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 7 5 460.69 2.09 2 2 73 71 30.70 0.65 3 2 76 74 25.88 0.12 4 2 127 125 22.41 0.47 5 2 128 126 22.22 0.37 6 3 6 3 467.61 5.50 7 3 7 4 460.75 2.07 8 4 7 3 482.22 1.80 9 4 8 4 460.94 1.99 10 5 8 3 471.59 2.65 11 5 9 4 460.98 2.00 12 6 9 3 471.10 2.89 13 6 10 4 469.64 2.32 14 6 124 118 49.34 1.05 15 6 127 121 49.34 1.05 16 7 10 3 478.25 0.72 17 7 11 4 469.64 2.31 18 7 73 66 49.40 1.03 19 7 74 67 49.40 1.03 20 8 11 3 472.39 3.65 21 8 12 4 469.64 2.31 22 9 12 3 478.25 0.72 23 9 13 4 465.79 0.39 24 9 121 112 65.19 0.85 25 9 124 115 65.11 0.85 26 10 13 3 472.99 2.08 27 10 14 4 465.43 0.57 28 10 70 60 65.14 0.84 29 10 124 114 65.19 0.85 30 10 125 115 65.14 0.84 31 10 128 118 65.13 0.84 32 11 14 3 479.49 1.68 33 11 15 4 463.17 1.45 34 11 70 59 65.23 0.85 35 11 71 60 65.27 0.84 36 11 73 62 65.25 0.85 37 12 15 3 470.82 2.11 38 12 16 4 463.24 1.42 39 13 16 3 468.14 0.78 40 13 17 4 468.14 0.78 41 13 113 100 81.65 0.66 42 13 121 108 72.44 1.50 43 13 125 112 65.61 0.87 44 14 17 3 471.38 0.84 45 14 18 4 466.01 0.29 46 14 21 7 390.99 9.50 47 14 63 49 77.15 0.09 48 14 66 52 67.22 0.04 49 14 67 53 67.24 0.05 50 14 70 56 65.57 0.86 51 14 109 95 81.43 0.59 52 15 18 3 468.00 1.28 53 16 113 97 90.28 0.81 54 16 116 100 84.00 1.79 55 17 20 3 478.57 2.12 56 17 21 4 442.01 1.81 57 17 24 7 400.28 15.14 58 17 109 92 84.00 1.80 59 17 113 96 91.85 0.05 60 18 21 3 490.50 3.02 61 20 23 3 472.62 2.29 62 20 24 4 469.85 3.67 63 21 24 3 477.22 0.00 64 21 25 4 467.50 1.37 65 21 63 42 94.89 1.44 66 22 25 3 477.24 0.01 67 22 26 4 471.00 3.12 68 22 60 38 96.66 2.24 69 22 63 41 96.66 2.23 70 23 26 3 479.55 0.74 71 23 27 4 471.00 3.12 72 24 27 3 477.66 0.20 73 24 28 4 470.97 3.15 74 24 108 84 119.99 0.07 75 24 109 85 121.92 0.85 76 24 112 88 132.93 1.26 77 25 28 3 477.65 0.21 78 25 29 4 470.30 3.43 79 25 59 34 119.70 0.06 80 25 63 38 119.55 0.05 81 25 105 80 120.17 0.03 82 26 29 3 475.25 0.85 83 26 30 4 469.79 3.58 84 26 55 29 131.10 1.69 85 26 56 30 129.27 0.77 86 26 59 33 125.42 2.60 87 27 30 3 476.67 0.15 88 27 31 4 469.82 3.58 89 27 108 81 134.23 1.76 90 27 112 85 134.55 1.69 91 28 31 3 470.20 3.39 92 28 32 4 470.25 3.42 93 28 101 73 134.00 1.74 94 28 104 76 134.00 1.74 95 28 105 77 134.00 1.74 96 28 108 80 134.34 1.74 97 29 32 3 474.35 1.37 98 29 33 4 469.91 3.61 99 29 55 26 134.32 1.79 100 29 58 29 134.31 1.79 101 29 59 30 134.22 1.76 102 29 62 33 134.24 1.77 103 29 101 72 134.04 1.74 104 30 33 3 481.07 2.00 105 30 34 4 471.49 2.83 106 30 50 20 134.84 1.57 107 30 55 25 134.47 1.72 108 31 34 3 477.15 0.04 109 31 35 4 471.48 2.83 110 31 104 73 134.37 1.60 111 31 107 76 134.59 1.62 112 31 108 77 134.75 1.58 113 31 111 80 134.89 1.57 114 32 35 3 477.14 0.04 115 32 36 4 448.84 2.08 116 32 39 7 273.26 58.08 117 32 100 68 134.45 1.64 118 32 101 69 134.44 1.64 119 32 104 72 134.52 1.65 120 33 37 4 414.76 13.07 121 33 39 6 259.08 38.97 122 33 40 7 206.71 30.32 123 33 43 10 135.06 1.68 124 33 48 15 134.90 1.57 125 33 55 22 134.89 1.57 126 36 39 3 494.93 1.44 127 36 100 64 134.53 1.67 128 36 103 67 134.88 1.55 129 36 104 68 134.88 1.55 130 37 40 3 481.47 1.80 131 38 41 3 486.20 1.54 132 39 42 3 492.90 0.07 133 39 43 4 485.99 1.64 134 39 97 58 134.41 1.60 135 39 100 61 134.84 1.51 136 40 43 3 485.99 1.64 137 40 48 8 139.28 0.20 138 41 44 3 498.86 3.05 139 42 93 51 134.32 1.62 140 42 94 52 134.74 1.50 141 42 97 55 134.84 1.50 142 43 46 3 480.13 0.27 143 43 48 5 406.52 10.37 144 43 58 15 135.12 1.59 145 45 54 9 142.02 0.98 146 46 54 8 141.94 1.01 147 46 55 9 142.01 0.98 148 46 58 12 141.94 1.01 149 47 52 5 312.28 21.77 150 47 54 7 142.03 0.97 151 47 55 8 142.05 0.98 152 48 55 7 204.41 32.11 153 49 52 3 481.85 1.31 154 51 56 5 458.29 1.91 155 52 55 3 477.01 2.33 156 52 56 4 474.99 1.32 157 53 56 3 478.26 0.30 158 53 57 4 475.00 1.32 159 54 57 3 480.36 0.74 160 54 58 4 475.15 1.25 161 55 58 3 475.16 1.25 162 55 59 4 467.92 2.20 163 56 59 3 479.48 0.93 164 56 60 4 471.64 2.36 165 57 60 3 486.95 2.11 166 57 61 4 474.06 3.56 167 58 61 3 476.23 2.48 168 58 62 4 471.65 2.35 169 59 62 3 476.29 2.44 170 59 63 4 471.63 2.36 171 60 63 3 476.40 2.50 172 60 64 4 469.75 1.42 173 61 64 3 474.14 3.62 174 61 65 4 462.79 0.49 175 62 65 3 469.61 1.43 176 62 66 4 462.79 0.50 177 62 101 39 158.77 2.02 178 63 66 3 473.09 2.43 179 63 67 4 465.46 0.83 180 64 67 3 469.06 0.36 181 64 68 4 466.06 1.15 182 65 68 3 474.48 2.40 183 65 69 4 465.02 1.67 184 65 80 15 158.71 1.97 185 65 83 18 158.16 2.26 186 66 69 3 473.09 1.92 187 66 70 4 465.00 1.69 188 66 105 39 191.73 1.73 189 66 128 62 201.56 3.18 190 66 129 63 182.25 6.33 191 66 132 66 181.85 6.15 192 67 70 3 468.81 0.22 193 67 71 4 457.63 0.09 194 68 71 3 466.00 2.83 195 68 72 4 464.56 3.55 196 68 79 11 181.94 6.11 197 69 72 3 473.69 3.75 198 69 73 4 451.29 3.26 199 69 76 7 270.61 5.88 200 69 80 11 181.97 6.10 201 69 128 59 212.82 0.35 202 69 132 63 182.34 6.28 203 70 73 3 455.30 4.45 204 70 128 58 210.02 1.05 205 72 75 3 473.22 2.94 206 72 76 4 449.75 0.07 207 72 79 7 269.42 1.01 208 73 76 3 481.94 1.39 209 73 128 55 249.56 2.35 210 75 78 3 481.51 1.61 211 75 79 4 469.38 4.01 212 76 79 3 479.77 0.74 213 76 80 4 437.68 11.84 214 76 128 52 258.58 3.76 215 76 131 55 253.09 1.32 216 76 132 56 250.00 2.54 217 76 135 59 249.99 2.54 218 77 81 4 454.99 3.18 219 77 135 58 250.00 2.54 220 78 81 3 469.38 4.02 221 80 83 3 482.08 1.39 222 80 84 4 459.32 0.13 223 80 132 52 258.91 3.79 224 80 135 55 258.72 3.77 225 80 136 56 258.74 3.77 226 81 84 3 477.65 3.60 227 81 85 4 475.80 2.68 228 81 139 58 258.81 3.79 229 82 85 3 475.81 2.67 230 82 86 4 475.80 2.67 231 83 86 3 477.35 1.90 232 83 87 4 475.81 2.67 233 83 136 53 259.23 3.71 234 84 87 3 480.63 4.68 235 84 88 4 465.43 2.52 236 84 135 51 259.22 3.71 237 84 136 52 259.22 3.71 238 84 138 54 259.21 3.70 239 84 139 55 259.00 3.79 240 85 88 3 477.91 3.44 241 85 89 4 450.79 4.80 242 85 139 54 259.00 3.80 243 86 89 3 481.81 1.48 244 86 90 4 450.75 4.80 245 86 91 5 439.52 3.08 246 87 91 4 399.43 10.46 247 87 92 5 325.52 6.85 248 87 93 6 308.83 6.59 249 87 98 11 277.69 2.00 250 87 140 53 259.18 3.71 251 88 92 4 385.20 17.57 252 88 139 51 259.22 3.71 253 88 140 52 258.99 3.80 254 89 92 3 476.44 2.62 255 89 139 50 259.24 3.71 256 93 97 4 484.38 0.84 257 93 98 5 475.56 0.97 258 93 140 47 259.27 3.70 259 94 97 3 502.07 3.62 260 95 98 3 493.29 0.61 261 95 137 42 259.68 3.54 262 95 140 45 259.47 3.64 263 96 99 3 500.34 1.74 264 96 100 4 490.29 2.12 265 97 100 3 482.25 1.90 266 97 101 4 478.54 0.04 267 98 101 3 482.32 1.86 268 98 102 4 475.88 1.38 269 98 133 35 259.96 3.56 270 98 136 38 259.99 3.58 271 98 137 39 259.95 3.56 272 98 140 42 259.95 3.57 273 99 102 3 478.99 2.93 274 99 103 4 471.24 1.11 275 100 103 3 487.63 1.39 276 100 104 4 471.24 1.11 277 101 104 3 479.16 2.84 278 101 105 4 471.24 1.12 279 102 105 3 479.79 3.16 280 102 106 4 468.70 0.14 281 102 129 27 260.57 3.56 282 102 133 31 260.46 3.55 283 103 106 3 473.66 2.64 284 103 107 4 469.87 0.96 285 104 107 3 472.13 2.10 286 104 108 4 472.37 0.29 287 105 108 3 477.15 2.10 288 105 109 4 477.15 2.11 289 105 129 24 261.38 3.48 290 106 109 3 480.20 0.59 291 106 110 4 477.15 2.11 292 106 117 11 263.02 3.11 293 106 122 16 261.88 3.29 294 106 125 19 261.83 3.29 295 106 126 20 261.66 3.37 296 106 129 23 261.39 3.48 297 107 110 3 480.04 0.67 298 107 111 4 477.16 2.10 299 108 111 3 482.35 1.82 300 108 112 4 470.72 4.00 301 109 112 3 470.72 4.00 302 109 113 4 457.18 2.76 303 109 117 8 263.67 2.81 304 109 125 16 261.91 3.29 305 110 113 3 478.48 0.12 306 110 117 7 263.05 3.12 307 113 116 3 478.94 0.81 308 113 117 4 328.09 12.68 309 115 118 3 522.28 0.70 310 116 121 5 427.44 4.52 311 117 121 4 458.68 0.29 312 117 122 5 430.05 3.21 313 117 125 8 420.75 7.87 314 118 121 3 470.69 1.56 315 118 122 4 460.44 1.16 316 119 122 3 476.67 1.43 317 119 123 4 460.48 1.18 318 120 123 3 473.00 0.16 319 120 124 4 460.48 1.19 320 121 124 3 472.32 1.61 321 121 125 4 462.50 0.17 322 122 125 3 475.25 2.77 323 122 126 4 466.28 1.72 324 123 126 3 475.91 1.48 325 123 127 4 457.19 6.26 326 124 127 3 476.43 1.92 327 124 128 4 454.13 4.74 328 125 128 3 469.64 3.01 329 125 129 4 456.30 3.66 330 126 129 3 473.92 0.88 331 126 130 4 469.64 3.01 332 127 130 3 475.06 0.31 333 127 131 4 459.75 4.02 334 128 131 3 479.01 5.61 335 128 132 4 464.31 1.75 336 129 132 3 473.67 2.20 337 129 133 4 461.00 3.41 338 130 133 3 473.67 2.20 339 130 134 4 468.55 0.36 340 131 134 3 468.55 0.36 341 131 135 4 468.54 0.36 342 132 135 3 483.06 5.67 343 132 136 4 468.66 1.79 344 133 136 3 476.38 2.06 345 133 137 4 470.06 1.09 346 134 137 3 476.38 2.06 347 134 138 4 454.78 8.72 348 135 138 3 475.36 1.55 349 136 140 4 492.69 1.15 350 137 140 3 492.69 1.15