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 2 134 132 65.78 1.78 2 3 44 41 65.88 1.77 3 3 45 42 65.86 1.77 4 3 47 44 65.91 1.79 5 3 48 45 65.91 1.79 6 3 71 68 65.80 1.78 7 3 74 71 65.91 1.78 8 3 133 130 65.80 1.78 9 3 134 131 65.78 1.78 10 3 136 133 65.78 1.77 11 4 42 38 67.64 1.42 12 4 43 39 65.90 1.78 13 4 44 40 65.89 1.77 14 4 134 130 65.81 1.77 15 4 135 131 65.80 1.78 16 4 136 132 65.78 1.77 17 5 41 36 72.45 0.21 18 5 42 37 69.19 0.70 19 5 43 38 66.16 1.88 20 5 45 40 66.45 1.99 21 5 69 64 65.81 1.77 22 5 70 65 65.89 1.79 23 5 71 66 65.95 1.78 24 5 128 123 65.79 1.78 25 5 136 131 65.80 1.78 26 6 40 34 72.79 0.25 27 6 41 35 72.42 0.20 28 6 42 36 69.19 0.70 29 6 136 130 65.82 1.77 30 6 137 131 65.80 1.78 31 6 138 132 65.80 1.78 32 7 34 27 72.86 0.24 33 7 40 33 72.86 0.24 34 7 41 34 72.64 0.18 35 7 54 47 72.66 0.30 36 7 69 62 66.47 2.00 37 7 138 131 65.80 1.78 38 7 140 133 65.77 1.77 39 8 40 32 72.86 0.24 40 8 138 130 65.82 1.77 41 8 139 131 65.78 1.78 42 8 140 132 65.78 1.78 43 9 41 32 73.23 0.09 44 9 56 47 73.75 0.27 45 9 140 131 65.78 1.78 46 9 142 133 65.78 1.78 47 10 139 129 65.86 1.77 48 10 140 130 65.81 1.78 49 10 141 131 65.78 1.78 50 10 142 132 65.77 1.77 51 11 17 6 214.74 64.05 52 11 18 7 81.73 2.44 53 11 142 131 65.77 1.78 54 12 141 129 65.85 1.77 55 12 142 130 65.81 1.78 56 12 143 131 65.78 1.78 57 13 122 109 85.34 3.21 58 13 143 130 65.81 1.78 59 15 122 107 104.50 1.08 60 16 58 42 243.22 52.25 61 16 60 44 243.22 52.25 62 16 61 45 243.17 52.27 63 16 122 106 122.16 1.05 64 17 57 40 243.27 52.24 65 17 58 41 243.25 52.23 66 18 56 38 243.24 52.23 67 18 57 39 243.27 52.24 68 18 58 40 243.27 52.25 69 18 63 45 243.28 52.25 70 18 64 46 243.25 52.24 71 18 65 47 243.25 52.24 72 18 122 104 134.56 2.12 73 18 124 106 130.42 0.10 74 18 142 124 65.75 1.78 75 19 56 37 244.59 52.90 76 19 57 38 245.72 53.45 77 19 59 40 247.06 53.02 78 20 41 21 247.36 52.84 79 20 55 35 245.60 53.40 80 20 56 36 245.88 53.48 81 21 55 34 247.30 52.89 82 21 56 35 247.09 53.00 83 21 57 36 247.08 53.00 84 22 54 32 250.14 51.62 85 22 55 33 249.97 51.58 86 22 89 67 204.19 28.28 87 22 90 68 203.81 28.44 88 22 91 69 204.74 27.96 89 23 34 11 251.18 51.12 90 23 36 13 251.53 51.08 91 23 41 18 251.14 51.18 92 23 53 30 250.16 51.61 93 23 54 31 250.16 51.61 94 24 34 10 251.57 51.06 95 24 52 28 251.11 51.16 96 24 53 29 251.08 51.16 97 24 90 66 204.79 27.98 98 24 91 67 204.77 27.96 99 24 94 70 204.56 27.86 100 25 32 7 251.59 51.06 101 25 33 8 251.59 51.06 102 25 34 9 251.59 51.06 103 25 43 18 251.58 51.06 104 25 51 26 251.25 51.12 105 25 52 27 251.22 51.11 106 25 94 69 205.00 27.79 107 26 31 5 389.51 4.44 108 26 50 24 251.47 51.02 109 26 51 25 251.44 51.03 110 26 94 68 205.03 27.81 111 26 95 69 204.92 27.75 112 26 98 72 205.14 27.48 113 27 31 4 375.44 2.60 114 28 31 3 465.50 0.44 115 28 49 21 257.33 52.94 116 28 50 22 253.04 50.88 117 28 98 70 205.96 27.23 118 29 46 17 258.52 53.50 119 29 47 18 258.11 53.32 120 29 48 19 258.12 53.33 121 29 50 21 257.88 53.19 122 30 46 16 261.40 52.13 123 31 45 14 261.62 52.13 124 31 46 15 261.55 52.11 125 31 50 19 261.18 52.02 126 32 44 12 266.92 49.53 127 32 45 13 265.69 50.10 128 33 42 9 326.38 20.45 129 33 43 10 267.88 49.56 130 33 44 11 267.30 49.34 131 34 41 7 353.76 6.83 132 34 42 8 326.38 20.44 133 34 43 9 267.94 49.56 134 34 52 18 267.13 49.18 135 34 53 19 267.14 49.18 136 34 54 20 267.10 49.15 137 34 69 35 261.17 46.20 138 35 41 6 362.29 2.60 139 35 42 7 326.38 20.45 140 36 40 4 421.41 7.58 141 36 41 5 362.34 2.63 142 37 40 3 466.85 0.13 143 37 42 5 374.22 0.18 144 41 54 13 272.42 46.49 145 41 56 15 272.42 46.48 146 43 51 8 272.49 46.51 147 43 52 9 272.47 46.50 148 43 69 26 266.46 43.52 149 45 50 5 373.18 2.75 150 45 51 6 370.54 2.53 151 45 70 25 293.94 29.78 152 45 71 26 295.80 28.85 153 48 71 23 314.72 19.38 154 48 73 25 314.63 19.30 155 48 74 26 314.17 19.08 156 49 71 22 314.92 19.27 157 49 98 49 270.67 5.15 158 50 70 20 315.18 19.14 159 50 71 21 315.17 19.14 160 50 98 48 270.75 5.27 161 51 68 17 317.39 18.22 162 51 69 18 316.22 18.68 163 51 70 19 314.94 19.02 164 51 77 26 269.41 3.79 165 51 94 43 270.97 5.21 166 51 98 47 270.71 5.30 167 52 68 16 317.60 18.12 168 52 69 17 316.70 18.43 169 52 94 42 270.88 5.25 170 53 66 13 318.11 18.00 171 53 67 14 317.76 18.10 172 53 68 15 317.61 18.12 173 53 90 37 271.43 5.35 174 53 94 41 270.80 5.29 175 54 66 12 318.12 18.00 176 54 67 13 318.08 18.00 177 54 69 15 317.79 18.09 178 55 65 10 318.27 18.01 179 55 66 11 318.12 18.00 180 55 84 29 271.89 5.48 181 55 88 33 271.81 5.52 182 55 89 34 271.72 5.51 183 55 90 35 271.45 5.50 184 56 64 8 318.57 17.93 185 56 65 9 318.44 17.97 186 56 140 84 65.83 1.77 187 57 63 6 366.55 3.25 188 57 64 7 318.57 17.93 189 58 61 3 484.81 2.04 190 58 62 4 430.91 5.13 191 58 63 5 366.55 3.25 192 59 62 3 441.23 2.82 193 61 120 59 213.00 31.69 194 62 120 58 213.05 31.66 195 63 118 55 213.06 31.67 196 63 120 57 212.74 31.51 197 63 122 59 206.13 28.99 198 64 82 18 299.64 19.39 199 64 84 20 299.55 19.37 200 65 80 15 300.23 19.59 201 65 81 16 300.17 19.61 202 65 82 17 299.66 19.39 203 65 84 19 299.62 19.39 204 65 124 59 186.59 20.38 205 65 140 75 65.85 1.77 206 65 142 77 65.78 1.77 207 66 80 14 300.23 19.59 208 66 81 15 300.18 19.60 209 66 84 18 299.72 19.39 210 66 90 24 299.00 19.22 211 66 93 27 298.92 19.34 212 67 79 12 300.38 19.60 213 67 80 13 300.26 19.62 214 67 126 59 185.49 20.18 215 67 140 73 65.78 1.77 216 68 77 9 303.91 21.14 217 68 78 10 301.07 19.91 218 68 79 11 300.39 19.57 219 68 94 26 298.94 19.36 220 68 97 29 298.92 19.46 221 68 126 58 185.50 20.18 222 69 77 8 303.91 21.14 223 69 78 9 303.42 21.08 224 69 126 57 185.51 20.18 225 69 128 59 185.04 20.03 226 69 138 69 65.82 1.77 227 70 76 6 364.85 5.15 228 70 77 7 309.23 23.75 229 71 74 3 481.94 0.09 230 71 75 4 401.24 4.34 231 71 76 5 318.49 28.32 232 71 77 6 318.49 28.32 233 71 136 65 88.28 1.60 234 72 75 3 468.00 2.19 235 72 77 5 397.31 0.14 236 72 107 35 265.86 35.72 237 72 108 36 265.82 35.70 238 72 110 38 265.10 35.74 239 73 110 37 265.74 35.74 240 75 110 35 264.62 35.52 241 76 110 34 263.72 35.78 242 76 112 36 250.53 36.43 243 76 128 52 185.19 20.03 244 76 131 55 115.94 0.57 245 76 136 60 86.50 0.74 246 77 97 20 299.25 19.53 247 77 98 21 299.25 19.53 248 77 107 30 265.79 35.77 249 77 110 33 245.63 33.95 250 77 111 34 240.94 36.30 251 77 128 51 185.47 20.16 252 78 111 33 235.99 34.02 253 78 113 35 232.27 35.43 254 78 114 36 218.94 34.34 255 78 126 48 185.53 20.17 256 78 128 50 185.50 20.18 257 79 97 18 298.79 19.55 258 79 106 27 265.54 35.88 259 79 114 35 213.36 31.56 260 79 126 47 185.80 20.11 261 80 114 34 213.45 31.62 262 80 116 36 213.05 31.62 263 80 124 44 186.47 20.14 264 80 125 45 186.38 20.11 265 80 126 46 186.02 20.22 266 80 140 60 65.84 1.76 267 81 84 3 516.51 1.27 268 81 93 12 299.04 19.42 269 81 97 16 298.55 19.66 270 81 103 22 266.00 35.64 271 82 116 34 213.09 31.64 272 82 117 35 213.08 31.64 273 82 118 36 212.76 31.50 274 82 124 42 187.58 19.91 275 83 118 35 212.75 31.50 276 83 119 36 212.75 31.50 277 84 88 4 445.98 5.50 278 85 88 3 466.24 3.83 279 87 92 5 451.84 0.99 280 88 92 4 451.84 0.99 281 88 93 5 451.16 1.31 282 88 103 15 406.83 0.97 283 89 92 3 460.57 1.42 284 89 93 4 455.13 0.65 285 90 93 3 459.30 1.43 286 90 94 4 456.01 1.09 287 91 95 4 468.43 1.54 288 92 95 3 481.86 0.74 289 92 96 4 478.10 2.62 290 93 96 3 481.86 0.74 291 93 97 4 481.86 0.74 292 93 103 10 415.86 1.40 293 94 97 3 491.60 0.17 294 94 98 4 487.30 1.98 295 95 98 3 490.25 0.50 296 96 99 3 477.15 2.04 297 96 100 4 451.38 2.92 298 96 103 7 417.50 2.15 299 97 103 6 430.25 4.23 300 97 104 7 415.86 1.39 301 97 106 9 415.94 1.36 302 97 107 10 415.86 1.40 303 98 104 6 430.25 4.25 304 98 107 9 420.50 0.26 305 99 104 5 442.44 0.31 306 100 103 3 461.93 1.14 307 100 104 4 450.99 1.94 308 101 104 3 456.60 0.85 309 101 105 4 461.69 0.85 310 102 105 3 469.99 3.29 311 102 106 4 461.70 0.84 312 103 106 3 464.69 3.89 313 103 107 4 458.47 0.78 314 104 107 3 466.18 3.15 315 104 108 4 458.48 0.78 316 105 108 3 464.67 2.33 317 105 109 4 458.47 0.78 318 106 109 3 468.21 3.94 319 107 110 3 479.91 2.69 320 111 114 3 500.53 0.29 321 111 128 17 185.66 20.13 322 112 127 15 185.78 20.10 323 112 128 16 185.50 20.18 324 112 131 19 175.41 23.24 325 113 126 13 186.17 20.01 326 113 127 14 185.65 20.16 327 114 125 11 186.44 20.07 328 114 126 12 186.31 20.07 329 115 123 8 187.88 19.77 330 115 124 9 187.68 19.80 331 115 125 10 186.44 20.08 332 116 123 7 187.80 19.81 333 116 124 8 187.71 19.82 334 117 122 5 371.52 0.24 335 117 123 6 187.76 19.83 336 118 121 3 464.97 2.55 337 118 122 4 409.66 10.78 338 118 124 6 403.23 13.98 339 122 142 20 65.84 1.77 340 122 143 21 65.79 1.78 341 123 143 20 65.77 1.78 342 124 141 17 65.83 1.77 343 124 142 18 65.78 1.78 344 125 140 15 65.84 1.76 345 125 141 16 65.79 1.77 346 126 138 12 65.91 1.75 347 126 139 13 65.84 1.76 348 126 140 14 65.79 1.77 349 127 138 11 65.91 1.75 350 127 139 12 65.86 1.76 351 127 141 14 65.84 1.76 352 128 131 3 470.42 3.12 353 128 136 8 185.44 50.70 354 128 137 9 74.15 5.86 355 128 138 10 65.83 1.76 356 129 137 8 83.34 1.80 357 129 138 9 74.05 5.80 358 129 139 10 74.05 5.80 359 130 135 5 416.14 1.39 360 130 136 6 229.28 66.14 361 130 137 7 85.71 0.66 362 131 136 5 379.30 2.00 363 132 136 4 452.13 3.82 364 133 136 3 487.63 0.70