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 1 132 131 27.63 0.95 2 1 133 132 26.97 0.59 3 1 136 135 25.12 0.79 4 2 132 130 28.78 1.14 5 3 7 4 490.30 0.04 6 3 8 5 490.11 0.13 7 3 11 8 451.30 5.04 8 3 78 75 36.03 0.97 9 3 129 126 30.69 0.59 10 3 132 129 29.25 1.25 11 3 133 130 29.18 1.27 12 4 7 3 490.69 0.14 13 4 8 4 490.69 0.15 14 5 8 3 490.80 0.18 15 5 9 4 490.96 0.09 16 6 9 3 498.44 3.64 17 6 10 4 491.10 0.03 18 7 10 3 509.90 3.29 19 7 11 4 491.09 0.03 20 7 129 122 48.37 0.35 21 8 11 3 509.80 3.34 22 8 12 4 492.03 0.45 23 8 78 70 48.40 0.34 24 9 12 3 512.85 1.80 25 9 13 4 491.05 0.02 26 10 13 3 499.65 3.20 27 10 14 4 491.30 0.12 28 10 126 116 67.06 0.85 29 11 14 3 504.94 3.88 30 11 15 4 491.59 0.01 31 11 129 118 65.31 0.03 32 11 130 119 65.29 0.03 33 12 15 3 492.76 0.58 34 12 16 4 492.11 0.26 35 13 16 3 503.91 2.50 36 13 17 4 501.19 3.85 37 14 17 3 509.54 0.32 38 14 18 4 500.25 4.32 39 14 114 100 89.55 0.39 40 14 118 104 90.47 0.72 41 14 121 107 89.70 0.34 42 14 122 108 89.56 0.38 43 14 126 112 88.92 0.68 44 14 130 116 87.02 1.08 45 15 18 3 497.80 1.94 46 15 68 53 89.41 0.46 47 15 71 56 86.98 1.10 48 15 72 57 85.04 0.14 49 15 75 60 84.70 0.03 50 15 114 99 89.61 0.42 51 15 130 115 89.38 0.45 52 17 118 101 99.17 1.31 53 17 121 104 106.31 1.56 54 18 23 5 400.57 12.32 55 18 68 50 95.30 0.58 56 18 114 96 96.11 0.18 57 18 118 100 110.45 0.48 58 19 22 3 513.75 1.16 59 19 23 4 405.62 9.80 60 20 65 45 97.86 1.83 61 20 68 48 95.31 0.57 62 21 65 44 110.89 2.69 63 22 25 3 496.20 1.17 64 22 26 4 489.02 1.52 65 22 117 95 140.46 1.31 66 23 26 3 492.34 0.14 67 23 27 4 489.02 1.52 68 23 68 45 120.70 0.40 69 23 110 87 120.78 0.37 70 23 113 90 132.50 3.79 71 23 117 94 140.46 1.31 72 24 27 3 511.56 3.57 73 24 28 4 488.50 1.78 74 24 64 40 120.74 0.39 75 24 65 41 120.74 0.39 76 24 68 44 120.70 0.40 77 25 28 3 506.82 5.94 78 25 29 4 488.64 1.85 79 25 60 35 140.21 1.12 80 25 61 36 135.60 1.18 81 25 64 39 128.26 3.74 82 26 29 3 495.57 0.32 83 26 30 4 488.58 0.76 84 26 55 29 142.25 1.45 85 26 113 87 141.41 1.52 86 26 116 90 142.04 1.53 87 26 117 91 142.10 1.50 88 27 30 3 493.28 0.31 89 27 31 4 488.59 0.77 90 27 109 82 141.32 1.54 91 27 110 83 141.20 1.41 92 27 113 86 141.49 1.48 93 28 31 3 498.37 2.26 94 28 32 4 496.19 3.02 95 28 42 14 142.86 1.80 96 28 60 32 142.09 1.44 97 28 63 35 141.98 1.39 98 28 64 36 141.75 1.33 99 28 106 78 141.36 1.53 100 29 32 3 499.36 1.45 101 29 33 4 496.19 3.02 102 29 54 25 142.66 1.65 103 29 55 26 142.67 1.65 104 29 60 31 142.17 1.48 105 30 33 3 501.91 0.17 106 30 34 4 496.18 3.02 107 30 55 25 142.94 1.73 108 30 109 79 141.80 1.72 109 30 113 83 142.19 1.60 110 30 116 86 142.30 1.56 111 31 34 3 508.62 0.45 112 31 35 4 483.97 3.08 113 31 38 7 344.05 6.52 114 31 105 74 141.78 1.73 115 31 106 75 141.74 1.72 116 31 109 78 142.00 1.69 117 32 36 4 460.06 7.94 118 32 38 6 344.05 6.52 119 32 39 7 305.36 5.54 120 32 42 10 323.75 3.63 121 32 54 22 143.09 1.68 122 32 60 28 142.66 1.65 123 33 36 3 506.32 0.07 124 33 51 18 143.09 1.68 125 33 54 21 143.10 1.68 126 33 55 22 143.09 1.68 127 35 38 3 509.31 1.12 128 35 105 70 141.81 1.74 129 35 109 74 142.47 1.73 130 36 39 3 508.84 1.36 131 37 40 3 515.50 1.52 132 37 102 65 142.31 1.71 133 37 105 68 142.54 1.70 134 38 41 3 515.94 1.74 135 38 42 4 508.66 1.44 136 38 102 64 142.02 1.82 137 39 42 3 508.66 1.44 138 39 43 4 494.50 1.34 139 39 48 9 144.19 1.59 140 40 43 3 515.48 1.97 141 40 99 59 142.29 1.76 142 41 96 55 141.78 1.95 143 41 97 56 141.85 1.93 144 41 98 57 141.88 1.92 145 41 102 61 142.50 1.73 146 42 45 3 507.69 0.01 147 42 48 6 370.20 24.91 148 42 63 21 143.09 1.65 149 43 46 3 518.41 1.03 150 43 48 5 370.20 24.91 151 44 59 15 146.14 1.06 152 45 57 12 146.24 1.10 153 45 59 14 144.88 1.33 154 45 60 15 144.89 1.34 155 45 63 18 144.88 1.33 156 46 57 11 146.28 1.10 157 47 53 6 327.18 13.25 158 47 57 10 212.97 34.41 159 48 53 5 408.94 17.71 160 48 54 6 321.04 16.32 161 48 57 9 271.99 4.95 162 48 60 12 271.69 4.96 163 49 53 4 485.63 2.41 164 50 53 3 488.39 1.03 165 50 54 4 485.63 2.41 166 51 54 3 491.92 0.72 167 51 55 4 486.88 1.79 168 52 55 3 493.06 0.15 169 52 56 4 486.85 1.81 170 53 56 3 497.81 1.02 171 53 57 4 486.84 1.82 172 54 57 3 494.63 0.70 173 54 60 6 409.80 8.96 174 57 60 3 489.59 0.45 175 57 61 4 488.81 4.54 176 58 61 3 498.00 0.05 177 58 62 4 488.80 4.54 178 59 62 3 498.00 0.05 179 59 63 4 492.32 2.91 180 60 63 3 498.02 0.07 181 60 64 4 488.64 4.75 182 61 64 3 498.01 0.07 183 61 65 4 493.70 2.23 184 62 65 3 500.66 1.25 185 62 66 4 493.71 2.21 186 63 66 3 488.43 0.43 187 63 67 4 488.41 0.43 188 64 67 3 494.15 1.08 189 64 68 4 490.86 1.67 190 65 68 3 498.90 2.35 191 65 69 4 487.73 0.12 192 66 69 3 495.82 0.81 193 66 70 4 495.25 0.52 194 67 70 3 507.05 3.58 195 67 71 4 496.42 1.10 196 67 106 39 181.69 0.24 197 68 71 3 499.25 0.32 198 68 72 4 492.70 3.00 199 68 110 42 184.16 0.91 200 69 72 3 499.30 0.29 201 69 73 4 492.70 3.00 202 70 73 3 499.30 0.29 203 70 74 4 494.98 1.86 204 70 85 15 181.99 0.07 205 70 88 18 181.85 0.13 206 71 74 3 505.49 2.16 207 71 75 4 494.99 1.87 208 71 110 39 200.33 4.95 209 71 134 63 184.24 0.87 210 71 137 66 182.04 0.10 211 72 75 3 499.97 0.61 212 72 76 4 495.00 1.88 213 73 76 3 500.40 0.82 214 73 77 4 495.00 1.88 215 73 84 11 205.00 2.81 216 74 77 3 495.00 1.89 217 74 78 4 490.88 1.76 218 74 81 7 290.12 1.96 219 74 84 10 239.19 14.29 220 74 85 11 239.19 14.29 221 75 78 3 507.17 1.88 222 75 133 58 230.78 6.79 223 77 80 3 501.50 0.96 224 77 81 4 478.68 4.32 225 77 84 7 394.90 1.76 226 78 81 3 501.11 1.17 227 78 133 55 245.66 5.92 228 80 83 3 512.82 2.52 229 80 84 4 485.70 5.17 230 81 84 3 483.17 6.44 231 81 85 4 472.69 1.20 232 81 136 55 245.82 5.96 233 81 137 56 245.83 5.96 234 81 140 59 245.78 5.96 235 82 85 3 496.70 0.17 236 82 86 4 469.70 2.68 237 82 139 57 245.84 5.96 238 82 140 58 245.80 5.97 239 82 143 61 245.78 5.96 240 83 86 3 489.28 3.39 241 85 88 3 500.25 3.58 242 85 89 4 475.80 2.73 243 85 137 52 255.31 2.17 244 85 140 55 250.29 4.43 245 85 141 56 255.05 2.04 246 86 89 3 495.99 3.75 247 86 90 4 487.71 1.55 248 87 90 3 496.19 3.65 249 87 91 4 483.03 0.79 250 88 91 3 501.96 0.38 251 88 92 4 479.25 1.09 252 88 141 53 257.68 2.88 253 89 92 3 494.22 3.49 254 89 93 4 471.85 2.61 255 89 140 51 257.69 2.88 256 89 141 52 257.68 2.88 257 89 143 54 257.66 2.88 258 89 144 55 257.68 2.88 259 90 93 3 504.48 1.64 260 90 94 4 458.36 1.54 261 90 95 5 458.21 1.61 262 90 144 54 257.68 2.88 263 91 95 4 420.01 17.49 264 91 96 5 420.00 17.50 265 92 96 4 377.85 6.26 266 92 97 5 376.07 7.14 267 92 98 6 322.26 5.52 268 92 103 11 278.89 1.25 269 92 141 49 258.06 2.87 270 93 97 4 334.64 1.21 271 93 141 48 258.08 2.88 272 93 142 49 257.99 2.89 273 93 144 51 257.88 2.94 274 93 145 52 257.72 2.86 275 94 144 50 257.96 2.90 276 97 145 48 258.11 2.86 277 98 102 4 484.51 0.29 278 98 103 5 478.45 2.79 279 98 145 47 258.39 2.86 280 99 102 3 502.20 0.57 281 100 103 3 498.29 1.39 282 100 104 4 490.40 2.92 283 100 142 42 258.56 2.81 284 100 145 45 258.45 2.87 285 101 104 3 497.21 1.93 286 101 105 4 484.84 0.12 287 102 105 3 490.38 2.90 288 102 106 4 485.77 2.63 289 103 106 3 501.26 0.10 290 103 107 4 488.51 4.00 291 103 138 35 258.72 2.77 292 103 141 38 258.73 2.77 293 103 142 39 258.69 2.77 294 103 145 42 258.72 2.77 295 104 107 3 498.73 1.10 296 104 108 4 483.56 6.48 297 104 138 34 258.75 2.77 298 105 108 3 490.19 2.43 299 105 109 4 482.70 6.05 300 106 109 3 491.18 2.67 301 106 110 4 486.01 4.40 302 107 110 3 490.32 2.24 303 107 111 4 481.14 1.96 304 107 134 27 258.98 2.69 305 108 111 3 483.71 0.67 306 108 112 4 481.12 1.96 307 109 112 3 487.29 4.86 308 109 113 4 476.25 4.22 309 110 113 3 488.86 2.08 310 110 114 4 494.59 0.78 311 110 134 24 259.62 2.80 312 111 114 3 496.69 0.77 313 111 115 4 494.59 0.78 314 111 122 11 275.23 3.91 315 111 127 16 259.81 2.82 316 111 130 19 259.77 2.81 317 111 131 20 259.70 2.78 318 111 134 23 259.67 2.78 319 112 115 3 507.23 3.03 320 112 116 4 494.57 0.79 321 113 116 3 502.31 3.08 322 113 117 4 480.62 7.75 323 114 117 3 484.74 1.48 324 114 118 4 472.22 3.56 325 114 122 8 294.68 3.35 326 114 130 16 259.97 2.74 327 115 118 3 497.32 0.30 328 115 119 4 457.09 1.83 329 115 122 7 278.26 5.27 330 118 121 3 503.03 0.70 331 118 122 4 469.52 0.79 332 119 122 3 507.22 2.79 333 120 123 3 518.83 0.39 334 122 126 4 466.12 1.28 335 122 127 5 464.51 0.50 336 122 130 8 457.59 2.28 337 123 126 3 482.96 6.44 338 123 127 4 469.44 0.32 339 124 127 3 480.54 0.66 340 124 128 4 483.16 7.17 341 125 128 3 483.69 7.45 342 125 129 4 485.39 8.30 343 126 129 3 486.11 7.96 344 126 130 4 485.39 8.30 345 127 130 3 502.20 0.75 346 127 131 4 482.60 8.02 347 128 131 3 501.35 0.33 348 128 132 4 500.64 0.68 349 129 132 3 498.96 0.17 350 129 133 4 498.95 0.17 351 130 133 3 495.35 1.96 352 130 134 4 482.61 0.29 353 131 134 3 504.50 2.96 354 131 135 4 481.45 0.87 355 132 135 3 494.87 1.35 356 132 136 4 483.00 0.54 357 133 136 3 494.67 1.45 358 133 137 4 482.99 0.54 359 134 137 3 502.50 1.03 360 134 138 4 480.38 0.77 361 135 138 3 502.51 1.04 362 135 139 4 480.39 0.76 363 136 139 3 500.51 0.04 364 136 140 4 471.64 3.62 365 137 140 3 479.52 7.55 366 137 141 4 472.19 5.92 367 138 141 3 491.78 6.37 368 138 142 4 472.12 5.96 369 139 142 3 495.00 0.19 370 139 143 4 465.87 2.70 371 139 146 7 448.90 2.52 372 140 143 3 496.94 1.88 373 142 145 3 504.00 0.81 374 142 146 4 490.84 3.46 375 143 146 3 497.75 2.31