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 0.10 2 3 6 3 501.84 0.48 3 3 7 4 494.31 0.79 4 3 91 88 24.87 0.46 5 3 94 91 24.79 0.45 6 3 95 92 22.88 0.07 7 3 141 138 17.30 0.01 8 3 144 141 17.18 0.05 9 3 145 142 17.17 0.05 10 4 7 3 501.85 0.48 11 4 8 4 501.72 2.92 12 4 91 87 26.25 0.51 13 4 95 91 24.95 0.45 14 5 8 3 506.47 0.54 15 5 9 4 504.20 1.67 16 6 9 3 511.65 1.23 17 6 141 135 22.21 0.68 18 6 144 138 23.03 0.26 19 7 10 3 517.13 1.51 20 7 90 83 32.93 0.18 21 7 91 84 32.79 0.11 22 7 141 134 25.59 0.83 23 9 137 128 37.15 0.48 24 10 14 4 462.72 0.49 25 10 15 5 460.99 0.35 26 10 18 8 458.09 1.82 27 10 84 74 53.95 0.26 28 10 90 80 48.41 1.27 29 10 137 127 37.38 0.57 30 10 138 128 37.38 0.59 31 10 141 131 37.27 0.53 32 11 14 3 497.50 1.09 33 11 15 4 494.09 2.98 34 12 15 3 502.19 1.07 35 12 16 4 502.19 1.07 36 13 16 3 502.20 1.06 37 13 17 4 502.19 1.07 38 14 17 3 511.17 3.41 39 14 18 4 502.19 1.06 40 14 134 120 71.48 0.81 41 14 137 123 70.11 0.12 42 15 18 3 506.85 1.25 43 15 19 4 498.01 3.16 44 15 84 69 75.72 1.19 45 16 19 3 506.85 1.25 46 16 20 4 498.00 3.15 47 17 20 3 502.13 1.07 48 17 21 4 497.78 3.25 49 17 130 113 92.33 1.02 50 17 131 114 92.27 1.00 51 17 134 117 92.08 1.10 52 18 21 3 513.23 0.53 53 18 22 4 492.19 2.91 54 18 81 63 95.92 0.80 55 18 84 66 96.00 0.79 56 18 134 116 92.27 1.01 57 18 135 117 92.03 1.08 58 18 138 120 92.03 1.08 59 19 22 3 503.87 2.65 60 19 23 4 492.19 2.91 61 19 81 62 96.03 0.77 62 19 84 65 96.01 0.79 63 19 85 66 102.56 0.21 64 20 23 3 502.84 1.57 65 20 127 107 107.98 1.16 66 20 131 111 105.56 0.15 67 21 24 3 508.07 2.76 68 21 25 4 479.79 3.94 69 21 122 101 106.45 0.51 70 21 127 106 107.89 1.21 71 21 131 110 105.58 0.15 72 21 135 114 105.55 0.16 73 22 25 3 506.63 3.48 74 22 26 4 469.33 0.29 75 22 29 7 456.09 2.46 76 22 74 52 192.34 0.23 77 22 77 55 105.55 0.17 78 22 78 56 105.57 0.16 79 22 81 59 105.53 0.18 80 22 135 113 105.84 0.28 81 23 27 4 478.32 4.20 82 24 27 3 508.95 1.63 83 24 125 101 117.88 1.86 84 24 127 103 109.95 2.09 85 25 28 3 526.43 0.19 86 25 32 7 312.04 7.94 87 25 74 49 194.88 0.40 88 25 121 96 109.99 2.08 89 25 122 97 109.98 2.08 90 25 125 100 118.97 2.21 91 26 29 3 513.64 0.72 92 28 31 3 505.96 2.09 93 28 32 4 487.83 2.88 94 29 33 4 487.82 2.88 95 29 74 45 204.49 2.46 96 29 75 46 204.47 2.46 97 29 78 49 204.47 2.46 98 30 33 3 498.49 0.59 99 30 34 4 493.92 0.17 100 30 61 31 217.80 4.17 101 30 67 37 216.15 4.33 102 30 71 41 211.65 5.94 103 31 34 3 509.32 0.49 104 31 35 4 494.02 0.23 105 31 61 30 217.80 4.17 106 32 35 3 494.03 0.23 107 32 36 4 493.92 0.19 108 32 74 42 215.75 4.14 109 32 121 89 159.61 2.32 110 32 125 93 168.73 0.98 111 33 36 3 495.00 0.73 112 33 37 4 495.00 0.73 113 33 70 37 216.28 3.88 114 33 74 41 215.72 4.16 115 34 37 3 497.68 2.06 116 34 38 4 494.99 0.73 117 34 60 26 217.81 4.17 118 34 61 27 217.81 4.17 119 34 67 33 216.82 4.09 120 34 70 36 216.73 4.12 121 35 38 3 504.84 1.71 122 35 39 4 499.44 1.42 123 35 121 86 171.49 1.13 124 36 39 3 503.19 0.45 125 36 40 4 499.44 1.42 126 36 73 37 216.84 4.13 127 36 74 38 216.80 4.12 128 36 114 78 171.88 1.14 129 36 117 81 171.77 1.17 130 36 118 82 171.76 1.17 131 36 121 85 171.50 1.12 132 37 40 3 507.86 1.27 133 37 41 4 499.44 1.42 134 37 51 14 237.87 1.77 135 37 66 29 217.71 4.18 136 37 69 32 217.24 3.98 137 37 70 33 216.91 4.11 138 37 73 36 216.90 4.11 139 38 41 3 499.45 1.42 140 38 42 4 493.76 4.26 141 38 60 22 217.91 4.14 142 39 42 3 488.69 1.72 143 39 43 4 488.69 1.72 144 39 117 78 171.78 1.16 145 39 120 81 171.74 1.18 146 40 43 3 513.01 5.56 147 40 44 4 471.73 6.67 148 40 47 7 361.68 23.28 149 40 113 73 171.94 1.12 150 40 114 74 171.95 1.14 151 40 117 77 171.81 1.15 152 41 45 4 430.77 6.65 153 41 48 7 281.13 7.82 154 41 51 10 266.56 0.52 155 41 57 16 222.97 2.73 156 41 66 25 219.49 4.45 157 43 120 77 171.94 1.13 158 44 47 3 516.50 2.43 159 44 113 69 172.17 1.10 160 45 48 3 518.74 1.30 161 46 49 3 523.08 0.86 162 46 113 67 172.97 0.95 163 47 50 3 515.82 0.16 164 47 51 4 510.17 2.98 165 47 110 63 173.41 0.78 166 47 113 66 172.43 1.20 167 48 51 3 510.17 2.98 168 48 52 4 500.00 2.09 169 48 57 9 238.19 2.22 170 49 52 3 516.34 0.10 171 50 104 54 174.33 1.02 172 50 105 55 174.34 1.03 173 50 106 56 174.31 1.03 174 50 110 60 173.88 0.90 175 51 54 3 503.25 0.42 176 51 69 18 225.85 3.79 177 52 55 3 519.22 1.90 178 53 65 12 249.79 2.69 179 54 57 3 532.64 0.49 180 54 63 9 273.35 8.20 181 54 65 11 242.22 6.46 182 54 66 12 242.21 6.46 183 54 69 15 231.51 1.12 184 56 59 3 522.75 1.85 185 56 63 7 289.28 0.27 186 57 60 3 511.77 0.27 187 57 63 6 290.76 0.47 188 57 66 9 273.12 8.31 189 59 62 3 503.77 2.21 190 59 63 4 429.84 12.34 191 60 63 3 510.19 0.70 192 60 66 6 321.61 0.21 193 61 67 6 317.60 2.25 194 63 66 3 502.50 0.19 195 63 67 4 496.55 0.14 196 64 67 3 497.44 0.30 197 64 68 4 491.76 2.25 198 65 68 3 503.14 2.41 199 65 69 4 491.77 2.25 200 66 69 3 497.00 0.21 201 66 70 4 492.34 2.54 202 67 70 3 507.23 0.42 203 67 71 4 499.38 4.29 204 68 71 3 516.39 4.19 205 68 72 4 505.58 1.22 206 69 72 3 505.99 1.02 207 69 73 4 505.55 1.20 208 70 73 3 516.37 4.20 209 70 74 4 505.56 1.19 210 71 74 3 506.90 0.54 211 71 75 4 505.56 1.19 212 72 75 3 509.17 0.84 213 72 76 4 505.56 1.19 214 73 76 3 505.19 1.01 215 73 77 4 505.48 0.86 216 74 77 3 500.69 1.54 217 74 78 4 499.65 2.06 218 75 78 3 503.35 0.21 219 75 79 4 499.66 2.06 220 76 79 3 504.19 0.21 221 76 80 4 502.22 0.78 222 76 97 21 175.91 1.65 223 77 80 3 511.55 3.89 224 77 81 4 502.22 0.78 225 77 135 58 171.27 1.09 226 78 81 3 502.56 0.60 227 78 82 4 502.17 0.76 228 79 82 3 507.65 3.15 229 79 83 4 501.46 1.10 230 79 93 14 235.54 5.70 231 80 83 3 505.02 2.89 232 80 84 4 501.45 1.09 233 80 90 10 243.72 4.63 234 80 93 13 238.53 7.20 235 80 94 14 235.55 5.70 236 80 97 17 235.55 5.70 237 80 138 58 171.16 1.14 238 80 142 62 170.68 1.30 239 81 84 3 513.62 4.96 240 81 135 54 171.62 1.17 241 81 138 57 171.28 1.08 242 83 86 3 501.66 1.43 243 83 89 6 299.03 4.37 244 83 90 7 268.96 0.36 245 83 93 10 269.02 0.34 246 84 90 6 317.04 3.73 247 86 89 3 502.10 0.80 248 86 90 4 496.20 3.68 249 87 90 3 496.20 3.68 250 87 91 4 496.25 3.71 251 88 91 3 502.20 0.85 252 88 92 4 496.25 3.71 253 89 92 3 505.51 0.92 254 89 93 4 496.25 3.71 255 90 93 3 505.51 0.92 256 90 94 4 494.07 4.79 257 90 138 48 171.19 1.14 258 91 94 3 501.12 1.27 259 91 95 4 498.80 2.43 260 92 95 3 503.06 0.30 261 92 96 4 498.81 2.42 262 93 96 3 503.88 0.12 263 93 97 4 501.31 1.16 264 94 97 3 507.58 2.14 265 94 98 4 501.13 1.08 266 94 141 47 170.43 1.41 267 94 142 48 169.03 2.04 268 94 145 51 162.05 0.72 269 95 98 3 505.97 3.47 270 95 99 4 501.14 1.08 271 96 99 3 509.00 2.24 272 97 101 4 498.47 2.22 273 97 111 14 259.34 0.43 274 97 142 45 168.31 1.71 275 98 101 3 509.04 0.56 276 98 102 4 489.26 0.30 277 98 145 47 162.04 0.72 278 98 146 48 162.03 0.72 279 99 102 3 505.56 1.18 280 99 103 4 489.26 0.30 281 100 103 3 506.03 0.95 282 100 104 4 498.29 4.82 283 101 104 3 499.61 2.26 284 101 105 4 491.76 1.66 285 101 106 5 434.63 4.00 286 101 111 10 294.45 2.02 287 101 146 45 161.68 0.86 288 102 105 3 490.42 3.93 289 102 145 43 162.08 0.72 290 102 146 44 161.34 1.02 291 106 110 4 473.11 2.26 292 106 111 5 472.87 2.31 293 106 146 40 159.72 1.74 294 107 110 3 496.70 4.99 295 107 111 4 496.75 0.57 296 107 146 39 159.82 1.53 297 108 111 3 502.29 2.20 298 108 112 4 496.76 0.56 299 108 143 35 162.27 0.62 300 108 146 38 157.58 0.67 301 109 112 3 505.38 0.66 302 109 113 4 505.38 0.66 303 110 113 3 508.68 1.58 304 111 114 3 517.67 0.24 305 111 139 28 170.68 1.24 306 111 142 31 167.99 1.34 307 111 143 32 162.37 0.67 308 111 146 35 157.58 0.67 309 112 115 3 508.99 0.32 310 112 139 27 170.38 1.09 311 112 143 31 162.37 0.67 312 113 116 3 527.77 0.04 313 113 117 4 509.19 0.97 314 114 117 3 506.48 0.40 315 114 118 4 506.18 0.41 316 114 139 25 170.38 1.09 317 115 118 3 506.30 0.48 318 115 119 4 506.10 0.45 319 115 136 21 171.03 1.13 320 115 139 24 170.68 1.24 321 116 119 3 515.12 4.04 322 116 120 4 506.10 0.45 323 117 120 3 504.28 1.35 324 117 121 4 499.07 3.95 325 118 121 3 506.26 2.34 326 118 122 4 492.49 0.66 327 118 135 17 171.08 1.14 328 118 139 21 170.69 1.25 329 119 122 3 507.91 7.05 330 119 123 4 497.33 1.76 331 119 129 10 237.01 1.04 332 119 132 13 171.19 1.12 333 120 123 3 498.53 1.16 334 120 124 4 497.38 1.77 335 121 124 3 501.40 2.62 336 121 125 4 497.39 1.77 337 122 125 3 503.38 0.63 338 122 126 4 497.38 1.77 339 122 127 5 410.09 8.73 340 122 131 9 271.33 0.17 341 122 132 10 243.12 2.00 342 122 135 13 236.12 1.49 343 123 126 3 497.38 1.77 344 123 127 4 496.02 2.44 345 127 131 4 474.48 4.29 346 128 131 3 506.86 0.52 347 128 132 4 487.40 2.17 348 129 132 3 491.02 0.35 349 129 133 4 498.78 3.54 350 130 133 3 515.75 4.84 351 130 134 4 498.78 3.54 352 131 134 3 501.87 2.00 353 131 135 4 498.11 3.89 354 132 135 3 512.69 5.10 355 132 136 4 499.17 3.37 356 133 136 3 512.71 5.09 357 133 137 4 496.88 2.22 358 134 137 3 517.68 5.08 359 134 138 4 498.11 1.61 360 135 138 3 510.66 8.59 361 135 139 4 496.62 2.36 362 136 139 3 496.62 2.36 363 136 140 4 496.68 3.27 364 137 140 3 499.96 1.65 365 137 141 4 501.98 0.64 366 138 141 3 513.81 4.15 367 138 142 4 504.65 0.70 368 139 142 3 511.60 4.17 369 139 143 4 502.00 0.61 370 140 143 3 502.00 0.61 371 140 144 4 501.76 0.49 372 141 144 3 506.81 0.49 373 141 145 4 502.00 0.38 374 142 145 3 507.18 0.19 375 142 146 4 502.00 0.38 376 143 146 3 507.18 0.18