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 14.72 0.21 2 3 6 3 499.88 2.06 3 3 7 4 499.74 2.00 4 3 91 88 26.21 0.12 5 3 141 138 16.04 0.33 6 3 144 141 15.21 0.43 7 4 7 3 499.88 2.06 8 4 8 4 489.93 2.91 9 4 88 84 32.79 0.15 10 4 91 87 30.20 0.60 11 5 8 3 512.35 3.97 12 5 9 4 507.03 6.63 13 6 9 3 517.75 1.27 14 6 141 135 23.55 1.34 15 6 144 138 23.55 1.34 16 7 10 3 515.04 5.10 17 7 90 83 33.60 0.26 18 7 91 84 32.76 0.14 19 7 141 134 28.16 1.17 20 9 14 5 483.60 2.00 21 9 137 128 37.44 0.45 22 10 14 4 483.60 2.00 23 10 15 5 477.92 0.83 24 10 18 8 453.00 3.02 25 10 84 74 48.70 0.16 26 10 90 80 46.81 0.12 27 10 137 127 41.70 1.47 28 10 138 128 38.95 0.10 29 10 141 131 38.94 0.10 30 11 14 3 499.39 0.88 31 11 15 4 494.25 1.69 32 12 15 3 501.06 1.72 33 12 16 4 501.06 1.71 34 13 16 3 501.05 1.72 35 13 17 4 499.48 2.50 36 14 17 3 505.86 0.69 37 14 18 4 499.47 2.52 38 14 134 120 65.07 0.04 39 14 137 123 65.13 0.07 40 15 18 3 500.45 2.02 41 15 19 4 499.53 2.50 42 15 84 69 74.92 0.41 43 16 19 3 500.55 2.07 44 16 20 4 499.47 2.52 45 17 20 3 499.53 2.50 46 17 21 4 499.47 2.52 47 17 130 113 93.56 0.30 48 17 131 114 93.50 0.34 49 17 134 117 93.48 0.34 50 18 21 3 506.19 1.49 51 18 22 4 492.80 2.10 52 18 81 63 93.64 0.31 53 18 84 66 95.34 0.48 54 18 134 116 93.56 0.30 55 18 135 117 93.48 0.34 56 18 138 120 93.47 0.35 57 19 22 3 494.38 2.89 58 19 23 4 492.80 2.10 59 19 81 62 93.97 0.20 60 19 84 65 96.70 0.31 61 19 85 66 101.39 0.14 62 20 23 3 506.81 1.19 63 20 127 107 104.64 0.03 64 20 131 111 104.05 0.14 65 21 24 3 510.34 0.58 66 21 25 4 491.78 2.60 67 21 122 101 104.17 0.12 68 21 127 106 104.64 0.03 69 21 131 110 104.05 0.15 70 21 135 114 103.42 0.46 71 22 25 3 500.60 1.82 72 22 26 4 476.98 1.47 73 22 29 7 464.54 8.37 74 22 74 52 144.18 19.81 75 22 77 55 103.43 0.46 76 22 78 56 103.50 0.50 77 22 81 59 103.33 0.50 78 22 135 113 103.51 0.42 79 23 27 4 490.69 3.14 80 24 27 3 507.19 0.99 81 24 125 101 113.95 3.83 82 24 127 103 113.84 3.89 83 25 28 3 514.03 1.17 84 25 32 7 312.42 4.58 85 25 74 49 155.95 25.39 86 25 122 97 105.64 0.21 87 25 125 100 113.97 3.84 88 25 135 110 105.61 0.23 89 26 29 3 507.25 0.96 90 28 31 3 507.56 1.02 91 28 32 4 482.98 4.59 92 29 33 4 462.39 4.57 93 29 74 45 164.50 21.16 94 29 75 46 164.53 21.17 95 29 78 49 164.50 21.16 96 30 33 3 508.82 2.84 97 30 34 4 488.88 1.65 98 30 61 31 190.03 13.50 99 30 67 37 184.52 15.32 100 30 71 41 175.03 18.71 101 31 34 3 504.97 0.29 102 31 35 4 498.85 3.33 103 31 61 30 190.38 13.34 104 32 35 3 499.41 3.06 105 32 36 4 498.75 3.37 106 32 74 42 183.13 14.77 107 32 121 89 152.77 0.52 108 33 36 3 504.92 0.27 109 33 37 4 499.40 3.04 110 33 70 37 187.45 13.36 111 33 74 41 183.13 14.77 112 34 37 3 500.78 2.34 113 34 38 4 499.42 3.02 114 34 60 26 190.46 13.33 115 34 61 27 190.47 13.33 116 34 67 33 189.50 13.22 117 34 70 36 188.75 13.09 118 35 38 3 506.61 0.58 119 35 39 4 497.12 0.49 120 35 121 86 164.46 0.74 121 36 39 3 502.94 2.41 122 36 40 4 497.13 0.50 123 36 73 37 189.51 13.09 124 36 74 38 189.43 13.07 125 36 77 41 189.40 13.09 126 36 117 81 164.71 0.93 127 36 118 82 164.70 0.94 128 36 121 85 164.57 0.72 129 37 40 3 498.50 0.18 130 37 41 4 497.16 0.49 131 37 51 14 244.21 1.62 132 37 66 29 190.28 13.27 133 37 69 32 189.72 13.11 134 37 70 33 189.49 13.05 135 37 73 36 189.59 13.11 136 37 114 77 165.04 1.03 137 38 41 3 501.18 1.52 138 38 42 4 495.75 1.20 139 38 60 22 190.66 13.35 140 38 66 28 190.49 13.27 141 39 42 3 497.11 0.52 142 39 43 4 492.24 2.95 143 39 117 78 164.81 0.95 144 39 120 81 164.92 0.89 145 40 43 3 505.37 2.23 146 40 44 4 471.67 7.41 147 40 47 7 317.57 3.56 148 40 51 11 273.82 2.62 149 40 113 73 165.02 1.08 150 40 114 74 165.03 1.05 151 40 117 77 164.85 0.93 152 41 45 4 438.75 2.70 153 41 48 7 272.58 2.00 154 41 51 10 272.60 2.02 155 41 57 16 219.22 0.59 156 41 66 25 217.34 0.26 157 43 120 77 165.21 0.85 158 44 47 3 510.41 2.50 159 44 113 69 165.08 1.08 160 45 48 3 510.40 2.50 161 46 113 67 165.64 1.11 162 47 50 3 513.79 0.96 163 47 51 4 513.38 0.75 164 47 113 66 165.42 1.13 165 48 51 3 514.04 0.83 166 48 57 9 246.03 1.29 167 49 52 3 507.45 1.04 168 50 106 56 165.50 1.49 169 50 110 60 165.76 1.33 170 51 54 3 500.87 1.71 171 51 69 18 231.47 1.59 172 52 55 3 509.46 0.09 173 53 65 12 240.46 1.09 174 54 57 3 534.39 0.39 175 54 63 9 270.01 2.44 176 54 65 11 235.97 3.33 177 54 66 12 235.90 3.31 178 54 69 15 235.90 3.31 179 56 59 3 514.29 0.46 180 56 63 7 280.38 2.58 181 57 60 3 507.41 2.17 182 57 63 6 291.20 0.40 183 57 66 9 265.19 0.18 184 59 62 3 509.43 1.19 185 59 63 4 448.55 5.80 186 60 63 3 508.36 1.15 187 60 66 6 348.99 15.36 188 61 67 6 352.37 13.67 189 63 66 3 494.65 2.32 190 63 67 4 494.70 1.58 191 64 67 3 494.71 1.58 192 64 68 4 490.89 0.32 193 65 68 3 499.99 1.06 194 65 69 4 490.94 0.29 195 66 69 3 499.23 0.68 196 66 70 4 494.69 1.59 197 67 70 3 501.91 0.19 198 67 71 4 495.60 2.50 199 68 71 3 501.91 0.19 200 68 72 4 495.61 2.50 201 69 72 3 504.81 1.64 202 69 73 4 499.29 4.34 203 70 73 3 505.00 1.54 204 70 74 4 506.68 0.69 205 71 74 3 506.70 0.70 206 71 75 4 506.69 0.70 207 72 75 3 506.69 0.69 208 72 76 4 501.96 3.05 209 73 76 3 506.69 0.69 210 73 77 4 501.96 3.05 211 73 114 41 168.18 0.56 212 74 77 3 513.61 2.78 213 74 78 4 498.94 1.55 214 75 78 3 497.95 1.36 215 75 79 4 498.31 1.18 216 76 79 3 499.90 0.40 217 76 80 4 500.72 2.32 218 76 97 21 188.96 9.20 219 77 80 3 502.23 1.56 220 77 81 4 500.73 2.31 221 77 135 58 172.05 3.23 222 78 81 3 509.89 2.27 223 78 82 4 498.36 1.09 224 79 82 3 501.44 0.39 225 79 83 4 498.82 0.86 226 79 93 14 192.47 10.46 227 80 83 3 501.61 0.54 228 80 84 4 498.82 0.86 229 80 90 10 236.19 5.11 230 80 93 13 225.32 0.32 231 80 94 14 192.47 10.46 232 80 97 17 192.47 10.46 233 80 138 58 172.40 3.43 234 80 142 62 172.02 3.26 235 81 84 3 501.94 1.71 236 81 135 54 173.67 3.92 237 81 138 57 172.44 3.44 238 83 86 3 505.03 3.83 239 83 89 6 296.51 10.63 240 83 90 7 260.70 2.00 241 83 93 10 260.69 2.00 242 84 90 6 303.78 0.10 243 86 89 3 502.10 0.99 244 86 90 4 497.56 1.25 245 87 90 3 497.56 1.25 246 87 91 4 497.56 1.25 247 88 91 3 505.78 2.52 248 88 92 4 497.56 1.25 249 89 92 3 505.66 2.58 250 89 93 4 488.29 3.39 251 90 93 3 505.81 2.50 252 90 94 4 483.03 3.45 253 91 94 3 495.62 2.81 254 91 95 4 487.71 0.71 255 92 95 3 493.90 1.32 256 92 96 4 486.70 0.78 257 93 96 3 491.70 1.23 258 93 97 4 485.06 1.60 259 94 97 3 501.44 0.22 260 94 98 4 497.10 1.95 261 94 141 47 176.91 5.70 262 94 142 48 176.48 5.58 263 94 145 51 176.03 5.79 264 95 98 3 504.53 1.76 265 95 99 4 501.44 0.22 266 95 145 50 176.03 5.79 267 96 99 3 515.48 1.11 268 97 100 3 536.98 3.10 269 97 101 4 508.18 0.06 270 97 111 14 271.31 10.73 271 97 142 45 176.81 5.84 272 98 101 3 510.43 0.13 273 98 102 4 503.00 0.80 274 98 145 47 176.17 5.84 275 98 146 48 176.15 5.86 276 99 102 3 507.98 0.05 277 99 103 4 501.87 1.36 278 100 103 3 504.67 1.60 279 100 104 4 501.88 1.38 280 101 104 3 503.06 0.80 281 101 105 4 487.07 8.79 282 101 106 5 420.50 8.38 283 101 111 10 303.18 1.87 284 101 146 45 176.63 6.10 285 102 105 3 496.17 4.24 286 102 145 43 176.90 6.16 287 102 146 44 176.50 6.04 288 106 110 4 504.45 1.69 289 106 111 5 504.45 1.69 290 107 110 3 510.84 1.51 291 107 111 4 505.52 1.17 292 107 146 39 176.41 6.46 293 108 111 3 512.34 0.76 294 108 112 4 505.66 1.10 295 108 143 35 177.19 6.33 296 108 146 38 174.33 7.77 297 109 112 3 508.44 2.50 298 109 113 4 507.24 1.79 299 110 113 3 521.62 4.98 300 111 114 3 514.49 1.41 301 111 139 28 178.01 6.23 302 111 142 31 177.54 6.46 303 111 143 32 177.43 6.49 304 111 146 35 176.89 6.71 305 112 115 3 511.75 2.92 306 112 143 31 177.52 6.50 307 113 117 4 501.45 1.24 308 114 117 3 508.04 2.06 309 114 118 4 497.15 0.81 310 115 118 3 501.43 1.23 311 115 119 4 497.14 0.81 312 115 136 21 179.28 6.86 313 115 139 24 179.24 6.84 314 116 119 3 505.44 3.35 315 116 120 4 485.50 0.66 316 117 120 3 490.28 2.62 317 117 121 4 489.80 2.77 318 118 121 3 507.88 1.82 319 118 122 4 489.80 2.77 320 118 135 17 179.38 6.82 321 118 139 21 179.28 6.86 322 119 122 3 507.88 1.82 323 119 123 4 489.80 2.77 324 119 129 10 233.34 1.59 325 119 132 13 185.13 9.68 326 120 123 3 506.56 2.59 327 120 124 4 497.67 1.84 328 121 124 3 507.97 3.29 329 121 125 4 501.91 0.27 330 122 125 3 506.46 2.54 331 122 126 4 497.98 1.69 332 122 127 5 387.41 1.69 333 122 131 9 276.08 7.05 334 122 132 10 267.41 10.21 335 122 135 13 243.08 5.42 336 123 126 3 497.77 6.88 337 123 127 4 460.51 11.73 338 127 131 4 473.00 4.58 339 128 131 3 512.74 0.33 340 128 132 4 499.81 3.33 341 129 132 3 499.82 3.33 342 129 133 4 499.82 3.33 343 130 133 3 512.24 2.88 344 130 134 4 499.82 3.33 345 131 134 3 509.00 1.26 346 131 135 4 497.30 2.07 347 132 135 3 500.29 3.11 348 132 136 4 497.72 4.16 349 133 136 3 509.81 1.89 350 133 137 4 497.81 4.12 351 134 137 3 511.76 0.91 352 134 138 4 497.81 4.12 353 135 138 3 508.94 1.46 354 135 139 4 495.53 5.25 355 136 139 3 505.91 1.70 356 136 140 4 499.38 5.94 357 137 140 3 508.65 1.31 358 137 141 4 499.68 5.80 359 138 141 3 508.90 1.19 360 138 142 4 508.92 1.18 361 139 142 3 508.93 1.18 362 139 143 4 508.92 1.18 363 140 143 3 499.79 3.40 364 140 144 4 495.18 5.71 365 141 144 3 511.34 0.42 366 141 145 4 508.55 0.98 367 142 145 3 508.56 0.97 368 142 146 4 508.55 0.97 369 143 146 3 508.56 0.97