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 90 89 220.22 0.51 2 1 91 90 220.15 0.51 3 1 92 91 220.14 0.51 4 2 31 29 350.26 0.05 5 2 32 30 350.23 0.07 6 2 38 36 349.43 0.38 7 2 92 90 220.14 0.51 8 2 94 92 220.11 0.49 9 3 30 27 350.42 0.09 10 3 31 28 350.26 0.05 11 3 32 29 350.26 0.05 12 3 91 88 220.25 0.51 13 3 92 89 220.21 0.52 14 3 93 90 220.13 0.48 15 3 94 91 220.12 0.49 16 4 29 25 350.62 0.01 17 4 30 26 350.44 0.09 18 4 32 28 350.31 0.03 19 4 38 34 349.51 0.38 20 4 41 37 349.40 0.37 21 4 42 38 349.38 0.37 22 4 93 89 220.20 0.52 23 4 94 90 220.17 0.51 24 4 96 92 220.12 0.49 25 5 27 22 351.11 0.03 26 5 28 23 350.99 0.01 27 5 29 24 350.81 0.09 28 5 42 37 349.42 0.36 29 5 93 88 220.28 0.51 30 5 94 89 220.22 0.52 31 5 95 90 220.16 0.51 32 5 96 91 220.16 0.51 33 6 27 21 351.12 0.03 34 6 28 22 351.11 0.03 35 6 42 36 349.49 0.37 36 6 46 40 349.27 0.42 37 6 96 90 220.18 0.51 38 6 98 92 219.58 0.30 39 7 14 7 355.49 0.13 40 7 27 20 351.12 0.03 41 7 75 68 220.24 0.52 42 7 95 88 220.28 0.51 43 7 96 89 220.21 0.52 44 7 97 90 220.16 0.51 45 7 98 91 220.11 0.49 46 7 128 121 70.50 1.01 47 7 132 125 61.30 0.46 48 8 14 6 356.24 0.49 49 8 15 7 355.48 0.14 50 8 46 38 349.49 0.35 51 8 52 44 347.82 0.26 52 8 54 46 317.92 2.43 53 8 98 90 220.17 0.51 54 8 99 91 220.12 0.49 55 8 100 92 220.02 0.48 56 8 110 102 146.04 0.04 57 9 13 4 375.50 3.20 58 9 14 5 356.24 0.50 59 9 132 123 65.52 1.02 60 9 133 124 64.20 0.37 61 9 136 127 56.20 0.43 62 10 13 3 474.11 4.70 63 10 100 90 220.21 0.52 64 10 110 100 146.37 0.06 65 12 112 100 145.88 0.03 66 12 113 101 144.96 0.34 67 13 110 97 146.31 0.02 68 13 111 98 145.88 0.04 69 13 112 99 144.73 0.44 70 14 109 95 146.41 0.03 71 14 110 96 145.28 0.34 72 14 111 97 144.94 0.35 73 14 113 99 142.22 0.03 74 14 129 115 70.56 1.03 75 15 28 13 353.93 0.94 76 15 46 31 349.47 0.35 77 15 50 35 348.69 0.32 78 15 52 37 348.38 0.24 79 15 105 90 149.84 0.69 80 15 109 94 146.27 0.01 81 15 110 95 145.20 0.30 82 16 25 9 354.82 1.17 83 16 26 10 354.65 1.18 84 16 27 11 354.01 0.98 85 16 108 92 146.29 0.01 86 16 109 93 146.25 0.01 87 16 111 95 144.94 0.35 88 16 116 100 86.61 3.98 89 16 121 105 73.75 2.19 90 16 125 109 73.52 2.10 91 17 25 8 354.94 1.12 92 17 26 9 354.78 1.19 93 17 28 11 354.08 0.94 94 17 49 32 348.75 0.32 95 17 50 33 348.69 0.32 96 17 108 91 146.31 0.02 97 18 23 5 360.08 0.88 98 18 24 6 360.06 0.88 99 18 25 7 354.94 1.12 100 18 109 91 146.34 0.01 101 19 22 3 458.10 0.05 102 19 23 4 360.38 0.73 103 19 24 5 360.08 0.88 104 19 26 7 354.97 1.12 105 19 84 65 221.25 0.73 106 21 84 63 221.24 0.72 107 21 86 65 221.41 0.71 108 21 87 66 221.41 0.71 109 22 82 60 220.76 0.59 110 22 84 62 221.17 0.73 111 22 122 100 73.60 2.13 112 24 120 96 73.74 2.18 113 24 121 97 73.62 2.14 114 24 122 98 73.62 2.13 115 25 109 84 146.29 0.03 116 25 119 94 73.77 2.18 117 25 120 95 73.75 2.19 118 25 121 96 73.62 2.14 119 25 122 97 73.61 2.14 120 25 125 100 73.55 2.11 121 26 122 96 73.39 2.04 122 26 125 99 72.63 2.00 123 27 95 68 220.24 0.52 124 27 125 98 72.53 1.99 125 27 128 101 70.51 1.01 126 28 46 18 349.16 0.47 127 28 49 21 348.35 0.24 128 28 50 22 348.20 0.32 129 29 45 16 349.23 0.42 130 29 49 20 348.33 0.25 131 30 45 15 349.20 0.41 132 31 44 13 357.66 1.43 133 31 91 60 220.38 0.46 134 32 36 4 454.70 4.12 135 32 37 5 419.28 9.67 136 32 38 6 369.62 2.42 137 32 41 9 357.68 1.42 138 33 36 3 482.07 1.56 139 33 44 11 370.14 1.65 140 36 40 4 465.96 2.86 141 36 41 5 465.47 2.64 142 36 44 8 448.66 2.47 143 37 40 3 475.30 1.43 144 37 41 4 471.45 0.48 145 38 41 3 475.29 1.44 146 38 42 4 471.45 0.48 147 38 94 56 220.31 0.48 148 38 96 58 220.27 0.49 149 39 42 3 484.51 3.15 150 39 43 4 478.14 0.04 151 39 56 17 225.66 1.55 152 39 71 32 221.07 0.11 153 39 72 33 221.00 0.14 154 39 96 57 220.28 0.49 155 40 43 3 483.04 1.73 156 40 44 4 475.30 1.46 157 41 44 3 478.14 0.04 158 41 45 4 471.25 0.51 159 42 45 3 479.68 2.41 160 42 46 4 471.17 0.55 161 42 56 14 226.22 1.28 162 42 96 54 220.25 0.51 163 42 98 56 220.09 0.52 164 43 46 3 485.67 5.41 165 43 47 4 470.81 0.41 166 43 54 11 260.13 0.22 167 43 56 13 235.45 0.73 168 44 47 3 477.90 3.29 169 44 48 4 476.78 3.44 170 45 48 3 484.54 1.67 171 45 49 4 470.18 0.14 172 46 49 3 488.48 0.30 173 46 50 4 470.16 0.12 174 46 51 5 470.15 0.12 175 46 52 6 443.20 7.24 176 46 54 8 369.16 1.04 177 46 98 52 220.18 0.51 178 47 50 3 488.48 0.30 179 47 51 4 454.67 1.37 180 47 52 5 440.19 5.73 181 47 53 6 403.03 10.41 182 49 107 58 146.31 0.01 183 50 104 54 153.91 2.44 184 50 105 55 149.06 1.07 185 50 106 56 147.01 0.09 186 50 107 57 146.31 0.01 187 51 103 52 154.12 2.37 188 51 104 53 153.93 2.45 189 51 106 55 147.05 0.07 190 52 100 48 219.66 0.62 191 52 102 50 184.91 0.24 192 52 103 51 153.95 2.45 193 52 104 52 153.91 2.44 194 52 105 53 149.93 0.63 195 53 100 47 219.78 0.58 196 53 101 48 216.58 1.30 197 53 102 49 178.78 0.90 198 53 103 50 162.07 1.18 199 54 98 44 220.21 0.53 200 54 99 45 220.12 0.51 201 54 100 46 219.72 0.64 202 54 101 47 217.42 0.47 203 55 98 43 220.21 0.53 204 55 99 44 220.19 0.52 205 55 101 46 219.69 0.60 206 56 72 16 222.06 0.57 207 56 96 40 220.38 0.53 208 56 97 41 220.34 0.51 209 56 98 42 220.21 0.53 210 57 72 15 222.09 0.58 211 57 97 40 220.38 0.53 212 57 98 41 220.27 0.52 213 57 99 42 220.25 0.53 214 57 136 79 51.86 0.35 215 58 72 14 222.11 0.58 216 58 73 15 222.09 0.58 217 58 139 81 38.81 0.35 218 59 72 13 222.14 0.58 219 59 73 14 222.11 0.58 220 59 135 76 52.37 0.11 221 59 138 79 49.11 0.46 222 59 139 80 38.83 0.34 223 59 142 83 33.06 0.66 224 60 70 10 223.52 0.72 225 60 72 12 222.16 0.58 226 61 70 9 223.56 0.72 227 62 70 8 223.54 0.73 228 63 69 6 223.63 0.73 229 63 70 7 223.56 0.72 230 64 68 4 405.86 6.02 231 64 69 5 223.62 0.70 232 65 68 3 484.17 1.12 233 72 96 24 220.53 0.49 234 74 77 3 515.36 1.00 235 74 94 20 220.66 0.51 236 74 95 21 220.62 0.52 237 74 96 22 220.54 0.49 238 75 95 20 220.67 0.51 239 75 96 21 220.62 0.51 240 75 97 22 220.54 0.49 241 75 128 53 70.36 1.02 242 75 131 56 63.87 0.50 243 75 132 57 61.30 0.46 244 75 135 60 51.95 0.39 245 76 95 19 220.66 0.50 246 76 128 52 70.34 1.02 247 76 131 55 63.87 0.50 248 77 92 15 224.62 0.50 249 77 93 16 223.13 0.14 250 77 94 17 220.88 0.57 251 78 91 13 226.48 0.36 252 78 92 14 225.62 0.00 253 78 93 15 224.57 0.50 254 78 95 17 223.12 0.14 255 78 124 46 72.55 2.04 256 78 128 50 70.25 1.03 257 79 90 11 226.71 0.30 258 79 91 12 225.83 0.04 259 79 92 13 225.62 0.00 260 80 90 10 226.71 0.30 261 80 91 11 226.65 0.29 262 80 93 13 225.78 0.06 263 80 122 42 73.12 1.92 264 81 88 7 305.95 34.04 265 81 89 8 238.97 5.79 266 81 90 9 226.75 0.28 267 82 88 6 250.62 0.01 268 82 89 7 238.97 5.79 269 82 91 9 226.93 0.23 270 82 122 40 72.66 1.68 271 83 88 5 250.62 0.01 272 84 87 3 492.14 2.66 273 84 88 4 383.01 0.18 274 84 89 5 406.57 11.60 275 95 128 33 70.30 1.04 276 97 132 35 61.30 0.46 277 97 135 38 52.38 0.18 278 97 136 39 51.76 0.29 279 97 139 42 38.85 0.35 280 100 110 10 146.38 0.05 281 105 108 3 530.52 1.60 282 105 110 5 479.14 0.83 283 111 116 5 404.32 2.67 284 111 119 8 250.59 1.82 285 112 115 3 477.98 0.03 286 112 116 4 472.26 2.80 287 113 116 3 477.65 0.14 288 113 129 16 73.45 2.27 289 113 133 20 72.01 1.79 290 115 118 3 498.18 1.61 291 115 119 4 473.78 0.18 292 116 119 3 473.78 0.18 293 116 121 5 462.34 1.47 294 116 126 10 73.73 2.18 295 117 126 9 238.47 2.65 296 119 126 7 424.36 2.93 297 121 125 4 452.78 5.88 298 121 126 5 435.27 2.89 299 122 125 3 481.10 1.78 300 124 127 3 467.51 2.10 301 124 128 4 463.23 1.73 302 125 128 3 475.69 2.17 303 125 129 4 465.44 0.66 304 126 129 3 481.99 0.27 305 126 130 4 465.48 0.67 306 127 130 3 490.44 0.44 307 127 131 4 480.71 0.34 308 128 131 3 474.10 3.65 309 128 132 4 474.10 3.65 310 129 132 3 479.32 1.04 311 129 133 4 474.00 3.70 312 130 133 3 481.20 2.33 313 130 134 4 465.39 0.58 314 131 134 3 483.94 0.78 315 131 135 4 463.27 1.62 316 132 135 3 478.41 2.85 317 132 136 4 465.55 0.33 318 133 136 3 488.50 1.72 319 133 137 4 469.12 1.79 320 134 137 3 475.59 0.47 321 134 138 4 473.67 1.43 322 135 138 3 482.49 3.64 323 135 139 4 460.88 0.01 324 136 139 3 473.47 0.10 325 136 140 4 467.60 3.37 326 137 140 3 470.11 2.12 327 137 141 4 466.96 3.70 328 138 141 3 471.18 2.06 329 138 142 4 469.84 2.26 330 139 142 3 472.98 0.70 331 139 143 4 469.84 2.25 332 140 143 3 483.61 0.69 333 140 144 4 475.68 2.46 334 141 144 3 481.64 0.52 335 141 145 4 474.12 3.25 336 142 145 3 478.10 1.26 337 142 146 4 467.24 0.19 338 143 146 3 473.80 0.08 339 143 147 4 469.35 0.87 340 144 147 3 469.35 0.87 341 144 148 4 469.28 0.91 342 145 148 3 469.35 0.91