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 46 44 119.69 25.73 2 2 134 132 64.36 1.90 3 3 44 41 120.20 25.98 4 3 45 42 120.00 25.89 5 3 47 44 120.19 25.98 6 3 48 45 120.19 25.98 7 3 71 68 119.84 25.82 8 3 74 71 120.27 26.03 9 3 133 130 64.41 1.89 10 3 134 131 64.36 1.90 11 3 136 133 64.36 1.90 12 4 42 38 120.42 26.08 13 4 43 39 120.25 26.02 14 4 44 40 120.25 26.01 15 4 134 130 64.44 1.89 16 4 135 131 64.41 1.89 17 4 136 132 64.38 1.90 18 5 41 36 123.23 25.50 19 5 42 37 121.51 25.89 20 5 43 38 120.42 26.08 21 5 45 40 120.44 26.07 22 5 69 64 120.23 26.03 23 5 70 65 120.26 26.02 24 5 71 66 120.29 26.03 25 5 128 123 64.40 1.89 26 5 136 131 64.39 1.89 27 6 40 34 123.38 25.54 28 6 41 35 123.22 25.50 29 6 42 36 121.52 25.89 30 6 136 130 64.44 1.89 31 6 137 131 64.41 1.89 32 6 138 132 64.40 1.89 33 7 34 27 123.34 25.50 34 7 40 33 123.38 25.54 35 7 41 34 123.27 25.48 36 7 54 47 123.23 25.50 37 7 69 62 120.79 26.25 38 7 138 131 64.41 1.89 39 7 140 133 64.36 1.89 40 8 40 32 123.42 25.53 41 8 138 130 64.43 1.89 42 8 139 131 64.41 1.89 43 8 140 132 64.40 1.89 44 9 41 32 123.59 25.61 45 9 56 47 123.94 25.37 46 9 140 131 64.41 1.89 47 9 142 133 64.38 1.88 48 10 139 129 64.45 1.88 49 10 140 130 64.42 1.89 50 10 141 131 64.40 1.89 51 10 142 132 64.38 1.88 52 11 17 6 359.69 0.29 53 11 18 7 125.81 24.52 54 11 142 131 64.39 1.89 55 12 141 129 64.45 1.88 56 12 142 130 64.42 1.89 57 12 143 131 64.39 1.88 58 13 122 109 88.62 4.86 59 13 143 130 64.42 1.89 60 15 122 107 106.12 1.90 61 16 58 42 347.64 0.03 62 16 60 44 347.69 0.04 63 16 61 45 347.67 0.04 64 16 122 106 115.19 2.65 65 17 57 40 347.72 0.04 66 17 58 41 347.68 0.04 67 18 56 38 347.63 0.03 68 18 57 39 347.72 0.04 69 18 58 40 347.72 0.04 70 18 63 45 349.38 0.80 71 18 64 46 347.72 0.04 72 18 65 47 347.72 0.04 73 18 122 104 115.73 8.71 74 18 124 106 106.42 9.60 75 18 142 124 64.40 1.89 76 19 56 37 348.54 0.35 77 19 57 38 349.19 0.68 78 19 59 40 350.38 0.57 79 20 41 21 352.38 1.56 80 20 55 35 350.29 0.79 81 20 56 36 350.49 0.62 82 21 55 34 350.60 0.65 83 21 56 35 350.59 0.64 84 21 57 36 350.60 0.64 85 22 54 32 350.62 0.66 86 22 55 33 350.61 0.66 87 22 89 67 256.31 1.30 88 22 90 68 256.16 1.32 89 22 91 69 256.27 1.28 90 23 34 11 354.00 0.81 91 23 36 13 354.15 0.79 92 23 41 18 354.01 0.83 93 23 53 30 350.73 0.65 94 23 54 31 350.65 0.66 95 24 34 10 354.31 0.68 96 24 52 28 352.56 0.21 97 24 53 29 350.96 0.75 98 24 90 66 256.32 1.29 99 24 91 67 256.32 1.29 100 24 94 70 256.15 1.31 101 25 32 7 355.11 1.00 102 25 33 8 355.04 1.02 103 25 34 9 355.03 1.02 104 25 43 18 354.33 0.67 105 25 51 26 353.29 0.29 106 25 52 27 352.69 0.15 107 25 94 69 256.26 1.31 108 26 31 5 380.31 9.04 109 26 50 24 353.95 0.48 110 26 51 25 353.39 0.24 111 26 94 68 256.30 1.29 112 26 95 69 256.21 1.31 113 26 98 72 255.59 1.24 114 27 31 4 364.27 1.02 115 28 31 3 469.86 0.56 116 28 49 21 354.63 0.20 117 28 50 22 354.28 0.38 118 28 98 70 256.19 1.30 119 29 48 19 354.89 0.09 120 29 49 20 354.88 0.10 121 29 50 21 354.62 0.21 122 31 50 19 354.99 0.01 123 32 44 12 355.63 0.17 124 32 45 13 355.44 0.14 125 33 42 9 357.66 0.40 126 33 43 10 357.12 0.63 127 33 44 11 355.69 0.18 128 34 41 7 358.99 0.23 129 34 42 8 357.64 0.40 130 34 43 9 357.49 0.46 131 34 52 18 354.50 0.29 132 34 53 19 354.49 0.29 133 34 54 20 354.42 0.30 134 34 69 35 350.69 0.47 135 35 41 6 359.01 0.24 136 35 42 7 358.95 0.26 137 36 40 4 401.68 2.29 138 36 41 5 359.06 0.21 139 37 40 3 464.30 1.41 140 37 42 5 390.05 8.09 141 41 54 13 354.37 0.35 142 41 56 15 354.37 0.35 143 43 51 8 355.08 0.07 144 43 52 9 354.43 0.33 145 43 69 26 350.67 0.48 146 45 50 5 375.91 0.15 147 45 51 6 365.57 5.02 148 45 70 25 350.69 0.48 149 45 71 26 350.67 0.48 150 48 71 23 350.62 0.48 151 48 72 24 350.62 0.48 152 48 73 25 350.49 0.53 153 48 74 26 347.94 0.18 154 49 71 22 350.61 0.48 155 50 70 20 350.61 0.48 156 50 71 21 350.58 0.48 157 50 98 48 255.76 1.28 158 51 68 17 350.80 0.42 159 51 69 18 350.61 0.48 160 51 70 19 350.48 0.42 161 51 77 26 258.18 1.55 162 51 94 43 256.23 1.31 163 51 98 47 255.54 1.23 164 52 68 16 350.78 0.41 165 52 69 17 350.75 0.40 166 52 94 42 256.19 1.30 167 53 66 13 350.82 0.40 168 53 67 14 350.79 0.41 169 53 68 15 350.68 0.35 170 53 90 37 256.30 1.29 171 53 94 41 255.69 1.28 172 54 66 12 350.81 0.40 173 54 67 13 350.77 0.40 174 54 69 15 350.73 0.38 175 55 65 10 350.83 0.39 176 55 66 11 350.75 0.36 177 55 84 29 256.52 1.29 178 55 89 34 256.25 1.29 179 55 90 35 256.12 1.30 180 56 64 8 350.87 0.37 181 56 65 9 350.84 0.39 182 56 140 84 64.45 1.89 183 57 63 6 379.83 3.41 184 57 64 7 350.88 0.36 185 58 61 3 482.94 2.98 186 58 62 4 439.67 0.76 187 58 63 5 379.87 3.40 188 59 62 3 453.11 1.62 189 61 120 59 129.93 9.67 190 62 120 58 129.91 9.66 191 63 118 55 130.09 9.67 192 63 120 57 129.90 9.67 193 63 122 59 123.70 12.69 194 64 82 18 256.49 1.29 195 64 84 20 256.35 1.29 196 65 80 15 256.63 1.29 197 65 81 16 256.58 1.28 198 65 82 17 256.50 1.30 199 65 84 19 256.44 1.28 200 65 124 59 111.00 15.64 201 65 140 75 64.47 1.89 202 65 142 77 64.39 1.89 203 66 80 14 256.62 1.28 204 66 81 15 256.60 1.28 205 66 84 18 256.54 1.30 206 66 90 24 256.12 1.31 207 66 93 27 256.12 1.30 208 67 79 12 256.78 1.33 209 67 80 13 256.66 1.29 210 67 126 59 105.18 18.07 211 67 140 73 64.41 1.89 212 68 77 9 307.51 26.24 213 68 78 10 257.57 1.57 214 68 79 11 256.83 1.31 215 68 94 26 255.94 1.24 216 68 97 29 255.39 1.28 217 69 77 8 307.51 26.24 218 69 78 9 257.64 1.54 219 69 126 57 105.20 18.07 220 69 128 59 101.70 19.70 221 69 138 69 64.45 1.89 222 70 76 6 369.30 2.93 223 70 77 7 307.53 26.24 224 71 74 3 481.94 0.09 225 71 75 4 400.35 3.29 226 71 76 5 374.25 0.46 227 71 77 6 369.30 2.93 228 71 136 65 74.53 6.92 229 72 75 3 461.03 1.18 230 72 77 5 396.96 5.22 231 72 107 35 193.43 0.70 232 72 108 36 193.22 0.60 233 72 110 38 192.80 0.61 234 73 110 37 193.17 0.58 235 75 110 35 192.33 0.68 236 76 110 34 190.36 0.88 237 76 112 36 148.35 15.86 238 76 128 52 101.91 19.64 239 76 131 55 86.52 12.91 240 76 136 60 74.11 6.71 241 77 97 20 255.65 1.21 242 77 98 21 255.65 1.21 243 77 107 30 193.06 0.59 244 77 110 33 146.35 14.41 245 77 111 34 143.21 12.87 246 77 128 51 102.04 19.61 247 78 111 33 143.07 12.79 248 78 113 35 135.32 9.06 249 78 114 36 131.46 9.55 250 78 126 48 105.56 18.11 251 78 128 50 102.06 19.62 252 79 97 18 255.46 1.24 253 79 106 27 193.09 0.60 254 79 114 35 133.41 8.58 255 79 126 47 105.45 17.96 256 80 114 34 133.41 8.58 257 80 116 36 131.06 9.46 258 80 124 44 107.66 17.33 259 80 125 45 107.42 17.21 260 80 126 46 107.38 17.21 261 80 140 60 64.45 1.89 262 81 84 3 515.15 1.95 263 81 93 12 256.12 1.30 264 81 97 16 254.60 0.90 265 81 103 22 193.49 0.67 266 82 116 34 131.07 9.45 267 82 117 35 130.92 9.38 268 82 118 36 129.84 9.64 269 82 124 42 114.83 16.66 270 83 118 35 129.84 9.63 271 83 119 36 129.84 9.63 272 84 88 4 431.01 2.61 273 84 93 9 390.80 6.97 274 85 88 3 457.81 0.38 275 87 92 5 449.31 0.41 276 88 92 4 453.30 1.58 277 88 93 5 440.94 2.14 278 88 103 15 404.91 3.81 279 89 92 3 462.08 0.67 280 89 93 4 456.07 0.20 281 90 93 3 461.91 2.04 282 90 94 4 460.36 2.35 283 91 95 4 475.59 1.36 284 92 95 3 486.16 2.90 285 92 96 4 478.10 2.61 286 93 96 3 481.86 0.74 287 93 97 4 481.86 0.74 288 93 103 10 414.78 7.15 289 94 97 3 491.60 0.17 290 94 98 4 487.30 1.98 291 95 98 3 490.25 0.50 292 96 99 3 477.50 1.86 293 96 100 4 453.35 1.88 294 96 103 7 426.46 5.67 295 97 103 6 422.10 3.49 296 97 104 7 414.78 7.15 297 97 106 9 414.14 0.48 298 97 107 10 406.79 3.15 299 98 104 6 428.54 0.28 300 98 107 9 414.15 0.49 301 99 104 5 445.92 0.09 302 100 103 3 461.11 1.14 303 100 104 4 456.82 1.00 304 101 104 3 469.37 3.60 305 101 105 4 457.85 0.49 306 102 105 3 470.37 3.50 307 102 106 4 459.24 1.18 308 103 106 3 464.68 3.90 309 103 107 4 458.42 0.77 310 104 107 3 464.27 0.68 311 104 108 4 458.16 0.64 312 105 108 3 466.07 1.62 313 105 109 4 456.66 1.38 314 106 109 3 472.70 1.69 315 107 110 3 479.91 2.69 316 111 114 3 500.53 0.29 317 111 128 17 105.47 18.16 318 112 127 15 105.53 18.16 319 112 128 16 102.10 19.64 320 112 131 19 89.33 14.30 321 113 126 13 105.89 18.18 322 113 127 14 105.50 18.14 323 114 125 11 108.03 18.78 324 114 126 12 105.75 18.10 325 115 123 8 116.70 17.61 326 115 124 9 110.70 18.73 327 115 125 10 108.03 18.78 328 116 123 7 223.86 71.17 329 116 124 8 115.33 18.23 330 117 122 5 371.68 0.30 331 117 123 6 223.86 71.17 332 118 121 3 464.97 2.55 333 118 122 4 409.34 10.95 334 118 124 6 409.33 10.95 335 122 142 20 64.45 1.89 336 122 143 21 64.39 1.89 337 123 143 20 64.37 1.90 338 124 141 17 64.44 1.88 339 124 142 18 64.34 1.88 340 125 140 15 64.45 1.88 341 125 141 16 64.42 1.89 342 126 138 12 64.47 1.89 343 126 139 13 64.45 1.88 344 126 140 14 64.42 1.89 345 127 138 11 64.47 1.88 346 127 139 12 64.45 1.88 347 127 141 14 64.44 1.88 348 128 131 3 470.42 3.12 349 128 136 8 227.77 70.15 350 128 137 9 73.47 6.38 351 128 138 10 64.44 1.89 352 129 137 8 74.05 6.67 353 129 138 9 73.28 6.29 354 129 139 10 73.21 6.25 355 130 135 5 424.84 3.04 356 130 136 6 258.88 54.61 357 130 137 7 227.74 70.17 358 131 136 5 391.68 11.10 359 132 136 4 444.95 2.12 360 133 136 3 495.82 2.73