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 6 4 466.88 0.47 2 2 7 5 463.32 2.23 3 2 10 8 444.35 8.81 4 2 74 72 30.07 0.85 5 2 127 125 24.95 0.57 6 2 128 126 23.34 0.21 7 2 131 129 23.05 0.35 8 3 6 3 469.16 1.59 9 3 7 4 471.71 1.88 10 4 7 3 479.13 0.04 11 4 8 4 478.94 0.03 12 5 8 3 487.90 0.35 13 5 9 4 483.25 1.99 14 6 9 3 485.99 0.61 15 6 10 4 483.25 1.98 16 6 124 118 52.70 0.89 17 6 127 121 52.70 0.88 18 7 10 3 490.54 1.67 19 7 11 4 483.25 1.98 20 7 74 67 53.23 0.63 21 8 11 3 485.36 0.14 22 8 12 4 487.56 0.47 23 9 12 3 487.78 0.58 24 9 13 4 487.57 0.47 25 9 124 115 62.23 2.27 26 10 13 3 485.78 0.43 27 10 14 4 483.26 1.69 28 10 71 61 62.22 2.27 29 10 74 64 62.23 2.27 30 10 124 114 62.24 2.28 31 10 125 115 62.23 2.28 32 10 128 118 62.23 2.28 33 11 14 3 499.07 1.86 34 11 15 4 486.82 0.09 35 11 71 60 62.23 2.27 36 11 74 63 62.23 2.27 37 12 15 3 492.31 0.23 38 13 16 3 486.75 0.96 39 13 17 4 481.84 1.51 40 13 110 97 79.62 2.62 41 13 114 101 87.17 0.88 42 13 121 108 63.46 2.04 43 13 125 112 63.11 1.98 44 14 17 3 482.66 1.92 45 14 18 4 481.83 1.51 46 14 68 54 63.09 1.98 47 14 71 57 63.11 1.98 48 15 18 3 482.84 1.58 49 15 19 4 482.17 1.35 50 16 19 3 482.28 1.30 51 16 20 4 481.85 1.52 52 16 24 8 406.06 10.88 53 16 114 98 89.64 0.14 54 17 20 3 484.72 0.09 55 17 21 4 455.40 1.11 56 17 24 7 406.02 10.89 57 17 64 47 121.54 17.45 58 17 68 51 64.14 1.72 59 18 21 3 474.93 4.98 60 18 68 50 64.14 1.71 61 20 23 3 486.23 0.28 62 20 24 4 473.42 1.04 63 21 24 3 487.70 2.34 64 21 25 4 463.53 1.83 65 21 61 40 142.65 17.63 66 21 64 43 140.46 18.73 67 21 65 44 140.47 18.73 68 22 25 3 481.23 0.90 69 22 26 4 468.55 4.10 70 22 57 35 153.54 14.77 71 22 61 39 143.84 17.84 72 23 26 3 488.50 2.81 73 23 27 4 471.36 2.69 74 24 27 3 473.49 3.75 75 24 28 4 472.34 3.19 76 24 64 40 152.85 14.14 77 24 109 85 138.90 4.42 78 24 110 86 140.55 3.42 79 24 113 89 144.18 1.33 80 24 114 90 144.27 1.30 81 25 28 3 481.21 1.24 82 25 29 4 475.65 1.54 83 25 60 35 152.94 14.11 84 25 64 39 152.87 14.14 85 26 29 3 481.19 1.24 86 26 30 4 475.65 1.54 87 26 51 25 162.74 10.40 88 26 56 30 162.25 10.43 89 26 57 31 162.25 10.43 90 26 60 34 159.34 11.05 91 27 30 3 482.38 2.23 92 27 31 4 475.65 1.54 93 27 51 24 163.06 10.47 94 27 109 82 144.68 1.53 95 28 31 3 478.81 1.89 96 28 32 4 475.40 1.42 97 28 64 36 161.68 9.88 98 28 102 74 144.94 1.65 99 28 105 77 144.85 1.61 100 28 106 78 144.84 1.60 101 28 109 81 144.83 1.56 102 29 32 3 480.81 0.89 103 29 33 4 475.66 3.27 104 29 56 27 162.99 10.46 105 29 59 30 162.58 10.28 106 29 60 31 162.54 10.29 107 29 102 73 144.94 1.65 108 30 33 3 484.14 0.96 109 30 34 4 475.55 1.34 110 30 49 19 165.64 11.77 111 30 51 21 163.16 10.54 112 31 34 3 480.93 1.34 113 31 35 4 475.55 1.34 114 31 105 74 144.85 1.61 115 31 108 77 144.97 1.53 116 31 109 78 144.99 1.52 117 31 112 81 144.98 1.51 118 32 35 3 487.14 3.75 119 32 36 4 463.10 1.52 120 32 39 7 380.88 0.65 121 32 101 69 145.03 1.70 122 32 102 70 144.96 1.64 123 32 105 73 144.98 1.54 124 33 36 3 480.77 4.46 125 33 37 4 448.49 6.04 126 33 39 6 372.50 4.83 127 33 40 7 302.32 3.54 128 33 43 10 291.19 0.69 129 33 46 13 230.06 2.98 130 33 49 16 166.91 12.32 131 33 56 23 166.85 12.35 132 34 37 3 492.52 1.42 133 35 105 70 145.03 1.54 134 36 39 3 494.73 0.96 135 36 101 65 145.24 1.65 136 37 40 3 490.37 1.23 137 38 41 3 493.36 0.83 138 39 42 3 499.38 1.58 139 39 43 4 490.99 0.36 140 39 98 59 145.24 1.66 141 40 43 3 488.86 1.43 142 40 49 9 240.83 0.29 143 42 92 50 145.86 2.14 144 42 93 51 145.84 2.12 145 42 94 52 145.77 2.08 146 42 95 53 145.90 2.06 147 42 98 56 145.81 1.91 148 43 46 3 482.60 1.72 149 43 49 6 396.27 38.31 150 43 59 16 228.22 5.61 151 45 55 10 276.04 8.98 152 46 49 3 531.67 1.94 153 46 55 9 274.25 8.15 154 46 56 10 278.41 7.91 155 46 59 13 274.25 8.15 156 47 53 6 313.37 0.88 157 47 55 8 313.25 0.89 158 48 53 5 313.37 0.88 159 48 56 8 313.32 0.89 160 49 56 7 313.33 0.89 161 50 53 3 483.84 0.17 162 50 56 6 417.24 4.74 163 51 56 5 433.74 3.50 164 51 57 6 417.26 4.75 165 52 57 5 460.39 9.83 166 53 56 3 468.78 5.67 167 53 57 4 461.97 9.07 168 54 57 3 473.63 3.24 169 54 58 4 461.97 9.07 170 55 58 3 480.04 0.03 171 55 59 4 473.65 3.23 172 56 59 3 473.64 3.21 173 56 60 4 473.62 3.21 174 57 60 3 478.38 0.53 175 57 61 4 470.94 1.86 176 58 61 3 482.84 0.73 177 58 62 4 478.55 0.75 178 59 62 3 479.20 1.08 179 59 63 4 477.36 1.34 180 60 63 3 481.55 0.53 181 60 64 4 473.97 1.62 182 61 64 3 487.43 2.67 183 61 65 4 472.46 1.07 184 62 65 3 476.69 1.66 185 62 66 4 475.30 0.96 186 63 66 3 478.98 0.88 187 63 67 4 478.98 0.88 188 63 102 39 157.02 4.32 189 64 67 3 475.97 2.38 190 64 68 4 475.84 2.31 191 64 106 42 159.05 5.48 192 65 68 3 478.87 0.80 193 65 69 4 476.53 1.97 194 66 69 3 485.05 0.34 195 66 70 4 479.10 0.62 196 66 84 18 157.84 3.93 197 67 70 3 484.61 0.56 198 67 71 4 483.42 1.15 199 67 106 39 164.61 8.20 200 67 128 61 167.04 10.25 201 67 129 62 163.65 8.59 202 67 132 65 155.00 6.33 203 68 71 3 486.77 1.65 204 68 72 4 488.03 3.46 205 69 72 3 491.11 1.93 206 69 73 4 486.38 4.27 207 69 80 11 260.90 6.12 208 70 73 3 491.06 1.95 209 70 74 4 479.17 0.70 210 70 77 7 343.01 1.91 211 70 80 10 243.68 7.92 212 70 81 11 230.47 1.32 213 70 128 58 168.71 11.02 214 71 74 3 497.08 0.52 215 71 128 57 168.68 11.04 216 73 76 3 486.62 1.06 217 73 77 4 444.71 3.54 218 73 80 7 318.32 6.63 219 74 77 3 477.11 1.72 220 74 128 54 169.84 11.54 221 76 79 3 490.74 1.23 222 76 80 4 462.98 5.12 223 77 80 3 476.38 1.57 224 77 81 4 451.61 3.29 225 77 131 54 170.37 11.84 226 77 132 55 170.83 12.08 227 77 135 58 169.11 12.42 228 78 81 3 494.60 1.57 229 78 82 4 446.00 0.49 230 78 135 57 169.11 12.42 231 79 82 3 480.95 2.38 232 81 84 3 484.74 1.06 233 81 85 4 469.16 3.87 234 81 132 51 170.41 13.04 235 81 135 54 169.80 13.02 236 81 136 55 169.09 13.37 237 82 85 3 479.76 1.43 238 82 86 4 460.36 0.54 239 83 86 3 474.72 3.95 240 83 87 4 465.44 3.22 241 84 87 3 466.29 3.64 242 84 88 4 466.28 3.64 243 84 136 52 168.85 13.86 244 85 88 3 480.53 3.48 245 85 89 4 446.31 4.00 246 85 135 50 169.32 13.66 247 85 136 51 168.84 13.86 248 85 138 53 168.75 13.89 249 85 139 54 168.58 13.98 250 86 89 3 484.61 2.31 251 86 90 4 422.33 7.92 252 86 91 5 421.89 8.13 253 86 139 53 168.60 13.97 254 87 91 4 405.12 16.36 255 87 92 5 356.18 8.05 256 88 92 4 326.86 1.81 257 88 93 5 318.48 6.00 258 88 94 6 300.78 14.79 259 88 99 11 265.72 6.14 260 88 136 48 168.90 13.89 261 89 93 4 318.44 6.00 262 89 139 50 168.61 14.00 263 89 140 51 168.60 14.01 264 90 93 3 487.69 1.88 265 90 139 49 168.66 14.00 266 93 140 47 168.65 14.03 267 94 98 4 468.75 3.12 268 94 99 5 468.75 3.12 269 94 140 46 168.78 14.09 270 95 98 3 473.37 0.82 271 96 99 3 490.66 1.68 272 96 137 41 169.11 14.10 273 96 140 44 167.89 14.56 274 97 100 3 470.11 2.69 275 97 101 4 466.53 4.48 276 98 101 3 476.47 0.48 277 98 102 4 465.15 5.17 278 99 102 3 472.03 2.98 279 99 103 4 472.93 1.28 280 99 133 34 169.57 13.88 281 99 136 37 169.16 14.12 282 99 137 38 169.16 14.12 283 100 103 3 472.97 1.30 284 100 104 4 472.96 1.30 285 101 104 3 485.85 1.98 286 101 105 4 472.96 1.30 287 102 105 3 476.50 3.07 288 102 106 4 472.95 1.30 289 103 106 3 478.73 1.59 290 103 107 4 466.67 4.44 291 103 129 26 169.76 13.96 292 104 107 3 480.84 5.25 293 104 108 4 472.94 1.30 294 105 108 3 480.07 4.87 295 105 109 4 471.23 0.46 296 106 109 3 481.54 2.59 297 106 110 4 467.35 1.49 298 106 129 23 170.81 14.46 299 107 110 3 474.25 1.05 300 107 111 4 467.31 1.54 301 107 117 10 242.41 12.19 302 107 122 15 172.85 13.53 303 107 125 18 172.59 13.65 304 107 129 22 170.83 14.48 305 108 111 3 468.88 2.32 306 108 112 4 467.31 1.54 307 109 112 3 483.11 0.45 308 109 113 4 460.05 0.93 309 110 113 3 466.78 1.45 310 110 114 4 436.80 1.27 311 110 117 7 248.86 8.96 312 110 125 15 172.73 13.71 313 111 117 6 224.09 3.02 314 114 117 3 507.36 1.02 315 117 121 4 453.32 4.61 316 117 122 5 445.66 3.24 317 117 125 8 433.05 1.03 318 118 121 3 475.25 5.54 319 118 122 4 464.20 5.46 320 119 122 3 468.14 3.50 321 119 123 4 464.20 5.46 322 120 123 3 469.35 3.24 323 120 124 4 462.28 0.15 324 121 124 3 469.00 1.83 325 121 125 4 457.92 2.33 326 122 125 3 466.86 4.15 327 122 126 4 459.48 1.42 328 123 126 3 486.44 7.32 329 123 127 4 459.49 1.46 330 124 127 3 475.54 0.97 331 124 128 4 459.44 1.48 332 125 128 3 466.09 3.75 333 125 129 4 457.16 2.62 334 126 129 3 473.21 1.93 335 126 130 4 458.31 2.04 336 127 130 3 461.79 3.77 337 127 131 4 458.31 2.04 338 128 131 3 456.37 1.53 339 128 132 4 468.36 2.89 340 129 132 3 467.98 4.12 341 129 133 4 456.30 8.92 342 130 133 3 478.26 0.38 343 130 134 4 462.56 5.79 344 131 134 3 473.41 2.04 345 131 135 4 462.56 5.78 346 132 135 3 483.99 4.95 347 132 136 4 452.55 0.78 348 133 136 3 487.53 3.18 349 133 137 4 454.78 0.34 350 134 137 3 487.53 3.18 351 134 138 4 457.91 1.95 352 134 141 7 427.95 7.51 353 135 138 3 473.44 2.12 354 137 140 3 492.81 2.01 355 137 141 4 477.78 0.19 356 138 141 3 479.35 0.04