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 5 460.03 1.85 2 2 73 71 31.62 0.32 3 2 127 125 23.70 0.33 4 2 128 126 19.30 1.14 5 3 6 3 474.36 2.10 6 3 7 4 465.59 2.29 7 4 7 3 475.25 1.65 8 4 8 4 470.66 0.25 9 5 8 3 481.97 3.30 10 5 9 4 468.43 0.91 11 6 9 3 481.36 5.54 12 6 10 4 468.44 0.91 13 6 124 118 48.59 0.51 14 6 127 121 48.59 0.51 15 7 10 3 480.95 4.91 16 7 11 4 474.90 5.11 17 7 73 66 49.12 0.76 18 7 74 67 49.52 0.95 19 8 11 3 478.39 6.19 20 8 12 4 474.89 5.11 21 9 12 3 482.65 4.07 22 9 13 4 468.73 2.04 23 9 121 112 56.84 3.93 24 9 124 115 56.80 3.93 25 10 13 3 486.81 1.99 26 10 14 4 468.66 2.04 27 10 70 60 56.81 3.92 28 10 124 114 56.84 3.93 29 10 125 115 56.84 3.93 30 10 128 118 56.80 3.92 31 11 14 3 479.50 2.80 32 11 15 4 467.18 1.39 33 11 70 59 56.83 3.93 34 11 73 62 56.84 3.93 35 12 15 3 480.69 2.21 36 12 16 4 468.20 0.86 37 13 16 3 473.21 1.54 38 13 17 4 466.88 1.54 39 13 121 108 59.41 2.74 40 13 125 112 59.35 2.73 41 14 17 3 465.72 2.21 42 14 18 4 464.48 1.58 43 14 21 7 398.84 4.69 44 14 63 49 73.38 1.97 45 14 66 52 59.46 2.69 46 14 67 53 59.46 2.69 47 14 70 56 59.45 2.69 48 14 109 95 77.06 2.86 49 15 18 3 472.95 2.33 50 16 113 97 82.91 0.02 51 16 116 100 82.83 0.06 52 17 20 3 482.62 2.10 53 17 21 4 445.50 0.18 54 17 24 7 378.55 10.71 55 17 109 92 82.83 0.03 56 17 113 96 93.28 0.58 57 18 21 3 493.04 1.24 58 20 23 3 483.87 1.45 59 20 24 4 475.50 0.45 60 21 24 3 480.73 3.02 61 21 25 4 473.06 1.67 62 21 63 42 103.53 2.18 63 22 25 3 485.88 0.44 64 22 26 4 478.24 4.26 65 22 59 37 109.33 0.26 66 22 60 38 105.31 1.70 67 22 63 41 105.25 1.71 68 23 26 3 480.66 3.06 69 23 27 4 473.42 1.49 70 24 27 3 475.36 0.51 71 24 28 4 473.41 1.48 72 24 108 84 131.68 4.37 73 24 109 85 136.36 2.04 74 24 112 88 141.49 3.33 75 24 113 89 141.90 3.48 76 25 28 3 480.98 2.88 77 25 29 4 473.41 1.49 78 25 59 34 123.30 0.28 79 26 29 3 485.32 0.70 80 26 30 4 473.39 1.48 81 26 55 29 138.78 5.23 82 26 56 30 138.78 5.23 83 26 59 33 125.20 0.67 84 27 30 3 479.75 2.55 85 27 31 4 467.99 1.50 86 27 108 81 142.70 3.88 87 27 112 85 142.95 3.75 88 28 31 3 476.23 0.79 89 28 32 4 467.73 1.62 90 28 101 73 142.85 3.98 91 28 104 76 142.70 3.89 92 28 105 77 142.68 3.89 93 28 108 80 142.71 3.89 94 29 32 3 480.17 1.19 95 29 33 4 476.75 2.90 96 29 55 26 152.81 8.76 97 29 58 29 142.47 3.60 98 29 59 30 142.35 3.54 99 29 62 33 142.34 3.54 100 29 101 72 143.13 4.11 101 30 33 3 489.25 0.76 102 30 34 4 472.62 0.94 103 30 50 20 157.97 11.31 104 31 34 3 489.25 0.76 105 31 35 4 479.23 4.25 106 31 104 73 143.05 4.01 107 31 107 76 143.24 3.91 108 31 108 77 143.11 3.84 109 32 35 3 489.25 0.76 110 32 36 4 458.44 0.24 111 32 39 7 325.27 5.56 112 32 100 68 143.19 4.08 113 32 101 69 143.21 4.09 114 32 104 72 143.19 4.05 115 33 37 4 418.94 9.18 116 33 39 6 340.03 5.28 117 33 40 7 293.22 6.57 118 33 43 10 287.94 9.20 119 33 48 15 167.78 16.12 120 34 37 3 491.58 3.45 121 36 39 3 488.97 0.53 122 36 100 64 143.46 4.22 123 36 103 67 143.68 4.11 124 36 104 68 143.65 4.09 125 37 40 3 485.15 1.09 126 38 41 3 498.25 1.26 127 39 42 3 498.25 1.26 128 39 43 4 490.75 0.10 129 39 97 58 143.56 4.25 130 39 100 61 143.72 4.15 131 40 43 3 490.88 0.17 132 40 44 4 488.31 0.21 133 40 48 8 250.53 0.86 134 41 44 3 490.95 0.20 135 42 91 49 143.72 4.33 136 42 92 50 143.75 4.32 137 42 93 51 143.70 4.33 138 42 94 52 143.75 4.32 139 42 97 55 143.89 4.21 140 43 46 3 482.55 0.71 141 43 48 5 420.94 15.91 142 43 58 15 225.25 1.78 143 45 54 9 299.59 12.08 144 46 54 8 260.91 7.24 145 46 58 12 249.35 1.46 146 47 52 5 329.01 2.62 147 47 54 7 299.60 12.09 148 47 55 8 299.60 12.09 149 48 55 7 299.62 12.08 150 49 52 3 466.19 5.71 151 50 56 6 461.55 3.31 152 51 56 5 461.57 3.31 153 52 55 3 481.86 0.55 154 52 56 4 477.70 2.45 155 53 56 3 483.88 0.47 156 53 57 4 480.30 1.31 157 54 57 3 491.19 6.77 158 54 58 4 480.30 1.32 159 55 58 3 480.31 1.32 160 55 59 4 480.30 1.32 161 56 59 3 487.22 2.14 162 56 60 4 480.27 1.33 163 57 60 3 482.58 0.17 164 57 61 4 476.64 3.13 165 58 61 3 481.01 0.94 166 58 62 4 470.85 1.42 167 59 62 3 476.41 1.36 168 59 63 4 472.85 0.42 169 60 63 3 477.81 2.59 170 60 64 4 472.86 0.42 171 61 64 3 487.24 2.12 172 61 65 4 475.57 0.94 173 62 65 3 481.03 0.98 174 62 66 4 475.58 0.94 175 63 66 3 476.39 1.34 176 63 67 4 473.24 2.10 177 64 67 3 477.59 0.07 178 64 68 4 473.24 2.10 179 65 68 3 480.26 1.42 180 65 69 4 473.23 2.10 181 65 83 18 156.97 1.10 182 66 69 3 473.23 2.10 183 66 70 4 473.20 2.10 184 66 105 39 162.42 4.48 185 66 129 63 160.19 4.70 186 66 132 66 154.17 2.58 187 67 70 3 476.16 0.58 188 67 71 4 474.89 1.20 189 68 71 3 474.89 1.19 190 68 72 4 474.88 1.19 191 68 79 11 236.66 3.12 192 69 72 3 470.10 1.21 193 69 73 4 469.05 1.73 194 69 76 7 279.24 7.65 195 69 80 11 227.19 7.86 196 69 128 59 167.43 7.98 197 69 132 63 155.25 2.48 198 70 73 3 469.05 1.73 199 70 128 58 170.63 9.55 200 72 75 3 479.84 0.28 201 72 76 4 429.10 18.34 202 72 79 7 310.85 12.38 203 73 76 3 481.00 0.30 204 73 128 55 181.96 15.18 205 75 78 3 494.97 1.02 206 75 79 4 469.21 1.69 207 76 79 3 476.69 5.42 208 76 80 4 469.22 1.69 209 76 128 52 182.47 15.50 210 76 131 55 181.52 15.62 211 76 132 56 181.51 15.61 212 76 135 59 181.35 15.62 213 77 80 3 480.37 2.62 214 77 81 4 456.82 7.88 215 77 135 58 181.21 15.69 216 78 81 3 474.29 0.85 217 80 83 3 487.71 2.41 218 80 84 4 475.70 0.16 219 80 132 52 182.02 15.99 220 80 135 55 181.27 16.12 221 80 136 56 181.12 16.21 222 81 84 3 486.73 2.90 223 81 85 4 479.51 2.02 224 82 85 3 489.82 1.35 225 82 86 4 482.12 0.72 226 83 86 3 482.12 0.72 227 83 87 4 480.31 1.62 228 83 136 53 181.02 16.59 229 84 87 3 480.32 1.62 230 84 88 4 469.31 1.81 231 84 135 51 180.97 16.58 232 84 136 52 180.44 16.80 233 84 139 55 179.30 17.37 234 85 88 3 474.25 3.23 235 85 89 4 436.75 7.37 236 85 90 5 418.02 3.91 237 85 139 54 179.39 17.32 238 86 90 4 377.53 7.26 239 86 91 5 377.52 7.26 240 87 91 4 377.48 7.25 241 87 92 5 344.31 9.20 242 87 93 6 332.47 15.07 243 87 98 11 251.65 2.10 244 87 136 49 180.53 16.89 245 88 92 4 344.31 9.21 246 88 136 48 180.55 16.89 247 88 139 51 177.52 18.32 248 88 140 52 176.97 18.53 249 89 139 50 179.46 17.35 250 92 140 48 176.81 18.75 251 93 97 4 480.12 1.98 252 93 98 5 477.98 0.92 253 93 140 47 176.84 18.75 254 94 97 3 491.12 1.72 255 95 98 3 491.12 1.72 256 95 137 42 177.13 18.63 257 95 140 45 176.49 18.95 258 96 99 3 490.04 2.98 259 96 100 4 485.92 5.04 260 97 100 3 485.93 5.05 261 97 101 4 485.92 5.04 262 98 101 3 489.97 3.02 263 98 102 4 477.41 0.81 264 98 133 35 180.94 16.88 265 98 136 38 179.48 17.62 266 98 137 39 177.25 18.71 267 99 102 3 490.74 2.64 268 99 103 4 477.40 0.80 269 100 103 3 482.26 1.59 270 100 104 4 477.39 0.80 271 101 104 3 476.94 0.57 272 101 105 4 472.64 2.69 273 102 105 3 479.10 0.52 274 102 106 4 472.64 2.69 275 102 129 27 181.96 16.50 276 102 133 31 181.06 16.94 277 103 106 3 478.17 0.06 278 103 107 4 472.64 2.69 279 104 107 3 472.63 2.71 280 104 108 4 468.28 0.55 281 105 108 3 470.75 1.78 282 105 109 4 468.27 0.55 283 105 129 24 182.81 16.91 284 106 109 3 474.82 0.42 285 106 110 4 459.48 3.79 286 106 117 11 197.71 10.93 287 106 122 16 189.09 14.30 288 106 125 19 182.93 16.96 289 106 126 20 182.92 16.95 290 106 129 23 182.88 16.94 291 107 110 3 475.23 3.97 292 107 111 4 459.50 3.79 293 108 111 3 484.38 0.61 294 108 112 4 462.73 5.41 295 109 112 3 488.25 1.18 296 109 113 4 450.72 8.19 297 109 125 16 189.25 14.34 298 110 117 7 215.56 2.77 299 113 116 3 473.87 2.36 300 113 117 4 424.88 1.02 301 115 118 3 522.48 0.68 302 116 121 5 442.72 9.95 303 117 122 5 431.75 0.22 304 117 125 8 415.87 3.48 305 118 121 3 466.49 5.54 306 118 122 4 455.83 4.62 307 119 122 3 475.15 1.19 308 119 123 4 469.78 1.51 309 120 123 3 475.67 1.44 310 120 124 4 469.06 1.86 311 121 124 3 472.07 0.37 312 121 125 4 470.50 1.40 313 122 125 3 478.97 0.38 314 122 126 4 470.63 1.44 315 123 126 3 472.96 0.75 316 123 127 4 470.65 1.43 317 124 127 3 471.34 1.08 318 124 128 4 470.64 1.44 319 125 128 3 472.95 0.76 320 125 129 4 470.64 1.44 321 126 129 3 483.78 0.23 322 126 130 4 470.51 1.45 323 127 130 3 470.68 1.53 324 127 131 4 470.68 1.54 325 128 131 3 474.66 2.75 326 128 132 4 465.98 0.72 327 129 132 3 472.87 0.68 328 129 133 4 470.56 1.59 329 130 133 3 484.38 5.30 330 130 134 4 471.38 1.56 331 131 134 3 475.99 3.87 332 131 135 4 471.41 1.56 333 132 135 3 472.50 2.10 334 132 136 4 470.90 1.82 335 133 136 3 481.05 1.34 336 133 137 4 470.84 1.85 337 134 137 3 484.74 1.76 338 134 138 4 469.49 2.27 339 134 141 7 422.34 1.81 340 135 138 3 469.77 2.39 341 137 140 3 491.71 1.64 342 137 141 4 491.50 1.74 343 138 141 3 497.68 2.52