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 7 5 403.12 6.96 2 4 7 3 463.22 2.67 3 4 10 6 403.18 6.99 4 4 36 32 257.34 8.76 5 4 106 102 79.98 2.58 6 5 103 98 80.00 2.58 7 5 106 101 80.64 2.26 8 6 9 3 460.54 1.38 9 6 10 4 454.84 0.67 10 6 106 100 97.77 3.71 11 7 10 3 472.26 2.35 12 7 11 4 455.63 1.06 13 7 44 37 262.78 11.47 14 8 11 3 466.71 0.43 15 8 12 4 455.63 1.06 16 8 48 40 262.63 11.47 17 8 53 45 262.08 11.21 18 9 12 3 466.00 0.08 19 9 13 4 451.95 0.76 20 9 71 62 174.90 0.67 21 9 75 66 172.81 0.79 22 9 106 97 132.22 1.21 23 10 13 3 456.52 0.17 24 10 14 4 451.75 0.84 25 10 34 24 267.47 10.01 26 10 102 92 133.73 0.70 27 10 105 95 133.43 0.81 28 10 106 96 131.84 1.40 29 11 14 3 452.99 0.20 30 11 15 4 452.93 0.17 31 11 30 19 267.16 10.04 32 11 34 23 267.50 10.02 33 11 36 25 267.44 10.03 34 11 40 29 267.11 9.97 35 11 41 30 265.97 10.29 36 11 44 33 264.69 10.60 37 11 45 34 264.51 10.65 38 11 48 37 264.50 10.64 39 12 15 3 452.95 0.08 40 12 16 4 452.79 0.10 41 12 48 36 264.51 10.65 42 12 53 41 264.24 10.53 43 12 71 59 175.22 0.62 44 12 72 60 174.45 0.80 45 13 16 3 458.24 2.83 46 13 17 4 458.25 2.84 47 13 75 62 174.56 0.62 48 13 76 63 173.62 0.64 49 13 79 66 173.03 0.89 50 13 98 85 134.41 0.60 51 13 102 89 133.87 0.64 52 13 105 92 133.85 0.64 53 14 17 3 461.56 1.66 54 14 18 4 452.73 0.08 55 14 30 16 267.47 10.00 56 14 33 19 267.59 9.99 57 14 34 20 267.57 9.99 58 15 18 3 460.74 2.07 59 15 19 4 458.25 2.84 60 15 25 10 267.01 9.95 61 15 30 15 267.49 10.01 62 15 54 39 264.35 10.56 63 15 62 47 263.95 10.37 64 15 64 49 263.18 10.02 65 16 19 3 466.59 1.32 66 16 20 4 457.75 3.09 67 16 64 48 263.38 10.09 68 16 72 56 181.05 3.49 69 16 73 57 177.29 0.44 70 16 76 60 175.11 0.58 71 16 133 117 52.37 0.65 72 17 20 3 449.23 1.81 73 17 21 4 449.19 1.79 74 17 76 59 175.13 0.58 75 18 21 3 457.76 3.09 76 18 22 4 452.12 0.27 77 18 23 5 392.10 19.21 78 18 25 7 280.00 6.17 79 18 29 11 277.68 5.40 80 18 33 15 277.69 5.38 81 19 22 3 444.26 4.21 82 19 25 6 307.39 1.09 83 19 64 45 263.91 10.31 84 19 69 50 239.46 1.06 85 20 80 60 191.04 3.40 86 21 33 12 279.82 6.33 87 23 29 6 401.29 4.28 88 24 29 5 445.41 0.16 89 24 61 37 270.05 7.52 90 25 61 36 270.80 7.15 91 25 62 37 266.24 9.33 92 26 29 3 454.61 0.70 93 26 30 4 450.29 1.35 94 26 59 33 271.14 7.05 95 26 60 34 271.08 7.03 96 27 30 3 453.56 0.28 97 27 31 4 446.69 0.44 98 27 41 14 272.39 7.59 99 27 45 18 272.32 7.58 100 27 56 29 271.23 7.09 101 27 60 33 271.08 7.02 102 27 62 35 270.95 6.96 103 28 31 3 455.23 0.84 104 28 32 4 446.49 0.34 105 28 60 32 271.12 7.03 106 29 32 3 463.45 0.26 107 29 33 4 449.07 1.96 108 30 33 3 461.64 1.17 109 30 34 4 435.75 2.69 110 30 41 11 272.41 7.59 111 30 45 15 272.38 7.58 112 30 62 32 270.75 7.07 113 31 34 3 462.78 1.74 114 31 35 4 407.56 1.06 115 31 36 5 373.12 13.80 116 31 37 6 358.07 21.32 117 31 41 10 276.49 5.54 118 32 35 3 435.44 12.88 119 36 40 4 442.39 0.74 120 36 41 5 426.19 5.54 121 37 40 3 453.06 1.49 122 37 41 4 452.84 1.60 123 38 41 3 459.72 0.78 124 38 42 4 452.84 1.60 125 39 42 3 461.62 1.73 126 39 43 4 455.49 4.79 127 40 43 3 473.78 0.66 128 40 44 4 455.12 2.98 129 41 44 3 461.56 1.75 130 41 45 4 456.81 2.15 131 42 45 3 458.18 1.47 132 42 46 4 449.92 1.32 133 43 46 3 449.94 1.31 134 43 47 4 449.96 1.31 135 44 47 3 449.97 1.31 136 44 48 4 452.78 1.36 137 45 48 3 459.82 0.57 138 45 49 4 455.11 1.79 139 45 56 11 272.55 6.36 140 45 62 17 272.39 6.29 141 46 49 3 470.86 4.46 142 47 50 3 460.76 0.10 143 47 51 4 460.72 0.07 144 48 51 3 468.88 2.56 145 48 52 4 453.42 0.96 146 48 53 5 384.85 6.87 147 48 54 6 301.63 4.50 148 49 52 3 456.88 3.44 149 49 54 5 356.42 21.08 150 49 56 7 280.52 2.47 151 52 65 13 271.87 5.72 152 53 64 11 271.87 5.73 153 53 65 12 271.87 5.72 154 53 67 14 271.54 5.62 155 53 68 15 247.06 6.58 156 53 71 18 248.66 5.78 157 54 62 8 272.85 6.08 158 54 63 9 272.50 5.98 159 54 64 10 271.98 5.78 160 54 65 11 271.87 5.73 161 55 61 6 273.26 5.95 162 55 62 7 272.88 6.08 163 55 63 8 272.77 6.03 164 55 65 10 272.51 5.92 165 56 60 4 290.12 1.12 166 56 61 5 273.25 5.95 167 56 62 6 272.89 6.08 168 57 60 3 453.74 8.36 169 57 61 4 279.50 5.03 170 64 68 4 385.32 8.91 171 64 69 5 366.28 0.47 172 64 72 8 349.30 2.27 173 65 68 3 447.46 2.81 174 65 69 4 440.10 5.83 175 66 70 4 444.38 3.73 176 67 70 3 452.50 0.30 177 67 71 4 450.48 0.69 178 68 71 3 454.24 2.47 179 68 72 4 450.56 0.64 180 69 72 3 450.80 0.58 181 69 73 4 443.69 2.83 182 70 73 3 454.31 1.19 183 70 74 4 450.29 4.12 184 71 74 3 450.30 4.12 185 71 75 4 450.34 4.09 186 72 75 3 456.68 1.99 187 72 76 4 450.37 4.09 188 73 76 3 456.28 2.19 189 73 77 4 454.07 2.23 190 73 133 60 52.34 0.66 191 73 134 61 52.02 0.80 192 74 77 3 468.83 4.83 193 74 78 4 454.94 2.65 194 75 78 3 463.99 2.41 195 75 79 4 457.74 1.45 196 75 105 30 133.84 0.66 197 75 106 31 133.83 0.65 198 76 79 3 464.41 0.04 199 76 80 4 457.74 1.45 200 76 133 57 52.38 0.65 201 77 80 3 459.65 1.18 202 77 81 4 457.53 1.34 203 77 110 33 133.46 0.61 204 77 113 36 125.77 1.56 205 77 132 55 52.77 0.64 206 77 133 56 52.56 0.57 207 77 134 57 52.36 0.66 208 77 135 58 52.13 0.76 209 77 137 60 49.05 0.30 210 77 138 61 42.96 0.14 211 78 81 3 459.62 2.33 212 78 82 4 454.81 2.68 213 78 105 27 133.93 0.65 214 78 108 30 133.83 0.64 215 78 109 31 133.82 0.64 216 78 110 32 133.52 0.64 217 78 113 35 125.77 1.56 218 79 82 3 458.83 2.73 219 79 83 4 454.82 2.68 220 79 98 19 134.72 0.68 221 79 101 22 133.99 0.62 222 79 102 23 134.00 0.62 223 79 105 26 133.90 0.66 224 80 83 3 458.82 0.66 225 80 84 4 452.16 1.34 226 80 126 46 65.42 2.80 227 80 130 50 59.80 1.49 228 80 131 51 58.58 0.91 229 80 132 52 52.80 0.65 230 80 133 53 52.83 0.64 231 81 84 3 456.18 0.67 232 81 85 4 463.23 0.55 233 81 113 32 126.51 1.23 234 81 116 35 117.62 0.57 235 81 117 36 117.27 0.65 236 81 120 39 105.92 1.76 237 81 123 42 65.43 2.79 238 81 132 51 56.37 0.37 239 81 135 54 52.48 0.61 240 81 138 57 49.28 0.19 241 82 85 3 463.24 0.54 242 82 86 4 463.24 0.54 243 82 101 19 134.64 0.61 244 82 104 22 134.59 0.64 245 82 108 26 133.87 0.65 246 83 86 3 463.24 0.54 247 83 87 4 463.24 0.54 248 83 97 14 134.83 0.63 249 83 98 15 134.94 0.58 250 83 101 18 134.71 0.64 251 83 126 43 65.51 2.83 252 83 127 44 65.46 2.81 253 83 128 45 65.47 2.81 254 84 87 3 464.64 1.24 255 84 88 4 454.60 3.78 256 84 120 36 106.62 1.42 257 84 122 38 94.65 0.32 258 84 125 41 65.52 2.83 259 84 126 42 65.52 2.83 260 84 127 43 65.48 2.81 261 85 88 3 461.18 3.06 262 85 89 4 436.31 1.30 263 85 90 5 425.81 3.33 264 85 104 19 135.09 0.65 265 85 116 31 120.53 0.54 266 85 120 35 106.61 1.42 267 86 90 4 410.75 4.20 268 86 91 5 409.66 4.75 269 86 92 6 315.55 6.07 270 86 97 11 135.27 0.69 271 86 100 14 135.26 0.69 272 86 101 15 135.23 0.68 273 86 104 18 135.11 0.67 274 87 91 4 363.96 18.09 275 87 97 10 135.31 0.67 276 87 127 40 65.66 2.85 277 88 120 32 111.43 1.71 278 89 120 31 114.62 0.75 279 90 104 14 139.83 1.18 280 92 96 4 453.73 2.54 281 92 97 5 381.44 9.43 282 92 100 8 346.25 8.19 283 93 96 3 458.99 0.08 284 93 97 4 451.04 3.89 285 94 97 3 456.97 0.92 286 94 127 33 65.62 2.88 287 94 128 34 65.67 2.89 288 96 99 3 470.22 1.07 289 96 100 4 453.31 2.77 290 97 100 3 470.22 1.07 291 97 101 4 453.72 2.56 292 97 127 30 65.54 2.84 293 97 128 31 65.64 2.89 294 98 101 3 465.62 3.37 295 98 102 4 453.85 2.52 296 99 102 3 463.06 2.08 297 99 103 4 454.82 2.03 298 100 103 3 461.12 1.09 299 100 104 4 454.84 2.02 300 101 104 3 455.76 1.71 301 101 105 4 453.38 1.30 302 102 105 3 475.81 0.92 303 102 106 4 471.25 3.20 304 103 106 3 482.69 2.40 305 104 107 3 464.10 0.37 306 104 108 4 447.14 0.61 307 105 108 3 460.28 1.31 308 108 112 4 452.78 1.07 309 108 113 5 434.68 1.55 310 108 116 8 413.01 8.80 311 109 112 3 454.04 1.70 312 109 113 4 448.21 3.35 313 110 113 3 452.78 1.06 314 110 114 4 448.21 3.35 315 110 138 28 42.34 0.44 316 111 114 3 453.63 1.49 317 111 115 4 453.05 0.93 318 112 115 3 452.49 0.65 319 112 116 4 447.63 3.08 320 113 116 3 455.76 0.27 321 113 117 4 448.80 2.48 322 113 138 25 42.84 0.42 323 114 117 3 468.02 1.59 324 114 118 4 448.20 0.18 325 114 138 24 44.45 0.21 326 115 118 3 465.50 0.03 327 115 119 4 443.89 2.33 328 116 119 3 447.76 0.40 329 116 120 4 442.97 2.72 330 117 120 3 455.82 3.62 331 117 123 6 219.31 34.20 332 117 135 18 52.86 0.73 333 117 138 21 51.80 0.93 334 120 123 3 490.30 1.08 335 123 132 9 65.99 2.82 336 123 135 12 63.18 2.75 337 124 131 7 66.06 2.81 338 124 132 8 66.00 2.82 339 125 129 4 300.67 3.50 340 125 130 5 223.41 29.91 341 125 131 6 66.07 2.81 342 125 132 7 66.06 2.81 343 126 129 3 457.85 2.18 344 126 130 4 292.48 2.41 345 126 132 6 177.49 52.88 346 132 135 3 498.15 2.10 347 134 137 3 465.12 1.24 348 134 138 4 451.81 1.90 349 135 138 3 453.34 1.13 350 135 139 4 453.34 1.12 351 136 139 3 455.76 2.25