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 2 144 142 16.68 0.06 2 3 6 3 499.31 2.04 3 3 7 4 491.78 0.45 4 3 91 88 26.12 1.09 5 3 94 91 24.64 0.53 6 3 95 92 23.67 0.32 7 3 141 138 20.36 0.30 8 3 144 141 18.36 0.69 9 3 145 142 17.30 0.15 10 4 7 3 503.09 0.14 11 4 8 4 498.40 1.57 12 4 91 87 27.57 0.36 13 4 95 91 26.32 0.99 14 5 8 3 509.04 0.57 15 5 9 4 502.45 0.46 16 6 9 3 509.41 0.39 17 6 141 135 24.28 0.76 18 6 144 138 24.29 0.76 19 7 10 3 510.93 0.38 20 7 90 83 38.82 0.24 21 7 91 84 30.61 0.40 22 7 141 134 26.16 1.06 23 9 137 128 39.69 0.21 24 10 14 4 474.21 0.68 25 10 15 5 474.16 0.69 26 10 18 8 424.54 8.21 27 10 84 74 53.19 0.49 28 10 90 80 50.53 1.00 29 10 137 127 39.93 0.30 30 10 138 128 39.74 0.21 31 10 141 131 39.74 0.21 32 11 14 3 499.75 0.03 33 11 15 4 487.93 0.93 34 12 15 3 499.87 0.09 35 12 16 4 494.91 2.56 36 13 16 3 496.75 1.64 37 13 17 4 488.31 0.73 38 14 17 3 512.39 2.80 39 14 18 4 496.81 4.99 40 14 134 120 68.31 0.21 41 14 137 123 68.30 0.20 42 15 18 3 502.66 2.07 43 15 19 4 491.47 7.67 44 15 84 69 70.28 1.11 45 16 19 3 498.57 4.12 46 16 20 4 491.48 7.66 47 17 20 3 501.21 2.80 48 17 21 4 496.56 5.12 49 17 130 113 92.74 0.50 50 17 131 114 92.05 0.30 51 17 134 117 91.97 0.34 52 18 21 3 511.77 1.65 53 18 22 4 491.06 2.36 54 18 81 63 92.43 0.29 55 18 84 66 92.52 0.27 56 18 134 116 92.06 0.29 57 18 135 117 91.97 0.34 58 18 138 120 91.97 0.34 59 19 22 3 501.94 1.36 60 19 23 4 491.06 2.36 61 19 81 62 92.53 0.27 62 19 84 65 92.53 0.27 63 19 85 66 98.24 0.83 64 20 23 3 504.28 0.86 65 21 24 3 504.28 0.86 66 21 25 4 484.91 2.27 67 21 122 101 102.42 1.14 68 21 127 106 102.43 1.14 69 21 131 110 101.42 0.65 70 21 135 114 101.36 0.65 71 22 25 3 499.26 0.21 72 22 26 4 465.75 7.29 73 22 29 7 420.88 7.99 74 22 74 52 196.97 1.45 75 22 77 55 141.59 18.46 76 22 78 56 102.42 1.12 77 22 81 59 101.42 0.62 78 22 135 113 101.45 0.64 79 23 27 4 483.53 1.59 80 24 27 3 506.33 2.94 81 24 125 101 114.12 3.75 82 24 127 103 106.18 0.23 83 25 28 3 521.49 3.92 84 25 32 7 317.88 1.15 85 25 74 49 198.56 0.67 86 25 121 96 106.19 0.18 87 25 122 97 106.17 0.20 88 25 125 100 117.73 1.96 89 26 29 3 508.27 1.97 90 26 74 48 198.56 0.67 91 28 31 3 498.93 2.68 92 28 32 4 478.98 3.73 93 29 33 4 480.22 4.35 94 29 74 45 202.81 0.37 95 29 75 46 214.04 5.99 96 29 78 49 214.03 5.98 97 30 33 3 499.76 0.01 98 30 34 4 488.05 1.96 99 30 61 31 221.27 4.56 100 30 67 37 220.38 4.25 101 30 71 41 217.03 5.75 102 31 34 3 505.16 1.58 103 31 35 4 493.92 0.98 104 31 61 30 221.27 4.56 105 32 35 3 496.35 0.32 106 32 36 4 492.45 1.72 107 32 74 42 220.23 4.23 108 32 121 89 157.97 3.39 109 32 125 93 165.34 0.38 110 33 36 3 505.86 5.07 111 33 37 4 494.70 0.59 112 33 70 37 220.30 4.25 113 33 74 41 220.17 4.20 114 34 37 3 496.23 1.35 115 34 38 4 488.74 1.75 116 34 61 27 221.28 4.56 117 34 67 33 220.85 4.42 118 34 70 36 220.62 4.32 119 35 38 3 497.01 0.96 120 35 39 4 487.91 2.21 121 35 121 86 166.30 0.78 122 36 39 3 504.65 2.87 123 36 40 4 493.37 4.46 124 36 73 37 220.78 4.40 125 36 74 38 220.77 4.40 126 36 77 41 220.62 4.37 127 36 114 78 167.22 0.93 128 36 117 81 166.78 0.83 129 36 118 82 166.77 0.83 130 36 121 85 166.34 0.80 131 37 40 3 509.11 0.64 132 37 41 4 493.37 4.46 133 37 51 14 273.49 1.25 134 37 66 29 221.27 4.55 135 37 69 32 221.24 4.55 136 37 70 33 220.87 4.42 137 37 73 36 220.81 4.40 138 38 41 3 504.47 1.09 139 38 42 4 487.88 2.23 140 38 60 22 221.85 4.32 141 39 42 3 499.82 3.41 142 39 43 4 487.87 2.22 143 39 117 78 166.80 0.83 144 39 120 81 166.78 0.84 145 40 43 3 503.06 1.79 146 40 44 4 487.84 2.23 147 40 47 7 328.76 2.81 148 40 51 11 298.31 0.68 149 40 113 73 167.38 0.98 150 40 114 74 167.24 0.94 151 40 117 77 166.81 0.84 152 41 45 4 436.39 0.01 153 41 47 6 339.20 4.49 154 41 48 7 304.81 3.94 155 41 51 10 298.31 0.69 156 41 57 16 223.66 4.33 157 41 66 25 222.00 4.37 158 42 45 3 518.51 3.25 159 43 120 77 167.19 0.95 160 44 47 3 507.56 1.97 161 44 113 69 167.43 0.98 162 45 48 3 509.04 1.22 163 46 113 67 167.84 1.07 164 47 50 3 515.28 0.42 165 47 51 4 506.30 1.08 166 47 113 66 167.80 1.07 167 48 51 3 510.13 3.00 168 49 52 3 512.92 1.60 169 50 106 56 168.56 1.18 170 50 110 60 168.59 1.17 171 51 54 3 504.49 1.04 172 51 69 18 225.38 3.89 173 52 55 3 520.02 1.50 174 53 65 12 239.93 5.83 175 54 57 3 532.95 0.61 176 54 63 9 265.19 4.10 177 54 65 11 239.85 5.87 178 54 66 12 239.85 5.87 179 54 69 15 239.85 5.87 180 56 59 3 521.74 2.36 181 56 63 7 302.70 5.21 182 57 60 3 514.21 0.48 183 57 63 6 318.80 2.83 184 57 66 9 265.01 4.23 185 59 62 3 510.09 0.30 186 59 63 4 437.01 16.98 187 60 63 3 507.87 0.35 188 60 66 6 334.54 4.96 189 61 67 6 332.01 8.51 190 63 66 3 496.40 0.83 191 63 67 4 497.79 0.78 192 64 67 3 498.69 0.32 193 64 68 4 489.21 3.51 194 65 68 3 496.23 3.33 195 65 69 4 491.06 2.59 196 66 69 3 490.71 0.57 197 66 70 4 490.76 0.54 198 67 70 3 503.07 2.50 199 67 71 4 495.28 0.98 200 68 71 3 517.63 4.82 201 68 72 4 506.82 0.59 202 69 72 3 506.84 0.59 203 69 73 4 506.84 0.60 204 70 73 3 517.66 4.80 205 70 74 4 506.88 0.59 206 71 74 3 508.20 0.07 207 71 75 4 506.88 0.59 208 72 75 3 508.29 1.28 209 72 76 4 506.88 0.59 210 73 76 3 506.93 0.59 211 73 77 4 506.44 0.38 212 74 77 3 505.33 3.10 213 74 78 4 500.88 1.43 214 75 78 3 503.07 2.52 215 75 79 4 498.84 2.45 216 76 79 3 505.42 0.84 217 76 80 4 503.44 0.14 218 76 97 21 170.54 0.60 219 77 80 3 505.47 0.82 220 77 81 4 503.39 0.12 221 77 135 58 165.91 0.85 222 78 81 3 503.41 0.12 223 78 82 4 502.68 0.48 224 79 82 3 507.85 3.05 225 79 83 4 502.69 0.48 226 79 93 14 199.65 12.48 227 80 83 3 502.70 0.48 228 80 84 4 502.69 0.48 229 80 90 10 205.83 15.55 230 80 93 13 199.68 12.48 231 80 94 14 198.93 12.12 232 80 97 17 198.91 12.11 233 80 138 58 165.82 0.81 234 80 142 62 165.05 0.70 235 81 84 3 506.81 1.49 236 81 135 54 166.16 0.78 237 81 138 57 165.81 0.81 238 83 86 3 502.15 1.67 239 83 89 6 353.24 22.52 240 83 90 7 258.23 5.74 241 83 93 10 261.28 4.19 242 84 90 6 319.88 4.80 243 84 138 54 166.11 0.78 244 86 89 3 503.24 1.36 245 86 90 4 493.98 2.64 246 87 90 3 497.34 4.31 247 87 91 4 495.12 5.41 248 88 91 3 509.94 1.99 249 88 92 4 495.12 5.42 250 89 92 3 502.44 1.76 251 89 93 4 494.97 5.49 252 90 93 3 502.28 1.84 253 90 94 4 492.45 6.75 254 91 94 3 498.69 0.27 255 91 95 4 496.07 1.06 256 92 95 3 500.33 1.06 257 92 96 4 495.82 0.92 258 93 96 3 500.88 1.61 259 93 97 4 498.32 0.34 260 94 97 3 504.75 3.56 261 94 98 4 491.23 3.90 262 94 141 47 165.65 0.89 263 94 142 48 165.02 0.70 264 94 145 51 163.35 0.07 265 95 98 3 504.75 3.56 266 95 99 4 498.33 0.35 267 96 99 3 510.25 1.61 268 97 101 4 492.85 0.58 269 97 111 14 260.49 1.01 270 97 142 45 165.02 0.69 271 98 101 3 502.17 1.62 272 98 102 4 487.75 1.98 273 98 145 47 163.34 0.07 274 98 146 48 163.32 0.08 275 99 102 3 506.81 1.80 276 99 103 4 495.88 4.95 277 100 103 3 500.69 4.87 278 100 104 4 498.20 6.11 279 101 104 3 491.79 2.90 280 101 105 4 488.89 1.46 281 101 106 5 400.42 2.14 282 101 111 10 360.25 22.21 283 101 146 45 163.24 0.06 284 102 105 3 495.05 1.62 285 102 145 43 163.56 0.01 286 102 146 44 163.24 0.06 287 106 110 4 473.92 1.10 288 106 111 5 474.88 3.78 289 106 146 40 163.09 0.10 290 107 110 3 481.50 0.48 291 107 111 4 487.29 2.52 292 107 146 39 162.53 0.01 293 108 111 3 496.69 0.60 294 108 112 4 490.47 1.03 295 108 143 35 163.52 0.01 296 108 146 38 160.44 1.06 297 109 112 3 507.02 1.09 298 109 113 4 506.63 1.28 299 110 113 3 508.55 1.56 300 111 114 3 512.98 0.95 301 111 139 28 165.58 0.83 302 111 142 31 164.45 0.42 303 111 143 32 163.53 0.00 304 111 146 35 161.79 0.35 305 112 115 3 510.02 0.83 306 112 139 27 165.57 0.83 307 112 143 31 163.53 0.01 308 113 116 3 523.96 1.02 309 113 117 4 504.29 2.03 310 114 117 3 507.65 1.05 311 114 118 4 499.56 2.89 312 115 118 3 505.69 0.07 313 115 119 4 507.32 1.06 314 115 136 21 165.66 0.80 315 115 139 24 165.65 0.86 316 116 119 3 507.97 0.76 317 116 120 4 507.35 1.07 318 117 120 3 507.98 0.76 319 117 121 4 500.33 4.58 320 118 121 3 505.32 2.08 321 118 122 4 500.32 4.58 322 118 135 17 166.95 0.23 323 118 139 21 166.93 0.23 324 119 122 3 506.86 1.31 325 119 123 4 491.80 0.32 326 119 132 13 166.96 0.23 327 120 123 3 510.36 5.83 328 120 124 4 489.56 3.31 329 121 124 3 501.31 1.67 330 121 125 4 498.51 1.17 331 122 125 3 504.64 0.00 332 122 126 4 489.56 3.31 333 122 127 5 424.75 1.90 334 122 131 9 256.84 3.62 335 122 132 10 239.27 0.07 336 122 135 13 239.27 0.07 337 123 126 3 489.98 0.70 338 123 127 4 442.87 4.75 339 127 131 4 488.04 3.08 340 128 131 3 504.44 0.70 341 128 132 4 488.05 3.08 342 129 132 3 491.63 1.28 343 129 133 4 488.05 3.07 344 130 133 3 503.07 1.36 345 130 134 4 488.07 3.06 346 131 134 3 501.92 1.96 347 131 135 4 490.20 1.80 348 132 135 3 510.44 6.22 349 132 136 4 490.18 1.81 350 133 136 3 497.25 2.02 351 133 137 4 490.39 1.71 352 134 137 3 499.34 0.98 353 134 138 4 496.65 2.33 354 135 138 3 494.70 0.64 355 135 139 4 491.12 0.43 356 136 139 3 498.91 0.77 357 136 140 4 496.15 2.08 358 137 140 3 504.23 1.89 359 137 141 4 496.86 1.78 360 138 141 3 507.01 0.49 361 138 142 4 499.53 3.11 362 139 142 3 512.58 3.68 363 139 143 4 497.49 1.68 364 140 143 3 497.49 1.68 365 140 144 4 503.28 1.22 366 141 144 3 505.78 0.03 367 141 145 4 503.28 1.22 368 142 145 3 508.43 0.82 369 142 146 4 503.25 1.24 370 143 146 3 501.79 2.50