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 1 76 75 18.66 0.22 2 1 131 130 17.75 0.09 3 2 6 4 467.64 0.43 4 2 7 5 457.94 0.90 5 2 73 71 27.45 1.03 6 2 127 125 23.46 2.18 7 2 128 126 20.82 0.86 8 3 6 3 468.29 0.76 9 3 7 4 467.69 0.46 10 4 7 3 471.31 0.58 11 4 8 4 466.20 1.21 12 5 8 3 480.03 5.12 13 5 9 4 462.50 3.05 14 6 9 3 470.25 0.83 15 6 10 4 466.53 5.15 16 6 124 118 46.95 0.06 17 6 127 121 47.91 0.42 18 7 10 3 475.56 0.64 19 7 11 4 468.74 4.06 20 7 73 66 48.01 0.40 21 7 74 67 49.61 1.20 22 8 11 3 475.59 0.65 23 8 12 4 475.57 0.65 24 9 12 3 475.57 0.65 25 9 13 4 465.85 5.50 26 9 124 115 59.12 0.13 27 10 13 3 479.98 1.43 28 10 14 4 466.01 0.29 29 10 70 60 59.08 0.15 30 10 73 63 59.16 0.12 31 10 124 114 59.17 0.12 32 10 125 115 59.16 0.12 33 10 128 118 59.12 0.14 34 11 14 3 472.30 1.35 35 11 15 4 469.59 1.48 36 11 70 59 59.16 0.12 37 11 73 62 59.20 0.14 38 12 15 3 481.64 4.55 39 12 16 4 469.60 1.47 40 13 16 3 485.01 4.13 41 13 17 4 466.06 0.30 42 13 121 108 59.83 0.28 43 13 125 112 59.75 0.31 44 14 17 3 474.68 0.14 45 14 18 4 466.06 0.30 46 14 21 7 439.05 1.19 47 14 66 52 59.62 0.24 48 14 67 53 59.62 0.24 49 14 70 56 59.62 0.24 50 14 109 95 86.38 1.02 51 15 18 3 465.81 0.45 52 16 113 97 95.81 1.58 53 16 116 100 92.50 0.01 54 17 20 3 487.72 2.52 55 17 21 4 457.29 0.72 56 17 24 7 431.10 2.92 57 17 109 92 92.30 0.09 58 17 113 96 97.00 1.01 59 18 21 3 498.43 0.95 60 20 23 3 471.09 0.61 61 20 24 4 459.19 1.67 62 21 24 3 471.09 0.61 63 21 25 4 459.21 1.68 64 21 63 42 97.37 0.82 65 21 67 46 97.23 0.89 66 22 25 3 467.63 2.34 67 22 26 4 459.25 1.67 68 22 59 37 99.30 0.78 69 22 60 38 97.64 0.72 70 22 63 41 97.59 0.72 71 23 26 3 477.13 0.04 72 23 27 4 464.38 0.39 73 24 27 3 472.88 2.59 74 24 28 4 461.93 0.84 75 24 108 84 119.36 1.05 76 24 109 85 128.11 2.13 77 24 112 88 134.15 0.22 78 24 113 89 134.24 0.18 79 25 28 3 477.60 0.23 80 25 29 4 467.24 0.23 81 25 59 34 113.42 0.34 82 25 62 37 112.53 0.71 83 26 29 3 472.87 2.04 84 26 30 4 467.24 0.24 85 26 56 30 123.13 2.27 86 26 59 33 115.48 0.69 87 27 30 3 468.25 0.27 88 27 31 4 468.17 0.32 89 27 108 81 134.50 0.25 90 27 112 85 134.81 0.35 91 28 31 3 468.75 0.57 92 28 32 4 468.20 0.29 93 28 101 73 134.30 0.28 94 28 104 76 134.41 0.29 95 28 105 77 134.34 0.30 96 28 108 80 134.52 0.26 97 29 32 3 471.00 1.70 98 29 33 4 471.00 1.70 99 29 55 26 134.59 0.24 100 29 58 29 134.58 0.23 101 29 59 30 134.51 0.24 102 29 62 33 134.56 0.23 103 29 101 72 134.45 0.28 104 30 33 3 472.93 2.66 105 30 34 4 471.00 1.70 106 30 55 25 134.80 0.33 107 31 34 3 477.05 0.00 108 31 35 4 470.98 1.71 109 31 104 73 134.47 0.27 110 31 107 76 134.78 0.32 111 31 108 77 134.77 0.34 112 31 111 80 134.94 0.33 113 32 35 3 472.23 2.41 114 32 36 4 463.19 5.60 115 32 39 7 315.95 9.67 116 32 100 68 134.44 0.29 117 32 101 69 134.43 0.29 118 32 104 72 134.53 0.26 119 33 37 4 446.44 2.77 120 33 39 6 282.51 11.44 121 33 40 7 256.33 5.52 122 33 43 10 253.78 6.79 123 33 48 15 134.97 0.34 124 33 55 22 134.94 0.33 125 36 39 3 492.52 0.24 126 36 100 64 134.43 0.29 127 36 103 67 134.87 0.34 128 36 104 68 134.88 0.34 129 37 40 3 489.25 2.09 130 38 41 3 500.50 0.95 131 39 42 3 512.56 1.34 132 39 43 4 498.25 0.17 133 39 97 58 134.38 0.31 134 39 100 61 134.85 0.34 135 40 43 3 496.98 0.81 136 40 48 8 334.12 1.31 137 42 93 51 134.37 0.31 138 42 94 52 134.62 0.28 139 42 97 55 134.88 0.34 140 43 48 5 459.32 2.69 141 43 58 15 135.06 0.29 142 44 47 3 473.72 2.07 143 44 48 4 471.30 3.29 144 45 48 3 478.24 2.75 145 45 49 4 466.37 0.83 146 45 50 5 459.33 2.69 147 46 49 3 476.62 0.62 148 46 50 4 454.13 0.12 149 46 51 5 454.13 0.12 150 47 51 4 450.09 0.45 151 47 54 7 300.47 4.65 152 47 55 8 300.51 4.62 153 48 55 7 280.50 14.64 154 52 55 3 478.68 1.50 155 52 56 4 457.01 2.62 156 53 56 3 479.83 1.50 157 53 57 4 465.86 3.38 158 54 57 3 473.38 0.99 159 54 58 4 462.62 5.01 160 55 58 3 474.54 1.58 161 55 59 4 462.62 5.01 162 56 59 3 463.18 4.74 163 56 60 4 464.46 4.10 164 57 60 3 473.56 1.42 165 57 61 4 468.62 3.89 166 58 61 3 474.62 1.60 167 58 62 4 468.62 3.89 168 59 62 3 471.67 4.75 169 59 63 4 468.14 4.11 170 60 63 3 470.62 2.88 171 60 64 4 460.25 1.34 172 61 64 3 468.30 2.66 173 61 65 4 457.40 0.09 174 62 65 3 480.78 2.18 175 62 66 4 457.40 0.09 176 63 66 3 474.43 1.62 177 63 67 4 460.60 1.51 178 64 67 3 483.07 1.04 179 64 68 4 467.50 1.86 180 65 68 3 476.19 2.48 181 65 69 4 467.51 1.85 182 65 80 15 145.31 4.01 183 65 83 18 145.31 4.01 184 66 69 3 476.98 2.87 185 66 70 4 467.51 1.85 186 66 105 39 180.91 7.05 187 66 128 62 183.84 5.58 188 66 129 63 176.29 9.33 189 66 132 66 148.84 2.37 190 67 70 3 476.98 2.88 191 67 71 4 471.44 0.11 192 68 71 3 476.80 2.06 193 68 72 4 471.09 3.15 194 68 79 11 155.91 1.13 195 69 72 3 476.80 2.06 196 69 73 4 467.10 5.15 197 69 76 7 248.00 2.64 198 69 80 11 155.82 1.18 199 69 128 59 197.87 4.42 200 69 132 63 176.27 9.34 201 70 73 3 489.10 4.08 202 70 128 58 197.87 4.42 203 72 75 3 477.49 0.04 204 72 76 4 449.02 2.36 205 72 79 7 273.95 5.12 206 73 76 3 479.10 2.81 207 73 128 55 221.90 5.63 208 75 78 3 477.98 3.38 209 75 79 4 463.44 10.64 210 76 79 3 477.78 3.48 211 76 80 4 442.14 5.72 212 76 131 55 224.58 4.32 213 76 132 56 224.55 4.31 214 76 135 59 215.87 2.54 215 77 81 4 409.50 8.58 216 77 135 58 224.53 4.30 217 80 83 3 481.63 0.58 218 80 84 4 472.51 1.08 219 80 132 52 228.18 5.40 220 80 135 55 227.64 5.19 221 81 84 3 485.59 1.41 222 81 85 4 476.88 2.96 223 81 139 58 227.67 5.20 224 82 85 3 485.56 6.00 225 82 86 4 472.53 1.08 226 83 86 3 474.12 0.29 227 83 87 4 472.52 1.08 228 83 136 53 228.62 5.20 229 84 87 3 470.29 1.06 230 84 88 4 468.19 1.07 231 84 89 5 453.09 6.41 232 84 135 51 228.62 5.20 233 84 136 52 228.62 5.20 234 84 138 54 228.60 5.20 235 84 139 55 228.40 5.17 236 85 89 4 432.12 5.64 237 85 90 5 432.12 5.64 238 85 139 54 228.50 5.20 239 86 90 4 413.29 0.41 240 86 91 5 413.28 0.41 241 87 91 4 413.25 0.42 242 87 92 5 413.25 0.42 243 87 93 6 302.58 5.17 244 87 98 11 261.52 0.73 245 88 92 4 359.76 27.16 246 88 136 48 228.78 5.22 247 88 137 49 228.72 5.21 248 88 139 51 228.63 5.18 249 88 140 52 228.44 5.19 250 89 92 3 481.75 1.58 251 89 139 50 228.62 5.17 252 89 140 51 228.38 5.21 253 89 141 52 228.30 5.19 254 92 140 48 228.66 5.19 255 93 97 4 484.38 0.84 256 93 98 5 475.98 0.13 257 93 140 47 228.80 5.19 258 94 97 3 486.28 0.11 259 95 98 3 486.39 0.17 260 95 137 42 229.35 5.13 261 95 140 45 229.34 5.13 262 96 99 3 486.56 0.84 263 96 100 4 466.63 0.42 264 97 100 3 477.85 5.20 265 97 101 4 462.23 2.25 266 98 101 3 477.86 5.19 267 98 102 4 466.23 0.26 268 98 133 35 229.62 5.17 269 98 136 38 229.63 5.17 270 98 137 39 229.59 5.19 271 99 102 3 471.60 2.94 272 99 103 4 466.60 0.45 273 100 103 3 474.69 2.06 274 100 104 4 466.60 0.45 275 101 104 3 478.53 3.98 276 101 105 4 461.89 3.49 277 102 105 3 464.55 2.17 278 102 106 4 461.94 3.51 279 102 129 27 230.16 4.98 280 102 133 31 230.13 4.96 281 103 106 3 482.97 1.15 282 103 107 4 471.86 2.17 283 104 107 3 472.30 1.96 284 104 108 4 471.87 2.17 285 105 108 3 472.37 1.92 286 105 109 4 472.35 1.92 287 105 129 24 230.59 5.09 288 106 109 3 474.62 0.79 289 106 110 4 472.36 1.92 290 106 117 11 235.95 3.35 291 106 122 16 231.23 5.01 292 106 125 19 230.94 5.08 293 106 126 20 231.13 4.98 294 106 129 23 230.83 5.12 295 107 110 3 474.86 0.66 296 107 111 4 474.85 0.66 297 108 111 3 474.86 0.66 298 108 112 4 469.60 1.97 299 109 112 3 473.82 0.58 300 109 113 4 465.08 1.35 301 109 117 8 241.13 2.58 302 109 125 16 235.39 3.14 303 110 114 4 410.55 11.10 304 110 117 7 261.80 16.27 305 111 114 3 490.20 2.25 306 113 116 3 481.50 0.77 307 113 117 4 466.29 2.50 308 114 117 3 483.55 1.43 309 115 118 3 514.13 1.10 310 116 121 5 452.34 3.00 311 117 121 4 452.36 2.98 312 117 122 5 440.70 8.81 313 117 125 8 424.36 0.64 314 118 121 3 477.26 4.67 315 118 122 4 452.40 3.00 316 119 122 3 471.68 0.51 317 119 123 4 466.67 1.70 318 120 123 3 472.14 0.28 319 120 124 4 459.00 2.15 320 121 124 3 476.49 1.78 321 121 125 4 454.79 4.24 322 122 125 3 475.66 1.35 323 122 126 4 468.59 0.74 324 123 126 3 470.30 0.18 325 123 127 4 469.31 1.10 326 124 127 3 477.87 2.45 327 124 128 4 467.36 2.07 328 125 128 3 477.14 2.81 329 125 129 4 456.10 3.56 330 126 129 3 480.81 0.97 331 126 130 4 467.36 2.08 332 127 130 3 474.80 0.43 333 127 131 4 461.52 0.83 334 128 131 3 475.07 0.29 335 128 132 4 461.51 0.82 336 129 132 3 477.05 3.64 337 129 133 4 459.21 4.48 338 130 133 3 476.11 4.12 339 130 134 4 459.24 0.30 340 131 134 3 482.08 6.15 341 131 135 4 478.03 3.16 342 132 135 3 484.50 4.94 343 132 136 4 474.50 4.92 344 133 136 3 472.51 0.40 345 133 137 4 462.04 1.31 346 134 137 3 479.44 0.06 347 134 138 4 453.95 2.73 348 135 138 3 474.92 0.85 349 137 140 3 512.69 0.05