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 17.28 0.23 2 3 6 3 502.13 0.38 3 3 7 4 495.63 3.62 4 3 91 88 25.16 0.60 5 3 94 91 24.10 0.27 6 3 95 92 21.77 0.46 7 3 141 138 19.16 0.69 8 3 144 141 17.29 0.23 9 3 145 142 17.11 0.13 10 4 7 3 512.09 2.27 11 4 8 4 502.12 0.38 12 4 91 87 27.41 0.52 13 4 95 91 25.20 0.59 14 5 8 3 505.13 0.38 15 5 9 4 497.16 2.10 16 6 9 3 508.41 0.89 17 6 141 135 23.46 0.58 18 6 144 138 23.46 0.58 19 7 10 3 515.41 2.62 20 7 90 83 36.02 1.15 21 7 91 84 32.13 0.36 22 7 141 134 25.14 0.61 23 9 137 128 37.43 0.48 24 10 14 4 467.98 3.79 25 10 15 5 468.00 3.77 26 10 84 74 49.97 0.71 27 10 90 80 49.93 0.70 28 10 137 127 40.13 1.82 29 10 138 128 37.45 0.48 30 10 141 131 37.45 0.49 31 11 14 3 498.90 0.61 32 11 15 4 493.95 3.05 33 12 15 3 500.20 0.07 34 12 16 4 493.94 3.06 35 13 16 3 494.35 2.86 36 13 17 4 494.49 2.78 37 14 17 3 511.38 3.31 38 14 18 4 495.81 4.49 39 14 134 120 68.31 0.44 40 14 137 123 68.03 0.30 41 15 18 3 501.66 1.57 42 15 19 4 490.32 7.24 43 15 84 69 73.41 0.14 44 16 19 3 497.57 3.62 45 16 20 4 495.54 4.63 46 17 20 3 500.30 2.26 47 17 21 4 497.96 3.41 48 17 130 113 91.08 0.33 49 17 131 114 90.61 0.12 50 17 134 117 90.45 0.13 51 18 21 3 510.78 2.15 52 18 22 4 495.53 1.49 53 18 81 63 91.00 0.30 54 18 84 66 91.06 0.29 55 18 134 116 90.79 0.21 56 18 135 117 90.52 0.10 57 18 138 120 90.45 0.13 58 19 22 3 503.84 2.67 59 19 23 4 493.16 0.30 60 19 81 62 91.06 0.29 61 19 84 65 94.75 1.56 62 19 85 66 98.94 0.47 63 20 23 3 508.66 3.06 64 21 24 3 506.89 3.60 65 21 25 4 475.14 1.62 66 21 122 101 102.02 0.49 67 21 127 106 103.64 0.29 68 21 131 110 99.16 0.48 69 21 135 114 99.14 0.48 70 22 25 3 491.95 2.44 71 22 26 4 468.34 4.91 72 22 29 7 459.95 0.71 73 22 74 52 103.80 0.28 74 22 77 55 101.86 0.42 75 22 78 56 101.50 0.62 76 22 81 59 99.21 0.48 77 22 135 113 99.22 0.49 78 23 27 4 482.22 1.56 79 24 27 3 509.19 1.51 80 24 125 101 110.09 2.21 81 24 127 103 110.08 2.21 82 25 28 3 520.49 3.42 83 25 32 7 326.03 2.31 84 25 74 49 109.98 2.21 85 25 121 96 110.07 2.21 86 25 122 97 110.03 2.23 87 25 125 100 111.86 3.10 88 26 29 3 518.03 2.91 89 26 74 48 109.98 2.21 90 28 31 3 505.81 1.76 91 28 32 4 458.69 0.04 92 29 33 4 475.36 8.29 93 29 74 45 126.28 2.83 94 29 75 46 125.91 0.57 95 29 78 49 122.74 1.06 96 30 33 3 494.00 2.84 97 30 34 4 487.02 2.48 98 30 61 31 163.49 0.86 99 30 67 37 152.31 0.66 100 30 71 41 149.92 0.29 101 31 34 3 505.28 1.52 102 31 35 4 490.18 0.91 103 31 61 30 164.00 1.12 104 32 35 3 492.94 0.48 105 32 36 4 487.62 2.19 106 32 74 42 152.39 0.63 107 32 121 89 152.61 0.56 108 32 125 93 162.54 0.84 109 33 36 3 494.81 0.45 110 33 37 4 494.80 0.45 111 33 70 37 159.69 2.57 112 33 74 41 152.38 0.63 113 34 37 3 497.92 2.19 114 34 38 4 487.38 0.82 115 34 60 26 164.12 1.09 116 34 61 27 164.09 1.08 117 34 67 33 163.38 1.02 118 34 70 36 162.75 1.19 119 35 38 3 498.92 4.67 120 35 39 4 494.01 4.13 121 35 121 86 163.10 1.01 122 36 39 3 504.25 0.98 123 36 40 4 495.19 3.54 124 36 73 37 163.82 1.16 125 36 77 41 163.22 1.01 126 36 114 78 162.89 1.04 127 36 117 81 162.94 1.07 128 36 118 82 162.95 1.02 129 36 121 85 163.16 1.03 130 37 40 3 504.05 0.89 131 37 41 4 495.19 3.54 132 37 51 14 259.75 0.04 133 37 66 29 164.00 1.15 134 37 69 32 163.90 1.15 135 37 70 33 163.83 1.15 136 37 73 36 163.84 1.16 137 38 41 3 499.62 1.33 138 38 42 4 493.99 4.15 139 38 60 22 164.23 1.06 140 38 66 28 164.09 1.12 141 39 42 3 494.60 1.09 142 39 43 4 489.01 1.70 143 39 117 78 163.02 1.04 144 39 120 81 163.24 1.02 145 40 43 3 497.53 0.88 146 40 44 4 488.93 1.69 147 40 47 7 385.89 25.64 148 40 113 73 162.99 1.04 149 40 114 74 163.02 1.04 150 40 117 77 163.14 1.03 151 41 44 3 495.57 0.10 152 41 45 4 453.00 2.87 153 41 48 7 296.58 1.54 154 41 51 10 284.33 7.66 155 41 57 16 193.30 15.55 156 41 66 25 164.47 1.16 157 43 120 77 163.56 1.14 158 44 47 3 506.54 2.46 159 44 113 69 163.09 1.04 160 45 48 3 506.53 0.96 161 46 113 67 163.47 1.13 162 47 50 3 510.56 2.79 163 47 51 4 498.77 1.68 164 47 113 66 163.36 1.08 165 48 51 3 522.70 3.28 166 48 57 9 242.99 4.51 167 49 52 3 516.59 0.23 168 50 106 56 162.78 1.21 169 50 110 60 163.19 1.01 170 51 54 3 503.49 0.54 171 51 69 18 198.00 17.88 172 52 55 3 514.28 4.37 173 53 65 12 245.26 5.50 174 54 57 3 537.42 2.63 175 54 63 9 275.31 7.48 176 54 65 11 245.09 5.58 177 54 66 12 238.81 2.46 178 54 69 15 238.81 2.46 179 56 59 3 520.82 2.82 180 56 63 7 283.64 3.33 181 57 60 3 511.78 0.26 182 57 66 9 275.32 7.48 183 59 62 3 509.09 0.20 184 59 63 4 443.36 0.97 185 60 63 3 506.87 0.85 186 60 66 6 332.08 0.41 187 61 67 6 332.08 0.41 188 63 66 3 492.66 2.69 189 63 67 4 490.05 3.11 190 64 67 3 496.81 0.27 191 64 68 4 492.80 1.74 192 65 68 3 501.05 1.82 193 65 69 4 492.78 1.75 194 66 69 3 497.38 0.02 195 66 70 4 494.35 1.52 196 67 70 3 507.48 0.29 197 67 71 4 500.56 1.57 198 68 71 3 516.64 4.32 199 68 72 4 500.51 1.61 200 69 72 3 506.24 0.89 201 69 73 4 505.84 1.04 202 70 73 3 516.60 4.33 203 70 74 4 505.85 1.03 204 71 74 3 507.13 0.40 205 71 75 4 505.85 1.03 206 72 75 3 505.85 1.03 207 72 76 4 503.73 0.02 208 73 76 3 502.30 2.45 209 73 77 4 499.87 1.91 210 74 77 3 507.90 1.82 211 74 78 4 499.90 1.94 212 75 78 3 502.00 2.98 213 75 79 4 499.90 1.94 214 76 79 3 504.56 1.70 215 76 80 4 502.47 0.65 216 77 80 3 502.47 0.65 217 77 81 4 502.47 0.65 218 77 135 58 198.74 1.33 219 78 81 3 502.44 0.64 220 78 82 4 499.30 2.17 221 79 82 3 508.88 2.54 222 79 83 4 501.68 0.96 223 79 93 14 211.24 4.94 224 80 83 3 503.73 0.04 225 80 84 4 501.66 0.96 226 80 90 10 247.14 3.00 227 80 93 13 227.13 12.88 228 80 94 14 227.12 12.88 229 80 97 17 227.12 12.88 230 80 138 58 198.77 1.35 231 80 142 62 198.72 1.32 232 81 84 3 507.00 1.40 233 81 135 54 199.00 1.38 234 81 138 57 198.88 1.34 235 83 86 3 499.92 0.56 236 83 89 6 298.25 0.46 237 83 90 7 269.19 0.23 238 83 93 10 269.19 0.23 239 84 90 6 348.15 22.89 240 86 89 3 502.24 0.86 241 86 90 4 495.45 4.30 242 87 90 3 495.47 4.30 243 87 91 4 495.45 4.30 244 88 91 3 509.16 2.38 245 88 92 4 501.34 1.37 246 89 92 3 509.16 2.38 247 89 93 4 497.90 3.10 248 90 93 3 505.72 0.82 249 90 94 4 495.51 4.28 250 90 138 48 222.84 3.90 251 91 94 3 500.90 1.60 252 91 95 4 495.65 0.85 253 92 95 3 503.29 0.42 254 92 96 4 500.87 1.63 255 93 96 3 500.88 1.63 256 93 97 4 501.36 1.87 257 94 97 3 508.48 1.69 258 94 98 4 501.35 1.88 259 94 141 47 222.83 3.90 260 94 142 48 222.62 3.79 261 94 145 51 222.39 3.90 262 95 98 3 501.35 1.88 263 95 99 4 502.05 1.53 264 95 145 50 222.38 3.91 265 96 99 3 507.63 1.27 266 96 100 4 502.09 1.51 267 97 100 3 507.62 1.27 268 97 101 4 502.11 1.49 269 97 111 14 259.47 0.49 270 97 142 45 222.85 3.91 271 98 101 3 507.62 1.27 272 98 102 4 501.47 1.16 273 98 145 47 222.56 3.84 274 98 146 48 222.41 3.92 275 99 102 3 501.47 1.16 276 99 103 4 494.57 2.29 277 100 103 3 503.79 2.32 278 100 104 4 503.79 2.32 279 101 104 3 494.44 2.35 280 101 105 4 494.44 2.35 281 101 106 5 425.56 8.79 282 101 111 10 288.95 8.00 283 101 146 45 222.83 3.92 284 102 105 3 490.15 4.07 285 102 145 43 224.80 4.63 286 102 146 44 222.81 3.92 287 106 110 4 478.49 4.96 288 106 111 5 461.70 2.81 289 106 146 40 225.87 4.29 290 107 110 3 495.34 3.46 291 107 111 4 489.38 0.48 292 107 146 39 225.87 4.29 293 108 111 3 502.54 2.33 294 108 112 4 494.11 1.89 295 108 143 35 226.33 4.48 296 108 146 38 226.22 4.45 297 109 112 3 505.75 0.72 298 109 113 4 506.35 0.42 299 110 113 3 508.66 0.52 300 111 114 3 514.87 1.89 301 111 139 28 227.37 4.36 302 111 142 31 227.11 4.48 303 111 143 32 226.86 4.42 304 111 146 35 226.81 4.42 305 112 115 3 509.93 0.10 306 112 139 27 227.43 4.37 307 112 143 31 227.03 4.51 308 113 116 3 528.02 0.17 309 113 117 4 507.53 1.81 310 114 117 3 509.46 0.85 311 114 118 4 507.17 1.99 312 114 139 25 227.81 4.49 313 115 118 3 509.31 0.92 314 115 119 4 506.35 0.57 315 115 136 21 228.13 4.64 316 115 139 24 227.93 4.54 317 116 119 3 506.35 0.57 318 116 120 4 506.35 0.57 319 117 120 3 499.34 4.08 320 117 121 4 499.33 4.08 321 118 121 3 506.30 2.58 322 118 122 4 499.31 4.08 323 118 135 17 228.37 4.54 324 118 139 21 228.37 4.54 325 119 122 3 504.17 1.67 326 119 123 4 497.57 1.65 327 119 132 13 228.36 4.54 328 120 123 3 498.79 1.04 329 120 124 4 497.60 1.66 330 121 124 3 498.80 1.07 331 121 125 4 497.60 1.66 332 122 125 3 503.63 0.50 333 122 126 4 497.59 1.66 334 122 127 5 396.82 9.48 335 122 131 9 257.67 2.25 336 122 132 10 254.47 3.79 337 122 135 13 250.89 5.56 338 123 126 3 497.63 1.64 339 123 127 4 455.20 5.68 340 127 131 4 483.46 0.75 341 128 131 3 502.84 0.89 342 128 132 4 483.50 0.77 343 129 132 3 487.05 1.01 344 129 133 4 483.97 0.53 345 130 133 3 515.29 5.32 346 130 134 4 487.73 2.40 347 131 134 3 502.10 1.87 348 131 135 4 493.17 0.32 349 132 135 3 507.72 7.58 350 132 136 4 493.17 0.32 351 133 136 3 499.42 3.25 352 133 137 4 499.19 3.35 353 134 137 3 506.96 0.53 354 134 138 4 500.64 2.63 355 135 138 3 499.94 2.98 356 135 139 4 487.37 2.36 357 136 139 3 500.23 3.40 358 136 140 4 490.74 0.30 359 137 140 3 496.72 0.94 360 137 141 4 496.32 2.19 361 138 141 3 506.01 0.01 362 138 142 4 496.94 1.88 363 139 142 3 511.57 4.17 364 139 143 4 496.13 2.32 365 140 143 3 502.25 0.73 366 140 144 4 502.25 0.73 367 141 144 3 504.78 0.53 368 141 145 4 502.48 0.62 369 142 145 3 507.43 0.32 370 142 146 4 502.25 0.73 371 143 146 3 507.43 0.31