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 6 27 21 65.81 0.66 2 6 28 22 65.90 0.66 3 6 29 23 65.89 0.66 4 6 30 24 65.81 0.66 5 6 31 25 65.84 0.67 6 6 35 29 65.55 0.77 7 6 127 121 65.36 0.79 8 6 135 129 65.38 0.79 9 6 136 130 65.28 0.76 10 6 137 131 65.20 0.73 11 6 138 132 65.19 0.73 12 7 27 20 65.94 0.66 13 7 28 21 65.94 0.66 14 7 29 22 65.95 0.66 15 7 138 131 65.20 0.73 16 7 140 133 65.19 0.73 17 8 25 17 66.09 0.67 18 8 26 18 66.07 0.67 19 8 27 19 65.95 0.66 20 8 40 32 65.36 0.78 21 8 42 34 65.27 0.76 22 8 127 119 65.77 0.71 23 8 137 129 65.38 0.79 24 8 138 130 65.30 0.76 25 8 139 131 65.20 0.73 26 8 140 132 65.20 0.73 27 9 25 16 66.10 0.67 28 9 26 17 66.11 0.67 29 9 140 131 65.20 0.73 30 10 23 13 67.15 0.29 31 10 24 14 66.25 0.72 32 10 25 15 66.11 0.67 33 10 42 32 65.36 0.78 34 10 104 94 66.26 0.73 35 10 119 109 65.21 0.73 36 10 140 130 65.34 0.78 37 10 141 131 65.23 0.74 38 10 142 132 65.15 0.73 39 10 143 133 65.17 0.74 40 11 23 12 67.17 0.29 41 11 24 13 66.27 0.72 42 11 26 15 66.36 0.67 43 11 142 131 65.22 0.74 44 11 143 132 65.21 0.73 45 12 116 104 73.59 3.12 46 12 142 130 65.25 0.74 47 12 143 131 65.21 0.73 48 12 145 133 65.19 0.74 49 13 21 8 79.39 0.91 50 13 22 9 73.61 0.04 51 13 23 10 68.28 0.32 52 13 24 11 67.74 0.05 53 13 143 130 65.29 0.76 54 13 144 131 65.21 0.74 55 13 145 132 65.19 0.74 56 14 145 131 65.20 0.74 57 15 19 4 447.13 0.34 58 15 21 6 363.63 3.02 59 15 108 93 127.48 0.94 60 15 144 129 65.37 0.78 61 15 145 130 65.28 0.74 62 15 146 131 65.19 0.73 63 15 147 132 65.15 0.75 64 16 19 3 473.10 2.33 65 16 108 92 143.10 0.39 66 16 146 130 65.27 0.75 67 16 147 131 65.18 0.73 68 17 108 91 150.71 0.56 69 17 109 92 151.38 0.40 70 17 110 93 151.66 0.40 71 17 112 95 151.88 0.48 72 17 146 129 65.36 0.78 73 17 147 130 65.29 0.75 74 18 107 89 153.10 0.69 75 18 108 90 151.94 0.28 76 18 110 92 151.95 0.28 77 19 107 88 157.10 0.70 78 19 108 89 153.13 0.66 79 20 105 85 171.76 1.82 80 20 106 86 168.27 2.79 81 20 107 87 157.10 0.70 82 21 104 83 186.83 0.24 83 21 105 84 172.70 1.35 84 21 106 85 170.98 1.97 85 21 108 87 170.00 1.93 86 21 144 123 65.33 0.77 87 22 55 33 189.38 0.40 88 22 103 81 189.15 0.30 89 22 104 82 186.81 0.26 90 22 105 83 182.43 0.64 91 23 103 80 189.16 0.30 92 23 104 81 187.35 0.01 93 23 106 83 187.22 0.04 94 23 119 96 153.48 0.54 95 23 144 121 65.20 0.73 96 24 100 76 189.81 0.48 97 24 102 78 189.58 0.47 98 24 103 79 189.40 0.41 99 25 82 57 189.72 0.48 100 25 100 75 190.25 0.29 101 25 101 76 189.81 0.48 102 25 102 77 189.66 0.51 103 25 104 79 189.59 0.47 104 26 99 73 192.12 0.23 105 26 100 74 191.12 0.15 106 27 30 3 508.11 0.89 107 27 38 11 207.01 0.68 108 27 40 13 193.58 0.04 109 27 59 32 206.53 1.44 110 27 95 68 218.91 1.93 111 27 98 71 205.50 1.74 112 27 99 72 205.47 1.74 113 27 101 74 191.30 0.10 114 27 127 100 151.17 0.38 115 28 98 70 207.28 2.62 116 29 98 69 222.86 0.33 117 30 34 4 454.47 1.56 118 30 35 5 449.21 0.40 119 30 95 65 228.25 0.21 120 30 96 66 226.67 1.48 121 30 97 67 225.08 0.71 122 30 98 68 223.50 0.04 123 31 34 3 470.99 1.29 124 31 35 4 469.05 0.32 125 31 129 98 151.12 0.39 126 31 135 104 110.28 0.58 127 33 129 96 151.14 0.39 128 33 130 97 151.10 0.38 129 33 131 98 151.10 0.38 130 34 95 61 279.18 0.96 131 34 96 62 273.06 1.80 132 34 129 95 151.12 0.38 133 35 38 3 528.74 0.49 134 35 84 49 281.61 0.06 135 35 94 59 280.05 0.57 136 35 95 60 279.22 0.94 137 35 127 92 151.19 0.38 138 35 128 93 151.14 0.36 139 35 129 94 151.08 0.39 140 35 135 100 110.23 0.60 141 36 84 48 281.62 0.06 142 36 85 49 281.62 0.06 143 36 86 50 281.39 0.04 144 36 94 58 280.05 0.57 145 36 128 92 151.13 0.36 146 36 129 93 151.09 0.37 147 36 130 94 150.22 0.26 148 36 132 96 126.27 1.19 149 37 84 47 281.61 0.06 150 37 85 48 281.61 0.07 151 37 127 90 151.15 0.35 152 37 128 91 151.12 0.36 153 37 132 95 121.48 2.27 154 38 83 45 281.77 0.04 155 38 84 46 281.66 0.07 156 38 101 63 281.61 0.07 157 38 126 88 151.19 0.37 158 38 127 89 151.13 0.36 159 39 82 43 281.85 0.01 160 39 83 44 281.77 0.04 161 39 124 85 152.50 0.42 162 39 125 86 151.75 0.11 163 39 126 87 151.35 0.29 164 40 81 41 282.00 0.00 165 40 82 42 281.98 0.01 166 40 101 61 282.04 0.04 167 40 123 83 153.50 0.53 168 40 124 84 152.20 0.34 169 40 127 87 151.16 0.35 170 40 139 99 67.21 0.77 171 41 79 38 301.22 2.02 172 41 80 39 282.14 0.06 173 41 81 40 282.02 0.01 174 41 121 80 153.84 0.61 175 41 122 81 153.69 0.59 176 41 123 82 153.45 0.49 177 42 79 37 301.83 2.29 178 42 80 38 284.88 1.40 179 42 82 40 282.25 0.02 180 42 119 77 154.53 0.34 181 42 120 78 154.27 0.42 182 42 121 79 153.80 0.62 183 42 122 80 153.75 0.62 184 42 139 97 66.28 0.48 185 42 140 98 66.27 0.48 186 42 141 99 66.12 0.51 187 43 78 35 303.29 1.66 188 43 79 36 303.04 1.71 189 43 119 76 154.53 0.34 190 43 120 77 154.48 0.34 191 43 122 79 153.79 0.65 192 44 49 5 445.44 0.33 193 44 51 7 415.44 0.38 194 44 73 29 303.33 1.68 195 44 75 31 322.30 9.93 196 44 78 34 303.31 1.66 197 44 79 35 303.30 1.66 198 44 80 36 303.30 1.66 199 44 118 74 154.75 0.32 200 44 119 75 154.63 0.28 201 45 48 3 481.33 1.51 202 45 49 4 449.01 1.40 203 45 117 72 154.78 0.31 204 46 49 3 462.17 1.45 205 46 75 29 323.50 9.33 206 46 78 32 328.36 6.95 207 46 109 63 281.40 0.07 208 47 109 62 281.39 0.06 209 48 108 60 281.56 0.01 210 48 109 61 281.21 0.03 211 48 112 64 227.23 3.75 212 48 113 65 230.86 1.94 213 48 117 69 154.77 0.31 214 48 146 98 65.44 0.77 215 49 106 57 282.03 0.02 216 49 107 58 281.89 0.01 217 49 108 59 281.60 0.02 218 49 117 68 154.74 0.31 219 49 119 70 154.65 0.28 220 49 144 95 65.50 0.74 221 50 106 56 282.06 0.03 222 50 107 57 281.91 0.00 223 50 109 59 281.58 0.02 224 51 54 3 553.49 0.73 225 51 73 22 339.29 2.42 226 51 80 29 339.31 2.43 227 51 104 53 282.89 0.20 228 51 105 54 282.35 0.07 229 51 106 55 282.16 0.08 230 52 105 53 282.94 0.22 231 52 106 54 282.34 0.07 232 52 107 55 282.23 0.06 233 53 104 51 284.18 0.20 234 53 105 52 282.94 0.22 235 54 69 15 339.51 2.46 236 54 71 17 339.44 2.42 237 54 73 19 339.69 2.47 238 54 80 26 339.66 2.48 239 54 82 28 339.51 2.46 240 54 102 48 284.72 0.14 241 54 103 49 284.49 0.13 242 54 104 50 284.17 0.19 243 55 69 14 339.51 2.46 244 55 102 47 284.73 0.14 245 55 103 48 284.56 0.17 246 55 105 50 284.29 0.15 247 56 60 4 457.28 6.65 248 56 65 9 341.43 1.51 249 56 69 13 339.50 2.46 250 56 102 46 284.72 0.12 251 57 60 3 483.11 2.23 252 57 100 43 285.52 0.10 253 57 101 44 285.25 0.09 254 57 102 45 284.95 0.01 255 58 99 41 286.13 0.04 256 58 100 42 286.01 0.08 257 59 95 36 327.93 2.68 258 59 97 38 317.26 1.51 259 59 98 39 316.59 1.19 260 59 99 40 287.82 0.81 261 59 100 41 286.04 0.08 262 59 101 42 286.00 0.08 263 60 65 5 406.05 4.72 264 60 68 8 366.13 9.60 265 60 69 9 350.68 5.96 266 60 84 24 340.21 2.41 267 60 95 35 328.03 2.63 268 60 101 41 286.02 0.09 269 61 93 32 329.35 2.58 270 61 94 33 329.32 2.59 271 62 65 3 470.82 0.59 272 62 67 5 442.49 0.72 273 62 68 6 424.16 2.30 274 62 87 25 339.98 2.27 275 62 93 31 332.25 1.13 276 63 93 30 338.58 1.57 277 64 67 3 475.36 1.09 278 65 68 3 479.85 3.44 279 65 69 4 455.74 0.64 280 66 69 3 467.36 5.15 281 67 87 20 340.22 2.29 282 68 84 16 340.53 2.41 283 68 85 17 340.49 2.40 284 68 86 18 340.43 2.39 285 68 87 19 340.38 2.37 286 68 93 25 332.90 1.37 287 69 83 14 340.85 2.35 288 69 84 15 340.50 2.39 289 69 101 32 285.76 0.07 290 69 102 33 284.81 0.12 291 70 82 12 341.05 2.31 292 70 83 13 340.86 2.35 293 71 81 10 341.10 2.30 294 71 82 11 341.05 2.32 295 71 83 12 341.03 2.31 296 72 80 8 350.80 1.43 297 72 81 9 346.77 0.53 298 73 79 6 385.63 1.80 299 73 80 7 350.81 1.43 300 74 77 3 474.26 0.13 301 74 78 4 438.66 3.97 302 74 79 5 403.49 5.74 303 74 81 7 387.02 2.50 304 75 78 3 445.00 1.00 305 79 122 43 153.79 0.65 306 80 104 24 282.34 0.07 307 82 101 19 284.74 0.14 308 82 102 20 284.60 0.16 309 82 104 22 284.24 0.23 310 84 93 9 409.17 2.46 311 84 94 10 403.64 0.74 312 84 95 11 403.46 0.65 313 84 101 17 285.25 0.34 314 86 89 3 506.12 4.32 315 86 90 4 485.50 2.29 316 86 91 5 433.99 0.49 317 86 92 6 438.48 3.85 318 86 93 7 406.87 1.31 319 86 94 8 403.88 0.86 320 87 93 6 438.72 3.73 321 88 91 3 492.29 1.79 322 88 92 4 444.85 2.38 323 88 93 5 438.73 3.72 324 91 94 3 469.91 0.75 325 91 130 39 150.53 0.10 326 94 130 36 150.32 0.21 327 95 101 6 388.16 4.46 328 100 103 3 527.93 1.85 329 104 119 15 153.53 0.53 330 108 112 4 455.99 1.84 331 108 144 36 65.48 0.76 332 108 146 38 65.28 0.75 333 109 112 3 462.45 0.12 334 112 146 34 65.51 0.74 335 113 146 33 65.53 0.76 336 114 146 32 65.53 0.76 337 114 147 33 65.51 0.76 338 115 145 30 65.61 0.74 339 115 146 31 65.56 0.76 340 116 143 27 65.88 0.64 341 116 144 28 65.84 0.64 342 116 145 29 65.57 0.77 343 117 143 26 65.86 0.64 344 117 144 27 65.78 0.67 345 118 141 23 66.16 0.54 346 118 142 24 66.02 0.57 347 118 143 25 65.79 0.66 348 119 141 22 66.13 0.52 349 119 142 23 65.86 0.64 350 119 143 24 65.73 0.69 351 120 141 21 66.12 0.51 352 121 139 18 66.25 0.48 353 121 141 20 66.12 0.51 354 124 127 3 541.62 2.93 355 124 139 15 68.44 0.43 356 126 134 8 242.93 67.31 357 127 134 7 243.06 67.24 358 127 135 8 242.87 67.31 359 127 137 10 238.00 69.66 360 127 139 12 237.72 69.53 361 128 132 4 432.54 3.81 362 128 133 5 391.94 16.46 363 128 134 6 367.67 4.94 364 128 135 7 242.93 67.31 365 129 132 3 470.36 1.41 366 129 133 4 432.54 3.81 367 129 135 6 391.62 16.63