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 5 453.74 9.61 2 2 73 71 31.39 0.19 3 2 76 74 27.36 0.37 4 2 127 125 23.47 0.21 5 2 128 126 23.41 0.20 6 2 131 129 23.06 0.03 7 3 6 3 477.00 1.50 8 3 7 4 466.21 6.90 9 4 7 3 477.00 1.50 10 4 8 4 473.80 3.10 11 5 8 3 474.95 3.68 12 5 9 4 470.55 1.48 13 6 9 3 472.38 2.39 14 6 10 4 471.14 1.19 15 6 124 118 45.84 0.22 16 6 127 121 45.84 0.21 17 7 10 3 478.91 2.79 18 7 11 4 474.29 2.75 19 7 73 66 47.87 0.14 20 7 74 67 47.91 0.16 21 8 11 3 476.92 1.47 22 8 12 4 474.29 2.77 23 9 12 3 478.78 0.54 24 9 13 4 474.48 2.86 25 9 121 112 60.27 0.96 26 9 124 115 60.20 0.96 27 10 13 3 471.72 4.25 28 10 14 4 470.94 4.63 29 10 70 60 60.25 0.97 30 10 124 114 60.27 0.96 31 10 125 115 60.26 0.96 32 10 128 118 60.20 0.95 33 11 14 3 476.86 1.68 34 11 15 4 474.38 2.91 35 11 70 59 60.30 0.95 36 11 73 62 60.30 0.97 37 12 15 3 477.93 1.15 38 12 16 4 477.93 1.15 39 13 16 3 477.97 1.08 40 13 17 4 474.35 2.89 41 13 113 100 78.95 0.96 42 13 121 108 70.54 3.65 43 13 125 112 61.32 0.95 44 14 17 3 477.88 1.12 45 14 18 4 474.34 2.89 46 14 21 7 420.23 6.29 47 14 63 49 66.58 1.11 48 14 66 52 61.31 0.95 49 14 67 53 61.32 0.95 50 14 70 56 61.30 0.96 51 14 109 95 77.85 1.48 52 15 18 3 477.95 1.07 53 16 113 97 79.44 1.05 54 16 116 100 79.28 1.12 55 17 20 3 489.57 2.64 56 17 21 4 450.86 5.13 57 17 24 7 420.25 6.30 58 17 109 92 79.42 1.05 59 17 113 96 88.85 0.18 60 18 21 3 503.33 1.19 61 20 23 3 478.01 1.18 62 20 24 4 465.87 3.34 63 21 24 3 480.46 2.73 64 21 25 4 468.05 2.25 65 21 63 42 91.84 1.26 66 22 25 3 469.94 1.32 67 22 26 4 468.05 2.25 68 22 60 38 98.11 0.72 69 22 63 41 98.00 0.69 70 23 26 3 474.95 0.11 71 23 27 4 469.94 1.31 72 24 27 3 479.45 2.14 73 24 28 4 471.39 2.03 74 24 108 84 119.95 0.80 75 24 109 85 120.44 0.54 76 24 112 88 128.64 0.65 77 25 28 3 474.68 3.02 78 25 29 4 471.38 2.04 79 25 59 34 117.11 0.60 80 26 29 3 477.88 0.13 81 26 30 4 466.97 4.25 82 26 55 29 124.51 1.65 83 26 56 30 121.39 0.09 84 26 59 33 118.62 1.34 85 27 30 3 470.61 3.51 86 27 31 4 461.53 3.39 87 27 108 81 129.24 0.62 88 27 112 85 130.15 0.96 89 28 31 3 470.04 2.38 90 28 32 4 463.38 2.48 91 28 101 73 129.15 0.65 92 28 104 76 129.16 0.64 93 28 105 77 129.16 0.65 94 28 108 80 129.28 0.61 95 29 32 3 468.59 1.68 96 29 33 4 465.16 3.39 97 29 55 26 129.31 0.60 98 29 58 29 129.28 0.59 99 29 59 30 129.28 0.60 100 29 101 72 129.16 0.65 101 30 33 3 468.60 1.68 102 30 34 4 467.36 1.06 103 30 50 20 129.99 0.94 104 31 34 3 474.73 1.39 105 31 35 4 466.78 0.78 106 31 104 73 129.72 0.89 107 31 107 76 130.03 0.97 108 31 108 77 130.07 0.96 109 31 111 80 130.26 0.97 110 32 35 3 469.00 0.87 111 32 36 4 456.62 2.58 112 32 39 7 353.70 4.83 113 32 101 69 129.69 0.91 114 32 104 72 129.78 0.88 115 33 37 4 445.82 2.81 116 33 39 6 322.36 10.84 117 33 40 7 240.02 51.98 118 33 43 10 161.97 0.07 119 33 48 15 130.34 0.97 120 33 55 22 130.28 0.94 121 34 37 3 490.24 1.35 122 36 39 3 492.82 0.10 123 36 100 64 129.77 0.91 124 36 103 67 130.12 0.94 125 36 104 68 130.13 0.94 126 37 40 3 487.65 1.53 127 38 41 3 487.75 1.47 128 39 42 3 496.04 1.73 129 39 43 4 488.26 0.74 130 39 97 58 129.76 0.90 131 39 100 61 130.06 0.98 132 40 43 3 488.26 0.74 133 40 44 4 487.10 1.32 134 40 48 8 141.41 0.53 135 41 44 3 500.49 0.53 136 42 45 3 644.72 0.49 137 42 93 51 129.63 0.96 138 42 94 52 129.97 1.00 139 42 97 55 130.07 1.00 140 43 46 3 481.59 0.44 141 43 48 5 412.00 2.44 142 43 58 15 130.41 0.96 143 45 54 9 138.40 2.08 144 46 54 8 138.38 2.08 145 46 55 9 138.39 2.08 146 46 58 12 138.38 2.08 147 47 52 5 149.71 0.85 148 47 54 7 138.39 2.08 149 47 55 8 138.42 2.08 150 48 55 7 139.10 1.74 151 49 52 3 483.92 0.12 152 51 56 5 439.93 7.65 153 52 55 3 474.44 0.45 154 52 56 4 447.29 6.21 155 53 56 3 476.29 4.28 156 53 57 4 449.14 5.27 157 54 57 3 474.22 0.34 158 54 58 4 465.70 3.00 159 55 58 3 468.62 1.55 160 55 59 4 469.72 2.41 161 56 59 3 473.20 0.68 162 56 60 4 472.56 1.15 163 57 60 3 473.30 0.78 164 57 61 4 472.56 1.15 165 58 61 3 474.53 0.18 166 58 62 4 470.06 2.40 167 59 62 3 480.50 2.83 168 59 63 4 473.66 0.59 169 60 63 3 473.86 0.69 170 60 64 4 473.53 0.53 171 61 64 3 472.33 0.07 172 61 65 4 468.73 1.88 173 62 65 3 479.16 7.08 174 62 66 4 467.88 1.45 175 62 101 39 153.18 2.39 176 63 66 3 469.24 1.61 177 63 67 4 465.18 0.10 178 64 67 3 467.85 1.45 179 64 68 4 464.73 0.11 180 65 68 3 478.23 2.93 181 65 69 4 474.31 4.90 182 65 83 18 153.46 2.56 183 66 69 3 476.50 3.80 184 66 70 4 466.27 0.89 185 66 105 39 182.74 2.79 186 66 129 63 169.16 1.29 187 66 132 66 162.09 1.70 188 67 70 3 474.31 4.90 189 67 71 4 458.26 4.88 190 68 71 3 471.15 4.88 191 68 72 4 458.25 4.89 192 68 79 11 201.99 17.96 193 68 80 12 162.33 1.85 194 69 72 3 471.16 4.88 195 69 73 4 450.72 2.17 196 69 76 7 235.80 32.73 197 69 80 11 162.34 1.86 198 69 128 59 194.05 0.32 199 69 132 63 169.31 1.22 200 70 73 3 464.39 7.99 201 70 128 58 222.33 14.47 202 72 75 3 472.88 1.03 203 72 76 4 442.99 2.07 204 72 79 7 301.91 0.35 205 73 76 3 475.53 1.43 206 73 128 55 273.69 2.46 207 75 78 3 495.31 0.51 208 75 79 4 468.10 3.06 209 76 79 3 468.55 3.27 210 76 80 4 454.82 3.56 211 76 128 52 280.10 1.93 212 76 131 55 276.90 1.43 213 76 132 56 276.55 1.60 214 76 135 59 276.54 1.60 215 77 80 3 486.94 1.12 216 77 81 4 468.07 3.06 217 77 135 58 276.54 1.60 218 78 81 3 473.47 3.14 219 80 83 3 479.81 2.52 220 80 84 4 459.39 5.75 221 80 132 52 282.15 2.81 222 80 135 55 281.73 2.62 223 80 136 56 281.73 2.62 224 81 84 3 473.84 5.16 225 81 85 4 467.22 1.85 226 81 139 58 282.54 3.05 227 82 85 3 477.45 3.35 228 82 86 4 463.50 3.71 229 83 86 3 474.88 2.06 230 83 87 4 461.50 4.65 231 83 136 53 283.10 3.29 232 84 87 3 480.85 0.92 233 84 88 4 461.64 4.58 234 84 135 51 283.14 3.27 235 84 136 52 283.09 3.30 236 84 138 54 283.08 3.31 237 84 139 55 283.07 3.31 238 85 88 3 480.81 0.93 239 85 89 4 461.49 4.65 240 85 139 54 283.08 3.30 241 86 89 3 482.25 0.21 242 86 90 4 428.05 5.84 243 86 91 5 395.12 22.30 244 87 91 4 363.69 10.00 245 87 92 5 363.66 10.00 246 87 93 6 363.66 10.00 247 87 98 11 292.16 5.89 248 87 136 49 283.16 3.27 249 87 140 53 283.07 3.31 250 88 92 4 388.92 22.62 251 88 139 51 283.09 3.31 252 88 140 52 282.99 3.26 253 89 92 3 483.11 0.58 254 89 139 50 283.14 3.29 255 92 140 48 283.14 3.29 256 93 97 4 482.77 0.37 257 93 98 5 476.82 0.25 258 93 140 47 283.23 3.25 259 94 97 3 494.81 0.05 260 95 98 3 494.81 0.05 261 95 137 42 283.47 3.29 262 95 140 45 283.33 3.22 263 96 99 3 493.31 0.38 264 96 100 4 482.78 0.36 265 97 100 3 475.95 1.54 266 97 101 4 480.56 3.85 267 98 101 3 480.56 3.85 268 98 102 4 472.97 3.04 269 98 133 35 283.67 3.21 270 98 136 38 283.69 3.21 271 98 137 39 283.64 3.23 272 98 140 42 283.66 3.23 273 99 102 3 480.55 3.86 274 99 103 4 472.97 3.04 275 100 103 3 482.68 2.79 276 100 104 4 477.38 5.45 277 101 104 3 482.68 2.80 278 101 105 4 472.37 1.86 279 102 105 3 482.68 2.80 280 102 106 4 478.49 4.91 281 102 129 27 284.05 3.29 282 102 133 31 284.05 3.29 283 103 106 3 479.47 4.42 284 103 107 4 479.19 4.55 285 104 107 3 479.22 4.54 286 104 108 4 473.11 1.50 287 105 108 3 480.21 1.55 288 105 109 4 469.97 3.56 289 105 129 24 284.38 3.33 290 106 109 3 481.23 4.16 291 106 110 4 476.72 3.33 292 106 117 11 285.82 3.48 293 106 122 16 284.86 3.06 294 106 125 19 284.65 3.19 295 106 126 20 284.61 3.18 296 106 129 23 284.64 3.20 297 107 110 3 480.25 1.56 298 107 111 4 472.05 5.67 299 108 111 3 484.82 0.72 300 108 112 4 459.25 0.96 301 109 112 3 480.24 1.55 302 109 113 4 459.19 0.93 303 109 125 16 284.90 3.09 304 110 113 3 480.25 1.55 305 110 117 7 285.41 3.25 306 113 116 3 477.07 0.03 307 113 117 4 437.99 0.79 308 115 118 3 550.22 3.54 309 116 121 5 443.97 3.65 310 117 122 5 444.31 3.81 311 117 125 8 393.04 0.03 312 118 121 3 475.29 2.04 313 118 122 4 468.84 5.26 314 119 122 3 476.19 6.23 315 119 123 4 472.60 3.38 316 120 123 3 475.30 2.03 317 120 124 4 472.60 3.38 318 121 124 3 474.91 2.23 319 121 125 4 472.64 3.35 320 122 125 3 483.92 2.97 321 122 126 4 462.81 1.58 322 123 126 3 478.19 0.57 323 123 127 4 471.12 2.56 324 124 127 3 478.31 0.48 325 124 128 4 471.11 2.56 326 125 128 3 478.50 0.39 327 125 129 4 472.62 3.32 328 126 129 3 490.55 0.29 329 126 130 4 469.89 3.18 330 127 130 3 483.85 3.06 331 127 131 4 472.24 1.92 332 128 131 3 473.62 1.53 333 128 132 4 473.62 1.53 334 129 132 3 473.62 1.52 335 129 133 4 463.82 2.29 336 130 133 3 472.15 1.86 337 130 134 4 463.67 2.38 338 131 134 3 467.11 0.67 339 131 135 4 463.62 2.41 340 132 135 3 465.33 1.55 341 132 136 4 463.62 2.41 342 133 136 3 470.19 3.18 343 133 137 4 461.12 0.17 344 134 137 3 474.73 2.12 345 134 138 4 458.92 1.23 346 135 138 3 474.12 1.43 347 136 140 4 494.06 3.52 348 137 140 3 486.87 0.07