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 75 73 251.47 2.27 2 2 76 74 251.44 2.27 3 2 77 75 251.44 2.27 4 3 77 74 251.44 2.27 5 4 69 65 251.50 2.27 6 4 76 72 251.50 2.27 7 4 77 73 251.47 2.27 8 4 78 74 251.43 2.27 9 4 79 75 251.43 2.27 10 5 33 28 277.72 15.39 11 5 34 29 277.69 15.38 12 5 79 74 251.44 2.27 13 6 31 25 277.98 15.52 14 6 32 26 277.73 15.40 15 6 33 27 277.73 15.38 16 6 34 28 277.70 15.38 17 6 78 72 251.50 2.27 18 6 79 73 251.47 2.27 19 6 80 74 251.43 2.27 20 6 81 75 251.43 2.27 21 7 31 24 278.01 15.50 22 7 32 25 278.01 15.50 23 7 34 27 277.83 15.41 24 7 40 33 277.51 15.30 25 7 43 36 277.42 15.25 26 7 44 37 277.35 15.21 27 7 80 73 251.46 2.27 28 7 81 74 251.44 2.27 29 8 30 22 278.06 15.52 30 8 31 23 278.02 15.50 31 8 44 36 277.42 15.25 32 8 80 72 251.51 2.27 33 8 81 73 251.47 2.27 34 8 82 74 251.44 2.27 35 8 83 75 251.44 2.27 36 9 29 20 278.23 15.59 37 9 30 21 278.10 15.54 38 9 48 39 277.39 15.19 39 9 82 73 251.47 2.27 40 9 83 74 251.44 2.27 41 9 85 76 251.33 2.24 42 10 17 7 297.54 6.73 43 10 29 19 278.46 15.69 44 10 62 52 251.53 2.27 45 10 82 72 251.52 2.27 46 10 83 73 251.47 2.27 47 10 84 74 251.43 2.27 48 10 85 75 251.42 2.27 49 10 121 111 59.01 0.75 50 10 122 112 58.91 0.74 51 10 125 115 46.98 0.43 52 11 17 6 297.56 6.72 53 11 18 7 287.37 11.81 54 11 48 37 277.64 15.28 55 11 54 43 274.64 13.81 56 11 56 45 263.82 8.43 57 11 85 74 251.42 2.27 58 11 86 75 251.41 2.28 59 11 87 76 251.29 2.28 60 11 103 92 136.52 0.85 61 12 16 4 335.76 3.23 62 12 17 5 299.71 5.67 63 12 84 72 251.53 2.26 64 12 85 73 251.46 2.27 65 12 86 74 251.42 2.28 66 12 87 75 251.41 2.28 67 12 106 94 131.25 1.00 68 12 122 110 59.39 0.82 69 12 125 113 58.94 0.64 70 12 126 114 58.51 0.57 71 12 129 117 45.61 0.07 72 12 134 122 20.09 0.31 73 13 16 3 425.74 3.96 74 13 87 74 251.40 2.29 75 13 103 90 136.65 0.89 76 15 106 91 134.97 1.22 77 16 103 87 136.62 0.87 78 16 104 88 136.27 0.73 79 16 105 89 134.99 1.21 80 16 106 90 132.88 0.19 81 17 29 12 311.45 2.16 82 17 103 86 136.50 0.86 83 17 104 87 135.72 0.84 84 17 106 89 127.38 0.29 85 17 109 92 105.03 1.71 86 17 122 105 59.44 0.80 87 18 30 12 311.44 2.15 88 18 48 30 280.15 13.91 89 18 52 34 279.66 13.56 90 18 54 36 277.37 12.60 91 18 92 74 140.75 0.41 92 18 102 84 136.73 0.93 93 18 103 85 136.10 0.69 94 19 27 8 311.85 2.16 95 19 28 9 311.52 2.14 96 19 29 10 311.45 2.16 97 19 101 82 137.33 0.88 98 19 102 83 136.75 0.86 99 19 104 85 136.59 0.93 100 19 109 90 92.63 3.44 101 19 112 93 60.70 0.70 102 19 113 94 60.58 0.76 103 20 27 7 312.07 2.23 104 20 28 8 311.56 2.14 105 20 29 9 311.54 2.14 106 20 30 10 311.50 2.14 107 20 52 32 279.60 13.53 108 20 98 78 138.66 0.70 109 20 100 80 137.80 0.92 110 20 101 81 136.91 0.93 111 21 25 4 382.54 11.74 112 21 26 5 329.89 6.66 113 21 27 6 312.07 2.23 114 21 98 77 138.68 0.70 115 21 99 78 138.62 0.71 116 21 100 79 137.84 0.90 117 22 25 3 419.87 2.92 118 22 26 4 369.88 18.07 119 22 28 6 329.89 6.67 120 22 99 77 138.68 0.70 121 23 97 74 138.78 0.69 122 23 99 76 138.69 0.70 123 25 99 74 138.67 0.70 124 26 114 88 60.55 0.75 125 26 115 89 60.55 0.76 126 27 100 73 138.12 0.77 127 27 102 75 137.17 0.79 128 27 104 77 136.39 0.76 129 27 112 85 60.56 0.78 130 27 113 86 60.55 0.76 131 28 113 85 60.49 0.75 132 28 115 87 60.22 0.70 133 28 118 90 59.60 0.95 134 29 82 53 251.48 2.27 135 29 113 84 60.52 0.76 136 29 118 89 59.09 0.71 137 29 121 92 59.05 0.73 138 29 122 93 58.99 0.70 139 30 48 18 280.37 13.68 140 30 51 21 277.86 12.37 141 30 52 22 277.84 12.37 142 31 47 16 280.47 13.63 143 31 51 20 277.88 12.35 144 31 67 36 251.66 2.21 145 31 78 47 251.66 2.21 146 31 80 49 251.50 2.26 147 31 82 51 251.47 2.27 148 32 43 11 308.56 5.01 149 32 47 15 282.43 12.62 150 33 43 10 308.89 5.10 151 33 46 13 308.89 5.10 152 34 38 4 380.38 0.13 153 34 40 6 325.96 8.52 154 34 43 9 308.89 5.10 155 35 38 3 432.62 0.19 156 35 46 11 347.38 0.73 157 38 42 4 421.25 1.30 158 38 43 5 421.22 1.29 159 38 46 8 392.21 3.94 160 39 42 3 431.90 1.48 161 39 43 4 424.79 1.03 162 40 43 3 430.86 2.00 163 40 44 4 423.95 0.62 164 40 81 41 251.50 2.25 165 40 83 43 251.47 2.27 166 41 44 3 435.44 1.42 167 41 45 4 428.62 1.67 168 41 58 17 254.47 0.77 169 41 83 42 251.47 2.27 170 42 45 3 443.14 2.43 171 42 46 4 428.63 1.67 172 43 46 3 434.88 1.45 173 43 47 4 423.94 0.68 174 44 47 3 443.14 2.43 175 44 48 4 423.93 0.68 176 44 58 14 254.48 0.77 177 44 83 39 251.47 2.26 178 45 48 3 437.69 1.44 179 45 49 4 429.96 2.43 180 45 56 11 259.21 0.77 181 45 58 13 254.49 0.77 182 45 85 40 251.44 2.26 183 46 49 3 437.13 1.16 184 46 50 4 423.85 0.65 185 47 50 3 430.29 1.83 186 47 51 4 423.85 0.65 187 48 51 3 437.69 1.20 188 48 52 4 421.59 1.78 189 48 53 5 410.99 1.81 190 48 54 6 387.20 0.99 191 48 85 37 251.43 2.27 192 49 52 3 430.22 2.53 193 49 53 4 391.57 3.20 194 49 54 5 379.51 2.75 195 49 55 6 379.47 2.73 196 49 93 44 151.58 5.82 197 50 93 43 151.57 5.82 198 50 95 45 138.63 0.65 199 51 93 42 140.74 0.41 200 51 94 43 139.65 0.21 201 51 95 44 138.63 0.65 202 51 97 46 138.59 0.67 203 51 98 47 138.46 0.67 204 52 92 40 140.76 0.41 205 52 93 41 140.73 0.41 206 52 101 49 137.18 0.99 207 53 90 37 167.65 1.59 208 53 93 40 151.58 5.81 209 54 87 33 251.28 2.23 210 54 89 35 186.03 0.32 211 54 90 36 166.53 1.03 212 54 91 37 164.82 1.88 213 54 92 38 151.66 5.78 214 55 87 32 251.31 2.25 215 55 88 33 232.61 7.16 216 55 89 34 188.67 1.19 217 56 85 29 251.47 2.23 218 56 86 30 251.41 2.26 219 56 88 32 231.54 7.70 220 57 85 28 251.50 2.23 221 57 86 29 251.42 2.27 222 57 88 31 251.16 2.19 223 58 83 25 251.69 2.21 224 58 84 26 251.66 2.20 225 58 85 27 251.50 2.23 226 59 84 25 251.69 2.21 227 59 86 27 251.58 2.25 228 59 132 73 25.70 0.53 229 59 134 75 23.14 0.61 230 60 83 23 251.78 2.19 231 60 84 24 251.69 2.21 232 60 128 68 43.85 0.00 233 60 132 72 27.36 0.41 234 61 81 20 251.84 2.21 235 61 82 21 251.80 2.19 236 61 83 22 251.78 2.19 237 61 128 67 43.38 0.23 238 62 82 20 251.82 2.21 239 62 83 21 251.79 2.19 240 62 84 22 251.78 2.19 241 62 121 59 58.93 0.74 242 62 124 62 46.99 0.43 243 62 125 63 46.95 0.45 244 62 128 66 42.45 0.69 245 63 81 18 252.00 2.14 246 63 82 19 251.84 2.21 247 63 121 58 58.91 0.74 248 64 79 15 252.16 2.11 249 64 80 16 252.09 2.12 250 64 81 17 252.00 2.14 251 64 121 57 58.91 0.74 252 65 79 14 252.30 2.04 253 65 80 15 252.14 2.12 254 65 82 17 252.11 2.12 255 65 117 52 58.84 0.72 256 65 120 55 58.91 0.74 257 65 121 56 58.76 0.70 258 66 77 11 282.85 13.13 259 66 78 12 268.68 6.11 260 66 79 13 252.30 2.04 261 67 77 10 283.18 13.28 262 67 78 11 268.80 6.12 263 67 80 13 268.69 6.10 264 68 75 7 318.69 4.00 265 68 76 8 317.36 3.64 266 68 77 9 283.18 13.28 267 69 75 6 318.73 4.00 268 69 76 7 317.70 3.65 269 69 78 9 317.43 3.60 270 70 74 4 362.19 10.86 271 70 75 5 327.34 0.30 272 70 76 6 318.73 4.00 273 71 74 3 425.97 3.13 274 71 76 5 401.80 8.94 275 82 121 39 58.91 0.74 276 84 125 41 46.97 0.45 277 84 128 44 42.45 0.69 278 84 129 45 42.39 0.68 279 84 132 48 26.65 0.06 280 84 134 50 20.62 0.98 281 85 134 49 20.62 0.98 282 86 134 48 20.62 0.98 283 87 103 16 136.69 0.91 284 92 101 9 137.47 1.01 285 92 102 10 137.27 1.03 286 92 103 11 137.26 1.03 287 93 101 8 137.60 0.96 288 94 98 4 346.08 1.59 289 94 99 5 343.33 2.96 290 94 100 6 206.43 34.87 291 94 101 7 205.90 35.10 292 95 98 3 431.78 0.76 293 104 108 4 424.24 0.23 294 104 109 5 409.61 2.05 295 104 112 8 373.88 4.22 296 105 108 3 432.93 3.19 297 105 109 4 424.24 0.23 298 106 109 3 438.68 4.83 299 106 110 4 424.24 0.23 300 106 122 16 161.40 49.81 301 106 126 20 59.37 0.57 302 107 110 3 426.75 1.49 303 107 111 4 424.19 0.21 304 108 111 3 426.89 0.50 305 108 112 4 422.13 1.02 306 109 112 3 423.01 0.53 307 109 113 4 422.03 0.98 308 109 122 13 177.47 57.86 309 110 122 12 188.04 63.13 310 110 126 16 160.90 50.05 311 113 118 5 405.13 1.61 312 113 119 6 400.54 3.89 313 113 122 9 364.34 8.30 314 114 119 5 416.56 0.99 315 115 118 3 430.00 1.94 316 115 119 4 423.10 1.38 317 116 119 3 435.04 2.10 318 116 120 4 423.10 1.38 319 117 120 3 434.13 2.56 320 117 121 4 424.73 0.56 321 118 121 3 428.93 0.04 322 118 122 4 424.73 0.53 323 119 122 3 427.57 1.83 324 119 123 4 425.91 1.12 325 120 123 3 442.91 0.29 326 120 124 4 425.92 1.13 327 121 124 3 428.74 0.35 328 121 125 4 425.90 1.12 329 122 125 3 425.89 1.13 330 122 126 4 425.84 1.16 331 123 126 3 426.12 1.02 332 123 127 4 428.06 0.04 333 124 127 3 434.56 0.12 334 124 128 4 428.93 0.47 335 125 128 3 435.84 2.98 336 125 129 4 427.14 0.42 337 126 129 3 448.45 3.32 338 126 130 4 431.70 0.93 339 127 130 3 450.86 2.12 340 128 131 3 450.86 2.12 341 128 132 4 443.05 6.03 342 129 132 3 427.94 0.02 343 129 133 4 422.33 2.78 344 129 134 5 359.19 2.24 345 130 133 3 422.33 2.78