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 2 144 142 17.02 0.13 2 3 6 3 503.73 3.92 3 3 7 4 495.54 3.64 4 3 91 88 21.77 0.44 5 3 94 91 21.75 0.43 6 3 95 92 21.74 0.42 7 3 141 138 17.96 0.28 8 3 144 141 17.23 0.08 9 3 145 142 17.23 0.08 10 4 7 3 500.77 1.02 11 4 8 4 489.17 0.84 12 4 91 87 23.39 1.23 13 5 8 3 501.20 0.17 14 5 9 4 494.55 1.55 15 6 9 3 512.61 0.75 16 6 140 134 22.12 0.58 17 6 141 135 22.11 0.58 18 6 144 138 22.12 0.59 19 7 10 3 511.65 1.23 20 7 91 84 31.53 0.74 21 7 141 134 24.87 0.47 22 9 137 128 37.84 0.42 23 10 14 4 486.50 4.42 24 10 15 5 459.60 1.07 25 10 18 8 445.01 3.29 26 10 84 74 52.55 0.43 27 10 90 80 49.73 0.60 28 10 137 127 37.86 0.42 29 10 138 128 37.89 0.41 30 10 141 131 37.91 0.45 31 11 14 3 498.06 0.81 32 11 15 4 499.82 2.24 33 12 15 3 499.82 2.24 34 12 16 4 499.82 2.25 35 13 16 3 507.31 1.49 36 13 17 4 502.18 1.07 37 14 17 3 511.17 3.42 38 14 18 4 502.18 1.06 39 14 134 120 69.53 0.17 40 14 137 123 69.53 0.17 41 15 18 3 502.17 1.06 42 15 19 4 499.97 2.16 43 15 84 69 74.90 0.60 44 16 19 3 503.02 1.49 45 16 20 4 491.50 2.08 46 17 20 3 500.66 1.81 47 17 21 4 496.18 0.26 48 17 130 113 91.51 0.62 49 17 131 114 91.27 0.70 50 17 134 117 91.25 0.69 51 18 21 3 513.23 0.53 52 18 22 4 496.20 0.26 53 18 81 63 91.45 0.63 54 18 84 66 91.50 0.61 55 18 134 116 91.28 0.69 56 18 135 117 91.26 0.70 57 18 138 120 91.26 0.70 58 19 22 3 501.33 1.67 59 19 23 4 496.21 0.27 60 19 81 62 91.50 0.61 61 19 84 65 91.64 0.68 62 19 85 66 101.02 0.56 63 20 23 3 504.60 0.69 64 21 24 3 506.64 3.48 65 21 25 4 491.51 2.60 66 21 122 101 104.19 0.84 67 21 127 106 104.14 0.82 68 21 131 110 103.95 0.86 69 21 135 114 102.22 0.30 70 22 25 3 487.92 4.42 71 22 26 4 468.02 4.91 72 22 29 7 432.94 13.99 73 22 74 52 196.31 1.76 74 22 77 55 103.91 0.84 75 22 78 56 102.75 0.26 76 22 81 59 102.57 0.17 77 22 135 113 103.98 0.86 78 23 27 4 486.69 0.92 79 24 27 3 512.15 0.03 80 24 125 101 118.75 2.31 81 24 127 103 109.78 2.15 82 25 28 3 523.19 1.81 83 25 32 7 344.60 4.34 84 25 74 49 198.97 0.40 85 25 121 96 109.81 2.12 86 25 122 97 109.81 2.12 87 25 125 100 120.47 1.46 88 25 135 110 109.72 2.13 89 26 29 3 518.04 2.66 90 28 31 3 505.96 2.09 91 28 32 4 489.88 0.94 92 29 32 3 505.56 1.88 93 29 33 4 488.47 0.23 94 29 74 45 209.05 3.34 95 29 75 46 209.41 3.52 96 29 78 49 209.05 3.34 97 30 33 3 498.51 0.61 98 30 34 4 495.01 0.38 99 30 61 31 220.74 3.25 100 30 67 37 219.66 3.18 101 30 71 41 214.56 5.25 102 31 34 3 509.32 0.49 103 31 35 4 495.13 0.32 104 31 61 30 220.74 3.25 105 32 35 3 495.14 0.32 106 32 36 4 495.14 0.33 107 32 74 42 217.50 4.25 108 32 121 89 156.34 3.64 109 33 36 3 504.65 4.43 110 33 37 4 495.03 0.39 111 33 70 37 219.33 3.56 112 33 74 41 218.51 3.75 113 34 37 3 498.81 1.51 114 34 38 4 491.94 1.93 115 34 60 26 220.77 3.25 116 34 61 27 220.77 3.25 117 34 67 33 220.04 3.33 118 34 70 36 219.94 3.35 119 35 38 3 509.43 0.48 120 35 39 4 492.45 1.68 121 35 121 86 171.28 1.24 122 36 39 3 499.47 1.41 123 36 40 4 499.44 1.42 124 36 73 37 220.15 3.35 125 36 74 38 220.10 3.35 126 36 77 41 220.08 3.35 127 36 117 81 171.81 1.14 128 36 118 82 171.81 1.14 129 36 121 85 171.45 1.22 130 37 40 3 503.80 0.76 131 37 41 4 499.44 1.42 132 37 51 14 259.48 0.33 133 37 66 29 220.72 3.29 134 37 69 32 220.54 3.22 135 37 70 33 220.25 3.37 136 37 73 36 220.20 3.35 137 38 41 3 499.37 1.46 138 38 42 4 499.12 1.57 139 38 60 22 221.24 3.06 140 38 66 28 220.77 3.27 141 39 42 3 497.88 0.80 142 39 43 4 491.81 2.08 143 39 117 78 171.82 1.14 144 39 120 81 171.83 1.14 145 40 43 3 513.01 5.56 146 40 44 4 486.42 0.61 147 40 47 7 399.38 17.27 148 40 51 11 314.29 8.76 149 40 113 73 172.01 1.08 150 40 114 74 171.94 1.12 151 40 117 77 171.85 1.14 152 41 44 3 496.82 2.08 153 41 45 4 473.89 6.79 154 41 48 7 295.37 9.82 155 41 51 10 280.98 7.89 156 41 57 16 226.06 4.04 157 41 66 25 222.16 3.14 158 42 45 3 520.59 0.96 159 43 120 77 171.94 1.10 160 44 47 3 510.20 0.72 161 44 113 69 172.31 0.96 162 45 48 3 516.42 2.46 163 46 113 67 172.79 0.89 164 47 50 3 510.31 2.91 165 47 51 4 510.13 3.00 166 47 110 63 172.87 0.93 167 47 113 66 172.60 0.89 168 48 51 3 522.45 3.16 169 48 57 9 239.22 1.93 170 49 52 3 516.34 0.10 171 50 106 56 172.91 0.93 172 50 110 60 172.92 0.93 173 51 54 3 512.49 1.47 174 51 69 18 230.13 2.04 175 52 55 3 513.54 4.74 176 53 65 12 247.92 1.75 177 54 57 3 538.88 1.90 178 54 63 9 272.54 6.08 179 54 65 11 232.84 1.23 180 54 66 12 232.84 1.23 181 54 69 15 232.83 1.23 182 56 59 3 520.49 2.98 183 56 63 7 289.26 0.26 184 57 60 3 511.53 0.39 185 57 63 6 311.98 4.55 186 57 66 9 273.07 5.78 187 59 62 3 508.84 0.33 188 59 63 4 442.99 16.51 189 60 63 3 508.19 1.70 190 60 66 6 325.97 2.41 191 61 67 6 314.20 4.88 192 63 66 3 503.97 0.14 193 63 67 4 496.59 0.12 194 64 67 3 503.59 0.34 195 64 68 4 497.13 0.15 196 65 68 3 499.75 1.57 197 65 69 4 493.72 1.87 198 66 69 3 503.44 0.27 199 66 70 4 493.72 1.87 200 67 70 3 507.23 0.42 201 67 71 4 505.99 1.02 202 68 71 3 518.39 3.19 203 68 72 4 506.01 1.02 204 69 72 3 506.01 1.02 205 69 73 4 505.60 1.23 206 70 73 3 516.42 4.17 207 70 74 4 505.59 1.23 208 71 74 3 506.95 0.56 209 71 75 4 505.62 1.22 210 72 75 3 505.63 1.22 211 72 76 4 505.57 1.18 212 73 76 3 505.61 1.19 213 73 77 4 505.61 1.19 214 74 77 3 499.76 1.74 215 74 78 4 503.50 0.13 216 75 78 3 499.65 2.06 217 75 79 4 497.06 3.36 218 76 79 3 504.19 0.21 219 76 80 4 502.22 0.78 220 76 97 21 175.14 0.33 221 77 80 3 511.55 3.89 222 77 81 4 502.21 0.78 223 77 135 58 171.06 1.15 224 78 81 3 502.22 0.78 225 78 82 4 502.15 0.74 226 79 82 3 505.02 2.89 227 79 83 4 501.44 1.09 228 79 93 14 197.94 11.39 229 79 97 18 176.46 0.72 230 80 83 3 515.13 2.67 231 80 84 4 501.43 1.09 232 80 90 10 231.12 5.16 233 80 93 13 198.00 11.40 234 80 94 14 197.96 11.40 235 80 97 17 197.96 11.40 236 80 138 58 170.78 1.18 237 80 142 62 169.96 1.28 238 81 84 3 505.03 2.89 239 81 135 54 171.12 1.18 240 81 138 57 171.03 1.15 241 83 86 3 500.90 1.04 242 83 89 6 305.39 9.23 243 83 90 7 268.96 0.37 244 83 93 10 268.98 0.38 245 84 90 6 365.18 20.66 246 86 89 3 502.56 1.02 247 86 90 4 496.11 3.68 248 87 90 3 498.84 2.32 249 87 91 4 496.13 3.69 250 88 91 3 508.73 2.60 251 88 92 4 499.17 2.21 252 89 92 3 509.23 2.35 253 89 93 4 499.18 2.21 254 90 93 3 513.83 4.65 255 90 94 4 498.78 2.42 256 90 138 48 171.10 1.17 257 91 94 3 501.92 0.85 258 91 95 4 496.16 3.75 259 92 95 3 503.07 0.31 260 92 96 4 498.62 2.53 261 93 96 3 503.90 0.10 262 93 97 4 498.66 2.51 263 94 97 3 512.38 0.26 264 94 98 4 498.88 2.44 265 94 141 47 170.19 1.23 266 94 142 48 168.99 1.64 267 94 145 51 162.43 0.62 268 95 98 3 501.37 1.19 269 95 99 4 501.38 1.20 270 95 145 50 162.36 0.59 271 96 99 3 507.35 1.41 272 96 100 4 501.38 1.20 273 97 100 3 499.38 2.20 274 97 101 4 498.91 2.44 275 98 101 3 509.04 0.56 276 98 102 4 496.10 3.84 277 98 145 47 162.36 0.58 278 98 146 48 162.31 0.58 279 99 102 3 497.84 2.98 280 99 103 4 496.09 3.85 281 100 103 3 510.37 0.19 282 100 104 4 503.47 2.23 283 101 104 3 497.05 0.98 284 101 105 4 490.70 1.17 285 101 106 5 412.44 2.23 286 101 111 10 276.88 1.97 287 101 146 45 162.26 0.55 288 102 105 3 496.02 1.49 289 102 145 43 162.41 0.60 290 102 146 44 162.28 0.56 291 106 110 4 474.44 2.68 292 106 111 5 472.85 2.28 293 106 146 40 161.97 0.66 294 107 110 3 499.19 1.35 295 107 111 4 493.85 2.02 296 107 146 39 161.68 0.69 297 108 111 3 502.30 2.19 298 108 112 4 495.58 1.16 299 108 143 35 162.37 0.58 300 108 146 38 161.44 0.72 301 109 112 3 505.38 0.66 302 109 113 4 506.63 1.28 303 110 113 3 508.55 1.65 304 111 114 3 520.58 1.22 305 111 139 28 170.22 1.15 306 111 142 31 164.25 0.93 307 111 143 32 162.44 0.62 308 111 146 35 161.52 0.69 309 112 115 3 516.31 3.35 310 112 143 31 163.08 0.35 311 113 116 3 524.88 1.49 312 113 117 4 506.96 2.08 313 114 117 3 506.94 2.10 314 114 118 4 504.12 0.71 315 114 139 25 170.38 1.09 316 115 118 3 506.93 2.10 317 115 119 4 506.23 0.38 318 115 136 21 170.41 1.07 319 115 139 24 170.38 1.09 320 116 119 3 515.11 4.05 321 116 120 4 506.18 0.41 322 117 120 3 506.28 0.36 323 117 121 4 504.29 1.35 324 118 121 3 506.26 2.33 325 118 122 4 503.98 1.51 326 118 135 17 170.83 1.17 327 118 139 21 170.66 1.24 328 119 122 3 514.49 3.76 329 119 123 4 495.49 2.76 330 119 129 10 206.41 15.25 331 119 132 13 173.02 2.26 332 120 123 3 498.62 1.21 333 120 124 4 495.50 2.77 334 121 124 3 501.40 2.62 335 121 125 4 495.50 2.77 336 122 125 3 495.47 2.75 337 122 126 4 495.45 2.75 338 122 127 5 413.36 26.75 339 122 131 9 250.39 0.91 340 122 132 10 245.62 3.29 341 122 135 13 237.98 0.54 342 123 126 3 495.43 2.74 343 123 127 4 483.88 8.51 344 127 131 4 476.70 3.13 345 128 131 3 506.94 0.54 346 128 132 4 486.81 1.85 347 129 132 3 486.82 1.85 348 129 133 4 486.85 1.86 349 130 133 3 503.42 5.10 350 130 134 4 487.30 1.66 351 131 134 3 501.85 2.00 352 131 135 4 487.31 1.66 353 132 135 3 515.28 3.80 354 132 136 4 506.79 0.45 355 133 136 3 515.29 3.79 356 133 137 4 506.80 0.45 357 134 137 3 515.29 3.79 358 134 138 4 506.80 0.45 359 135 138 3 506.80 0.45 360 135 139 4 504.50 1.58 361 136 139 3 506.84 0.40 362 136 140 4 496.43 2.18 363 137 140 3 500.20 2.93 364 137 141 4 504.65 0.70 365 138 141 3 513.81 4.15 366 138 142 4 504.65 0.70 367 139 142 3 511.59 4.17 368 139 143 4 504.64 0.70 369 140 143 3 502.05 0.60 370 140 144 4 501.98 0.62 371 141 144 3 506.81 0.49 372 141 145 4 502.04 0.59 373 142 145 3 505.00 0.90 374 142 146 4 497.83 1.45 375 143 146 3 506.38 0.21