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 5 448.42 1.79 2 2 73 71 29.76 0.82 3 2 76 74 24.80 1.61 4 2 127 125 23.41 0.43 5 2 128 126 22.55 0.01 6 3 6 3 472.52 1.36 7 3 7 4 466.79 4.24 8 4 7 3 474.74 0.26 9 4 8 4 464.55 5.36 10 5 8 3 482.59 1.22 11 5 9 4 475.19 0.04 12 6 9 3 478.48 0.83 13 6 10 4 469.97 2.58 14 6 124 118 46.66 0.53 15 6 127 121 46.67 0.52 16 7 10 3 477.71 1.22 17 7 11 4 469.97 2.58 18 7 73 66 49.18 1.13 19 7 74 67 49.18 1.13 20 8 11 3 475.21 0.05 21 8 12 4 469.94 2.56 22 9 12 3 476.31 0.27 23 9 13 4 469.93 2.57 24 9 121 112 60.52 0.34 25 9 124 115 60.52 0.33 26 10 13 3 478.69 1.86 27 10 14 4 459.36 2.70 28 10 70 60 60.51 0.31 29 10 124 114 60.53 0.33 30 10 125 115 60.50 0.32 31 10 128 118 60.49 0.32 32 11 15 4 457.00 4.00 33 11 70 59 60.52 0.30 34 11 71 60 60.67 0.23 35 11 73 62 60.52 0.30 36 12 15 3 464.94 4.12 37 12 16 4 470.29 1.44 38 13 16 3 478.57 1.04 39 13 17 4 466.24 0.59 40 13 113 100 79.89 0.38 41 13 121 108 61.75 0.08 42 13 125 112 61.65 0.05 43 14 17 3 470.30 1.43 44 14 18 4 467.56 1.26 45 14 21 7 380.67 15.50 46 14 63 49 67.96 2.94 47 14 66 52 61.63 0.04 48 14 67 53 61.63 0.04 49 14 70 56 61.63 0.04 50 15 18 3 472.74 1.07 51 16 113 97 94.50 1.02 52 16 116 100 91.66 0.40 53 17 20 3 485.70 0.31 54 17 21 4 443.76 0.27 55 17 24 7 395.43 6.21 56 17 109 92 91.60 0.38 57 17 113 96 94.69 1.09 58 18 21 3 495.98 4.77 59 20 23 3 474.24 0.67 60 20 24 4 469.77 0.47 61 21 24 3 469.81 0.49 62 21 25 4 467.79 1.50 63 21 63 42 97.00 0.15 64 22 25 3 471.36 1.27 65 22 26 4 468.89 0.95 66 22 60 38 102.02 1.24 67 22 63 41 100.91 1.79 68 23 26 3 482.58 4.34 69 23 27 4 461.03 4.87 70 24 27 3 482.56 4.36 71 24 28 4 461.03 4.87 72 24 108 84 117.72 0.49 73 24 109 85 122.33 0.17 74 24 112 88 127.83 0.31 75 25 28 3 471.44 0.35 76 25 29 4 469.74 3.06 77 25 59 34 117.98 0.16 78 25 63 38 116.64 0.14 79 26 29 3 465.53 0.04 80 26 30 4 465.53 0.04 81 26 55 29 126.92 0.97 82 26 56 30 126.48 1.28 83 26 59 33 123.28 2.78 84 27 30 3 464.62 0.50 85 27 31 4 464.25 0.68 86 27 108 81 129.82 0.96 87 27 112 85 130.93 0.87 88 28 31 3 474.10 1.71 89 28 32 4 471.55 2.98 90 28 101 73 129.41 0.83 91 28 104 76 129.54 0.89 92 28 105 77 129.42 0.83 93 28 108 80 129.84 0.96 94 29 32 3 474.41 1.55 95 29 33 4 469.06 4.22 96 29 55 26 129.66 0.86 97 29 58 29 129.63 0.85 98 29 59 30 129.61 0.86 99 29 101 72 129.64 0.88 100 30 33 3 479.57 3.14 101 30 34 4 464.13 2.58 102 30 50 20 130.99 0.94 103 31 34 3 464.36 2.48 104 31 35 4 464.12 2.59 105 31 104 73 129.91 0.93 106 31 107 76 130.90 0.89 107 31 108 77 130.91 0.89 108 32 35 3 474.09 0.40 109 32 36 4 452.47 3.24 110 32 39 7 165.50 4.56 111 32 100 68 129.90 0.93 112 32 101 69 129.91 0.93 113 32 104 72 130.38 0.70 114 33 37 4 426.27 9.65 115 33 39 6 226.23 34.12 116 33 40 7 165.49 4.57 117 33 43 10 155.41 0.47 118 33 48 15 131.18 0.93 119 33 55 22 131.03 0.93 120 36 39 3 487.41 3.04 121 36 100 64 129.91 0.93 122 36 103 67 130.99 0.88 123 36 104 68 130.99 0.88 124 37 40 3 482.93 1.38 125 38 41 3 483.01 1.33 126 39 42 3 488.34 1.17 127 39 43 4 490.63 4.38 128 39 97 58 129.91 0.94 129 39 100 61 130.94 0.90 130 40 43 3 495.03 2.18 131 40 48 8 149.34 1.94 132 41 44 3 498.83 0.28 133 42 93 51 129.57 0.83 134 42 94 52 130.59 0.94 135 42 97 55 130.88 0.87 136 43 46 3 474.34 0.74 137 43 48 5 433.73 3.16 138 43 58 15 138.81 3.66 139 45 54 9 149.91 1.84 140 46 54 8 149.90 1.84 141 46 55 9 155.11 0.77 142 46 58 12 149.87 1.85 143 47 52 5 164.25 3.80 144 47 54 7 155.12 0.76 145 47 55 8 155.12 0.76 146 48 52 4 400.05 9.31 147 48 55 7 155.12 0.76 148 49 52 3 476.71 0.50 149 51 56 5 451.16 1.25 150 52 55 3 471.16 2.27 151 52 56 4 471.00 2.19 152 53 56 3 471.00 2.19 153 53 57 4 462.62 6.38 154 54 57 3 472.52 1.44 155 54 58 4 472.49 1.45 156 55 58 3 472.49 1.45 157 55 59 4 473.22 1.08 158 56 59 3 475.10 1.30 159 56 60 4 473.27 1.10 160 57 60 3 485.67 4.09 161 57 61 4 473.28 1.10 162 58 61 3 475.57 0.04 163 58 62 4 473.29 1.11 164 59 62 3 475.60 0.04 165 59 63 4 472.48 1.53 166 60 63 3 473.31 1.11 167 60 64 4 469.09 3.21 168 61 64 3 469.22 3.16 169 61 65 4 474.82 0.35 170 62 65 3 483.90 0.03 171 62 66 4 474.82 0.35 172 62 101 39 154.14 1.89 173 63 66 3 476.43 1.15 174 63 67 4 471.10 1.52 175 64 67 3 469.51 0.72 176 64 68 4 468.91 0.42 177 65 68 3 468.92 0.42 178 65 69 4 468.93 0.41 179 65 80 15 154.16 1.91 180 65 83 18 143.81 3.27 181 66 69 3 468.94 0.41 182 66 70 4 468.94 0.41 183 66 105 39 174.09 7.34 184 66 129 63 173.77 7.62 185 66 132 66 154.50 1.72 186 67 70 3 473.87 2.06 187 67 71 4 468.94 0.41 188 68 71 3 475.80 0.82 189 68 72 4 467.30 0.41 190 68 79 11 162.94 2.59 191 69 72 3 476.14 0.99 192 69 73 4 455.47 5.48 193 69 76 7 280.59 1.23 194 69 80 11 163.81 2.06 195 69 128 59 188.93 0.08 196 69 132 63 174.31 7.29 197 70 73 3 465.44 4.37 198 70 128 58 209.98 10.44 199 72 75 3 472.17 0.08 200 72 76 4 445.50 13.42 201 72 79 7 283.72 0.36 202 73 76 3 480.25 1.91 203 75 78 3 480.63 1.72 204 75 79 4 466.50 0.04 205 76 79 3 466.50 0.03 206 76 80 4 437.79 4.96 207 76 128 52 273.91 0.42 208 76 131 55 272.54 0.06 209 76 132 56 272.42 0.06 210 76 135 59 272.42 0.07 211 77 81 4 437.78 4.96 212 77 135 58 272.41 0.07 213 78 81 3 469.92 1.05 214 80 83 3 481.60 0.93 215 80 84 4 463.93 0.70 216 80 132 52 275.13 0.27 217 80 135 55 274.24 0.27 218 80 136 56 274.24 0.27 219 81 84 3 479.63 1.90 220 81 85 4 479.62 1.90 221 81 139 58 274.25 0.27 222 82 85 3 480.87 1.29 223 82 86 4 479.63 1.91 224 83 86 3 479.64 1.90 225 83 87 4 472.94 5.25 226 83 136 53 275.46 0.39 227 84 87 3 484.22 0.39 228 84 88 4 472.94 5.25 229 84 135 51 275.50 0.38 230 84 136 52 275.46 0.40 231 84 138 54 275.42 0.42 232 84 139 55 275.30 0.45 233 85 88 3 479.38 2.80 234 85 89 4 461.44 0.48 235 85 139 54 275.29 0.48 236 86 89 3 484.18 0.40 237 86 90 4 447.41 4.61 238 86 91 5 443.59 2.71 239 87 91 4 405.54 16.32 240 87 92 5 398.72 14.88 241 87 98 11 280.97 1.43 242 87 136 49 275.53 0.39 243 87 140 53 275.29 0.46 244 88 92 4 396.42 13.63 245 88 139 51 275.43 0.42 246 88 140 52 275.12 0.45 247 89 92 3 490.81 2.11 248 92 140 48 275.51 0.39 249 93 97 4 480.99 1.27 250 93 98 5 475.61 3.96 251 93 140 47 275.64 0.34 252 94 97 3 488.20 0.80 253 95 98 3 482.00 1.06 254 95 140 45 275.74 0.35 255 96 99 3 481.73 0.92 256 96 100 4 480.42 1.57 257 97 100 3 475.62 3.97 258 97 101 4 475.62 3.97 259 98 101 3 483.06 0.26 260 98 102 4 469.87 1.11 261 98 133 35 276.26 0.35 262 98 136 38 276.27 0.35 263 98 137 39 276.25 0.35 264 98 140 42 276.10 0.42 265 99 102 3 479.78 1.90 266 99 103 4 469.79 1.15 267 100 103 3 474.04 0.97 268 100 104 4 468.88 0.73 269 101 104 3 474.03 0.97 270 101 105 4 466.34 0.20 271 102 105 3 466.78 0.41 272 102 106 4 466.77 0.41 273 102 129 27 276.43 0.40 274 102 133 31 276.40 0.40 275 103 106 3 469.25 1.26 276 103 107 4 463.58 1.19 277 104 107 3 467.22 2.46 278 104 108 4 462.67 0.69 279 105 108 3 470.56 4.04 280 105 109 4 466.75 2.70 281 105 129 24 277.44 0.27 282 106 109 3 470.64 4.18 283 106 110 4 462.70 0.68 284 106 117 11 278.98 0.36 285 106 122 16 277.57 0.27 286 106 125 19 277.54 0.27 287 106 126 20 277.53 0.25 288 106 129 23 277.46 0.26 289 107 110 3 472.86 2.75 290 107 111 4 462.69 0.68 291 108 111 3 470.66 4.65 292 108 112 4 461.74 0.21 293 109 112 3 464.20 1.02 294 109 113 4 454.98 0.47 295 109 117 8 279.32 0.49 296 109 125 16 278.14 0.28 297 110 117 7 279.28 0.51 298 113 116 3 478.60 0.18 299 113 117 4 425.37 16.27 300 114 117 3 479.17 2.13 301 115 118 3 525.34 0.43 302 116 121 5 466.46 2.38 303 117 121 4 466.47 2.37 304 117 122 5 454.43 2.03 305 117 125 8 412.92 6.13 306 118 121 3 467.23 2.02 307 118 122 4 466.48 2.37 308 119 122 3 466.55 2.36 309 119 123 4 466.55 2.37 310 120 123 3 467.10 2.10 311 120 124 4 466.55 2.37 312 121 124 3 475.47 2.08 313 121 125 4 475.44 2.10 314 122 125 3 475.56 2.16 315 122 126 4 475.44 2.10 316 123 126 3 477.42 1.23 317 123 127 4 464.07 0.61 318 124 127 3 475.58 2.04 319 124 128 4 472.47 3.58 320 125 128 3 470.43 0.53 321 125 129 4 468.64 0.35 322 126 129 3 477.24 4.31 323 126 130 4 469.64 0.86 324 127 130 3 477.24 4.31 325 127 131 4 469.65 0.86 326 128 131 3 477.23 4.31 327 128 132 4 467.16 2.10 328 129 132 3 476.62 3.26 329 129 133 4 461.33 0.70 330 130 133 3 463.62 1.84 331 130 134 4 461.31 0.70 332 131 134 3 466.37 1.70 333 131 135 4 461.72 0.48 334 132 135 3 475.75 4.45 335 132 136 4 464.94 1.12 336 133 136 3 470.39 0.34 337 133 137 4 462.19 0.30 338 134 137 3 474.38 0.82 339 134 138 4 455.25 3.77 340 135 138 3 469.98 0.17 341 136 140 4 487.00 0.96 342 137 140 3 486.25 1.34