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 1 46 45 68.05 1.01 2 1 132 131 68.00 1.01 3 2 43 41 68.08 1.01 4 2 44 42 68.06 1.01 5 2 46 44 68.06 1.01 6 2 47 45 68.06 1.01 7 2 69 67 68.05 1.01 8 2 72 70 68.06 1.00 9 2 131 129 68.05 1.01 10 2 132 130 67.98 1.00 11 2 134 132 68.00 1.01 12 3 41 38 68.10 1.00 13 3 42 39 68.07 1.01 14 3 43 40 68.08 1.01 15 3 132 129 68.05 1.00 16 3 133 130 68.02 1.02 17 3 134 131 68.01 1.02 18 4 41 37 68.64 0.73 19 4 42 38 68.07 1.01 20 4 44 40 68.13 1.00 21 4 67 63 68.06 1.00 22 4 68 64 68.06 1.00 23 4 69 65 68.08 1.01 24 4 126 122 68.02 1.02 25 4 134 130 68.02 1.02 26 4 136 132 68.00 1.02 27 5 39 34 70.31 0.98 28 5 40 35 70.05 0.95 29 5 41 36 68.66 0.74 30 5 134 129 68.06 1.00 31 5 135 130 68.02 1.02 32 5 136 131 68.01 1.02 33 6 33 27 70.44 0.93 34 6 39 33 70.34 0.99 35 6 40 34 70.31 0.98 36 6 53 47 70.20 0.93 37 6 67 61 68.09 1.01 38 6 136 130 68.02 1.02 39 6 138 132 67.99 1.02 40 7 39 32 70.39 1.01 41 7 136 129 68.05 1.01 42 7 137 130 68.01 1.02 43 7 138 131 68.00 1.02 44 8 40 32 70.54 0.97 45 8 55 47 71.73 0.94 46 8 138 130 68.01 1.02 47 8 140 132 68.00 1.02 48 9 137 128 68.06 1.00 49 9 138 129 68.03 1.02 50 9 139 130 68.00 1.02 51 9 140 131 68.00 1.02 52 10 16 6 363.77 1.79 53 10 17 7 78.31 1.97 54 10 140 130 68.02 1.01 55 11 139 128 68.06 1.00 56 11 140 129 68.03 1.01 57 11 141 130 68.02 1.02 58 12 15 3 503.00 0.88 59 12 120 108 91.17 1.92 60 12 141 129 68.03 1.01 61 14 120 106 108.94 0.46 62 15 57 42 346.80 0.27 63 15 59 44 346.82 0.27 64 15 120 105 110.98 0.56 65 16 57 41 346.83 0.27 66 16 58 42 346.87 0.27 67 17 55 38 346.81 0.27 68 17 56 39 346.85 0.26 69 17 57 40 346.85 0.26 70 17 61 44 346.83 0.27 71 17 62 45 346.83 0.27 72 17 63 46 346.83 0.27 73 17 120 103 131.51 0.49 74 17 122 105 129.74 0.61 75 17 140 123 68.01 1.00 76 18 55 37 346.86 0.27 77 18 56 38 347.06 0.27 78 19 40 21 357.51 0.26 79 19 54 35 346.96 0.22 80 19 55 36 347.06 0.27 81 20 54 34 348.41 0.12 82 20 55 35 348.37 0.10 83 20 56 36 348.35 0.09 84 21 53 32 348.43 0.12 85 21 54 33 348.42 0.12 86 21 87 66 252.32 0.84 87 21 88 67 252.22 0.90 88 21 89 68 252.27 0.86 89 22 33 11 359.07 0.30 90 22 35 13 359.18 0.30 91 22 40 18 359.00 0.23 92 22 52 30 348.44 0.12 93 22 53 31 348.44 0.12 94 23 33 10 359.18 0.32 95 23 51 28 348.99 0.12 96 23 52 29 348.93 0.12 97 23 88 65 252.37 0.84 98 23 89 66 252.31 0.86 99 23 92 69 252.06 0.77 100 24 30 6 359.26 0.40 101 24 31 7 359.21 0.36 102 24 32 8 359.18 0.35 103 24 33 9 359.19 0.33 104 24 42 18 359.00 0.22 105 24 50 26 350.42 0.23 106 24 51 27 349.73 0.03 107 24 92 68 252.37 0.84 108 25 30 5 382.32 8.55 109 25 49 24 350.66 0.21 110 25 50 25 350.54 0.15 111 25 92 67 252.37 0.83 112 25 93 68 252.36 0.83 113 25 96 71 251.78 0.79 114 27 30 3 466.44 2.12 115 27 48 21 357.02 0.01 116 27 49 22 355.31 0.51 117 27 96 69 252.22 0.85 118 28 45 17 358.87 0.16 119 28 46 18 358.76 0.12 120 28 47 19 358.72 0.14 121 28 48 20 357.60 0.26 122 28 49 21 357.02 0.01 123 29 45 16 358.80 0.12 124 30 44 14 358.94 0.12 125 30 45 15 358.85 0.14 126 30 49 19 352.92 0.69 127 31 43 12 358.94 0.12 128 31 44 13 358.92 0.11 129 32 41 9 366.29 2.42 130 32 42 10 363.02 0.96 131 32 43 11 361.72 1.38 132 33 40 7 366.38 2.42 133 33 41 8 366.31 2.44 134 33 42 9 363.04 0.96 135 33 51 18 350.60 0.15 136 33 52 19 350.58 0.15 137 33 53 20 350.54 0.17 138 34 40 6 372.61 0.67 139 34 41 7 366.32 2.43 140 35 38 3 490.07 1.28 141 35 39 4 404.50 10.85 142 35 40 5 372.36 0.55 143 36 39 3 460.14 1.24 144 36 41 5 402.35 3.16 145 40 53 13 350.49 0.14 146 42 50 8 350.78 0.20 147 42 51 9 350.60 0.15 148 42 67 25 348.82 0.16 149 44 49 5 367.50 2.89 150 44 50 6 351.36 0.09 151 44 68 24 348.82 0.15 152 44 69 25 348.75 0.15 153 47 69 22 348.77 0.17 154 47 71 24 348.43 0.14 155 47 72 25 347.12 0.07 156 48 69 21 348.76 0.18 157 49 68 19 348.77 0.18 158 49 69 20 348.75 0.18 159 49 96 47 251.92 0.88 160 50 66 16 348.87 0.17 161 50 67 17 348.79 0.18 162 50 68 18 348.51 0.29 163 50 75 25 254.19 0.94 164 50 92 42 252.37 0.83 165 50 96 46 251.81 0.92 166 51 66 15 348.87 0.17 167 51 67 16 348.83 0.16 168 51 92 41 252.25 0.86 169 52 64 12 349.01 0.17 170 52 65 13 348.95 0.17 171 52 66 14 348.87 0.17 172 52 88 36 252.30 0.87 173 52 92 40 251.71 0.70 174 53 64 11 349.02 0.17 175 53 65 12 348.97 0.16 176 53 67 14 348.94 0.18 177 54 63 9 349.11 0.18 178 54 64 10 349.03 0.16 179 54 82 28 253.09 0.96 180 54 87 33 252.28 0.87 181 54 88 34 252.14 0.92 182 55 62 7 349.16 0.18 183 55 63 8 349.15 0.18 184 55 138 83 68.06 0.99 185 56 60 4 457.18 4.25 186 56 61 5 387.95 0.84 187 56 62 6 349.18 0.18 188 57 60 3 467.72 1.36 189 57 61 4 403.31 7.66 190 59 120 61 144.91 0.01 191 61 116 55 145.12 0.12 192 61 118 57 144.90 0.01 193 61 120 59 144.72 0.01 194 62 80 18 253.08 0.97 195 62 81 19 252.98 0.95 196 62 82 20 252.50 0.83 197 63 78 15 253.22 0.97 198 63 79 16 253.16 0.97 199 63 80 17 253.08 0.97 200 63 82 19 252.87 0.93 201 63 122 59 142.03 0.57 202 63 138 75 68.09 0.99 203 63 140 77 68.00 1.01 204 64 78 14 253.22 0.97 205 64 79 15 253.16 0.97 206 64 82 18 253.09 0.96 207 64 88 24 252.27 0.86 208 64 91 27 252.00 0.83 209 65 77 12 253.32 0.98 210 65 78 13 253.24 0.97 211 65 124 59 138.99 0.72 212 65 138 73 68.02 1.01 213 66 75 9 253.91 0.90 214 66 76 10 253.37 0.97 215 66 77 11 253.33 0.98 216 66 95 29 251.12 0.80 217 67 75 8 308.92 28.41 218 67 124 57 139.03 0.71 219 67 126 59 138.29 0.76 220 67 136 69 68.05 0.99 221 68 74 6 375.62 4.55 222 68 75 7 313.44 30.59 223 69 72 3 476.11 3.46 224 69 73 4 404.67 1.12 225 69 74 5 384.04 0.35 226 69 75 6 375.62 4.55 227 69 134 65 80.24 2.48 228 70 73 3 466.40 1.06 229 70 75 5 395.80 0.20 230 70 105 35 194.77 1.18 231 70 106 36 194.73 1.16 232 70 108 38 192.88 0.55 233 71 108 37 194.47 1.04 234 73 108 35 192.41 0.42 235 73 130 57 115.27 0.49 236 74 108 34 187.10 1.72 237 74 110 36 178.57 0.93 238 74 126 52 138.48 0.82 239 74 129 55 115.67 0.28 240 74 130 56 114.81 0.28 241 74 134 60 77.62 3.79 242 75 95 20 251.88 0.89 243 75 96 21 251.94 0.92 244 75 105 30 194.03 1.01 245 75 108 33 177.06 1.68 246 75 109 34 171.85 0.69 247 75 126 51 138.99 0.72 248 76 109 33 171.84 0.68 249 76 111 35 159.14 0.66 250 76 112 36 146.63 0.29 251 76 124 48 139.13 0.67 252 76 126 50 139.00 0.71 253 77 95 18 251.23 0.94 254 77 104 27 194.05 0.99 255 77 112 35 146.01 0.01 256 77 124 47 139.18 0.67 257 78 112 34 146.00 0.01 258 78 114 36 145.40 0.17 259 78 122 44 142.31 0.68 260 78 123 45 141.06 0.15 261 78 124 46 139.23 0.72 262 79 82 3 518.82 3.11 263 79 91 12 252.16 0.75 264 79 95 16 249.31 0.10 265 79 101 22 194.71 1.16 266 80 114 34 145.38 0.16 267 80 116 36 144.93 0.04 268 80 122 42 144.47 0.01 269 81 116 35 145.09 0.12 270 81 117 36 144.93 0.04 271 82 86 4 448.51 8.29 272 82 91 9 377.24 2.54 273 83 86 3 461.09 2.01 274 85 90 5 452.89 0.82 275 86 90 4 452.89 0.82 276 86 91 5 452.88 0.80 277 87 90 3 472.31 1.37 278 87 91 4 465.78 0.07 279 88 91 3 466.54 0.30 280 88 92 4 464.31 0.81 281 89 92 3 466.00 0.03 282 89 93 4 464.94 0.48 283 90 93 3 476.20 1.43 284 90 94 4 473.36 0.85 285 91 94 3 473.37 0.85 286 91 95 4 473.37 0.85 287 91 101 10 417.80 1.08 288 92 95 3 482.50 4.69 289 92 96 4 484.44 3.72 290 93 96 3 484.44 3.72 291 93 97 4 473.37 0.86 292 94 97 3 465.72 0.15 293 94 98 4 453.64 3.88 294 94 101 7 422.13 1.08 295 95 101 6 417.80 1.08 296 95 102 7 417.78 1.08 297 95 104 9 416.97 0.67 298 95 105 10 416.95 0.67 299 96 102 6 424.17 0.07 300 96 105 9 417.02 0.69 301 97 102 5 444.97 2.58 302 98 101 3 467.42 3.85 303 98 102 4 456.62 2.34 304 99 102 3 472.37 1.38 305 99 103 4 466.91 1.71 306 100 103 3 468.69 0.82 307 100 104 4 466.91 1.71 308 101 104 3 464.19 1.43 309 101 105 4 462.44 0.54 310 102 105 3 477.62 1.25 311 102 106 4 462.42 0.55 312 103 106 3 469.32 2.91 313 103 107 4 459.49 2.01 314 104 107 3 474.29 0.42 315 105 108 3 466.92 1.71 316 109 112 3 499.73 3.75 317 110 125 15 139.13 0.67 318 110 126 16 139.03 0.70 319 110 129 19 115.50 0.00 320 111 124 13 139.42 0.77 321 111 125 14 139.13 0.67 322 112 123 11 142.38 0.64 323 112 124 12 139.30 0.70 324 113 121 8 145.97 0.62 325 113 122 9 144.71 0.00 326 113 123 10 143.31 0.18 327 114 121 7 145.97 0.62 328 114 122 8 144.75 0.01 329 115 119 4 393.48 9.10 330 115 120 5 369.72 0.10 331 115 121 6 254.64 54.95 332 116 119 3 448.91 2.45 333 116 120 4 406.88 6.83 334 116 122 6 374.18 2.32 335 120 140 20 68.08 1.00 336 120 141 21 67.99 1.01 337 121 141 20 67.83 1.05 338 122 139 17 68.06 0.99 339 122 140 18 68.00 1.01 340 123 138 15 68.08 0.99 341 123 139 16 68.02 1.02 342 124 136 12 68.10 1.00 343 124 137 13 68.08 0.99 344 124 138 14 68.02 1.02 345 125 136 11 68.10 1.00 346 125 137 12 68.08 0.99 347 125 139 14 68.06 0.99 348 126 129 3 445.60 1.85 349 126 134 8 226.56 70.70 350 126 135 9 75.68 2.79 351 126 136 10 68.07 0.99 352 127 135 8 77.56 3.73 353 127 136 9 76.06 2.99 354 127 137 10 76.06 2.99 355 128 133 5 407.80 2.18 356 128 134 6 227.07 70.45 357 128 135 7 77.58 3.74 358 129 134 5 374.00 1.84 359 130 134 4 430.44 1.95 360 131 134 3 499.25 2.16