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 5 453.64 1.15 2 2 10 8 441.55 7.19 3 2 73 71 28.85 0.31 4 2 124 122 33.34 0.18 5 2 127 125 25.11 0.16 6 2 128 126 25.08 0.16 7 3 6 3 473.44 1.31 8 3 7 4 471.61 2.23 9 4 7 3 478.34 0.45 10 4 8 4 472.67 1.70 11 5 8 3 480.11 0.44 12 5 9 4 471.60 2.23 13 6 9 3 488.02 1.86 14 6 10 4 464.20 2.04 15 6 124 118 48.48 0.09 16 6 127 121 49.19 0.26 17 7 10 3 479.70 0.23 18 7 11 4 464.64 3.45 19 7 73 66 50.85 0.58 20 7 74 67 51.53 0.24 21 8 11 3 472.31 0.16 22 8 12 4 469.34 0.52 23 9 12 3 483.86 1.53 24 9 13 4 471.98 0.80 25 9 120 111 68.67 0.27 26 9 121 112 68.42 0.14 27 9 124 115 68.37 0.13 28 10 13 3 479.66 0.57 29 10 14 4 473.09 1.34 30 10 70 60 68.34 0.12 31 10 73 63 68.41 0.15 32 10 124 114 68.41 0.14 33 10 125 115 68.37 0.12 34 10 128 118 68.34 0.12 35 11 14 3 475.49 0.15 36 11 15 4 473.09 1.34 37 11 70 59 68.41 0.15 38 12 15 3 493.53 0.68 39 12 16 4 487.37 3.77 40 13 16 3 492.90 2.29 41 13 17 4 487.36 3.77 42 13 109 96 83.19 0.68 43 13 113 100 85.37 0.15 44 13 121 108 81.11 0.01 45 13 125 112 81.07 0.04 46 14 17 3 478.78 1.54 47 14 18 4 472.74 1.49 48 14 63 49 84.21 0.44 49 14 66 52 82.94 0.92 50 14 67 53 80.39 0.35 51 14 70 56 80.25 0.42 52 14 105 91 85.11 0.07 53 14 125 111 83.06 0.74 54 15 18 3 482.61 1.08 55 15 19 4 473.57 0.54 56 16 19 3 485.66 0.45 57 16 113 97 98.42 0.18 58 16 116 100 98.37 0.15 59 17 20 3 482.67 1.94 60 17 21 4 464.68 1.62 61 17 24 7 369.35 6.37 62 17 63 46 90.82 0.32 63 17 105 88 88.91 0.80 64 17 109 92 90.66 0.04 65 18 21 3 478.61 3.97 66 20 23 3 483.18 0.65 67 20 24 4 466.48 1.12 68 21 24 3 490.58 1.90 69 21 25 4 465.44 0.60 70 21 60 39 106.12 0.06 71 21 63 42 106.02 0.10 72 21 64 43 106.02 0.10 73 22 25 3 483.19 0.66 74 22 26 4 470.89 0.74 75 22 56 34 120.47 0.24 76 22 60 38 109.91 0.33 77 23 26 3 487.13 1.32 78 23 27 4 469.52 1.44 79 23 56 33 121.69 0.23 80 24 27 3 477.81 2.03 81 24 28 4 469.45 1.48 82 24 63 39 121.46 0.24 83 24 108 84 131.31 0.38 84 24 109 85 130.75 0.03 85 24 112 88 135.80 0.29 86 25 28 3 484.23 2.79 87 25 29 4 465.72 1.46 88 25 59 34 123.04 1.01 89 25 63 38 121.45 0.24 90 26 29 3 473.97 2.34 91 26 30 4 466.02 1.31 92 26 55 29 135.54 0.17 93 26 56 30 134.22 0.50 94 26 59 33 127.57 2.99 95 27 30 3 486.41 3.88 96 27 31 4 474.28 2.19 97 27 108 81 136.27 0.24 98 27 112 85 137.62 0.44 99 28 31 3 478.91 3.17 100 28 32 4 466.31 1.19 101 28 101 73 135.93 0.34 102 28 104 76 135.96 0.36 103 28 105 77 135.96 0.36 104 28 108 80 136.44 0.18 105 29 32 3 481.98 1.64 106 29 33 4 468.39 2.23 107 29 55 26 137.13 0.33 108 29 58 29 136.96 0.41 109 29 59 30 136.81 0.40 110 29 62 33 136.72 0.34 111 29 101 72 136.01 0.37 112 30 33 3 488.67 1.71 113 30 34 4 465.45 0.43 114 30 50 20 138.31 0.47 115 30 51 21 138.30 0.47 116 30 55 25 137.31 0.27 117 31 34 3 475.56 1.35 118 31 35 4 468.73 2.06 119 31 104 73 136.96 0.47 120 31 107 76 137.75 0.49 121 31 108 77 137.97 0.55 122 32 35 3 478.49 0.12 123 32 36 4 456.24 4.19 124 32 39 7 325.75 8.15 125 32 43 11 273.85 9.44 126 32 100 68 136.94 0.46 127 32 101 69 136.96 0.47 128 32 104 72 137.00 0.45 129 33 36 3 473.09 2.59 130 33 37 4 420.34 4.90 131 33 39 6 351.35 20.96 132 33 40 7 292.81 0.04 133 33 43 10 273.85 9.44 134 33 48 15 138.49 0.48 135 33 55 22 138.41 0.45 136 34 37 3 471.70 3.52 137 36 39 3 494.30 0.06 138 36 100 64 136.94 0.46 139 36 103 67 137.97 0.51 140 36 104 68 138.02 0.53 141 37 40 3 484.60 1.70 142 38 41 3 491.85 0.92 143 39 42 3 495.19 0.76 144 39 97 58 136.91 0.48 145 39 100 61 137.94 0.53 146 40 43 3 489.59 3.56 147 40 48 8 196.62 28.46 148 41 44 3 490.49 3.12 149 42 91 49 136.86 0.46 150 42 92 50 136.87 0.46 151 42 93 51 136.86 0.46 152 42 94 52 137.83 0.51 153 42 97 55 138.03 0.53 154 43 46 3 489.49 2.11 155 43 48 5 417.05 12.38 156 43 58 15 141.61 0.79 157 45 54 9 218.24 37.88 158 46 54 8 198.93 28.28 159 46 55 9 198.94 28.28 160 46 58 12 198.93 28.28 161 47 52 5 293.49 0.27 162 47 54 7 218.25 37.89 163 47 55 8 218.25 37.89 164 48 55 7 278.53 7.75 165 49 52 3 473.19 0.75 166 49 55 6 416.69 7.17 167 51 56 5 439.16 4.05 168 52 55 3 469.48 4.33 169 52 56 4 461.36 1.04 170 53 56 3 470.23 1.21 171 53 57 4 454.34 3.35 172 54 57 3 467.92 1.86 173 54 58 4 456.17 2.43 174 55 58 3 467.41 0.40 175 55 59 4 456.30 2.37 176 56 59 3 472.18 0.19 177 56 60 4 466.37 2.65 178 57 60 3 476.30 1.87 179 57 61 4 476.31 1.88 180 58 61 3 476.31 1.88 181 58 62 4 475.87 2.10 182 59 62 3 478.06 2.75 183 59 63 4 476.31 1.88 184 60 63 3 476.32 1.88 185 60 64 4 473.89 3.08 186 61 64 3 466.69 3.21 187 61 65 4 463.88 1.93 188 62 65 3 477.68 2.29 189 62 66 4 463.88 1.92 190 62 101 39 176.68 1.94 191 63 66 3 470.43 1.32 192 63 67 4 459.73 0.26 193 63 105 42 184.14 1.76 194 64 67 3 474.80 1.76 195 64 68 4 460.00 0.40 196 65 68 3 473.09 2.67 197 65 69 4 464.45 2.11 198 65 83 18 172.46 3.41 199 66 69 3 488.69 4.17 200 66 70 4 474.51 2.92 201 66 105 39 199.11 5.33 202 66 128 62 203.05 6.46 203 66 129 63 198.88 5.22 204 66 132 66 184.22 1.68 205 67 70 3 476.76 1.79 206 67 71 4 459.97 0.42 207 68 71 3 472.06 4.15 208 68 72 4 459.40 0.14 209 68 79 11 184.41 1.74 210 69 72 3 470.44 1.34 211 69 73 4 459.38 0.14 212 69 76 7 275.09 1.17 213 69 80 11 211.70 12.06 214 69 128 59 220.83 2.27 215 69 132 63 202.91 6.38 216 70 73 3 468.81 2.17 217 70 128 58 218.89 0.95 218 72 75 3 479.19 3.24 219 72 76 4 443.83 8.44 220 72 79 7 289.99 0.18 221 73 76 3 482.28 1.70 222 73 128 55 225.65 0.81 223 75 78 3 491.88 0.89 224 75 79 4 472.26 1.95 225 76 79 3 472.26 1.95 226 76 80 4 464.00 2.18 227 76 131 55 226.61 0.96 228 76 132 56 226.22 0.82 229 76 135 59 226.22 0.82 230 77 80 3 474.17 2.90 231 77 81 4 442.40 8.05 232 77 135 58 226.22 0.82 233 77 138 61 226.47 0.94 234 78 81 3 464.01 2.19 235 80 83 3 474.55 0.60 236 80 84 4 467.06 3.52 237 80 132 52 233.69 3.66 238 80 135 55 233.35 3.80 239 80 136 56 232.75 3.85 240 81 84 3 474.81 0.33 241 81 85 4 470.79 1.68 242 82 85 3 474.99 3.77 243 82 86 4 475.46 0.19 244 83 86 3 475.47 0.18 245 83 87 4 475.46 0.19 246 83 136 53 236.77 3.62 247 84 87 3 477.38 1.14 248 84 88 4 475.45 0.19 249 84 135 51 236.77 3.62 250 84 136 52 236.76 3.62 251 84 138 54 236.76 3.62 252 84 139 55 236.66 3.58 253 85 88 3 475.98 0.07 254 85 89 4 458.78 8.53 255 85 90 5 456.53 8.73 256 85 139 54 236.66 3.60 257 86 90 4 446.46 4.12 258 86 91 5 399.42 19.39 259 87 91 4 399.39 19.41 260 87 92 5 399.37 19.41 261 87 93 6 317.79 21.34 262 87 98 11 259.93 3.33 263 87 136 49 236.78 3.62 264 87 140 53 236.79 3.60 265 88 92 4 345.75 7.37 266 88 139 51 236.79 3.60 267 88 140 52 236.69 3.60 268 89 139 50 236.80 3.61 269 92 140 48 236.91 3.63 270 93 97 4 477.91 2.06 271 93 98 5 466.14 0.79 272 93 140 47 237.09 3.58 273 94 97 3 484.91 1.43 274 95 98 3 485.31 1.23 275 95 99 4 478.76 1.34 276 95 137 42 237.46 3.48 277 95 140 45 237.26 3.58 278 96 99 3 479.93 1.79 279 96 100 4 478.76 1.35 280 97 100 3 481.81 0.18 281 97 101 4 476.49 2.48 282 98 101 3 481.82 0.18 283 98 102 4 466.35 0.65 284 98 133 35 237.67 3.46 285 98 136 38 237.68 3.46 286 98 137 39 237.67 3.46 287 99 102 3 481.82 0.18 288 99 103 4 473.96 4.11 289 100 103 3 468.79 2.02 290 100 104 4 465.22 0.24 291 101 104 3 478.34 6.83 292 101 105 4 465.18 0.26 293 102 105 3 475.75 5.04 294 102 106 4 471.82 1.79 295 102 129 27 238.12 3.58 296 102 133 31 237.95 3.50 297 103 106 3 473.69 0.86 298 103 107 4 471.82 1.79 299 104 107 3 471.84 1.79 300 104 108 4 470.41 2.50 301 105 108 3 473.66 0.68 302 105 109 4 465.75 3.41 303 105 129 24 239.86 3.60 304 106 109 3 472.44 0.07 305 106 110 4 455.38 0.38 306 106 117 11 255.33 8.30 307 106 122 16 240.00 3.58 308 106 126 20 239.94 3.58 309 106 129 23 239.91 3.57 310 107 110 3 465.50 3.41 311 107 111 4 463.26 0.10 312 108 111 3 471.23 0.53 313 108 112 4 463.26 0.11 314 109 112 3 475.68 6.07 315 109 113 4 459.07 2.21 316 109 117 8 293.12 3.71 317 109 125 16 240.03 3.58 318 110 113 3 464.19 0.57 319 110 114 4 445.92 2.35 320 110 117 7 267.10 2.42 321 113 116 3 469.04 1.73 322 113 117 4 415.53 19.89 323 113 121 8 427.85 13.71 324 114 117 3 494.41 5.38 325 115 118 3 494.83 3.81 326 116 121 5 450.69 3.46 327 117 121 4 451.43 3.81 328 117 122 5 450.68 3.46 329 117 125 8 441.44 1.16 330 118 121 3 462.73 1.08 331 118 122 4 454.39 5.25 332 119 122 3 465.63 4.99 333 119 123 4 457.14 3.87 334 120 123 3 468.08 3.77 335 120 124 4 459.07 2.91 336 121 124 3 473.75 0.66 337 121 125 4 456.81 3.70 338 122 125 3 477.09 0.31 339 122 126 4 456.81 3.64 340 123 126 3 473.06 1.70 341 123 127 4 460.37 2.38 342 124 127 3 467.61 1.03 343 124 128 4 459.38 2.89 344 125 128 3 466.86 1.40 345 125 129 4 461.28 1.93 346 126 129 3 467.66 1.09 347 126 130 4 453.45 2.12 348 127 130 3 484.61 1.67 349 127 131 4 458.05 0.18 350 128 131 3 475.56 2.86 351 128 132 4 457.08 0.30 352 129 132 3 470.79 2.98 353 129 133 4 457.12 0.28 354 130 133 3 473.39 1.68 355 130 134 4 466.03 4.66 356 131 134 3 473.99 0.68 357 131 135 4 468.36 3.50 358 132 135 3 477.01 3.14 359 132 136 4 466.85 1.39 360 133 136 3 482.66 3.68 361 133 137 4 466.85 1.39 362 134 137 3 471.76 0.08 363 134 138 4 467.82 1.88 364 135 138 3 482.83 2.85 365 135 139 4 489.62 0.55 366 136 139 3 542.13 2.87 367 137 140 3 490.61 1.04 368 138 141 3 478.71 0.58