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 15.68 0.48 2 3 6 3 499.96 0.78 3 3 7 4 498.49 1.37 4 3 91 88 27.05 0.89 5 3 95 92 21.23 0.24 6 3 141 138 16.84 0.01 7 3 144 141 15.71 0.49 8 4 7 3 498.55 0.94 9 4 8 4 491.31 2.22 10 4 88 84 34.29 0.94 11 4 91 87 30.59 0.85 12 5 8 3 492.44 2.12 13 5 9 4 505.78 7.25 14 6 9 3 511.10 4.60 15 6 141 135 23.12 1.08 16 6 144 138 23.12 1.08 17 7 10 3 510.75 4.77 18 7 90 83 35.16 0.53 19 7 91 84 34.30 0.95 20 7 141 134 27.07 0.88 21 9 14 5 489.06 1.98 22 9 137 128 37.52 0.54 23 10 14 4 488.25 2.38 24 10 15 5 477.17 1.26 25 10 18 8 454.51 1.02 26 10 84 74 49.19 0.09 27 10 90 80 45.89 0.00 28 10 137 127 42.15 0.82 29 10 138 128 39.72 0.39 30 10 141 131 38.62 0.94 31 11 14 3 498.15 0.24 32 11 15 4 493.00 2.32 33 12 15 3 499.63 0.99 34 12 16 4 493.00 2.32 35 13 16 3 498.44 0.40 36 13 17 4 494.26 1.69 37 14 17 3 501.67 2.79 38 14 18 4 492.66 0.89 39 14 134 120 63.41 0.41 40 14 137 123 63.41 0.41 41 15 18 3 500.40 0.91 42 15 19 4 498.36 1.91 43 15 84 69 72.90 1.42 44 16 19 3 498.51 1.85 45 16 20 4 498.51 1.85 46 17 20 3 501.63 2.52 47 17 21 4 498.42 1.80 48 17 130 113 92.78 0.58 49 17 131 114 92.66 0.58 50 17 134 117 92.64 0.57 51 18 21 3 504.95 0.87 52 18 22 4 501.86 2.42 53 18 81 63 92.96 0.66 54 18 84 66 94.04 0.11 55 18 134 116 92.67 0.58 56 18 135 117 92.66 0.57 57 18 138 120 92.66 0.57 58 19 22 3 503.43 1.64 59 19 23 4 501.88 2.41 60 19 81 62 93.95 0.16 61 19 84 65 95.20 0.44 62 19 85 66 96.92 0.42 63 20 23 3 508.97 1.13 64 20 24 4 503.24 1.73 65 21 24 3 514.21 3.75 66 21 25 4 499.57 1.25 67 21 122 101 102.05 0.07 68 21 127 106 101.98 0.11 69 21 131 110 99.64 0.85 70 21 135 114 98.98 0.54 71 22 25 3 506.28 2.10 72 22 26 4 490.94 5.39 73 22 29 7 466.00 6.40 74 22 74 52 187.16 2.25 75 22 77 55 99.60 0.79 76 22 78 56 99.74 0.86 77 22 81 59 99.03 0.51 78 22 135 113 99.58 0.81 79 23 27 4 495.05 3.44 80 24 27 3 506.00 1.59 81 24 125 101 111.86 4.74 82 24 127 103 102.64 0.17 83 25 28 3 512.67 0.60 84 25 32 7 282.87 2.47 85 25 74 49 191.60 3.31 86 25 121 96 102.67 0.15 87 25 122 97 102.64 0.15 88 25 125 100 112.20 4.90 89 25 135 110 102.58 0.15 90 26 29 3 507.15 2.17 91 28 31 3 506.20 1.70 92 28 32 4 466.65 8.18 93 29 33 4 476.05 0.62 94 29 74 45 201.50 1.40 95 29 75 46 201.53 1.42 96 29 78 49 201.49 1.41 97 30 33 3 507.57 2.21 98 30 34 4 497.59 2.71 99 30 61 31 218.17 3.25 100 30 67 37 215.14 4.05 101 30 71 41 205.38 0.75 102 31 34 3 512.38 4.67 103 31 35 4 496.78 3.10 104 31 61 30 218.14 3.27 105 32 35 3 503.69 0.35 106 32 36 4 498.16 2.41 107 32 74 42 209.10 2.21 108 32 121 89 165.67 0.52 109 33 36 3 503.67 0.35 110 33 37 4 498.16 2.41 111 33 70 37 212.16 2.58 112 33 74 41 209.05 2.23 113 34 37 3 498.16 2.41 114 34 38 4 499.56 1.71 115 34 60 26 218.19 3.25 116 34 61 27 218.18 3.25 117 34 67 33 216.11 3.68 118 34 70 36 214.76 3.89 119 35 38 3 502.29 0.99 120 35 39 4 495.93 0.12 121 35 121 86 165.96 0.65 122 36 39 3 505.78 0.99 123 36 40 4 495.91 0.14 124 36 73 37 216.03 3.63 125 36 114 78 166.76 0.46 126 36 117 81 166.44 0.54 127 36 118 82 166.34 0.53 128 36 121 85 165.96 0.66 129 37 40 3 495.90 0.14 130 37 41 4 495.91 0.13 131 37 51 14 246.88 0.29 132 37 66 29 218.19 3.22 133 37 69 32 217.26 3.60 134 37 70 33 216.69 3.31 135 37 73 36 216.72 3.33 136 38 41 3 499.93 2.15 137 38 42 4 495.90 0.13 138 38 60 22 218.24 3.25 139 38 66 28 218.24 3.24 140 39 42 3 494.50 0.58 141 39 43 4 485.00 0.67 142 39 117 78 166.46 0.53 143 39 120 81 166.46 0.53 144 40 43 3 497.99 0.90 145 40 44 4 480.08 1.27 146 40 47 7 344.39 1.98 147 40 51 11 290.06 0.48 148 40 113 73 166.81 0.46 149 40 114 74 166.78 0.46 150 40 117 77 166.46 0.53 151 41 45 4 449.39 4.53 152 41 48 7 288.96 1.36 153 41 51 10 288.61 1.19 154 41 57 16 225.44 0.18 155 41 66 25 225.43 0.18 156 42 45 3 510.45 2.73 157 43 120 77 166.72 0.49 158 44 47 3 512.75 1.33 159 44 113 69 166.99 0.51 160 45 48 3 507.38 2.25 161 46 113 67 168.14 0.09 162 47 50 3 512.54 0.33 163 47 51 4 512.54 0.33 164 47 113 66 167.24 0.52 165 48 51 3 512.79 0.21 166 48 57 9 257.63 0.14 167 49 52 3 506.20 1.67 168 50 104 54 168.41 0.04 169 50 106 56 168.33 0.04 170 50 110 60 168.21 0.09 171 51 54 3 500.06 2.12 172 51 57 6 297.47 6.17 173 51 69 18 241.22 0.56 174 52 55 3 508.21 0.71 175 53 65 12 253.88 1.63 176 54 57 3 527.74 2.94 177 54 63 9 261.81 0.27 178 54 65 11 245.43 2.59 179 54 66 12 245.41 2.58 180 54 69 15 245.41 2.58 181 56 59 3 513.04 1.08 182 56 63 7 279.13 3.21 183 57 60 3 512.38 2.12 184 57 63 6 296.12 0.42 185 57 66 9 263.95 0.80 186 59 62 3 499.34 1.54 187 59 63 4 446.98 10.92 188 60 63 3 507.12 2.35 189 60 66 6 371.93 19.95 190 61 67 6 326.44 1.30 191 63 66 3 493.55 2.87 192 63 67 4 492.35 1.51 193 64 67 3 493.45 0.96 194 64 68 4 492.41 1.48 195 65 68 3 502.93 3.77 196 65 69 4 498.84 1.73 197 66 69 3 498.86 1.73 198 66 70 4 498.85 1.73 199 67 70 3 500.68 0.83 200 67 71 4 498.85 1.73 201 68 71 3 508.28 2.98 202 68 72 4 495.19 3.55 203 69 72 3 500.68 0.83 204 69 73 4 498.14 4.91 205 70 73 3 501.41 3.28 206 70 74 4 505.40 1.29 207 71 74 3 507.12 0.43 208 71 75 4 505.41 1.29 209 72 75 3 505.42 1.30 210 72 76 4 505.41 1.30 211 73 76 3 511.14 1.56 212 73 77 4 500.38 3.81 213 74 77 3 512.34 2.17 214 74 78 4 495.08 1.16 215 75 78 3 508.67 4.00 216 75 79 4 496.72 1.98 217 76 79 3 500.98 2.19 218 76 80 4 496.94 1.87 219 76 97 21 169.03 0.18 220 77 80 3 500.98 2.19 221 77 81 4 499.06 3.14 222 77 135 58 165.60 0.70 223 78 81 3 508.64 1.64 224 78 82 4 496.74 1.98 225 79 82 3 500.22 0.24 226 79 83 4 494.75 2.98 227 79 93 14 169.94 0.18 228 80 83 3 500.44 0.13 229 80 84 4 497.57 1.49 230 80 90 10 255.87 41.48 231 80 93 13 169.97 0.18 232 80 94 14 169.96 0.18 233 80 97 17 169.91 0.19 234 80 138 58 165.34 0.72 235 80 142 62 162.96 0.55 236 81 84 3 501.40 1.99 237 81 135 54 165.68 0.70 238 81 138 57 165.46 0.77 239 83 86 3 501.06 5.81 240 83 89 6 304.56 17.16 241 83 90 7 300.55 19.17 242 83 93 10 300.55 19.18 243 84 90 6 320.19 9.36 244 86 89 3 506.01 2.94 245 86 90 4 483.75 8.15 246 87 90 3 496.30 1.88 247 87 91 4 493.74 3.16 248 88 91 3 505.98 2.96 249 88 92 4 493.79 3.14 250 89 92 3 499.03 0.52 251 89 93 4 484.48 1.50 252 90 93 3 504.56 3.13 253 90 94 4 483.03 2.22 254 91 94 3 499.19 1.02 255 91 95 4 483.03 2.22 256 92 95 3 490.81 1.68 257 92 96 4 488.94 1.15 258 93 96 3 494.74 3.08 259 93 97 4 482.56 2.08 260 94 97 3 493.86 2.77 261 94 98 4 492.38 0.55 262 94 141 47 163.31 0.82 263 94 142 48 162.98 0.66 264 94 145 51 162.22 0.33 265 95 98 3 504.44 0.55 266 95 99 4 500.19 0.40 267 96 99 3 511.55 1.83 268 97 100 3 538.15 2.51 269 97 101 4 506.93 0.68 270 97 111 14 276.53 3.06 271 97 142 45 162.87 0.59 272 98 101 3 506.74 0.58 273 98 102 4 500.64 1.98 274 98 145 47 161.97 0.27 275 98 146 48 161.84 0.21 276 99 102 3 506.72 0.58 277 99 103 4 493.75 5.42 278 100 103 3 500.62 1.99 279 100 104 4 491.80 4.59 280 101 104 3 486.05 2.48 281 101 105 4 486.03 2.48 282 101 106 5 400.59 12.12 283 101 111 10 319.78 3.43 284 101 146 45 161.93 0.17 285 102 105 3 485.12 2.94 286 102 145 43 162.26 0.32 287 102 146 44 161.82 0.17 288 106 110 4 476.84 1.07 289 106 111 5 476.82 1.08 290 107 110 3 501.25 6.29 291 107 111 4 498.75 2.21 292 107 146 39 161.16 0.38 293 108 111 3 506.49 0.92 294 108 112 4 498.88 2.27 295 108 143 35 162.30 0.30 296 108 146 38 157.85 1.03 297 109 112 3 508.19 1.38 298 109 113 4 505.38 0.03 299 110 113 3 516.34 0.48 300 111 114 3 522.18 4.70 301 111 139 28 165.22 0.90 302 111 142 31 162.38 0.29 303 111 143 32 162.29 0.31 304 111 146 35 155.93 0.18 305 112 115 3 511.03 2.08 306 112 143 31 162.29 0.30 307 113 116 3 520.85 1.18 308 113 117 4 509.44 2.56 309 114 117 3 510.17 2.96 310 114 118 4 504.28 2.70 311 114 139 25 165.33 0.72 312 115 118 3 506.97 1.35 313 115 119 4 504.27 2.70 314 115 136 21 165.61 0.68 315 115 139 24 165.33 0.72 316 116 119 3 506.79 1.45 317 116 120 4 504.27 2.70 318 117 120 3 506.93 1.37 319 117 121 4 489.42 2.57 320 118 121 3 506.01 0.14 321 118 122 4 488.67 2.20 322 118 135 17 165.66 0.70 323 118 139 21 165.16 0.81 324 119 122 3 507.42 0.84 325 119 123 4 505.24 1.92 326 119 132 13 165.72 0.72 327 120 123 3 507.41 0.84 328 120 124 4 505.22 1.92 329 121 124 3 506.15 2.38 330 121 125 4 505.21 1.92 331 122 125 3 505.23 1.92 332 122 126 4 500.66 0.35 333 122 127 5 385.81 0.71 334 122 131 9 244.30 4.75 335 122 132 10 213.93 19.93 336 122 135 13 209.44 18.40 337 123 126 3 505.21 1.92 338 123 127 4 466.45 8.70 339 127 131 4 474.48 6.58 340 128 131 3 511.49 0.30 341 128 132 4 505.41 1.99 342 129 132 3 508.01 0.69 343 129 133 4 505.41 1.99 344 130 133 3 508.17 0.60 345 130 134 4 497.76 1.83 346 131 134 3 505.23 1.90 347 131 135 4 497.77 1.83 348 132 135 3 508.01 0.70 349 132 136 4 499.06 4.83 350 133 136 3 503.19 2.13 351 133 137 4 507.67 0.54 352 134 137 3 507.68 0.54 353 134 138 4 507.68 0.54 354 135 138 3 507.67 0.54 355 135 139 4 497.00 5.87 356 136 139 3 507.69 0.83 357 136 140 4 504.14 2.29 358 137 140 3 507.69 0.83 359 137 141 4 504.15 2.29 360 138 141 3 507.94 0.70 361 138 142 4 497.25 1.17 362 139 142 3 500.74 2.90 363 139 143 4 499.59 3.48 364 140 143 3 499.59 3.48 365 140 144 4 499.59 3.48 366 141 144 3 511.25 0.46 367 141 145 4 507.28 0.36 368 142 145 3 507.28 0.36 369 142 146 4 507.28 0.36 370 143 146 3 510.56 1.28