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 91 90 219.81 0.78 2 1 92 91 219.79 0.79 3 2 31 29 294.02 36.20 4 2 32 30 294.00 36.20 5 2 92 90 219.81 0.78 6 2 94 92 219.72 0.74 7 3 30 27 294.07 36.18 8 3 31 28 294.03 36.20 9 3 32 29 294.01 36.20 10 3 91 88 219.99 0.81 11 3 92 89 219.94 0.81 12 3 93 90 219.81 0.78 13 3 94 91 219.80 0.78 14 4 29 25 294.12 36.19 15 4 30 26 294.11 36.18 16 4 32 28 294.07 36.18 17 4 38 34 293.81 36.13 18 4 41 37 293.76 36.08 19 4 42 38 293.72 36.09 20 4 45 41 293.79 36.02 21 4 93 89 219.94 0.81 22 4 94 90 219.84 0.78 23 4 96 92 219.81 0.78 24 5 27 22 294.48 36.30 25 5 28 23 294.45 36.29 26 5 29 24 294.12 36.18 27 5 42 37 293.81 36.10 28 5 93 88 220.03 0.80 29 5 94 89 219.96 0.80 30 5 95 90 219.83 0.78 31 5 96 91 219.82 0.78 32 6 27 21 294.63 36.31 33 6 28 22 294.49 36.28 34 6 42 36 293.89 36.09 35 6 46 40 293.75 36.02 36 6 96 90 219.88 0.80 37 6 98 92 219.49 0.66 38 7 14 7 340.57 14.81 39 7 27 20 294.69 36.32 40 7 75 68 220.03 0.80 41 7 95 88 220.03 0.80 42 7 96 89 219.93 0.80 43 7 97 90 219.81 0.77 44 7 98 91 219.72 0.73 45 7 128 121 69.45 3.65 46 7 132 125 62.49 0.50 47 8 14 6 334.64 17.77 48 8 15 7 331.98 18.32 49 8 46 38 294.08 36.02 50 8 52 44 287.70 32.83 51 8 54 46 250.32 14.25 52 8 98 90 219.81 0.79 53 8 99 91 219.71 0.74 54 8 100 92 219.66 0.74 55 8 110 102 146.47 1.58 56 9 13 4 416.88 5.79 57 9 14 5 334.23 17.56 58 9 132 123 68.16 3.29 59 9 133 124 62.59 0.52 60 9 136 127 56.92 1.52 61 10 13 3 490.35 4.62 62 10 100 90 219.80 0.81 63 10 110 100 146.80 1.46 64 12 112 100 146.37 1.56 65 12 113 101 146.18 1.51 66 13 110 97 146.67 1.51 67 13 111 98 146.40 1.54 68 13 112 99 146.06 1.47 69 13 113 100 145.91 1.46 70 14 109 95 146.83 1.45 71 14 110 96 146.40 1.55 72 14 111 97 146.18 1.52 73 14 113 99 143.34 0.49 74 14 116 102 125.50 0.85 75 14 129 115 69.47 3.66 76 15 28 13 313.38 29.89 77 15 46 31 297.56 34.33 78 15 50 35 297.32 34.20 79 15 52 37 297.26 34.23 80 15 105 90 154.72 1.10 81 15 108 93 146.84 1.45 82 15 109 94 146.71 1.46 83 15 110 95 146.34 1.52 84 16 25 9 317.80 29.16 85 16 26 10 316.86 28.76 86 16 27 11 315.00 29.07 87 16 108 92 146.80 1.46 88 16 109 93 146.72 1.47 89 16 111 95 146.16 1.51 90 16 116 100 113.78 0.84 91 16 121 105 79.59 3.18 92 16 125 109 79.04 3.00 93 17 25 8 317.88 29.14 94 17 26 9 317.51 29.07 95 17 28 11 315.79 29.46 96 17 49 32 297.52 34.13 97 17 50 33 297.51 34.13 98 17 108 91 146.69 1.47 99 18 23 5 356.23 10.02 100 18 24 6 356.21 10.02 101 18 25 7 320.25 27.96 102 18 109 91 146.74 1.49 103 19 22 3 473.61 1.07 104 19 23 4 370.79 2.83 105 19 24 5 356.23 10.02 106 19 26 7 320.22 27.98 107 19 84 65 224.06 1.78 108 19 122 103 79.45 3.19 109 21 84 63 224.05 1.78 110 21 89 68 224.01 1.76 111 22 82 60 223.53 1.74 112 22 84 62 224.02 1.77 113 22 122 100 79.50 3.20 114 24 120 96 79.58 3.21 115 24 121 97 79.53 3.19 116 24 122 98 79.48 3.20 117 25 109 84 146.72 1.47 118 25 119 94 79.64 3.21 119 25 120 95 79.58 3.19 120 25 121 96 79.49 3.18 121 25 122 97 79.46 3.19 122 25 125 100 79.27 3.12 123 26 122 96 79.03 3.23 124 26 125 99 72.93 3.55 125 27 95 68 220.02 0.80 126 27 125 98 72.92 3.55 127 27 128 101 69.45 3.65 128 28 46 18 304.19 30.82 129 28 49 21 298.00 27.71 130 28 50 22 297.98 27.71 131 29 45 16 304.20 30.82 132 29 49 20 297.98 27.70 133 30 45 15 310.48 27.66 134 31 44 13 360.38 6.12 135 31 45 14 332.86 16.52 136 31 91 60 220.40 0.97 137 32 36 4 463.53 0.32 138 32 37 5 395.06 4.03 139 32 38 6 385.50 0.11 140 32 41 9 360.38 6.12 141 33 36 3 490.72 0.85 142 33 44 11 395.28 3.91 143 36 40 4 476.57 2.35 144 36 41 5 473.12 1.56 145 36 44 8 455.06 3.16 146 37 40 3 485.53 1.73 147 37 41 4 476.60 2.37 148 38 41 3 480.43 4.28 149 38 42 4 478.95 3.54 150 38 94 56 220.12 0.84 151 38 96 58 220.09 0.84 152 39 42 3 496.65 0.58 153 39 43 4 480.44 4.28 154 39 56 17 253.12 12.10 155 39 71 32 226.25 4.12 156 39 72 33 226.47 4.02 157 39 96 57 220.10 0.83 158 40 43 3 493.41 2.21 159 40 44 4 489.70 4.05 160 41 44 3 493.65 2.08 161 41 45 4 489.70 4.05 162 42 45 3 499.06 0.62 163 42 46 4 489.71 4.05 164 42 56 14 255.38 12.84 165 42 96 54 220.02 0.81 166 42 98 56 219.83 0.78 167 43 46 3 493.81 4.04 168 43 47 4 477.58 2.01 169 43 54 11 299.77 22.39 170 43 55 12 265.05 13.17 171 43 56 13 255.56 12.76 172 44 47 3 495.78 3.06 173 44 48 4 475.05 0.74 174 45 48 3 491.20 0.77 175 45 49 4 470.63 2.75 176 46 49 3 501.85 5.62 177 46 50 4 469.97 3.08 178 46 52 6 432.17 13.62 179 46 54 8 301.56 21.54 180 46 98 52 219.83 0.78 181 47 50 3 501.30 5.90 182 47 51 4 441.00 0.05 183 47 52 5 395.56 3.14 184 47 53 6 383.87 2.16 185 49 107 58 146.78 1.46 186 50 105 55 148.20 0.94 187 50 106 56 147.04 1.52 188 50 107 57 146.79 1.46 189 51 103 52 167.99 1.69 190 51 104 53 160.72 0.91 191 51 106 55 147.06 1.51 192 52 100 48 219.45 0.67 193 52 102 50 195.68 0.33 194 52 103 51 167.47 1.42 195 52 104 52 163.60 0.51 196 52 105 53 154.81 1.20 197 53 100 47 219.44 0.67 198 53 101 48 218.35 0.97 199 53 102 49 187.13 0.78 200 53 103 50 171.31 0.49 201 54 98 44 219.94 0.82 202 54 99 45 219.71 0.73 203 54 100 46 218.59 1.10 204 54 101 47 212.44 1.11 205 55 98 43 219.99 0.81 206 55 99 44 219.93 0.82 207 55 101 46 216.88 0.04 208 56 72 16 227.86 3.43 209 56 96 40 220.16 0.81 210 56 97 41 220.12 0.82 211 56 98 42 219.92 0.79 212 57 72 15 227.91 3.41 213 57 97 40 220.14 0.82 214 57 98 41 220.06 0.80 215 57 99 42 220.00 0.80 216 57 136 79 53.25 0.21 217 57 139 82 41.05 0.84 218 58 72 14 227.91 3.41 219 58 73 15 227.86 3.42 220 59 72 13 227.99 3.41 221 59 73 14 227.94 3.39 222 60 70 10 228.69 3.44 223 60 71 11 228.49 3.38 224 60 72 12 228.02 3.39 225 61 70 9 230.97 2.43 226 62 70 8 230.99 2.43 227 63 69 6 296.44 35.13 228 63 70 7 231.33 2.60 229 64 68 4 400.66 5.33 230 64 69 5 256.29 15.05 231 65 68 3 491.89 1.49 232 72 96 24 220.59 0.91 233 74 77 3 508.97 0.27 234 74 94 20 246.19 13.68 235 74 95 21 222.56 1.87 236 74 96 22 222.41 1.90 237 75 95 20 246.25 13.66 238 75 96 21 222.50 1.91 239 75 97 22 222.41 1.92 240 75 128 53 69.41 3.65 241 75 131 56 62.62 0.53 242 75 132 57 62.52 0.49 243 75 135 60 53.27 0.22 244 76 95 19 247.00 14.00 245 76 128 52 69.39 3.63 246 76 131 55 62.62 0.52 247 77 92 15 274.12 25.66 248 77 93 16 270.89 24.55 249 77 94 17 263.06 20.66 250 78 91 13 274.82 25.98 251 78 92 14 274.57 25.87 252 78 93 15 271.43 24.31 253 78 95 17 270.90 24.57 254 78 124 46 72.79 3.58 255 78 128 50 69.30 3.60 256 79 90 11 276.10 25.89 257 79 91 12 274.83 25.98 258 79 92 13 274.12 25.64 259 80 89 9 277.20 25.75 260 80 90 10 276.69 25.86 261 80 91 11 274.82 25.98 262 80 93 13 274.80 25.97 263 80 122 42 73.38 3.46 264 81 88 7 280.26 27.21 265 81 89 8 277.18 25.74 266 81 90 9 276.80 25.87 267 82 88 6 280.27 27.21 268 82 89 7 277.18 25.73 269 82 91 9 276.91 25.82 270 82 122 40 73.41 3.45 271 83 88 5 285.85 30.00 272 84 87 3 476.45 1.35 273 84 89 5 382.44 2.64 274 95 128 33 69.38 3.64 275 97 132 35 62.49 0.50 276 97 135 38 53.80 0.04 277 97 136 39 53.25 0.21 278 97 139 42 41.16 0.90 279 100 103 3 650.00 1.26 280 100 104 4 529.48 1.57 281 105 110 5 470.66 5.81 282 111 116 5 454.88 2.73 283 111 119 8 314.97 33.15 284 112 115 3 490.20 2.66 285 112 116 4 478.99 0.06 286 113 116 3 481.44 1.17 287 113 129 16 176.43 51.77 288 113 133 20 71.91 2.43 289 115 118 3 497.72 4.60 290 115 119 4 473.95 2.81 291 116 119 3 473.95 2.80 292 116 121 5 452.85 3.98 293 116 125 9 301.16 29.19 294 116 126 10 287.13 25.68 295 116 129 13 287.07 25.68 296 117 126 9 297.89 30.82 297 119 126 7 420.86 14.92 298 121 125 4 460.25 3.98 299 121 126 5 452.24 7.99 300 122 125 3 489.58 0.54 301 124 127 3 481.64 0.84 302 124 128 4 474.30 3.03 303 125 128 3 481.30 0.47 304 125 129 4 474.29 3.02 305 126 129 3 489.27 0.12 306 126 130 4 474.28 3.02 307 127 130 3 484.92 2.29 308 127 131 4 475.91 2.21 309 128 131 3 480.64 1.57 310 128 132 4 473.11 2.27 311 129 132 3 477.10 0.53 312 129 133 4 473.14 2.24 313 130 133 3 487.69 2.19 314 130 134 4 482.16 1.26 315 131 134 3 482.47 1.10 316 131 135 4 474.32 2.79 317 132 135 3 477.87 1.14 318 132 136 4 474.34 2.80 319 133 136 3 488.18 4.12 320 133 137 4 474.47 2.87 321 134 137 3 485.69 2.51 322 134 138 4 480.44 0.12 323 135 138 3 485.47 2.62 324 135 139 4 474.72 2.58 325 136 139 3 477.79 1.21 326 136 140 4 474.69 2.58 327 137 140 3 477.69 1.16 328 137 141 4 468.00 1.10 329 138 141 3 493.47 5.34 330 138 142 4 468.81 0.74 331 139 142 3 482.97 0.39 332 139 143 4 472.25 2.46 333 140 143 3 485.98 1.89 334 140 144 4 473.29 5.95 335 141 144 3 486.70 1.53 336 141 145 4 467.44 3.02 337 142 145 3 484.11 0.54 338 142 146 4 467.98 2.75 339 143 146 3 475.14 3.72 340 143 147 4 467.43 3.02 341 144 147 3 470.69 1.40 342 144 148 4 465.23 2.02 343 145 148 3 483.81 1.87 344 145 149 4 474.69 2.70 345 146 149 3 486.07 0.74 346 147 150 3 489.49 1.06