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 5 450.13 1.82 2 2 73 71 24.52 1.06 3 2 76 74 24.52 1.06 4 2 127 125 26.71 1.21 5 2 128 126 25.39 0.71 6 2 131 129 24.45 1.03 7 3 6 3 476.88 1.56 8 3 7 4 476.88 1.56 9 4 7 3 476.95 1.59 10 4 8 4 481.84 0.85 11 5 8 3 481.85 0.84 12 5 9 4 481.84 0.85 13 6 9 3 481.84 0.84 14 6 10 4 476.93 1.58 15 6 124 118 50.62 0.24 16 6 127 121 50.59 0.25 17 7 10 3 481.81 0.86 18 7 11 4 472.90 3.59 19 7 73 66 49.66 0.24 20 7 74 67 50.80 0.32 21 8 11 3 476.94 1.56 22 8 12 4 469.24 2.94 23 9 12 3 478.24 1.31 24 9 13 4 469.23 2.95 25 9 121 112 61.36 0.80 26 9 124 115 61.29 0.77 27 10 13 3 475.38 0.12 28 10 14 4 475.36 0.13 29 10 70 60 61.13 0.65 30 10 124 114 61.35 0.79 31 10 125 115 61.33 0.78 32 10 128 118 61.09 0.68 33 11 14 3 475.38 0.12 34 11 15 4 475.34 0.15 35 11 70 59 61.16 0.64 36 11 73 62 61.21 0.66 37 12 15 3 474.49 0.58 38 12 16 4 474.44 0.60 39 13 16 3 477.54 0.95 40 13 17 4 474.44 0.60 41 13 121 108 61.77 0.65 42 13 125 112 61.50 0.71 43 14 17 3 474.39 0.21 44 14 18 4 472.72 0.25 45 14 21 7 413.94 4.66 46 14 66 52 61.66 0.59 47 14 67 53 61.44 0.69 48 14 70 56 61.45 0.70 49 14 109 95 73.50 0.64 50 15 18 3 481.43 4.60 51 16 113 97 81.09 2.93 52 16 116 100 80.94 2.97 53 17 20 3 485.44 0.44 54 17 21 4 444.73 2.68 55 17 24 7 416.82 5.71 56 17 109 92 81.06 2.93 57 17 113 96 91.16 2.09 58 18 21 3 482.60 0.74 59 20 23 3 481.64 1.23 60 20 24 4 465.81 3.36 61 21 24 3 475.05 1.25 62 21 25 4 468.03 2.25 63 21 63 42 80.45 3.25 64 22 25 3 470.16 1.20 65 22 26 4 465.94 3.29 66 22 60 38 97.53 1.61 67 22 63 41 89.68 1.35 68 23 26 3 471.13 2.02 69 23 27 4 467.43 4.02 70 23 56 33 119.22 0.30 71 24 27 3 473.47 1.00 72 24 28 4 467.43 4.01 73 24 108 84 123.52 0.59 74 24 109 85 126.17 0.25 75 24 112 88 133.19 1.38 76 24 113 89 133.19 1.36 77 25 28 3 477.48 1.01 78 25 29 4 469.75 2.85 79 25 59 34 118.73 0.26 80 26 29 3 478.00 3.27 81 26 30 4 462.12 1.15 82 26 55 29 128.78 2.03 83 26 56 30 130.71 0.72 84 26 59 33 119.03 0.38 85 27 30 3 477.60 2.89 86 27 31 4 462.12 1.15 87 27 108 81 133.28 1.38 88 27 112 85 133.46 1.29 89 28 31 3 478.38 2.50 90 28 32 4 465.83 3.00 91 28 101 73 133.21 1.38 92 28 104 76 133.22 1.39 93 28 105 77 133.24 1.40 94 28 108 80 133.34 1.35 95 29 32 3 469.71 2.10 96 29 33 4 467.65 3.13 97 29 55 26 133.31 1.40 98 29 58 29 133.31 1.39 99 29 59 30 133.30 1.39 100 29 101 72 133.27 1.39 101 30 33 3 482.02 1.51 102 30 34 4 469.69 2.12 103 30 50 20 134.76 1.23 104 31 34 3 477.41 1.65 105 31 35 4 452.04 3.78 106 31 104 73 133.83 1.16 107 31 107 76 134.50 1.27 108 31 108 77 134.51 1.27 109 31 111 80 134.88 1.22 110 32 35 3 472.28 4.21 111 32 36 4 451.84 3.87 112 32 39 7 319.89 3.15 113 32 100 68 133.84 1.17 114 32 101 69 133.82 1.17 115 32 104 72 133.87 1.18 116 33 37 4 428.19 0.26 117 33 39 6 327.38 7.42 118 33 40 7 292.56 4.99 119 33 43 10 292.56 5.00 120 33 48 15 135.00 1.28 121 33 55 22 134.82 1.22 122 34 37 3 496.88 2.93 123 36 39 3 487.54 2.15 124 36 100 64 134.30 1.25 125 36 103 67 134.82 1.22 126 36 104 68 134.84 1.22 127 37 40 3 487.64 1.52 128 38 41 3 489.96 2.68 129 39 42 3 495.72 2.36 130 39 97 58 134.13 1.28 131 39 100 61 134.76 1.22 132 40 43 3 480.29 2.07 133 40 48 8 251.99 1.65 134 41 44 3 487.39 3.01 135 42 93 51 134.13 1.29 136 42 94 52 134.76 1.21 137 42 97 55 134.84 1.24 138 43 46 3 483.63 4.12 139 43 48 5 423.62 6.67 140 43 58 15 240.49 3.71 141 45 54 9 254.37 1.21 142 46 54 8 254.25 1.21 143 46 55 9 254.31 1.24 144 46 58 12 254.24 1.21 145 47 52 5 256.32 2.18 146 47 54 7 254.38 1.21 147 47 55 8 254.38 1.21 148 48 52 4 367.85 0.06 149 48 55 7 254.46 1.17 150 49 52 3 456.81 9.30 151 52 55 3 479.50 3.92 152 52 56 4 463.43 4.12 153 53 56 3 478.25 3.29 154 53 57 4 463.44 4.11 155 54 57 3 480.94 2.25 156 54 58 4 462.39 3.58 157 55 58 3 472.11 1.28 158 55 59 4 472.20 1.23 159 56 59 3 472.37 1.18 160 56 60 4 472.25 1.24 161 57 60 3 484.35 0.56 162 57 61 4 472.82 1.32 163 58 61 3 472.44 1.14 164 58 62 4 472.25 1.24 165 59 62 3 478.42 1.85 166 59 63 4 472.21 1.24 167 60 63 3 479.69 2.58 168 60 64 4 467.15 1.19 169 61 64 3 478.29 2.83 170 61 65 4 463.75 3.08 171 62 65 3 478.30 2.83 172 62 66 4 467.00 1.89 173 63 66 3 478.30 2.83 174 63 67 4 476.94 3.51 175 64 67 3 477.35 3.31 176 64 68 4 472.48 0.86 177 65 68 3 472.49 0.86 178 65 69 4 469.49 2.37 179 65 83 18 174.50 0.36 180 66 69 3 479.93 1.23 181 66 70 4 468.51 2.89 182 66 105 39 186.28 1.47 183 66 128 62 190.95 0.88 184 66 129 63 186.05 1.51 185 66 132 66 180.03 0.62 186 67 70 3 479.93 1.23 187 67 71 4 469.53 2.39 188 68 71 3 478.69 2.73 189 68 72 4 469.53 2.39 190 68 79 11 233.30 5.33 191 69 72 3 472.63 2.75 192 69 73 4 448.91 7.09 193 69 76 7 287.98 1.35 194 69 80 11 197.81 7.72 195 69 128 59 194.91 2.85 196 69 132 63 186.06 1.48 197 70 73 3 473.49 0.41 198 70 128 58 190.96 0.88 199 72 75 3 470.96 2.66 200 72 76 4 428.97 13.29 201 72 79 7 285.42 2.85 202 73 76 3 488.11 4.43 203 73 128 55 209.47 6.13 204 75 78 3 491.00 1.65 205 75 79 4 469.63 1.62 206 76 79 3 475.50 1.30 207 76 80 4 468.10 2.39 208 76 128 52 211.93 5.19 209 76 131 55 211.83 5.23 210 76 132 56 211.83 5.23 211 76 135 59 211.63 5.32 212 77 80 3 480.42 1.16 213 77 81 4 468.50 2.17 214 77 135 58 211.67 5.30 215 77 140 63 199.06 1.18 216 78 81 3 476.06 2.26 217 78 141 63 198.59 0.94 218 80 83 3 478.88 1.51 219 80 84 4 461.06 7.40 220 80 132 52 212.66 5.15 221 80 135 55 212.37 5.28 222 80 136 56 212.69 5.21 223 81 84 3 478.88 1.51 224 81 85 4 479.28 1.71 225 81 140 59 209.23 6.23 226 81 141 60 198.57 0.94 227 82 85 3 479.29 1.72 228 82 86 4 479.28 1.71 229 83 86 3 486.02 1.67 230 83 87 4 466.06 1.86 231 83 136 53 212.94 5.09 232 84 87 3 487.47 2.39 233 84 88 4 457.54 2.39 234 84 89 5 446.19 3.27 235 84 135 51 212.94 5.09 236 84 136 52 212.94 5.09 237 84 138 54 212.92 5.08 238 84 140 56 212.82 5.11 239 85 89 4 420.41 4.50 240 85 90 5 412.32 0.47 241 86 90 4 386.81 6.48 242 86 91 5 386.81 6.49 243 87 91 4 386.75 6.50 244 87 92 5 359.30 7.23 245 87 93 6 359.23 7.23 246 87 98 11 300.44 2.62 247 87 136 49 213.03 5.05 248 88 92 4 359.29 7.23 249 88 136 48 213.09 5.05 250 88 137 49 213.03 5.06 251 88 138 50 213.03 5.06 252 88 139 51 212.98 5.07 253 89 92 3 481.40 0.28 254 89 139 50 212.97 5.07 255 93 97 4 482.24 0.20 256 93 98 5 475.90 3.37 257 94 97 3 495.52 2.44 258 95 98 3 483.05 0.21 259 95 99 4 482.24 0.20 260 95 137 42 213.41 5.07 261 96 99 3 481.31 0.37 262 96 100 4 480.03 1.01 263 97 100 3 480.01 1.01 264 97 101 4 475.59 1.21 265 98 101 3 471.62 0.79 266 98 102 4 467.80 2.67 267 98 133 35 213.94 4.98 268 98 136 38 214.14 4.88 269 98 137 39 214.13 4.87 270 99 102 3 476.09 1.48 271 99 103 4 467.82 2.66 272 100 103 3 478.06 0.49 273 100 104 4 464.49 0.99 274 101 104 3 470.55 0.85 275 101 105 4 474.89 4.21 276 102 105 3 480.20 1.56 277 102 106 4 475.20 4.06 278 102 129 27 214.71 4.70 279 102 133 31 214.71 4.70 280 103 106 3 475.22 4.05 281 103 107 4 475.20 4.05 282 104 107 3 480.19 1.56 283 104 108 4 475.20 4.05 284 105 108 3 472.38 2.35 285 105 109 4 464.85 1.12 286 105 129 24 216.08 4.45 287 106 109 3 477.39 2.99 288 106 110 4 470.33 6.53 289 106 117 11 219.25 4.18 290 106 122 16 216.40 4.38 291 106 125 19 216.24 4.46 292 106 126 20 216.22 4.46 293 106 129 23 216.21 4.45 294 107 110 3 481.29 1.04 295 107 111 4 468.19 7.59 296 108 111 3 480.13 1.62 297 108 112 4 480.12 1.62 298 109 112 3 474.13 1.48 299 109 113 4 441.83 5.23 300 109 125 16 216.75 4.26 301 110 114 4 396.39 1.52 302 110 117 7 223.03 2.37 303 113 116 3 482.01 0.70 304 113 117 4 466.27 2.48 305 114 117 3 481.74 0.83 306 115 118 3 515.59 4.44 307 116 121 5 457.50 0.53 308 117 122 5 457.49 0.52 309 117 125 8 390.90 1.04 310 118 121 3 471.65 3.85 311 118 122 4 461.56 0.01 312 119 122 3 474.63 2.41 313 119 123 4 465.26 0.01 314 120 123 3 474.81 2.18 315 120 124 4 471.16 2.94 316 121 124 3 477.73 0.34 317 121 125 4 477.74 0.35 318 122 125 3 480.35 0.59 319 122 126 4 477.74 0.34 320 123 126 3 478.90 0.24 321 123 127 4 477.74 0.35 322 124 127 3 478.90 0.24 323 124 128 4 472.25 3.09 324 125 128 3 476.70 0.32 325 125 129 4 474.23 5.22 326 126 129 3 480.38 2.15 327 126 130 4 473.55 2.10 328 127 130 3 481.21 1.74 329 127 131 4 473.06 2.33 330 128 131 3 481.81 1.44 331 128 132 4 474.50 1.61 332 129 132 3 481.21 1.74 333 129 133 4 467.54 1.86 334 130 133 3 475.67 2.19 335 130 134 4 473.95 1.35 336 131 134 3 474.50 1.59 337 131 135 4 473.99 1.33 338 132 135 3 477.96 3.35 339 132 136 4 467.31 1.85 340 133 136 3 477.96 3.35 341 133 137 4 473.54 1.14 342 134 137 3 475.17 0.32 343 134 138 4 471.13 0.07 344 135 138 3 481.31 2.17 345 135 140 5 465.48 2.54