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 5 455.45 4.57 2 2 73 71 31.82 0.20 3 2 76 74 26.51 0.59 4 2 127 125 21.74 0.04 5 2 128 126 21.00 0.39 6 3 6 3 474.34 0.29 7 3 7 4 469.27 2.27 8 4 7 3 474.03 0.10 9 4 8 4 469.48 2.17 10 5 8 3 469.49 2.17 11 5 9 4 474.44 0.32 12 6 9 3 477.72 1.21 13 6 10 4 474.44 0.32 14 6 124 118 47.22 0.78 15 6 127 121 47.22 0.78 16 7 10 3 476.95 1.59 17 7 11 4 472.21 1.43 18 7 73 66 48.43 0.76 19 7 74 67 53.29 0.95 20 8 11 3 476.18 0.55 21 8 12 4 466.40 4.33 22 9 12 3 477.05 0.11 23 9 13 4 460.98 7.04 24 9 121 112 59.01 0.34 25 9 124 115 58.95 0.34 26 10 13 3 477.98 1.47 27 10 14 4 455.93 4.53 28 10 70 60 59.04 0.30 29 10 124 114 59.01 0.34 30 10 125 115 58.98 0.33 31 10 128 118 58.98 0.33 32 11 15 4 464.14 0.42 33 11 70 59 59.01 0.30 34 11 71 60 59.16 0.24 35 11 73 62 59.01 0.31 36 12 15 3 471.18 1.02 37 12 16 4 471.19 1.01 38 13 16 3 477.82 1.42 39 13 17 4 471.19 1.01 40 13 113 100 82.02 0.03 41 13 121 108 59.92 0.18 42 13 125 112 59.87 0.18 43 14 17 3 471.20 1.01 44 14 18 4 471.20 1.01 45 14 21 7 414.29 1.08 46 14 63 49 71.70 0.04 47 14 66 52 59.89 0.17 48 14 67 53 59.89 0.17 49 14 70 56 59.88 0.17 50 15 18 3 475.19 0.15 51 16 113 97 94.05 0.79 52 16 116 100 93.92 0.71 53 17 20 3 484.95 0.69 54 17 21 4 425.80 6.82 55 17 24 7 425.81 6.83 56 17 109 92 92.32 1.50 57 17 113 96 96.64 1.17 58 18 21 3 497.87 3.08 59 20 23 3 477.97 1.20 60 20 24 4 467.18 0.83 61 21 24 3 465.89 1.67 62 21 25 4 464.02 2.61 63 21 63 42 98.07 1.49 64 22 25 3 471.76 1.26 65 22 26 4 468.12 0.56 66 22 60 38 101.55 0.17 67 22 63 41 100.54 0.34 68 23 26 3 480.25 5.50 69 23 27 4 465.04 2.10 70 24 27 3 482.82 4.22 71 24 28 4 467.62 3.38 72 24 108 84 117.06 0.32 73 24 109 85 123.06 0.02 74 24 112 88 127.61 0.68 75 25 28 3 473.26 0.56 76 25 29 4 470.66 1.86 77 25 59 34 117.02 0.31 78 25 63 38 116.69 0.46 79 26 29 3 472.93 0.73 80 26 30 4 470.66 1.86 81 26 55 29 126.07 1.30 82 26 56 30 125.59 1.58 83 26 59 33 118.18 0.07 84 27 30 3 471.66 0.10 85 27 31 4 469.38 1.23 86 27 108 81 129.43 0.20 87 27 112 85 131.00 0.56 88 28 31 3 469.32 1.26 89 28 32 4 474.67 1.42 90 28 101 73 127.70 0.66 91 28 104 76 127.71 0.66 92 28 105 77 127.71 0.66 93 28 108 80 129.69 0.33 94 29 32 3 474.67 1.42 95 29 33 4 463.68 2.03 96 29 55 26 129.53 0.10 97 29 58 29 129.41 0.16 98 29 59 30 129.40 0.17 99 29 101 72 129.38 0.18 100 30 33 3 479.88 1.18 101 30 34 4 463.67 2.04 102 30 50 20 130.84 0.62 103 31 34 3 473.66 1.93 104 31 35 4 459.30 0.08 105 31 104 73 130.52 0.43 106 31 107 76 130.97 0.55 107 31 108 77 130.97 0.55 108 32 35 3 472.56 0.38 109 32 36 4 456.47 1.24 110 32 39 7 296.99 2.30 111 32 100 68 130.52 0.43 112 32 101 69 130.52 0.43 113 32 104 72 130.80 0.53 114 33 37 4 438.39 10.26 115 33 39 6 307.39 2.90 116 33 40 7 217.11 42.25 117 33 43 10 232.31 34.62 118 33 48 15 131.09 0.61 119 33 55 22 131.06 0.62 120 36 39 3 491.30 5.66 121 36 100 64 130.56 0.41 122 36 103 67 131.02 0.53 123 36 104 68 131.06 0.55 124 37 40 3 480.07 0.06 125 38 41 3 488.00 1.35 126 39 42 3 488.15 1.43 127 39 43 4 494.28 1.80 128 39 97 58 130.52 0.42 129 39 100 61 131.02 0.53 130 40 43 3 494.28 1.80 131 40 44 4 479.08 1.48 132 40 48 8 148.59 1.51 133 41 44 3 498.08 0.10 134 42 93 51 130.25 0.56 135 42 94 52 130.66 0.43 136 42 97 55 131.10 0.55 137 43 46 3 478.38 0.77 138 43 48 5 451.04 5.50 139 43 58 15 134.56 1.08 140 45 54 9 148.71 1.51 141 46 54 8 148.65 1.49 142 46 55 9 148.69 1.51 143 46 58 12 148.64 1.49 144 47 52 5 162.31 3.32 145 47 54 7 148.71 1.50 146 47 55 8 148.72 1.51 147 48 52 4 387.23 1.97 148 48 55 7 159.62 6.99 149 49 52 3 475.96 0.88 150 51 56 5 451.72 1.37 151 52 55 3 468.50 3.60 152 52 56 4 468.36 3.53 153 53 56 3 468.37 3.53 154 53 57 4 468.36 3.53 155 54 57 3 480.92 2.75 156 54 58 4 472.49 1.46 157 55 58 3 472.51 1.47 158 55 59 4 472.51 1.47 159 56 59 3 474.35 1.68 160 56 60 4 472.63 1.50 161 57 60 3 484.00 4.18 162 57 61 4 472.64 1.50 163 58 61 3 474.91 0.36 164 58 62 4 472.64 1.50 165 59 62 3 480.28 2.29 166 59 63 4 472.63 1.49 167 60 63 3 472.61 1.48 168 60 64 4 472.61 1.47 169 61 64 3 472.54 1.50 170 61 65 4 464.87 3.88 171 62 65 3 483.15 0.40 172 62 66 4 465.58 3.52 173 62 101 39 146.86 5.67 174 63 66 3 475.68 1.52 175 63 67 4 466.34 1.59 176 64 67 3 470.36 1.14 177 64 68 4 468.34 0.13 178 65 68 3 468.78 0.35 179 65 69 4 468.36 0.12 180 65 80 15 147.01 5.73 181 65 83 18 146.72 5.73 182 66 69 3 477.03 2.68 183 66 70 4 468.37 0.12 184 66 105 39 169.37 1.12 185 66 129 63 157.75 0.35 186 66 132 66 157.53 0.38 187 67 70 3 473.30 2.34 188 67 71 4 470.40 1.14 189 68 71 3 475.07 1.19 190 68 72 4 470.40 1.14 191 68 79 11 162.37 1.88 192 69 72 3 475.41 1.36 193 69 73 4 467.86 2.41 194 69 76 7 158.60 0.04 195 69 80 11 157.65 0.43 196 69 128 59 186.06 1.48 197 69 132 63 157.66 0.44 198 70 73 3 467.74 2.47 199 70 128 58 186.08 1.48 200 72 75 3 471.77 0.12 201 72 76 4 436.24 17.30 202 72 79 7 290.43 1.94 203 73 76 3 477.25 2.62 204 75 78 3 479.88 1.34 205 75 79 4 451.61 7.41 206 76 79 3 469.98 0.62 207 76 80 4 445.72 4.47 208 76 128 52 280.97 0.39 209 76 131 55 277.82 0.95 210 76 132 56 275.87 0.04 211 76 135 59 275.84 0.03 212 77 80 3 473.33 0.26 213 77 81 4 448.71 0.14 214 77 135 58 275.86 0.04 215 78 81 3 476.30 2.15 216 80 83 3 480.80 0.53 217 80 84 4 454.91 1.06 218 80 132 52 281.81 0.01 219 80 135 55 281.60 0.09 220 80 136 56 281.60 0.09 221 81 84 3 478.87 1.52 222 81 85 4 478.86 1.52 223 81 139 58 281.61 0.10 224 82 85 3 480.09 0.90 225 82 86 4 472.82 1.50 226 83 86 3 468.15 0.84 227 83 87 4 463.42 3.20 228 83 136 53 282.29 0.01 229 84 88 4 447.48 4.69 230 84 135 51 282.34 0.06 231 84 136 52 282.26 0.03 232 84 138 54 282.26 0.03 233 84 139 55 282.19 0.01 234 85 88 3 474.05 0.89 235 85 89 4 447.47 4.69 236 85 139 54 282.19 0.01 237 86 89 3 485.32 0.17 238 86 90 4 440.42 3.17 239 86 91 5 390.31 12.06 240 87 91 4 370.64 11.53 241 87 92 5 353.72 15.45 242 87 93 6 353.12 15.74 243 87 98 11 300.32 2.00 244 87 136 49 282.37 0.05 245 87 140 53 282.22 0.02 246 88 92 4 364.94 9.83 247 88 139 51 282.27 0.03 248 88 140 52 282.18 0.01 249 89 92 3 492.91 3.16 250 92 140 48 282.36 0.05 251 93 97 4 480.31 0.93 252 93 98 5 474.64 3.69 253 93 140 47 282.39 0.06 254 94 97 3 494.35 3.02 255 95 98 3 484.98 0.81 256 95 137 42 282.57 0.10 257 95 140 45 282.44 0.04 258 96 99 3 491.44 5.76 259 96 100 4 481.03 0.57 260 97 100 3 484.06 2.08 261 97 101 4 479.62 1.22 262 98 101 3 485.39 1.42 263 98 102 4 469.05 0.77 264 98 133 35 282.85 0.09 265 98 136 38 282.85 0.09 266 98 137 39 282.83 0.09 267 98 140 42 282.80 0.08 268 99 102 3 469.06 0.77 269 99 103 4 469.05 0.77 270 100 103 3 473.29 1.35 271 100 104 4 468.19 0.33 272 101 104 3 469.04 0.77 273 101 105 4 464.28 1.61 274 102 105 3 471.59 2.08 275 102 106 4 465.93 0.74 276 102 129 27 283.12 0.10 277 102 133 31 283.00 0.07 278 103 106 3 470.84 0.29 279 103 107 4 465.94 0.74 280 104 107 3 481.26 1.02 281 104 108 4 461.79 0.37 282 105 108 3 480.23 1.54 283 105 109 4 466.62 2.02 284 105 129 24 283.56 0.28 285 106 109 3 472.55 3.33 286 106 110 4 466.44 0.46 287 106 117 11 285.14 0.55 288 106 122 16 284.00 0.20 289 106 125 19 283.83 0.24 290 106 126 20 283.74 0.23 291 106 129 23 283.75 0.21 292 107 110 3 472.12 2.38 293 107 111 4 461.01 3.18 294 108 111 3 472.08 0.46 295 108 112 4 463.94 1.72 296 109 112 3 459.93 3.71 297 109 113 4 441.12 0.24 298 109 125 16 284.07 0.17 299 110 117 7 285.14 0.55 300 113 116 3 477.86 0.55 301 113 117 4 459.05 8.85 302 114 117 3 480.09 1.67 303 115 118 3 526.28 0.91 304 116 121 5 464.62 3.30 305 117 121 4 465.19 3.02 306 117 122 5 443.20 7.40 307 117 125 8 404.29 9.91 308 118 121 3 468.25 1.49 309 118 122 4 465.19 3.02 310 119 122 3 474.82 1.79 311 119 123 4 474.87 1.78 312 120 123 3 475.25 1.96 313 120 124 4 474.89 1.77 314 121 124 3 474.88 1.76 315 121 125 4 474.74 1.70 316 122 125 3 476.57 2.60 317 122 126 4 474.74 1.70 318 123 126 3 474.88 1.76 319 123 127 4 459.19 0.64 320 124 127 3 474.83 1.67 321 124 128 4 472.34 3.54 322 125 128 3 473.62 2.91 323 125 129 4 467.89 0.73 324 126 129 3 484.02 0.33 325 126 130 4 464.06 2.65 326 127 130 3 481.29 0.93 327 127 131 4 463.23 1.03 328 128 131 3 475.13 4.01 329 128 132 4 463.23 1.03 330 129 132 3 475.88 3.64 331 129 133 4 462.62 1.34 332 130 133 3 470.67 4.69 333 130 134 4 463.38 1.12 334 131 134 3 467.18 0.20 335 131 135 4 463.40 1.14 336 132 135 3 477.09 3.78 337 132 136 4 463.69 0.97 338 133 136 3 477.09 3.78 339 133 137 4 462.50 1.57 340 134 137 3 475.47 1.36 341 134 138 4 446.63 2.43 342 135 138 3 474.60 1.80 343 136 140 4 489.82 1.20 344 137 140 3 485.50 0.97