.22 3.06 234 72 75 3 461.03 1.18 235 72 77 5 397.45 2.97 236 72 107 35 193.44 0.69 237 72 108 36 193.21 0.59 238 72 110 38 192.67 0.55 239 73 110 37 193.16 0.58 240 75 110 35 192.46 0.62 241 76 110 34 187.99 0.86 242 76 112 36 146.47 15.60 243 76 128 52 109.09 18.97 244 76 131 55 91.97 11.42 245 76 136 60 74.99 2.94 246 77 97 20 260.66 0.25 247 77 98 21 260.67 0.25 248 77 107 30 193.09 0.58 249 77 110 33 146.54 15.46 250 77 111 34 142.16 13.27 251 77 128 51 109.38 18.84 252 78 111 33 141.02 12.70 253 78 113 35 138.43 11.50 254 78 114 36 132.80 8.76 255 78 126 48 109.92 19.09 256 78 128 50 109.39 18.84 257 79 97 18 260.50 0.21 258 79 106 27 192.94 0.48 259 79 114 35 132.81 8.75 260 79 126 47 110.17 18.96 261 80 114 34 132.81 8.75 262 80 116 36 132.53 8.63 263 80 124 44 112.45 17.87 264 80 125 45 110.31 18.93 265 80 126 46 110.20 18.96 266 80 140 60 66.34 1.39 267 81 84 3 515.15 1.95 268 81 93 12 260.70 0.25 269 81 97 16 258.96 0.10 270 81 103 22 193.45 0.64 271 82 116 34 132.53 8.63 272 82 117 35 132.53 8.63 273 82 118 36 131.37 9.18 274 82 124 42 115.54 16.57 275 83 118 35 132.33 8.71 276 83 119 36 132.01 8.86 277 84 88 4 425.42 0.96 278 84 93 9 403.13 5.79 279 85 88 3 457.36 0.18 280 87 92 5 456.07 0.20 281 88 92 4 456.08 0.20 282 88 93 5 452.43 1.93 283 88 103 15 407.92 3.81 284 89 92 3 465.94 0.80 285 89 93 4 461.79 2.02 286 90 93 3 466.16 0.69 287 90 94 4 461.47 1.43 288 91 94 3 480.13 1.38 289 91 95 4 477.56 0.38 290 92 95 3 481.86 0.74 291 92 96 4 477.41 2.96 292 93 96 3 481.86 0.74 293 93 97 4 481.86 0.74 294 93 103 10 409.74 4.62 295 94 97 3 490.88 0.18 296 94 98 4 487.30 1.98 297 95 98 3 490.25 0.50 298 96 99 3 480.48 0.38 299 96 100 4 438.99 2.44 300 96 103 7 409.75 4.62 301 97 103 6 409.75 4.62 302 97 104 7 409.69 4.62 303 97 106 9 409.73 4.62 304 97 107 10 409.69 4.62 305 98 104 6 426.42 1.30 306 98 107 9 419.12 0.08 307 99 104 5 442.84 1.62 308 100 103 3 462.34 1.19 309 100 104 4 456.86 1.00 310 101 104 3 469.37 3.60 311 101 105 4 456.89 1.02 312 102 105 3 466.85 4.86 313 102 106 4 458.16 0.64 314 103 106 3 468.72 1.88 315 103 107 4 457.94 0.52 316 104 107 3 468.13 2.17 317 104 108 4 457.93 0.52 318 105 108 3 466.07 1.62 319 105 109 4 456.45 1.26 320 106 109 3 464.38 2.48 321 107 110 3 479.91 2.69 322 111 114 3 500.53 0.29 323 111 128 17 109.92 19.09 324 112 127 15 109.95 19.10 325 112 128 16 109.88 19.10 326 112 131 19 98.08 14.42 327 113 126 13 110.22 18.98 328 113 127 14 109.95 19.10 329 114 125 11 110.33 18.94 330 114 126 12 110.23 18.97 331 115 123 8 115.73 16.66 332 115 124 9 115.30 16.64 333 115 125 10 110.33 18.95 334 116 123 7 115.70 16.64 335 116 124 8 115.50 16.59 336 117 122 5 231.01 70.49 337 117 123 6 116.46 16.12 338 118 121 3 464.97 2.55 339 118 122 4 418.85 6.17 340 118 124 6 375.82 0.29 341 122 142 20 66.37 1.38 342 122 143 21 66.30 1.39 343 123 143 20 66.25 1.37 344 124 141 17 66.35 1.38 345 124 142 18 66.27 1.38 346 125 140 15 66.36 1.39 347 125 141 16 66.30 1.39 348 126 138 12 66.39 1.38 349 126 139 13 66.36 1.38 350 126 140 14 66.31 1.39 351 127 138 11 66.39 1.38 352 127 139 12 66.37 1.38 353 127 141 14 66.35 1.38 354 128 131 3 470.42 3.12 355 128 136 8 74.45 2.65 356 128 137 9 66.39 1.38 357 128 138 10 66.34 1.39 358 129 137 8 66.41 1.38 359 129 138 9 66.38 1.39 360 129 139 10 66.38 1.38 361 130 135 5 421.13 4.89 362 130 136 6 87.40 4.80 363 130 137 7 74.27 2.56 364 131 136 5 260.31 70.95 365 132 136 4 450.53 4.62 366 133 136 3 493.85 1.75