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 5 442.02 1.97 2 2 73 71 29.28 0.70 3 2 76 74 24.89 0.89 4 2 127 125 24.30 0.44 5 2 128 126 23.66 0.12 6 2 131 129 23.24 0.07 7 3 6 3 474.43 2.78 8 3 7 4 474.67 2.66 9 4 7 3 489.93 4.89 10 4 8 4 474.72 2.69 11 5 8 3 478.25 2.02 12 5 9 4 474.72 2.69 13 6 9 3 474.72 2.69 14 6 10 4 474.72 2.69 15 6 124 118 46.90 0.34 16 6 127 121 45.75 0.18 17 7 10 3 478.91 2.79 18 7 11 4 474.70 2.69 19 7 73 66 48.09 0.25 20 7 74 67 48.09 0.25 21 8 11 3 474.69 2.69 22 8 12 4 471.38 1.06 23 9 12 3 475.62 1.04 24 9 13 4 471.70 1.22 25 9 121 112 60.29 0.95 26 9 124 115 60.18 0.95 27 10 13 3 473.00 3.59 28 10 14 4 467.89 3.12 29 10 70 60 60.25 0.92 30 10 124 114 60.30 0.95 31 10 125 115 60.27 0.96 32 10 128 118 60.20 0.96 33 11 14 3 474.06 0.05 34 11 15 4 465.91 4.12 35 11 70 59 60.34 0.94 36 11 73 62 60.34 0.94 37 12 15 3 477.08 1.56 38 12 16 4 469.15 5.19 39 13 16 3 477.68 0.93 40 13 17 4 468.61 5.46 41 13 113 100 75.40 0.64 42 13 121 108 67.62 3.60 43 13 125 112 61.01 0.72 44 14 17 3 474.74 2.40 45 14 18 4 473.44 3.04 46 14 21 7 421.44 7.04 47 14 63 49 64.45 0.01 48 14 66 52 61.02 0.73 49 14 67 53 61.02 0.73 50 14 70 56 61.01 0.72 51 14 109 95 74.88 0.83 52 15 18 3 473.44 3.04 53 16 113 97 83.81 2.39 54 16 116 100 77.88 0.57 55 17 20 3 489.22 2.81 56 17 21 4 443.75 5.49 57 17 24 7 424.00 4.39 58 17 109 92 77.28 0.29 59 17 113 96 87.61 3.85 60 18 21 3 503.33 1.19 61 20 23 3 478.01 1.17 62 20 24 4 468.04 2.27 63 21 24 3 480.74 2.58 64 21 25 4 468.07 2.27 65 21 63 42 90.61 2.44 66 22 25 3 469.87 1.38 67 22 26 4 468.09 2.25 68 22 60 38 98.20 0.98 69 22 63 41 97.77 0.77 70 23 26 3 477.71 1.49 71 23 27 4 468.09 2.25 72 24 27 3 482.22 0.76 73 24 28 4 468.07 2.23 74 24 108 84 122.20 1.73 75 24 109 85 122.03 1.34 76 24 112 88 129.03 0.69 77 25 28 3 472.04 1.71 78 25 29 4 466.06 1.23 79 25 59 34 118.20 0.43 80 25 105 80 120.00 0.82 81 26 29 3 477.88 0.13 82 26 30 4 466.05 1.24 83 26 55 29 124.73 1.54 84 26 56 30 121.58 0.04 85 26 59 33 118.47 0.30 86 27 30 3 475.05 1.28 87 27 31 4 463.94 2.21 88 27 108 81 129.27 0.61 89 27 112 85 130.34 1.05 90 28 31 3 467.16 3.81 91 28 32 4 463.97 2.23 92 28 101 73 129.06 0.69 93 28 104 76 129.15 0.65 94 28 105 77 129.15 0.65 95 28 108 80 129.97 0.95 96 29 32 3 467.50 1.13 97 29 33 4 464.50 2.51 98 29 55 26 130.26 1.08 99 29 58 29 129.31 0.61 100 29 59 30 129.31 0.61 101 29 101 72 129.16 0.65 102 30 33 3 468.87 1.81 103 30 34 4 467.38 1.07 104 30 50 20 130.43 1.16 105 31 34 3 478.72 0.61 106 31 35 4 467.37 1.07 107 31 104 73 130.22 1.17 108 31 107 76 130.37 1.15 109 31 108 77 130.49 1.16 110 31 111 80 130.66 1.18 111 32 35 3 461.89 3.83 112 32 36 4 447.04 2.21 113 32 39 7 315.07 1.28 114 32 100 68 130.22 1.18 115 32 101 69 130.18 1.16 116 32 104 72 130.33 1.14 117 33 37 4 422.19 7.56 118 33 39 6 316.44 1.96 119 33 40 7 291.42 1.64 120 33 43 10 298.89 6.80 121 33 48 15 130.59 1.13 122 34 37 3 490.24 1.35 123 36 39 3 492.82 0.10 124 36 100 64 130.23 1.17 125 36 103 67 130.58 1.17 126 36 104 68 130.59 1.18 127 37 40 3 488.63 1.03 128 38 41 3 487.57 1.56 129 39 42 3 496.05 1.72 130 39 43 4 488.26 0.74 131 39 97 58 130.15 1.18 132 39 100 61 130.46 1.19 133 40 43 3 488.26 0.74 134 40 44 4 487.09 1.32 135 40 48 8 146.75 0.74 136 41 44 3 500.49 0.53 137 42 45 3 646.57 0.43 138 42 93 51 130.00 1.18 139 42 94 52 130.35 1.20 140 42 97 55 130.47 1.20 141 43 46 3 485.53 1.53 142 43 48 5 414.87 1.06 143 43 58 15 134.45 2.94 144 45 54 9 140.82 3.79 145 46 54 8 140.81 3.79 146 46 55 9 140.80 3.79 147 46 58 12 140.80 3.79 148 47 52 5 148.75 1.33 149 47 54 7 140.84 3.80 150 47 55 8 140.84 3.80 151 48 55 7 140.83 3.81 152 49 52 3 472.44 1.05 153 51 56 5 451.54 1.42 154 52 55 3 471.84 0.85 155 52 56 4 468.46 0.38 156 53 56 3 476.29 4.28 157 53 57 4 461.04 3.33 158 54 57 3 471.39 1.07 159 54 58 4 458.18 1.57 160 55 58 3 475.78 2.04 161 55 59 4 463.91 3.18 162 56 59 3 471.54 0.19 163 56 60 4 473.34 0.74 164 57 60 3 473.38 0.73 165 57 61 4 473.34 0.74 166 58 61 3 474.50 0.17 167 58 62 4 467.51 1.39 168 59 62 3 480.49 2.83 169 59 63 4 467.60 1.32 170 60 63 3 468.71 1.86 171 60 64 4 467.57 1.31 172 61 64 3 477.25 3.47 173 61 65 4 467.59 1.31 174 62 65 3 485.18 0.49 175 62 66 4 467.57 1.31 176 62 101 39 147.15 5.38 177 63 66 3 468.38 1.19 178 63 67 4 466.46 0.77 179 64 67 3 469.38 0.68 180 64 68 4 469.41 0.68 181 65 68 3 478.23 2.93 182 65 69 4 477.44 3.33 183 65 80 15 147.35 5.48 184 65 83 18 147.28 5.51 185 66 69 3 477.43 3.33 186 66 70 4 474.30 4.91 187 66 105 39 173.83 3.25 188 66 132 66 148.80 5.38 189 67 70 3 477.32 3.39 190 67 71 4 471.53 3.23 191 68 71 3 474.60 4.75 192 68 72 4 471.53 3.23 193 68 79 11 169.29 4.82 194 68 80 12 169.29 4.82 195 69 72 3 472.99 3.96 196 69 73 4 456.32 4.37 197 69 76 7 284.29 1.70 198 69 80 11 169.30 4.82 199 69 128 59 227.21 0.15 200 69 132 63 168.94 1.40 201 70 73 3 459.15 2.96 202 70 128 58 237.22 4.87 203 72 75 3 470.97 0.07 204 72 76 4 444.34 5.24 205 72 79 7 285.38 2.87 206 73 76 3 478.20 2.77 207 73 128 55 271.32 1.25 208 75 78 3 495.31 0.51 209 75 79 4 463.31 0.67 210 76 79 3 466.35 2.18 211 76 80 4 454.84 3.56 212 76 128 52 277.42 0.98 213 76 131 55 274.87 1.64 214 76 132 56 272.83 1.70 215 76 135 59 272.82 1.70 216 77 80 3 486.94 1.12 217 77 81 4 468.09 3.06 218 77 135 58 272.83 1.70 219 78 81 3 470.86 4.44 220 80 83 3 479.30 2.77 221 80 84 4 459.42 5.74 222 80 132 52 278.68 1.50 223 80 135 55 277.86 1.09 224 80 136 56 277.75 1.15 225 81 84 3 468.67 2.52 226 81 85 4 463.49 3.71 227 81 139 58 277.88 1.32 228 82 85 3 473.29 1.27 229 82 86 4 463.49 3.71 230 83 86 3 474.88 2.06 231 83 87 4 467.30 1.80 232 83 136 53 278.81 1.56 233 84 87 3 481.78 1.78 234 84 88 4 467.30 1.81 235 84 135 51 278.81 1.56 236 84 136 52 278.77 1.57 237 84 138 54 278.75 1.57 238 84 139 55 278.58 1.65 239 85 88 3 474.80 2.06 240 85 89 4 463.14 0.27 241 85 139 54 278.57 1.65 242 86 89 3 477.76 2.04 243 86 90 4 444.90 2.60 244 86 91 5 425.03 7.03 245 87 91 4 396.25 1.77 246 87 92 5 346.92 2.00 247 87 98 11 282.49 2.10 248 87 136 49 278.85 1.56 249 87 140 53 278.60 1.65 250 88 92 4 368.94 7.35 251 88 139 51 278.63 1.63 252 88 140 52 278.50 1.66 253 89 92 3 483.19 0.62 254 92 140 48 278.67 1.61 255 93 97 4 482.77 0.36 256 93 98 5 473.85 1.74 257 93 140 47 278.83 1.61 258 94 97 3 494.81 0.05 259 95 98 3 491.98 1.47 260 95 137 42 279.37 1.67 261 95 140 45 279.10 1.56 262 96 99 3 490.80 0.88 263 96 100 4 482.77 0.37 264 97 100 3 474.38 0.78 265 97 101 4 480.55 3.85 266 98 101 3 480.56 3.85 267 98 102 4 469.59 1.63 268 98 133 35 279.56 1.58 269 98 136 38 279.62 1.61 270 98 137 39 279.61 1.61 271 98 140 42 279.60 1.61 272 99 102 3 480.56 3.85 273 99 103 4 474.44 0.80 274 100 103 3 480.56 3.85 275 100 104 4 480.56 3.85 276 101 104 3 481.57 3.35 277 101 105 4 472.37 1.86 278 102 105 3 475.98 3.67 279 102 106 4 472.37 1.86 280 102 129 27 279.90 1.68 281 102 133 31 279.71 1.58 282 103 106 3 476.36 2.86 283 103 107 4 472.38 1.86 284 104 107 3 475.19 0.46 285 104 108 4 465.07 2.50 286 105 108 3 482.66 2.78 287 105 109 4 466.45 1.80 288 105 129 24 280.50 1.67 289 106 109 3 479.80 4.88 290 106 110 4 460.21 0.07 291 106 117 11 281.54 1.78 292 106 122 16 281.04 1.86 293 106 125 19 280.92 1.83 294 106 126 20 280.85 1.80 295 106 129 23 280.56 1.68 296 107 110 3 480.29 1.58 297 107 111 4 464.01 1.83 298 108 111 3 483.36 3.10 299 108 112 4 459.07 3.06 300 109 112 3 474.43 4.46 301 109 113 4 450.57 0.50 302 109 125 16 281.16 1.89 303 110 113 3 480.25 1.55 304 110 117 7 281.56 1.79 305 113 116 3 477.07 0.03 306 113 117 4 425.57 11.64 307 115 118 3 537.79 1.93 308 116 121 5 469.47 3.75 309 117 122 5 474.13 1.42 310 117 125 8 392.29 0.23 311 118 121 3 474.14 1.43 312 118 122 4 474.17 1.43 313 119 122 3 479.99 4.33 314 119 123 4 474.18 1.43 315 120 123 3 474.18 1.43 316 120 124 4 474.19 1.43 317 121 124 3 474.19 1.43 318 121 125 4 474.17 1.43 319 122 125 3 483.92 2.97 320 122 126 4 471.42 2.76 321 123 126 3 477.11 0.03 322 123 127 4 471.42 2.75 323 124 127 3 477.20 0.07 324 124 128 4 471.47 2.71 325 125 128 3 477.41 0.17 326 125 129 4 471.47 2.71 327 126 129 3 485.19 2.97 328 126 130 4 476.98 0.39 329 127 130 3 483.86 3.05 330 127 131 4 472.30 1.95 331 128 131 3 477.21 0.28 332 128 132 4 472.29 1.94 333 129 132 3 477.21 0.28 334 129 133 4 464.93 1.74 335 130 133 3 467.13 0.68 336 130 134 4 464.94 1.73 337 131 134 3 467.06 0.64 338 131 135 4 464.95 1.70 339 132 135 3 473.50 1.49 340 132 136 4 463.60 1.02 341 133 136 3 473.53 1.51 342 133 137 4 461.51 0.03 343 134 137 3 474.73 2.12 344 134 138 4 462.57 2.12 345 135 138 3 477.37 0.19 346 136 140 4 497.40 1.85 347 137 140 3 486.87 0.07