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 5 459.04 6.96 2 2 73 71 29.98 0.55 3 2 76 74 25.26 0.68 4 2 127 125 22.81 0.58 5 2 128 126 22.68 0.64 6 2 131 129 22.65 0.62 7 3 6 3 477.00 1.50 8 3 7 4 476.99 1.50 9 4 7 3 477.00 1.50 10 4 8 4 470.71 1.14 11 5 8 3 478.25 2.02 12 5 9 4 470.89 1.05 13 6 9 3 474.89 1.14 14 6 10 4 471.07 1.15 15 6 124 118 45.67 0.21 16 6 127 121 44.92 0.59 17 7 10 3 478.91 2.79 18 7 11 4 471.07 1.15 19 7 73 66 47.85 0.13 20 7 74 67 47.85 0.13 21 8 11 3 477.54 1.28 22 8 12 4 471.07 1.16 23 9 12 3 476.35 0.68 24 9 13 4 474.44 2.84 25 9 121 112 60.27 0.96 26 9 124 115 60.20 0.95 27 10 13 3 477.09 1.55 28 10 14 4 466.37 6.88 29 10 70 60 60.25 0.92 30 10 124 114 60.33 0.94 31 10 125 115 60.27 0.97 32 10 128 118 60.22 0.95 33 11 14 3 477.92 1.14 34 11 15 4 469.44 5.34 35 11 70 59 60.30 0.96 36 11 73 62 60.30 0.97 37 12 15 3 482.79 1.29 38 12 16 4 477.89 1.12 39 13 16 3 488.11 1.36 40 13 17 4 477.88 1.12 41 13 113 100 74.60 0.97 42 13 121 108 61.03 0.71 43 13 125 112 61.01 0.72 44 14 17 3 474.31 2.91 45 14 18 4 474.31 2.91 46 14 21 7 411.69 8.70 47 14 63 49 72.43 1.80 48 14 66 52 61.02 0.73 49 14 67 53 61.02 0.73 50 14 70 56 61.02 0.73 51 14 109 95 74.06 1.24 52 15 18 3 477.96 1.07 53 16 113 97 75.50 0.60 54 16 116 100 74.69 0.96 55 17 20 3 485.39 4.73 56 17 21 4 431.02 0.96 57 17 24 7 417.78 5.65 58 17 109 92 74.61 0.96 59 17 113 96 81.36 3.52 60 18 21 3 503.33 1.19 61 20 23 3 478.01 1.17 62 20 24 4 468.41 2.06 63 21 24 3 482.81 1.55 64 21 25 4 468.01 2.25 65 21 63 42 94.75 0.26 66 22 25 3 476.12 1.79 67 22 26 4 468.03 2.25 68 22 60 38 96.91 1.23 69 22 63 41 96.88 1.23 70 23 26 3 474.95 0.11 71 23 27 4 468.03 2.25 72 24 27 3 469.36 2.91 73 24 28 4 461.56 1.32 74 24 108 84 122.02 1.81 75 24 109 85 125.01 0.33 76 24 112 88 129.40 0.27 77 25 28 3 470.38 2.53 78 25 29 4 461.55 1.31 79 25 59 34 118.15 0.07 80 25 105 80 120.02 0.81 81 26 29 3 477.88 0.13 82 26 30 4 461.53 1.32 83 26 55 29 127.04 0.39 84 26 56 30 123.41 0.82 85 26 59 33 119.70 0.78 86 27 30 3 477.88 0.13 87 27 31 4 461.48 1.31 88 27 108 81 129.77 0.37 89 27 112 85 129.85 0.40 90 28 31 3 473.64 0.58 91 28 32 4 465.15 3.40 92 28 101 73 129.69 0.38 93 28 104 76 129.71 0.36 94 28 105 77 129.69 0.38 95 28 108 80 129.77 0.37 96 29 32 3 466.68 2.64 97 29 33 4 466.68 2.64 98 29 55 26 129.80 0.36 99 29 58 29 129.80 0.37 100 29 59 30 129.78 0.38 101 29 101 72 129.74 0.35 102 30 33 3 478.72 0.61 103 30 34 4 467.36 1.06 104 30 50 20 130.56 0.66 105 31 34 3 480.61 1.55 106 31 35 4 464.57 0.33 107 31 104 73 130.29 0.60 108 31 107 76 130.55 0.72 109 31 108 77 130.59 0.74 110 31 111 80 130.75 0.77 111 32 35 3 469.28 1.54 112 32 36 4 446.37 1.72 113 32 39 7 339.81 20.21 114 32 43 11 290.78 1.13 115 32 101 69 130.28 0.61 116 32 104 72 130.35 0.64 117 33 37 4 432.04 5.29 118 33 39 6 373.50 3.33 119 33 40 7 299.91 0.26 120 33 43 10 285.63 1.45 121 33 48 15 176.08 23.41 122 33 55 22 130.78 0.77 123 34 37 3 489.17 0.82 124 36 39 3 492.82 0.10 125 36 100 64 130.33 0.62 126 36 103 67 130.70 0.76 127 36 104 68 130.70 0.75 128 37 40 3 488.63 1.03 129 38 41 3 490.32 2.08 130 39 42 3 493.76 0.58 131 39 43 4 488.26 0.74 132 39 97 58 130.35 0.65 133 39 100 61 130.66 0.74 134 40 43 3 488.25 0.73 135 40 44 4 487.09 1.32 136 40 48 8 182.10 25.00 137 41 44 3 500.49 0.53 138 42 45 3 646.57 0.43 139 42 93 51 130.37 0.67 140 42 94 52 130.55 0.71 141 42 97 55 130.67 0.75 142 43 46 3 481.59 0.44 143 43 48 5 414.69 11.37 144 43 58 15 176.03 23.34 145 45 54 9 178.13 23.62 146 46 54 8 178.11 23.62 147 46 58 12 178.06 23.59 148 47 52 5 265.86 5.50 149 47 54 7 191.52 29.79 150 47 55 8 191.53 29.79 151 48 55 7 191.52 29.79 152 49 52 3 483.92 0.12 153 51 56 5 451.44 1.47 154 52 55 3 478.04 1.02 155 52 56 4 461.44 3.13 156 53 56 3 479.19 2.83 157 53 57 4 465.69 3.01 158 54 57 3 472.76 0.39 159 54 58 4 465.72 3.02 160 55 58 3 475.80 2.02 161 55 59 4 465.72 3.02 162 56 59 3 473.38 0.73 163 56 60 4 473.30 0.76 164 57 60 3 482.92 2.25 165 57 61 4 473.29 0.76 166 58 61 3 474.50 0.17 167 58 62 4 468.67 1.88 168 59 62 3 480.49 2.83 169 59 63 4 468.63 1.92 170 60 63 3 478.50 1.97 171 60 64 4 468.64 1.91 172 61 64 3 475.45 1.60 173 61 65 4 468.68 1.90 174 62 65 3 483.66 0.27 175 62 66 4 467.56 1.33 176 62 101 39 161.96 1.33 177 63 66 3 477.49 3.35 178 63 67 4 477.20 3.49 179 64 67 3 477.22 3.48 180 64 68 4 477.19 3.50 181 65 68 3 478.24 2.93 182 65 69 4 474.94 4.58 183 65 80 15 173.09 2.92 184 65 83 18 172.05 3.44 185 66 69 3 476.50 3.80 186 66 70 4 474.94 4.58 187 66 105 39 184.34 2.00 188 66 128 62 185.74 1.34 189 66 129 63 185.28 1.53 190 66 132 66 173.12 2.91 191 67 70 3 475.75 4.18 192 67 71 4 466.94 0.58 193 68 71 3 475.75 4.18 194 68 72 4 460.53 3.79 195 68 79 11 193.91 5.25 196 68 80 12 191.86 4.22 197 69 72 3 477.42 1.74 198 69 73 4 447.19 0.45 199 69 76 7 282.78 4.17 200 69 80 11 183.77 8.22 201 69 128 59 185.87 1.31 202 69 132 63 185.27 1.52 203 70 73 3 474.62 2.87 204 70 128 58 186.21 1.48 205 72 75 3 479.25 0.56 206 72 76 4 439.00 2.49 207 72 79 7 274.16 1.54 208 73 76 3 478.20 2.77 209 73 128 55 221.88 15.00 210 75 78 3 495.31 0.51 211 75 79 4 451.71 1.93 212 76 79 3 465.49 1.79 213 76 80 4 432.02 0.23 214 76 128 52 225.69 16.61 215 76 131 55 224.87 16.40 216 76 132 56 223.68 15.80 217 76 135 59 223.66 15.80 218 77 81 4 437.79 3.12 219 77 135 58 223.59 15.84 220 78 81 3 469.89 4.92 221 80 83 3 476.86 0.20 222 80 84 4 457.87 10.55 223 80 132 52 225.72 16.65 224 80 135 55 225.55 16.71 225 80 136 56 225.54 16.72 226 81 84 3 475.85 1.56 227 81 85 4 471.25 3.87 228 81 139 58 225.54 16.73 229 82 85 3 474.90 2.04 230 82 86 4 465.59 6.69 231 83 86 3 474.89 2.06 232 83 87 4 474.86 2.05 233 83 136 53 225.81 16.71 234 84 87 3 480.84 0.92 235 84 88 4 472.74 1.02 236 84 135 51 225.85 16.70 237 84 136 52 225.69 16.77 238 84 139 55 225.65 16.79 239 85 88 3 480.84 0.92 240 85 89 4 470.59 0.05 241 85 139 54 225.69 16.77 242 86 89 3 482.26 0.21 243 86 90 4 431.10 4.28 244 86 91 5 431.05 4.30 245 87 91 4 421.27 2.58 246 87 92 5 400.45 7.83 247 87 98 11 267.88 1.98 248 87 136 49 225.91 16.68 249 87 140 53 225.68 16.77 250 88 92 4 400.49 7.82 251 88 139 51 225.72 16.77 252 88 140 52 225.66 16.77 253 89 92 3 485.18 1.61 254 93 97 4 480.39 1.54 255 93 98 5 474.62 0.84 256 93 140 47 226.03 16.75 257 94 97 3 494.81 0.05 258 95 98 3 494.81 0.05 259 95 137 42 226.49 16.71 260 95 140 45 226.38 16.75 261 96 99 3 490.80 0.88 262 96 100 4 476.81 0.24 263 97 100 3 474.62 0.85 264 97 101 4 480.57 3.85 265 98 101 3 480.57 3.85 266 98 102 4 474.44 0.80 267 98 133 35 227.34 16.48 268 98 136 38 227.37 16.49 269 98 137 39 227.31 16.48 270 98 140 42 227.31 16.48 271 99 102 3 480.56 3.85 272 99 103 4 474.44 0.80 273 100 103 3 480.56 3.85 274 100 104 4 480.56 3.86 275 101 104 3 474.23 0.94 276 101 105 4 475.98 3.67 277 102 105 3 475.98 3.67 278 102 106 4 476.00 3.66 279 102 129 27 227.66 16.60 280 102 133 31 227.64 16.60 281 103 106 3 476.00 3.66 282 103 107 4 473.08 1.51 283 104 107 3 473.39 1.66 284 104 108 4 466.55 1.77 285 105 108 3 470.06 3.52 286 105 109 4 466.46 1.80 287 105 129 24 228.58 16.60 288 106 109 3 479.82 4.86 289 106 110 4 466.45 1.80 290 106 117 11 239.59 11.63 291 106 122 16 229.47 16.53 292 106 125 19 229.34 16.52 293 106 126 20 229.25 16.55 294 106 129 23 229.21 16.53 295 107 110 3 480.29 1.58 296 107 111 4 462.49 2.60 297 108 111 3 476.78 0.19 298 108 112 4 459.36 2.91 299 109 112 3 474.45 2.17 300 109 113 4 457.00 1.74 301 109 125 16 230.15 16.21 302 110 113 3 480.25 1.55 303 110 117 7 239.59 11.64 304 113 116 3 477.07 0.03 305 113 117 4 430.04 15.16 306 115 118 3 537.25 2.19 307 116 121 5 457.68 0.24 308 117 121 4 457.71 0.26 309 117 122 5 457.67 0.24 310 117 125 8 404.22 2.49 311 118 121 3 473.77 1.26 312 118 122 4 465.39 2.96 313 119 122 3 479.98 4.33 314 119 123 4 471.39 0.04 315 120 123 3 468.31 1.51 316 120 124 4 465.42 2.96 317 121 124 3 468.31 1.52 318 121 125 4 464.53 3.40 319 122 125 3 483.92 2.97 320 122 126 4 465.98 2.68 321 123 126 3 473.77 1.22 322 123 127 4 473.74 1.21 323 124 127 3 473.75 1.21 324 124 128 4 471.00 2.58 325 125 128 3 476.97 0.39 326 125 129 4 471.04 2.56 327 126 129 3 478.50 0.38 328 126 130 4 471.11 2.52 329 127 130 3 477.23 0.27 330 127 131 4 472.55 2.07 331 128 131 3 477.22 0.27 332 128 132 4 472.55 2.07 333 129 132 3 477.20 0.28 334 129 133 4 464.82 1.79 335 130 133 3 469.18 0.39 336 130 134 4 464.79 1.79 337 131 134 3 467.06 0.65 338 131 135 4 464.06 2.14 339 132 135 3 466.37 2.07 340 132 136 4 460.61 0.42 341 133 136 3 473.68 1.58 342 133 137 4 464.14 1.34 343 134 137 3 474.73 2.12 344 134 138 4 460.56 0.41 345 135 138 3 469.22 3.88 346 136 140 4 494.06 3.52 347 137 140 3 486.87 0.07