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 5 449.03 1.27 2 2 73 71 31.85 0.16 3 2 76 74 25.91 0.31 4 2 127 125 22.87 0.32 5 2 128 126 22.84 0.30 6 2 131 129 22.11 0.06 7 3 6 3 475.94 0.52 8 3 7 4 463.91 4.96 9 4 7 3 474.03 0.10 10 4 8 4 474.44 0.30 11 5 8 3 474.44 0.30 12 5 9 4 474.47 0.32 13 6 9 3 477.72 1.21 14 6 10 4 474.45 0.34 15 6 124 118 45.92 0.14 16 6 127 121 45.93 0.14 17 7 10 3 476.95 1.58 18 7 11 4 469.24 2.94 19 7 73 66 47.80 1.07 20 7 74 67 48.43 0.81 21 8 11 3 474.70 0.21 22 8 12 4 469.23 2.94 23 9 12 3 475.56 0.64 24 9 13 4 469.12 2.92 25 9 121 112 61.48 0.89 26 9 124 115 61.48 0.89 27 10 13 3 478.88 1.02 28 10 14 4 464.17 0.46 29 10 70 60 61.45 0.91 30 10 124 114 61.50 0.89 31 10 125 115 61.47 0.90 32 10 128 118 61.46 0.90 33 11 14 3 477.06 1.93 34 11 15 4 455.38 4.78 35 11 70 59 61.47 0.91 36 11 71 60 61.80 1.07 37 11 73 62 61.80 1.07 38 12 15 3 469.58 1.81 39 12 16 4 469.57 1.81 40 13 16 3 477.82 1.42 41 13 17 4 469.56 1.81 42 13 113 100 79.67 1.04 43 13 121 108 61.98 1.07 44 13 125 112 61.96 1.07 45 14 17 3 465.62 0.16 46 14 18 4 465.62 0.16 47 14 21 7 404.56 8.33 48 14 66 52 61.97 1.07 49 14 67 53 61.97 1.07 50 14 70 56 61.97 1.07 51 15 18 3 467.20 0.95 52 16 113 97 93.05 2.75 53 16 116 100 91.41 2.03 54 17 20 3 484.95 0.69 55 17 21 4 444.39 0.59 56 17 24 7 417.38 1.93 57 17 109 92 91.34 2.00 58 17 113 96 93.08 2.83 59 18 21 3 497.87 3.08 60 20 23 3 473.49 1.03 61 20 24 4 469.03 0.10 62 21 24 3 469.04 0.10 63 21 25 4 469.04 0.10 64 21 63 42 98.21 1.46 65 22 25 3 473.39 0.50 66 22 26 4 474.38 0.00 67 22 60 38 101.62 0.14 68 22 63 41 98.33 1.51 69 23 26 3 482.84 4.21 70 23 27 4 468.95 2.71 71 23 56 33 117.34 0.14 72 24 27 3 482.82 4.22 73 24 28 4 466.39 1.44 74 24 108 84 121.03 2.07 75 24 109 85 126.17 0.50 76 24 112 88 128.22 0.15 77 24 113 89 128.25 0.12 78 25 28 3 470.70 0.71 79 25 29 4 468.94 2.71 80 25 59 34 117.20 0.21 81 25 63 38 116.78 0.01 82 26 29 3 472.92 0.73 83 26 30 4 465.52 0.70 84 26 55 29 124.91 1.25 85 26 56 30 125.48 1.53 86 26 59 33 119.59 1.40 87 27 30 3 465.53 0.70 88 27 31 4 463.54 0.27 89 27 108 81 128.55 0.08 90 27 112 85 129.19 0.09 91 28 31 3 466.09 1.55 92 28 32 4 458.34 2.28 93 28 101 73 128.32 0.12 94 28 104 76 128.34 0.12 95 28 105 77 128.31 0.12 96 28 108 80 128.62 0.07 97 29 32 3 469.26 0.27 98 29 33 4 463.66 2.05 99 29 55 26 129.15 0.10 100 29 58 29 128.89 0.18 101 29 59 30 128.77 0.14 102 29 101 72 128.38 0.10 103 30 33 3 485.40 0.53 104 30 34 4 463.68 2.04 105 30 50 20 129.41 0.04 106 31 34 3 482.74 1.86 107 31 35 4 463.66 2.04 108 31 104 73 128.87 0.10 109 31 107 76 128.94 0.10 110 31 108 77 128.99 0.10 111 31 111 80 129.41 0.05 112 32 35 3 473.35 0.02 113 32 36 4 463.66 2.05 114 32 39 7 317.95 7.19 115 32 101 69 128.85 0.12 116 32 104 72 128.89 0.10 117 33 37 4 442.56 2.31 118 33 39 6 324.21 3.98 119 33 40 7 297.00 2.31 120 33 43 10 296.98 2.30 121 33 48 15 129.57 0.01 122 34 37 3 482.88 0.90 123 36 39 3 488.00 1.92 124 36 100 64 128.87 0.10 125 36 103 67 129.27 0.04 126 36 104 68 129.28 0.04 127 37 40 3 480.06 0.06 128 38 41 3 483.26 0.90 129 39 42 3 487.59 1.54 130 39 43 4 483.04 0.58 131 39 97 58 128.84 0.12 132 39 100 61 129.21 0.01 133 40 43 3 489.88 4.00 134 40 48 8 242.14 0.38 135 41 44 3 494.37 1.76 136 42 93 51 128.84 0.10 137 42 94 52 128.94 0.07 138 42 97 55 129.24 0.01 139 43 46 3 477.87 1.02 140 43 48 5 391.75 24.14 141 43 58 15 233.55 2.66 142 45 54 9 246.83 2.23 143 46 54 8 246.80 2.24 144 46 58 12 246.79 2.24 145 47 52 5 266.06 3.83 146 47 54 7 246.88 2.25 147 47 55 8 246.93 2.25 148 48 52 4 393.25 6.67 149 48 55 7 246.90 2.24 150 49 52 3 475.97 0.88 151 52 55 3 470.25 2.56 152 52 56 4 465.84 4.77 153 53 56 3 470.25 2.56 154 53 57 4 455.45 0.42 155 54 57 3 480.35 3.04 156 54 58 4 462.08 3.73 157 55 58 3 473.63 2.04 158 55 59 4 464.04 2.77 159 56 59 3 474.35 1.68 160 56 60 4 471.12 0.77 161 57 60 3 483.44 4.46 162 57 61 4 471.12 0.78 163 58 61 3 473.41 0.38 164 58 62 4 470.59 1.03 165 59 62 3 473.93 0.12 166 59 63 4 470.58 1.02 167 60 63 3 471.89 1.20 168 60 64 4 470.55 1.01 169 61 64 3 471.53 1.00 170 61 65 4 462.41 3.56 171 62 65 3 483.15 0.40 172 62 66 4 467.16 2.73 173 63 66 3 475.68 1.52 174 63 67 4 466.45 2.38 175 64 67 3 465.09 1.55 176 64 68 4 461.94 3.33 177 65 68 3 468.75 0.35 178 65 69 4 457.98 3.39 179 65 80 15 163.21 2.55 180 65 83 18 162.71 2.32 181 66 69 3 472.69 4.85 182 66 70 4 459.92 4.34 183 66 105 39 180.35 4.19 184 66 128 62 180.50 4.26 185 66 129 63 180.37 4.32 186 66 132 66 163.43 2.62 187 67 70 3 474.59 1.70 188 67 71 4 461.95 5.36 189 68 71 3 475.08 1.19 190 68 72 4 461.96 5.37 191 68 79 11 237.61 9.70 192 69 72 3 475.42 1.35 193 69 73 4 450.62 2.71 194 69 76 7 267.98 3.17 195 69 80 11 188.25 14.98 196 69 128 59 180.68 4.21 197 69 132 63 180.48 4.26 198 70 73 3 470.32 1.19 199 70 128 58 180.70 4.21 200 72 75 3 471.41 0.30 201 72 76 4 439.52 2.83 202 72 79 7 300.62 13.10 203 73 76 3 477.25 2.62 204 75 78 3 479.88 1.34 205 75 79 4 444.14 11.14 206 76 79 3 469.94 0.60 207 76 80 4 428.51 13.52 208 76 128 52 201.02 5.39 209 76 131 55 200.81 5.40 210 76 132 56 200.56 5.27 211 77 81 4 425.25 11.87 212 77 135 58 195.77 2.88 213 78 81 3 469.17 1.42 214 80 83 3 479.44 0.58 215 80 84 4 474.36 0.75 216 80 132 52 201.25 5.33 217 80 135 55 201.17 5.29 218 81 84 3 478.88 1.51 219 81 85 4 478.91 1.53 220 81 139 58 201.14 5.31 221 82 85 3 480.13 0.92 222 82 86 4 478.90 1.53 223 83 86 3 478.91 1.54 224 83 87 4 472.09 4.92 225 83 136 53 201.28 5.29 226 84 87 3 483.50 0.75 227 84 88 4 472.07 4.93 228 84 135 51 201.33 5.32 229 84 136 52 201.27 5.29 230 84 139 55 201.24 5.29 231 85 88 3 478.63 3.18 232 85 89 4 460.55 0.79 233 85 139 54 201.18 5.32 234 86 89 3 486.91 0.96 235 86 90 4 448.14 2.38 236 86 91 5 438.99 2.96 237 87 91 4 398.35 17.36 238 87 92 5 368.42 11.64 239 87 98 11 270.56 3.38 240 87 136 49 201.68 5.25 241 87 140 53 201.25 5.30 242 88 92 4 359.20 4.90 243 88 139 51 201.33 5.33 244 88 140 52 201.12 5.34 245 89 92 3 492.91 3.16 246 92 140 48 201.71 5.17 247 93 97 4 477.08 0.42 248 93 98 5 471.75 2.24 249 93 140 47 202.25 5.34 250 94 97 3 487.44 0.42 251 95 98 3 480.95 0.54 252 95 137 42 202.88 5.12 253 95 140 45 202.87 5.12 254 96 99 3 483.34 2.44 255 96 100 4 477.10 0.43 256 97 100 3 480.25 0.89 257 97 101 4 473.32 2.32 258 98 101 3 476.58 2.99 259 98 102 4 469.26 0.66 260 98 133 35 203.43 5.19 261 98 136 38 203.43 5.19 262 98 137 39 203.43 5.19 263 98 140 42 203.43 5.19 264 99 102 3 476.62 1.89 265 99 103 4 473.29 1.35 266 100 103 3 473.30 1.35 267 100 104 4 473.29 1.35 268 101 104 3 476.91 0.46 269 101 105 4 466.21 0.88 270 102 105 3 471.87 1.94 271 102 106 4 466.22 0.88 272 102 129 27 203.94 5.12 273 102 133 31 203.92 5.12 274 103 106 3 469.12 0.57 275 103 107 4 466.23 0.88 276 104 107 3 466.10 0.82 277 104 108 4 466.10 0.83 278 105 108 3 472.45 2.35 279 105 109 4 464.43 1.66 280 105 129 24 206.00 4.37 281 106 109 3 472.62 2.44 282 106 110 4 464.43 1.66 283 106 117 11 207.98 4.49 284 106 122 16 206.78 4.34 285 106 125 19 206.65 4.41 286 106 126 20 206.28 4.26 287 106 129 23 206.14 4.33 288 107 110 3 472.12 2.37 289 107 111 4 464.25 1.56 290 108 111 3 476.59 2.71 291 108 112 4 463.59 1.90 292 109 112 3 479.81 1.83 293 109 113 4 459.62 1.53 294 109 125 16 207.33 4.60 295 110 117 7 216.17 0.40 296 113 116 3 477.86 0.55 297 113 117 4 469.31 3.72 298 114 117 3 481.58 2.41 299 115 118 3 524.59 0.06 300 116 121 5 459.00 0.21 301 117 121 4 459.00 0.21 302 117 122 5 454.10 2.25 303 117 125 8 412.31 6.58 304 118 121 3 472.83 1.66 305 118 122 4 463.42 0.94 306 119 122 3 467.54 1.12 307 119 123 4 466.57 0.64 308 120 123 3 470.39 0.44 309 120 124 4 466.56 0.64 310 121 124 3 479.39 0.64 311 121 125 4 461.54 0.03 312 122 125 3 474.83 1.78 313 122 126 4 463.69 1.10 314 123 126 3 474.72 1.73 315 123 127 4 468.85 1.21 316 124 127 3 474.72 1.73 317 124 128 4 466.14 0.13 318 125 128 3 474.00 2.71 319 125 129 4 467.89 0.73 320 126 129 3 482.05 1.31 321 126 130 4 467.89 0.73 322 127 130 3 475.13 4.01 323 127 131 4 466.14 0.14 324 128 131 3 476.48 4.69 325 128 132 4 464.69 1.69 326 129 132 3 475.88 3.64 327 129 133 4 464.62 1.73 328 130 133 3 474.06 3.00 329 130 134 4 463.50 1.14 330 131 134 3 467.79 0.98 331 131 135 4 463.54 1.12 332 132 135 3 477.09 3.78 333 132 136 4 464.68 0.54 334 133 136 3 470.03 0.24 335 133 137 4 462.60 0.51 336 134 137 3 475.47 1.36 337 134 138 4 462.59 0.51 338 135 138 3 474.63 1.79 339 136 140 4 494.56 1.17 340 137 140 3 486.25 0.59