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 5 446.37 3.79 2 2 73 71 31.43 0.01 3 2 76 74 28.34 1.55 4 2 127 125 24.12 0.29 5 2 128 126 23.98 0.23 6 2 131 129 23.49 0.47 7 3 6 3 474.34 0.29 8 3 7 4 463.88 4.94 9 4 7 3 473.99 0.12 10 4 8 4 474.42 0.34 11 5 8 3 481.84 0.84 12 5 9 4 474.42 0.34 13 6 9 3 477.72 1.21 14 6 10 4 472.19 1.46 15 6 124 118 47.23 0.82 16 6 127 121 47.23 0.82 17 7 10 3 476.95 1.59 18 7 11 4 472.19 1.46 19 7 73 66 50.34 0.12 20 7 74 67 50.75 0.32 21 8 11 3 474.70 0.21 22 8 12 4 469.22 2.95 23 9 12 3 477.06 0.10 24 9 13 4 469.13 2.91 25 9 121 112 61.48 0.90 26 9 124 115 61.12 0.74 27 10 13 3 486.09 2.59 28 10 14 4 458.73 2.25 29 10 70 60 61.45 0.91 30 10 124 114 61.52 0.92 31 10 125 115 61.44 0.91 32 10 128 118 61.11 0.74 33 11 14 3 476.73 2.10 34 11 15 4 446.81 0.20 35 11 70 59 61.50 0.94 36 11 71 60 61.95 0.90 37 11 73 62 61.51 0.94 38 12 15 3 464.19 4.50 39 12 16 4 468.39 2.39 40 13 16 3 477.25 1.13 41 13 17 4 465.01 0.45 42 13 113 100 79.36 0.97 43 13 121 108 62.07 0.90 44 13 125 112 62.05 0.90 45 14 17 3 469.55 1.81 46 14 18 4 469.75 2.81 47 14 21 7 407.78 1.17 48 14 63 49 71.56 2.21 49 14 66 52 62.04 0.90 50 14 67 53 62.04 0.91 51 14 70 56 62.04 0.91 52 15 18 3 478.38 1.50 53 16 113 97 93.97 0.75 54 16 116 100 93.92 0.71 55 17 20 3 482.36 0.62 56 17 21 4 432.17 5.53 57 17 24 7 403.44 2.56 58 17 109 92 93.77 0.78 59 17 113 96 94.27 0.60 60 18 21 3 495.86 2.06 61 20 23 3 469.20 1.10 62 20 24 4 465.51 0.74 63 21 24 3 465.52 0.74 64 21 25 4 461.28 1.38 65 21 63 42 98.07 1.49 66 22 25 3 469.69 1.35 67 22 26 4 469.22 2.58 68 22 60 38 101.63 0.14 69 22 63 41 99.03 1.16 70 23 26 3 482.83 4.22 71 23 27 4 463.49 2.10 72 24 27 3 482.82 4.22 73 24 28 4 468.66 2.86 74 24 108 84 117.71 0.34 75 24 109 85 121.58 0.18 76 24 112 88 129.45 0.50 77 25 28 3 478.16 1.90 78 25 29 4 474.38 0.01 79 25 59 34 117.64 0.34 80 25 63 38 116.91 0.07 81 26 29 3 474.60 0.11 82 26 30 4 467.37 0.21 83 26 55 29 125.34 1.47 84 26 56 30 124.75 1.76 85 26 59 33 117.83 0.43 86 27 30 3 476.44 2.30 87 27 31 4 469.38 1.23 88 27 108 81 129.77 0.36 89 27 112 85 131.85 0.06 90 28 31 3 469.38 1.23 91 28 32 4 465.72 1.05 92 28 101 73 129.66 0.39 93 28 104 76 129.69 0.38 94 28 105 77 129.69 0.40 95 28 108 80 129.77 0.36 96 29 32 3 476.85 2.10 97 29 33 4 461.69 1.36 98 29 55 26 130.44 0.47 99 29 58 29 130.23 0.58 100 29 59 30 129.94 0.44 101 29 101 72 129.76 0.36 102 30 33 3 478.82 2.76 103 30 34 4 465.80 3.42 104 30 50 20 132.22 0.13 105 31 34 3 476.56 1.23 106 31 35 4 461.62 1.34 107 31 104 73 131.49 0.03 108 31 107 76 131.82 0.09 109 31 108 77 131.87 0.10 110 31 111 80 132.34 0.07 111 32 35 3 472.56 0.38 112 32 36 4 451.67 3.60 113 32 39 7 325.24 5.48 114 32 100 68 131.43 0.01 115 32 101 69 131.48 0.04 116 32 104 72 131.55 0.04 117 33 37 4 419.64 6.16 118 33 39 6 325.25 5.48 119 33 40 7 304.89 1.65 120 33 43 10 283.04 9.29 121 33 48 15 132.45 0.12 122 33 55 22 132.35 0.07 123 34 37 3 487.84 1.57 124 36 39 3 486.72 3.39 125 36 100 64 131.49 0.04 126 36 103 67 132.19 0.10 127 36 104 68 132.17 0.12 128 37 40 3 480.01 0.08 129 38 41 3 485.85 0.68 130 39 42 3 488.76 2.32 131 39 43 4 489.88 4.00 132 39 97 58 131.40 0.03 133 39 100 61 132.16 0.10 134 40 43 3 494.28 1.80 135 40 48 8 136.23 1.51 136 41 44 3 498.08 0.10 137 42 93 51 131.47 0.06 138 42 94 52 131.79 0.07 139 42 97 55 132.16 0.10 140 43 46 3 472.86 3.54 141 43 48 5 418.80 10.62 142 43 58 15 132.53 0.07 143 45 54 9 136.71 1.56 144 46 54 8 136.69 1.57 145 46 55 9 136.71 1.57 146 46 58 12 136.69 1.58 147 47 52 5 240.64 33.24 148 47 54 7 157.34 5.84 149 47 55 8 159.66 7.01 150 48 52 4 383.54 1.16 151 48 55 7 159.65 7.01 152 49 52 3 474.92 1.40 153 51 56 5 465.84 4.77 154 52 55 3 468.53 3.58 155 52 56 4 468.42 3.53 156 53 56 3 470.30 2.59 157 53 57 4 471.81 1.83 158 54 57 3 471.84 1.84 159 54 58 4 471.92 1.80 160 55 58 3 472.00 1.77 161 55 59 4 471.94 1.79 162 56 59 3 474.35 1.68 163 56 60 4 472.56 1.51 164 57 60 3 485.00 3.68 165 57 61 4 472.58 1.51 166 58 61 3 474.88 0.35 167 58 62 4 472.58 1.51 168 59 62 3 480.23 2.31 169 59 63 4 471.97 1.81 170 60 63 3 471.91 1.83 171 60 64 4 462.01 0.46 172 61 64 3 469.68 2.42 173 61 65 4 465.10 3.76 174 62 65 3 483.15 0.40 175 62 66 4 467.17 2.73 176 62 101 39 153.24 2.34 177 63 66 3 478.30 2.83 178 63 67 4 467.17 2.73 179 64 67 3 467.45 2.60 180 64 68 4 459.85 1.17 181 65 68 3 462.42 0.29 182 65 69 4 459.64 1.31 183 65 80 15 153.47 2.30 184 65 83 18 142.10 3.38 185 66 69 3 479.93 1.23 186 66 70 4 461.84 0.22 187 66 105 39 177.29 5.46 188 66 129 63 162.23 2.60 189 66 132 66 153.53 2.33 190 67 70 3 472.24 2.88 191 67 71 4 467.46 2.60 192 68 71 3 475.32 1.33 193 68 72 4 469.43 4.01 194 68 79 11 209.19 20.53 195 69 72 3 475.41 1.36 196 69 73 4 447.85 7.12 197 69 76 7 264.58 6.99 198 69 80 11 157.56 0.37 199 69 128 59 240.59 7.99 200 69 132 63 160.94 1.25 201 70 73 3 470.30 1.19 202 70 128 58 240.63 8.00 203 72 75 3 471.41 0.29 204 72 76 4 430.24 11.38 205 72 79 7 278.04 1.24 206 73 76 3 477.38 2.69 207 75 78 3 479.88 1.34 208 75 79 4 463.11 1.64 209 76 79 3 467.21 0.41 210 76 80 4 460.89 0.54 211 76 128 52 254.32 7.69 212 76 131 55 252.49 7.44 213 76 132 56 250.85 6.71 214 76 135 59 250.84 6.71 215 77 80 3 472.18 0.32 216 77 81 4 460.86 0.54 217 77 135 58 246.00 9.07 218 78 81 3 469.21 1.40 219 80 83 3 480.80 0.53 220 80 84 4 454.97 1.07 221 80 132 52 256.44 8.60 222 80 135 55 256.25 8.50 223 80 136 56 256.25 8.50 224 81 84 3 468.85 5.87 225 81 85 4 454.98 1.06 226 81 139 58 256.31 8.53 227 82 85 3 480.10 0.91 228 82 86 4 478.86 1.52 229 83 86 3 471.24 5.33 230 83 87 4 469.51 6.19 231 83 136 53 256.69 8.69 232 84 88 4 454.81 1.03 233 84 135 51 256.69 8.68 234 84 136 52 256.68 8.67 235 84 138 54 256.67 8.69 236 84 139 55 256.59 8.65 237 85 88 3 470.24 2.79 238 85 89 4 446.77 5.04 239 85 139 54 256.58 8.65 240 86 89 3 475.32 4.83 241 86 90 4 438.36 5.66 242 86 91 5 411.05 9.23 243 87 91 4 398.09 15.71 244 87 92 5 380.58 24.42 245 87 93 6 353.04 15.73 246 87 98 11 304.69 4.21 247 87 136 49 256.93 8.65 248 87 140 53 256.72 8.72 249 88 92 4 380.69 24.43 250 88 139 51 256.61 8.67 251 88 140 52 256.50 8.62 252 89 92 3 492.91 3.16 253 92 140 48 256.79 8.72 254 93 97 4 482.50 0.34 255 93 98 5 480.81 1.18 256 93 140 47 256.92 8.68 257 94 97 3 495.75 2.32 258 94 98 4 484.89 0.86 259 95 98 3 496.92 1.20 260 95 140 45 257.04 8.63 261 96 99 3 494.80 4.09 262 96 100 4 484.06 2.08 263 97 100 3 479.71 1.18 264 97 101 4 479.70 1.17 265 98 101 3 477.85 2.35 266 98 102 4 470.49 1.27 267 98 133 35 257.52 8.54 268 98 136 38 257.52 8.54 269 98 137 39 257.51 8.54 270 98 140 42 257.49 8.55 271 99 102 3 477.79 2.38 272 99 103 4 470.48 1.27 273 100 103 3 470.45 1.28 274 100 104 4 469.20 0.75 275 101 104 3 472.20 2.00 276 101 105 4 469.25 0.73 277 102 105 3 469.48 0.65 278 102 106 4 469.49 0.66 279 102 129 27 257.98 8.39 280 102 133 31 257.89 8.40 281 103 106 3 480.51 4.55 282 103 107 4 469.50 0.66 283 104 107 3 471.11 0.15 284 104 108 4 469.49 0.66 285 105 108 3 472.50 2.33 286 105 109 4 469.24 0.74 287 105 129 24 258.80 8.21 288 106 109 3 472.54 2.48 289 106 110 4 464.06 1.71 290 106 117 11 265.99 5.88 291 106 122 16 259.44 8.39 292 106 125 19 259.22 8.28 293 106 126 20 259.08 8.21 294 106 129 23 259.10 8.22 295 107 110 3 474.02 1.43 296 107 111 4 466.50 0.49 297 108 111 3 470.90 0.14 298 108 112 4 467.38 0.05 299 109 112 3 475.38 4.05 300 109 113 4 449.73 1.24 301 109 117 8 268.32 7.04 302 109 125 16 259.47 8.38 303 110 117 7 265.99 5.88 304 113 116 3 477.86 0.55 305 113 117 4 460.89 7.92 306 114 117 3 473.97 1.39 307 115 118 3 526.28 0.91 308 116 121 5 463.89 3.71 309 117 121 4 466.37 2.48 310 117 122 5 463.89 3.71 311 117 125 8 413.62 4.68 312 118 121 3 468.28 1.52 313 118 122 4 466.37 2.48 314 119 122 3 466.51 2.41 315 119 123 4 474.87 1.77 316 120 123 3 481.19 1.02 317 120 124 4 474.88 1.77 318 121 124 3 474.88 1.77 319 121 125 4 474.88 1.78 320 122 125 3 476.56 2.61 321 122 126 4 468.29 5.07 322 123 126 3 474.45 1.99 323 123 127 4 472.81 2.81 324 124 127 3 473.61 2.29 325 124 128 4 466.81 0.20 326 125 128 3 473.32 3.06 327 125 129 4 467.89 0.73 328 126 129 3 482.05 1.31 329 126 130 4 467.89 0.73 330 127 130 3 481.29 0.93 331 127 131 4 466.14 0.14 332 128 131 3 478.31 2.42 333 128 132 4 465.71 2.03 334 129 132 3 478.04 4.71 335 129 133 4 459.86 0.03 336 130 133 3 474.92 2.57 337 130 134 4 460.82 0.04 338 131 134 3 473.22 1.72 339 131 135 4 460.50 0.33 340 132 135 3 474.12 5.26 341 132 136 4 462.12 0.74 342 133 136 3 476.43 4.11 343 133 137 4 462.62 0.52 344 134 137 3 474.19 2.00 345 134 138 4 455.82 3.90 346 135 138 3 474.63 1.79 347 136 140 4 488.99 0.78 348 137 140 3 485.50 0.97