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 5 462.56 4.98 2 2 74 72 29.34 0.54 3 2 77 75 24.40 0.12 4 2 128 126 23.07 1.20 5 2 129 127 22.98 1.16 6 3 6 3 477.97 7.82 7 3 7 4 472.39 0.56 8 4 7 3 482.85 5.38 9 4 8 4 472.86 0.36 10 5 8 3 486.00 3.80 11 5 9 4 473.85 0.85 12 6 9 3 478.49 3.17 13 6 10 4 473.85 0.85 14 6 125 119 49.55 0.10 15 6 128 122 47.74 0.81 16 7 10 3 484.49 2.98 17 7 11 4 473.84 0.86 18 7 74 67 49.55 0.09 19 7 75 68 50.18 0.12 20 8 11 3 487.56 1.45 21 8 12 4 473.35 1.01 22 9 12 3 485.96 0.65 23 9 13 4 473.36 1.02 24 9 125 116 56.05 2.33 25 10 13 3 473.38 1.02 26 10 14 4 473.38 1.02 27 10 71 61 56.13 2.37 28 10 74 64 56.15 2.36 29 10 125 115 56.11 2.33 30 10 126 116 56.08 2.33 31 10 129 119 56.08 2.33 32 11 14 3 476.38 0.47 33 11 15 4 469.88 2.78 34 11 71 60 56.16 2.36 35 11 74 63 56.16 2.36 36 11 75 64 56.19 2.35 37 12 15 3 470.44 2.50 38 12 16 4 469.88 2.78 39 13 16 3 484.80 3.77 40 13 17 4 469.88 2.78 41 13 117 104 68.31 0.66 42 13 118 105 65.19 0.78 43 13 122 109 60.06 1.67 44 13 126 113 60.00 1.64 45 14 17 3 479.81 0.87 46 14 18 4 458.25 2.98 47 14 21 7 420.89 6.54 48 14 64 50 61.97 1.02 49 14 67 53 60.11 1.69 50 14 68 54 60.11 1.69 51 14 71 57 60.07 1.68 52 16 19 3 534.06 2.55 53 16 117 101 80.83 1.60 54 17 20 3 503.28 1.39 55 17 24 7 437.71 1.80 56 17 110 93 81.01 1.58 57 17 114 97 93.65 0.24 58 18 21 3 480.52 2.10 59 20 23 3 481.42 2.56 60 20 24 4 476.36 1.11 61 20 114 94 122.58 2.39 62 21 24 3 476.36 1.11 63 21 25 4 476.12 1.24 64 21 64 43 138.29 18.26 65 22 25 3 477.77 1.43 66 22 26 4 470.78 1.44 67 22 61 39 140.89 17.57 68 23 26 3 477.56 1.54 69 23 27 4 474.72 0.13 70 23 113 90 142.77 1.81 71 24 27 3 483.93 0.17 72 24 28 4 474.71 0.13 73 24 64 40 151.74 12.22 74 24 109 85 141.74 6.88 75 24 110 86 141.72 6.88 76 24 113 89 142.78 1.81 77 24 114 90 144.04 2.41 78 25 28 3 479.98 2.14 79 25 29 4 474.71 0.13 80 25 60 35 151.91 12.30 81 25 64 39 151.74 12.22 82 26 29 3 489.23 2.48 83 26 30 4 469.17 2.63 84 26 52 26 160.43 10.31 85 26 56 30 158.77 9.56 86 26 57 31 157.24 10.27 87 26 60 34 154.08 11.22 88 27 30 3 482.07 1.17 89 27 31 4 482.07 1.17 90 27 109 82 147.69 3.95 91 27 113 86 147.09 3.17 92 28 31 3 482.14 1.19 93 28 32 4 474.95 4.73 94 28 102 74 148.49 4.37 95 28 105 77 148.46 4.36 96 28 106 78 148.25 4.25 97 28 109 81 148.02 4.08 98 29 32 3 479.87 0.06 99 29 33 4 469.73 2.12 100 29 56 27 158.97 9.53 101 29 59 30 158.87 9.49 102 29 60 31 158.69 9.41 103 29 63 34 158.77 9.45 104 29 102 73 148.50 4.36 105 30 33 3 489.23 0.49 106 30 34 4 472.37 0.69 107 30 51 21 161.19 9.94 108 30 52 22 161.19 9.94 109 30 56 26 160.91 9.97 110 31 34 3 480.46 0.18 111 31 35 4 463.69 0.08 112 31 105 74 149.19 4.00 113 31 108 77 149.27 3.91 114 31 109 78 149.18 3.94 115 31 112 81 149.28 3.85 116 32 35 3 483.07 0.23 117 32 36 4 448.19 1.48 118 32 39 7 355.48 21.71 119 32 43 11 338.50 30.19 120 32 101 69 149.26 4.03 121 32 102 70 149.16 4.08 122 32 105 73 149.24 3.98 123 33 37 4 419.06 10.05 124 33 39 6 355.48 21.71 125 33 40 7 338.50 30.19 126 33 49 16 174.59 16.30 127 33 50 17 174.59 16.30 128 33 51 18 174.45 16.33 129 33 56 23 174.03 16.28 130 34 37 3 477.91 1.32 131 34 51 17 174.54 16.27 132 36 39 3 497.18 3.60 133 36 101 65 149.40 4.10 134 36 104 68 149.56 4.01 135 36 105 69 149.56 4.01 136 37 40 3 491.06 1.51 137 38 41 3 505.36 0.93 138 38 101 63 149.73 4.11 139 39 42 3 497.39 1.82 140 39 43 4 491.06 1.51 141 39 98 59 149.49 4.21 142 39 101 62 149.69 4.09 143 40 43 3 490.78 1.95 144 40 44 4 485.99 0.45 145 40 49 9 182.97 20.30 146 41 44 3 484.04 0.18 147 42 45 3 556.69 2.56 148 42 93 51 149.69 4.30 149 42 94 52 149.66 4.29 150 42 95 53 149.74 4.24 151 42 98 56 149.83 4.19 152 43 46 3 491.48 0.28 153 43 49 6 247.81 7.24 154 43 59 16 174.47 16.31 155 46 49 3 506.01 0.37 156 46 55 9 187.69 22.57 157 46 56 10 187.69 22.57 158 46 59 13 187.66 22.58 159 47 55 8 200.09 28.68 160 50 53 3 476.72 0.19 161 50 56 6 410.31 5.82 162 52 56 4 459.24 0.48 163 52 57 5 454.61 1.83 164 53 56 3 466.54 2.43 165 53 57 4 460.23 0.98 166 54 57 3 466.38 1.11 167 54 58 4 475.38 1.97 168 55 58 3 477.32 2.94 169 55 59 4 475.40 1.98 170 56 59 3 475.42 1.99 171 56 60 4 475.41 1.98 172 57 60 3 488.07 3.88 173 57 61 4 476.56 2.56 174 58 61 3 481.63 0.03 175 58 62 4 476.55 2.57 176 59 62 3 484.16 1.24 177 59 63 4 476.51 2.58 178 60 63 3 486.55 2.48 179 60 64 4 476.19 2.72 180 61 64 3 482.69 1.16 181 61 65 4 471.83 4.89 182 62 65 3 478.96 3.69 183 62 66 4 476.59 2.50 184 63 66 3 484.88 1.65 185 63 67 4 476.59 2.50 186 63 102 39 176.13 9.45 187 63 106 43 176.37 9.80 188 64 67 3 487.25 0.46 189 64 68 4 469.45 1.06 190 65 68 3 476.56 2.50 191 65 69 4 469.16 1.21 192 66 69 3 477.23 0.23 193 66 70 4 467.17 0.21 194 66 84 18 176.88 9.23 195 67 70 3 477.30 0.19 196 67 71 4 467.18 0.21 197 67 106 39 176.65 9.75 198 67 129 62 181.22 15.76 199 67 130 63 171.91 12.01 200 67 133 66 170.17 12.69 201 68 71 3 481.56 2.74 202 68 72 4 470.14 1.70 203 69 72 3 480.86 0.63 204 69 73 4 469.37 1.34 205 69 80 11 212.72 6.24 206 69 81 12 209.95 7.13 207 69 84 15 209.91 7.12 208 70 73 3 480.12 2.01 209 70 74 4 459.97 0.62 210 70 77 7 294.77 6.63 211 70 81 11 209.91 7.12 212 70 129 59 183.03 16.57 213 70 133 63 171.24 12.22 214 71 74 3 459.94 0.64 215 71 129 58 194.27 22.18 216 73 76 3 490.59 1.54 217 73 77 4 438.31 10.13 218 73 80 7 274.23 2.46 219 74 77 3 488.73 1.04 220 74 129 55 197.02 23.51 221 76 79 3 487.04 2.23 222 76 80 4 457.72 2.63 223 77 80 3 475.25 2.39 224 77 81 4 466.68 1.85 225 77 129 52 197.80 23.88 226 77 132 55 196.75 24.25 227 77 133 56 195.87 24.22 228 77 136 59 194.45 24.81 229 78 81 3 484.49 3.88 230 78 82 4 465.59 0.01 231 78 136 58 194.46 24.82 232 78 139 61 193.84 25.12 233 79 82 3 473.91 0.25 234 81 84 3 485.71 3.44 235 81 85 4 468.47 1.34 236 81 133 52 196.91 24.85 237 81 136 55 195.67 25.47 238 81 137 56 195.19 25.41 239 82 85 3 485.71 3.44 240 82 86 4 469.67 0.74 241 83 86 3 488.95 0.89 242 83 87 4 477.67 4.75 243 84 87 3 484.97 1.10 244 84 88 4 478.70 4.24 245 84 137 53 195.09 25.80 246 85 88 3 478.71 4.24 247 85 89 4 467.51 0.80 248 85 136 51 195.69 25.61 249 85 137 52 193.52 26.57 250 85 139 54 193.43 26.62 251 85 140 55 192.36 27.09 252 86 89 3 472.38 1.06 253 86 90 4 467.50 0.80 254 86 140 54 192.93 26.76 255 87 91 4 407.63 0.68 256 87 92 5 382.44 4.36 257 88 92 4 352.61 2.29 258 88 93 5 330.42 12.46 259 88 94 6 283.78 1.59 260 88 99 11 280.62 0.05 261 88 141 53 192.37 27.15 262 89 93 4 344.24 5.55 263 89 140 51 192.47 27.17 264 89 141 52 192.24 27.16 265 90 93 3 485.67 2.33 266 90 140 50 193.12 26.89 267 94 98 4 491.62 0.79 268 94 99 5 476.26 0.89 269 94 141 47 191.19 27.86 270 95 98 3 496.87 0.48 271 96 99 3 491.62 0.78 272 96 100 4 484.18 3.06 273 96 138 42 193.44 27.00 274 96 141 45 191.46 27.99 275 97 100 3 491.93 0.62 276 97 101 4 477.73 0.17 277 98 101 3 479.48 0.71 278 98 102 4 470.65 2.35 279 99 102 3 480.36 1.45 280 99 103 4 470.63 2.43 281 99 134 35 195.69 26.04 282 99 137 38 193.81 27.01 283 99 141 42 191.62 28.07 284 100 103 3 480.43 1.42 285 100 104 4 476.81 0.45 286 101 104 3 483.06 0.09 287 101 105 4 472.97 4.02 288 102 105 3 483.07 0.09 289 102 106 4 476.81 0.45 290 103 106 3 480.36 1.28 291 103 107 4 480.35 1.28 292 103 130 27 197.03 25.43 293 103 134 31 195.88 25.99 294 104 107 3 480.36 1.28 295 104 108 4 476.85 0.48 296 105 108 3 476.82 0.49 297 105 109 4 479.39 0.80 298 106 109 3 489.42 5.80 299 106 110 4 479.39 0.80 300 106 130 24 198.49 25.19 301 107 110 3 486.17 0.29 302 107 111 4 476.61 0.58 303 107 118 11 237.88 7.03 304 107 123 16 199.79 24.95 305 107 126 19 199.68 24.98 306 107 127 20 199.57 25.04 307 107 130 23 199.06 25.28 308 108 111 3 479.88 1.11 309 108 112 4 476.53 0.54 310 109 112 3 479.34 0.81 311 109 113 4 470.48 3.56 312 110 113 3 488.72 2.35 313 110 114 4 467.20 5.20 314 110 118 8 239.50 6.22 315 110 126 16 199.70 25.00 316 111 115 4 425.50 8.69 317 111 118 7 239.88 6.04 318 112 115 3 495.54 0.52 319 114 117 3 477.99 6.03 320 114 118 4 447.81 4.67 321 115 118 3 489.31 0.64 322 116 119 3 520.95 2.85 323 117 122 5 449.97 11.53 324 118 122 4 449.97 11.53 325 118 123 5 448.38 12.38 326 118 126 8 417.81 0.42 327 119 122 3 483.50 1.16 328 119 123 4 463.38 4.88 329 120 123 3 483.50 1.16 330 120 124 4 467.47 6.92 331 121 124 3 487.56 2.37 332 121 125 4 471.89 4.71 333 122 125 3 480.62 1.10 334 122 126 4 455.84 12.72 335 123 126 3 489.02 3.10 336 123 127 4 468.07 6.61 337 124 127 3 476.26 2.47 338 124 128 4 472.10 0.39 339 125 128 3 477.87 0.26 340 125 129 4 473.93 2.23 341 126 129 3 473.93 2.23 342 126 130 4 472.90 1.88 343 127 130 3 476.34 1.02 344 127 131 4 472.92 1.88 345 128 131 3 474.92 0.88 346 128 132 4 472.91 1.88 347 129 132 3 472.92 1.88 348 129 133 4 464.19 2.48 349 130 133 3 471.90 3.22 350 130 134 4 471.90 3.22 351 131 134 3 475.71 1.32 352 131 135 4 467.48 5.44 353 132 135 3 477.89 0.23 354 132 136 4 463.81 2.06 355 133 136 3 472.43 0.38 356 133 137 4 466.48 3.35 357 134 137 3 471.44 1.85 358 134 138 4 466.50 3.35 359 135 138 3 466.50 3.35 360 135 139 4 466.50 3.35 361 136 139 3 467.87 2.67 362 137 141 4 486.75 1.01 363 138 141 3 478.50 5.13