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 11 140 129 74.36 1.42 2 12 36 24 74.99 1.47 3 12 40 28 74.80 1.41 4 12 140 128 74.36 1.42 5 12 141 129 74.35 1.42 6 12 142 130 74.28 1.41 7 13 35 22 75.06 1.47 8 13 36 23 74.99 1.47 9 13 37 24 74.82 1.42 10 13 40 27 74.81 1.42 11 13 43 30 74.67 1.35 12 13 130 117 74.47 1.39 13 13 138 125 74.55 1.39 14 13 140 127 74.45 1.40 15 13 141 128 74.36 1.42 16 13 142 129 74.36 1.42 17 14 34 20 75.06 1.47 18 14 35 21 75.06 1.47 19 14 36 22 75.06 1.47 20 14 39 25 75.07 1.47 21 14 142 128 74.36 1.41 22 15 32 17 75.07 1.47 23 15 33 18 75.07 1.47 24 15 34 19 75.06 1.47 25 15 124 109 74.37 1.42 26 15 130 115 74.94 1.48 27 15 141 126 74.52 1.41 28 15 142 127 74.47 1.40 29 15 143 128 74.36 1.42 30 15 144 129 74.36 1.42 31 16 32 16 75.08 1.48 32 16 33 17 75.08 1.48 33 16 144 128 74.36 1.42 34 17 30 13 75.12 1.49 35 17 31 14 75.12 1.49 36 17 32 15 75.08 1.48 37 17 50 33 74.48 1.41 38 17 122 105 74.35 1.42 39 17 124 107 74.45 1.40 40 17 144 127 74.47 1.40 41 17 145 128 74.37 1.41 42 17 146 129 74.32 1.43 43 18 30 12 75.12 1.49 44 18 31 13 75.12 1.49 45 18 146 128 74.36 1.41 46 18 147 129 74.36 1.41 47 19 30 11 75.36 1.49 48 19 31 12 75.36 1.49 49 19 146 127 74.46 1.40 50 19 147 128 74.37 1.41 51 20 28 8 75.52 1.52 52 20 29 9 75.50 1.52 53 20 30 10 75.46 1.53 54 20 147 127 74.47 1.40 55 20 148 128 74.36 1.42 56 20 149 129 74.36 1.42 57 21 28 7 331.87 3.60 58 21 148 127 74.46 1.40 59 21 149 128 74.36 1.42 60 22 26 4 422.88 0.09 61 22 28 6 375.06 1.61 62 22 111 89 123.99 5.04 63 22 149 127 74.47 1.40 64 22 150 128 74.36 1.41 65 22 151 129 74.34 1.42 66 23 26 3 463.79 1.74 67 23 111 88 142.05 0.86 68 23 150 127 74.45 1.40 69 23 151 128 74.36 1.42 70 23 152 129 74.34 1.42 71 24 111 87 147.22 1.04 72 24 112 88 148.99 1.61 73 24 113 89 149.62 1.35 74 24 114 90 149.64 1.36 75 24 150 126 74.50 1.40 76 24 151 127 74.47 1.40 77 24 152 128 74.36 1.42 78 25 111 86 149.98 1.23 79 26 110 84 155.21 0.59 80 26 111 85 151.33 1.02 81 27 60 33 168.47 1.00 82 27 108 81 169.08 1.20 83 27 109 82 163.96 2.14 84 27 110 83 155.85 0.92 85 28 108 80 169.24 1.25 86 28 109 81 167.37 0.45 87 28 111 83 158.73 0.29 88 28 148 120 74.47 1.40 89 29 106 77 190.11 0.70 90 29 107 78 182.59 3.05 91 29 108 79 169.49 1.34 92 30 106 76 192.53 0.12 93 30 107 77 188.71 0.01 94 30 109 79 186.97 0.85 95 30 148 118 74.36 1.42 96 31 103 72 193.72 0.12 97 31 105 74 193.18 0.02 98 31 106 75 193.13 0.04 99 32 48 16 193.89 0.23 100 32 50 18 193.46 0.09 101 32 86 54 193.78 0.24 102 32 103 71 193.73 0.12 103 32 104 72 193.71 0.13 104 32 105 73 193.43 0.08 105 32 107 75 193.27 0.01 106 33 102 69 203.38 1.15 107 33 103 70 193.75 0.12 108 34 37 3 492.03 0.24 109 34 43 9 391.89 1.47 110 34 46 12 335.88 3.10 111 34 67 33 218.19 1.69 112 34 98 64 224.59 0.66 113 34 101 67 209.05 1.59 114 34 102 68 207.12 0.69 115 34 104 70 200.19 2.77 116 34 130 96 149.68 1.30 117 35 101 66 218.25 1.72 118 36 39 3 459.18 3.08 119 36 40 4 445.97 1.52 120 36 101 65 225.30 1.46 121 37 40 3 459.18 3.08 122 37 41 4 445.97 1.52 123 37 42 5 422.74 0.32 124 37 43 6 422.49 0.43 125 37 98 61 235.96 1.35 126 37 99 62 233.74 0.88 127 37 100 63 231.97 0.00 128 37 101 64 229.33 0.56 129 38 41 3 451.25 0.77 130 38 42 4 432.51 2.14 131 40 132 92 149.53 1.28 132 40 138 98 119.40 0.35 133 40 140 100 119.25 0.35 134 41 132 91 149.52 1.30 135 41 133 92 149.47 1.30 136 42 97 55 296.91 0.53 137 42 98 56 295.44 0.49 138 42 99 57 288.63 0.45 139 42 132 90 149.46 1.31 140 42 133 91 147.87 1.22 141 42 138 96 119.69 0.31 142 43 46 3 523.35 2.56 143 43 88 45 297.70 0.72 144 43 97 54 297.36 0.75 145 43 98 55 296.55 0.38 146 43 131 88 149.58 1.33 147 43 132 89 149.00 1.09 148 43 138 95 119.38 0.34 149 44 88 44 297.86 0.69 150 44 89 45 297.80 0.69 151 44 90 46 297.80 0.69 152 44 97 53 297.50 0.68 153 44 131 87 149.62 1.31 154 44 132 88 149.46 1.29 155 44 133 89 146.75 1.50 156 44 135 91 130.57 1.41 157 45 88 43 297.86 0.69 158 45 89 44 297.81 0.70 159 45 130 85 149.66 1.31 160 45 131 86 149.47 1.29 161 45 135 90 128.66 0.45 162 46 87 41 298.00 0.65 163 46 88 42 297.95 0.66 164 46 104 58 297.90 0.68 165 46 129 83 149.69 1.30 166 46 130 84 149.51 1.30 167 47 86 39 298.10 0.65 168 47 87 40 298.01 0.65 169 47 128 81 149.69 1.30 170 47 129 82 149.68 1.30 171 48 85 37 298.16 0.64 172 48 86 38 298.12 0.64 173 48 104 56 298.17 0.67 174 48 124 76 152.94 1.49 175 48 130 82 149.58 1.27 176 49 83 34 298.57 0.72 177 49 84 35 298.18 0.64 178 49 85 36 298.18 0.65 179 49 124 75 152.91 1.48 180 49 125 76 152.80 1.46 181 49 127 78 150.05 1.38 182 49 128 79 149.74 1.27 183 50 83 33 299.17 0.42 184 50 84 34 298.19 0.65 185 50 86 36 298.25 0.65 186 50 107 57 298.13 0.66 187 50 122 72 153.30 1.59 188 50 123 73 152.97 1.50 189 50 124 74 152.91 1.48 190 50 125 75 152.84 1.49 191 51 82 31 300.61 1.03 192 51 122 71 153.30 1.59 193 51 123 72 153.20 1.56 194 51 125 74 152.79 1.53 195 52 57 5 425.48 4.38 196 52 59 7 407.97 0.54 197 52 82 30 300.63 1.03 198 52 83 31 300.63 1.03 199 52 84 32 300.63 1.03 200 52 109 57 298.12 0.66 201 52 121 69 153.49 1.53 202 52 122 70 153.29 1.60 203 53 56 3 460.57 1.88 204 53 57 4 442.19 1.73 205 53 120 67 153.81 1.53 206 54 57 3 447.97 1.17 207 54 81 27 315.90 6.45 208 54 82 28 310.39 3.85 209 54 112 58 297.44 0.52 210 55 112 57 297.45 0.51 211 56 111 55 297.80 0.68 212 56 112 56 297.35 0.47 213 56 114 58 297.17 0.39 214 56 118 62 198.01 0.60 215 56 120 64 153.74 1.50 216 56 150 94 74.56 1.39 217 57 109 52 298.16 0.67 218 57 110 53 298.11 0.66 219 57 111 54 297.81 0.68 220 57 112 55 297.45 0.52 221 57 120 63 153.57 1.57 222 57 122 65 153.34 1.61 223 57 148 91 74.62 1.39 224 57 150 93 74.48 1.40 225 58 109 51 298.17 0.68 226 58 110 52 298.14 0.68 227 58 112 54 298.08 0.65 228 59 62 3 544.21 1.78 229 59 79 20 325.66 3.38 230 59 84 25 325.65 3.38 231 59 107 48 298.43 0.66 232 59 108 49 298.41 0.66 233 59 109 50 298.16 0.69 234 60 108 48 298.43 0.65 235 60 109 49 298.41 0.66 236 60 110 50 298.31 0.62 237 61 107 46 298.58 0.60 238 61 108 47 298.43 0.65 239 62 75 13 326.00 3.27 240 62 77 15 325.93 3.29 241 62 84 22 325.88 3.33 242 62 86 24 325.94 3.29 243 62 106 44 298.69 0.64 244 62 107 45 298.58 0.60 245 62 108 46 298.56 0.59 246 63 75 12 326.00 3.27 247 63 105 42 298.88 0.69 248 63 106 43 298.79 0.68 249 63 108 45 298.69 0.64 250 64 68 4 429.62 0.89 251 64 71 7 398.08 9.46 252 64 75 11 329.98 1.28 253 64 104 40 298.97 0.70 254 64 105 41 298.88 0.69 255 65 68 3 473.71 1.18 256 65 103 38 298.96 0.70 257 65 104 39 298.96 0.70 258 65 105 40 298.89 0.68 259 66 103 37 299.12 0.72 260 67 98 31 319.70 1.40 261 67 100 33 300.12 0.99 262 67 101 34 299.49 0.68 263 67 102 35 299.19 0.70 264 67 103 36 299.09 0.70 265 67 104 37 299.08 0.70 266 68 71 3 475.12 1.74 267 68 75 7 389.98 2.57 268 68 88 20 329.36 3.36 269 68 98 30 320.50 1.79 270 68 104 36 299.02 0.68 271 69 74 5 430.38 0.01 272 69 96 27 324.66 3.06 273 69 97 28 325.27 2.75 274 69 99 30 324.62 3.08 275 70 73 3 470.63 1.25 276 70 74 4 438.33 3.91 277 70 96 26 325.63 2.79 278 71 74 3 444.50 1.16 279 71 75 4 430.24 0.04 280 73 91 18 329.35 3.36 281 74 88 14 329.39 3.35 282 74 89 15 329.36 3.35 283 74 90 16 329.36 3.36 284 74 91 17 329.35 3.36 285 74 96 22 329.07 3.44 286 75 86 11 330.52 3.18 287 75 87 12 330.37 3.18 288 75 88 13 329.39 3.35 289 75 104 29 298.96 0.68 290 75 105 30 298.91 0.68 291 76 86 10 330.54 3.18 292 76 87 11 330.47 3.16 293 77 85 8 330.81 3.23 294 77 86 9 330.54 3.18 295 78 84 6 353.38 4.60 296 78 85 7 330.80 3.23 297 79 83 4 415.82 9.92 298 79 84 5 353.39 4.60 299 80 83 3 453.41 1.11 300 83 125 42 152.91 1.51 301 84 107 23 298.41 0.67 302 84 109 25 298.31 0.65 303 86 104 18 298.88 0.70 304 86 105 19 298.69 0.65 305 86 107 21 298.56 0.59 306 88 96 8 422.12 1.58 307 88 98 10 375.44 6.71 308 88 104 16 298.94 0.69 309 89 135 46 129.19 0.21 310 90 93 3 450.16 1.42 311 90 94 4 451.88 0.56 312 90 95 5 436.92 0.20 313 90 96 6 410.93 1.56 314 90 97 7 394.94 1.21 315 90 135 45 141.22 0.20 316 92 95 3 464.47 2.17 317 92 96 4 451.99 2.34 318 93 97 4 466.01 4.65 319 93 135 42 147.07 0.80 320 94 97 3 481.41 1.48 321 97 133 36 147.03 1.36 322 97 135 38 144.14 0.29 323 98 104 6 383.79 8.47 324 103 106 3 523.22 5.92 325 109 122 13 153.05 1.57 326 109 148 39 74.51 1.39 327 111 148 37 74.65 1.38 328 111 150 39 74.37 1.42 329 112 150 38 74.59 1.38 330 114 118 4 444.75 2.53 331 114 150 36 74.67 1.38 332 114 152 38 74.47 1.40 333 115 152 37 74.64 1.39 334 116 152 36 74.66 1.38 335 117 149 32 74.73 1.40 336 117 150 33 74.70 1.39 337 117 151 34 74.69 1.39 338 117 152 35 74.67 1.39 339 118 149 31 74.72 1.39 340 118 150 32 74.70 1.39 341 119 147 28 74.81 1.35 342 119 148 29 74.73 1.39 343 119 149 30 74.70 1.39 344 120 147 27 74.81 1.35 345 120 148 28 74.72 1.39 346 120 150 30 74.70 1.39 347 121 146 25 74.81 1.35 348 121 147 26 74.70 1.39 349 122 145 23 74.81 1.35 350 122 146 24 74.72 1.39 351 122 147 25 74.70 1.39 352 122 148 26 74.70 1.39 353 123 145 22 74.72 1.38 354 124 143 19 74.83 1.35 355 124 144 20 74.82 1.35 356 124 145 21 74.71 1.38 357 129 137 8 351.11 1.75 358 130 137 7 351.15 1.75 359 130 138 8 351.05 1.77 360 130 141 11 349.21 1.77 361 130 143 13 213.39 65.39 362 131 135 4 379.13 9.69 363 131 136 5 378.93 9.76 364 131 137 6 352.79 0.93 365 131 138 7 351.12 1.75 366 132 135 3 439.95 2.91 367 132 136 4 416.44 3.98 368 132 138 6 352.79 0.93 369 138 141 3 502.61 2.41