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 5 450.48 4.94 2 2 74 72 26.25 0.24 3 2 128 126 21.83 0.09 4 2 129 127 21.30 0.22 5 3 6 3 466.28 1.46 6 3 7 4 464.69 0.53 7 4 7 3 476.49 6.38 8 4 8 4 479.21 0.09 9 5 8 3 485.89 1.67 10 5 9 4 471.12 4.14 11 6 9 3 481.06 0.75 12 6 10 4 478.89 0.26 13 6 125 119 46.05 0.10 14 6 128 122 46.05 0.10 15 7 10 3 483.96 2.46 16 7 11 4 478.89 0.25 17 7 74 67 48.38 0.10 18 7 75 68 48.38 0.11 19 8 11 3 483.75 2.57 20 8 12 4 472.03 3.19 21 9 12 3 480.43 1.01 22 9 13 4 475.13 1.63 23 9 125 116 56.59 0.64 24 10 13 3 476.86 0.75 25 10 14 4 474.84 1.48 26 10 71 61 56.55 0.66 27 10 74 64 56.57 0.65 28 10 125 115 56.63 0.66 29 10 126 116 56.58 0.65 30 10 129 119 56.58 0.65 31 11 14 3 481.88 1.76 32 11 15 4 481.60 1.89 33 11 74 63 57.49 1.13 34 12 15 3 481.62 1.89 35 12 16 4 481.61 1.90 36 13 16 3 481.62 1.90 37 13 17 4 481.41 1.99 38 13 117 104 79.69 0.12 39 13 118 105 79.67 0.12 40 13 126 113 59.00 1.12 41 14 17 3 476.66 0.39 42 14 18 4 461.75 5.09 43 14 21 7 441.62 3.62 44 14 64 50 161.16 2.10 45 14 67 53 64.81 1.61 46 14 68 54 64.84 1.60 47 14 71 57 58.99 1.13 48 16 19 3 518.01 2.02 49 16 117 101 93.68 0.51 50 17 20 3 492.26 1.16 51 17 21 4 474.72 1.37 52 17 24 7 422.04 6.92 53 17 110 93 92.38 0.00 54 17 114 97 94.01 0.47 55 18 21 3 478.70 0.40 56 20 23 3 489.01 1.51 57 20 24 4 468.82 1.60 58 20 114 94 121.26 0.01 59 21 24 3 483.63 1.18 60 21 25 4 477.42 1.93 61 21 64 43 162.01 1.73 62 22 25 3 485.44 1.61 63 22 26 4 475.18 0.81 64 22 61 39 165.01 2.34 65 23 26 3 479.51 1.36 66 23 27 4 479.56 1.39 67 23 113 90 141.99 0.87 68 24 27 3 485.70 2.14 69 24 28 4 479.56 1.39 70 24 64 40 162.77 1.47 71 24 106 82 151.74 0.90 72 24 109 85 151.36 0.99 73 24 110 86 151.35 0.98 74 24 113 89 142.59 0.58 75 24 114 90 145.02 0.64 76 25 28 3 483.07 3.14 77 25 29 4 479.56 1.38 78 25 60 35 164.90 2.23 79 25 64 39 162.72 1.45 80 26 29 3 490.06 2.23 81 26 30 4 479.56 1.38 82 26 56 30 166.23 2.36 83 26 57 31 166.22 2.35 84 26 60 34 165.62 2.06 85 27 30 3 477.06 1.68 86 27 31 4 469.54 2.08 87 27 109 82 151.41 0.99 88 27 113 86 150.25 0.44 89 28 31 3 477.37 1.52 90 28 32 4 476.71 1.51 91 28 102 74 152.12 0.96 92 28 105 77 151.99 0.92 93 28 106 78 151.86 0.89 94 28 109 81 151.56 0.99 95 29 32 3 476.73 1.51 96 29 33 4 476.69 1.52 97 29 43 14 260.61 4.04 98 29 56 27 167.50 2.41 99 29 59 30 166.82 2.23 100 29 60 31 166.50 2.18 101 29 63 34 166.26 2.29 102 29 102 73 152.12 0.96 103 30 33 3 482.68 1.48 104 30 34 4 475.31 0.83 105 30 51 21 170.97 3.71 106 30 56 26 167.77 2.12 107 31 34 3 480.20 0.24 108 31 35 4 465.32 2.38 109 31 105 74 152.09 0.95 110 31 108 77 152.05 0.95 111 31 109 78 152.00 0.96 112 31 112 81 151.89 1.01 113 32 35 3 474.44 2.19 114 32 36 4 460.51 0.01 115 32 39 7 304.29 2.10 116 32 43 11 304.23 2.12 117 32 101 69 152.16 0.96 118 32 102 70 152.15 0.96 119 32 105 73 152.09 0.95 120 33 37 4 430.47 6.63 121 33 39 6 303.32 2.58 122 33 40 7 293.58 6.04 123 33 43 10 293.61 6.05 124 33 49 16 203.57 0.93 125 33 56 23 199.95 0.45 126 34 37 3 492.00 5.37 127 34 51 17 202.69 1.55 128 36 39 3 499.80 1.55 129 36 101 65 152.47 1.01 130 36 104 68 152.49 1.02 131 36 105 69 152.38 0.99 132 37 40 3 504.21 0.65 133 38 41 3 515.77 4.41 134 38 42 4 509.43 0.20 135 38 98 60 152.81 1.04 136 38 101 63 152.80 1.03 137 39 42 3 506.31 0.26 138 39 43 4 498.53 3.15 139 39 98 59 152.75 1.02 140 40 43 3 505.81 0.50 141 40 44 4 488.40 2.27 142 41 44 3 496.73 5.04 143 42 45 3 560.15 4.51 144 42 93 51 153.28 1.07 145 42 94 52 153.22 1.09 146 42 95 53 153.22 1.07 147 42 98 56 153.15 1.06 148 43 46 3 496.66 0.03 149 43 49 6 273.62 5.24 150 43 59 16 206.00 2.56 151 46 49 3 500.91 0.68 152 46 55 9 266.17 1.54 153 46 56 10 282.38 9.61 154 46 59 13 268.91 2.89 155 47 55 8 291.81 4.95 156 48 53 5 303.86 10.96 157 48 55 7 291.81 4.95 158 49 53 4 413.73 18.45 159 49 56 7 311.94 2.33 160 50 53 3 471.37 0.15 161 50 56 6 404.12 10.86 162 51 56 5 436.81 3.39 163 52 57 5 458.75 6.62 164 53 56 3 473.93 5.61 165 53 57 4 458.76 6.62 166 54 57 3 468.63 1.68 167 54 58 4 458.81 6.59 168 55 58 3 476.21 4.47 169 55 59 4 476.84 0.12 170 56 59 3 481.11 2.02 171 56 60 4 472.65 1.98 172 57 60 3 482.38 2.89 173 57 61 4 482.47 2.93 174 58 61 3 488.58 0.12 175 58 62 4 482.46 2.94 176 59 62 3 483.59 2.37 177 59 63 4 480.64 3.84 178 60 63 3 487.88 0.23 179 60 64 4 480.12 4.10 180 61 64 3 486.94 0.69 181 61 65 4 474.39 1.24 182 62 65 3 476.03 1.33 183 62 66 4 474.31 1.28 184 63 66 3 474.97 0.95 185 63 67 4 474.29 1.29 186 63 102 39 152.12 0.96 187 64 67 3 471.36 0.28 188 64 68 4 474.62 1.47 189 64 106 42 151.95 0.92 190 65 68 3 474.84 1.36 191 65 69 4 474.62 1.48 192 66 69 3 480.67 0.64 193 66 70 4 478.25 0.33 194 66 84 18 182.51 3.54 195 67 70 3 484.60 2.85 196 67 71 4 469.69 4.86 197 67 106 39 151.94 0.92 198 67 129 62 147.04 1.75 199 67 130 63 146.59 1.74 200 68 71 3 476.43 1.50 201 68 72 4 469.68 4.86 202 69 72 3 486.75 1.76 203 69 73 4 465.52 6.11 204 69 80 11 228.31 3.50 205 69 81 12 214.69 5.74 206 69 84 15 211.12 3.99 207 70 73 3 480.48 1.38 208 70 74 4 451.12 13.29 209 70 77 7 283.90 2.03 210 70 81 11 211.16 3.97 211 70 129 59 147.15 1.73 212 70 133 63 145.84 2.07 213 71 74 3 475.78 1.82 214 71 129 58 147.14 1.74 215 73 76 3 494.73 0.18 216 73 77 4 421.45 9.05 217 73 80 7 283.28 2.35 218 74 77 3 486.04 4.18 219 74 129 55 147.23 1.73 220 76 79 3 487.91 1.27 221 76 80 4 465.24 2.86 222 77 80 3 464.89 3.05 223 77 81 4 462.62 4.17 224 77 129 52 147.21 1.72 225 77 132 55 146.88 1.67 226 77 133 56 146.28 1.95 227 77 136 59 144.40 1.64 228 78 81 3 494.90 0.34 229 78 82 4 473.19 1.10 230 78 136 58 144.33 1.60 231 78 139 61 143.68 1.76 232 79 82 3 485.84 0.03 233 81 84 3 481.01 0.38 234 81 85 4 461.31 1.11 235 81 133 52 145.78 1.88 236 81 136 55 144.08 1.62 237 81 137 56 143.99 1.59 238 82 85 3 478.29 2.68 239 82 86 4 471.40 6.11 240 82 139 57 143.61 1.76 241 82 140 58 143.38 1.86 242 83 86 3 488.25 2.31 243 83 87 4 454.72 2.23 244 84 87 3 484.61 0.49 245 84 88 4 467.67 3.23 246 84 137 53 143.62 1.76 247 85 88 3 481.74 0.95 248 85 89 4 460.20 6.96 249 85 136 51 143.66 1.75 250 85 137 52 143.61 1.76 251 85 139 54 143.45 1.81 252 85 140 55 141.18 1.02 253 86 89 3 476.99 0.63 254 86 90 4 452.72 3.22 255 86 140 54 141.19 1.01 256 87 91 4 385.46 8.13 257 87 92 5 379.72 10.99 258 88 92 4 356.44 22.63 259 88 93 5 297.43 6.87 260 88 94 6 297.42 6.87 261 88 99 11 229.26 1.62 262 88 141 53 141.06 1.06 263 89 93 4 297.41 6.86 264 89 140 51 141.18 1.02 265 89 141 52 139.98 1.57 266 90 93 3 465.93 4.92 267 90 140 50 143.09 1.95 268 94 141 47 136.43 0.06 269 95 98 3 494.85 0.92 270 96 99 3 492.61 0.72 271 96 141 45 130.04 0.22 272 97 100 3 511.07 0.74 273 98 101 3 481.75 0.58 274 98 102 4 484.85 3.06 275 99 102 3 486.29 2.34 276 99 103 4 478.66 1.43 277 99 134 35 143.91 1.46 278 99 137 38 141.72 0.86 279 99 141 42 134.90 0.39 280 100 103 3 480.19 0.67 281 100 104 4 478.66 1.43 282 101 104 3 478.75 1.39 283 101 105 4 472.38 1.71 284 102 105 3 473.09 1.44 285 102 106 4 470.73 0.88 286 103 106 3 483.41 2.65 287 103 107 4 474.49 1.79 288 103 130 27 146.30 1.55 289 103 134 31 143.93 1.47 290 104 107 3 483.38 2.66 291 104 108 4 473.21 1.55 292 105 108 3 486.58 1.05 293 105 109 4 473.22 1.55 294 106 109 3 486.61 1.06 295 106 110 4 473.22 1.56 296 106 130 24 146.50 1.47 297 107 110 3 479.43 4.66 298 107 111 4 473.23 1.56 299 107 118 11 243.39 3.22 300 107 123 16 164.82 7.27 301 107 126 19 146.90 1.59 302 107 127 20 146.84 1.61 303 107 130 23 146.56 1.50 304 108 111 3 473.01 1.68 305 108 112 4 472.13 2.11 306 109 112 3 480.66 1.28 307 109 113 4 472.12 2.11 308 110 113 3 479.19 2.02 309 110 114 4 469.20 0.67 310 110 118 8 250.89 0.53 311 110 126 16 173.93 11.92 312 111 115 4 421.34 4.34 313 111 118 7 243.39 3.22 314 112 115 3 486.12 1.31 315 114 117 3 479.36 2.06 316 114 118 4 439.26 5.00 317 116 119 3 524.88 3.99 318 117 122 5 458.15 2.64 319 118 122 4 458.84 2.29 320 118 123 5 458.03 2.70 321 118 126 8 440.23 1.01 322 119 122 3 472.92 0.90 323 119 123 4 469.09 2.81 324 120 123 3 473.47 1.52 325 120 124 4 469.68 2.52 326 121 124 3 484.21 0.87 327 121 125 4 475.30 5.33 328 122 125 3 482.62 0.29 329 122 126 4 470.45 2.91 330 123 126 3 470.57 2.96 331 123 127 4 469.06 2.21 332 124 127 3 469.05 2.22 333 124 128 4 469.06 2.22 334 125 128 3 469.04 2.23 335 125 129 4 469.04 2.23 336 126 129 3 468.97 2.27 337 126 130 4 466.95 1.26 338 127 130 3 468.81 2.34 339 127 131 4 466.96 1.41 340 128 131 3 476.84 3.53 341 128 132 4 466.95 1.41 342 129 132 3 466.95 1.42 343 129 133 4 466.94 1.41 344 130 133 3 466.95 1.42 345 130 134 4 466.94 1.41 346 131 134 3 468.12 2.01 347 131 135 4 466.91 1.42 348 132 135 3 479.93 3.60 349 132 136 4 468.11 2.02 350 133 136 3 479.79 3.50 351 133 137 4 467.91 2.13 352 134 137 3 488.70 0.78 353 134 138 4 467.91 2.13 354 135 138 3 481.93 3.19 355 135 139 4 468.47 1.85 356 136 139 3 478.51 1.49 357 137 141 4 494.34 1.92 358 138 141 3 487.00 1.75