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 5 462.73 4.12 2 2 73 71 28.49 0.51 3 2 76 74 26.71 0.38 4 2 127 125 23.64 0.04 5 2 128 126 23.64 0.04 6 3 6 3 465.94 2.57 7 3 7 4 467.24 1.92 8 4 7 3 475.21 2.07 9 4 8 4 466.96 2.06 10 5 8 3 467.25 1.91 11 5 9 4 467.05 2.00 12 6 9 3 479.02 3.98 13 6 10 4 467.22 1.91 14 6 124 118 46.90 0.56 15 6 127 121 47.05 0.64 16 7 10 3 482.98 2.00 17 7 11 4 467.18 1.92 18 7 73 66 47.11 0.64 19 7 74 67 47.65 0.65 20 8 11 3 478.45 0.26 21 8 12 4 468.32 1.30 22 9 12 3 472.69 0.88 23 9 13 4 468.32 1.30 24 9 120 111 63.38 0.90 25 9 121 112 63.22 0.83 26 9 124 115 63.17 0.83 27 10 13 3 475.38 2.83 28 10 14 4 466.82 2.04 29 10 70 60 63.12 0.86 30 10 124 114 63.19 0.83 31 10 125 115 63.16 0.83 32 10 128 118 63.16 0.84 33 11 14 3 479.17 2.52 34 11 15 4 465.05 1.07 35 11 70 59 63.16 0.84 36 11 73 62 63.23 0.85 37 12 15 3 479.61 1.60 38 12 16 4 465.09 1.05 39 13 16 3 481.67 2.65 40 13 17 4 465.09 1.05 41 13 113 100 78.36 0.21 42 13 121 108 64.14 0.52 43 13 125 112 63.31 0.86 44 14 17 3 465.50 0.50 45 14 18 4 464.07 0.55 46 14 21 7 390.42 8.34 47 14 66 52 63.37 0.84 48 14 67 53 68.73 1.84 49 14 70 56 63.30 0.87 50 14 109 95 78.10 0.34 51 15 18 3 474.85 5.94 52 16 113 97 90.46 2.94 53 16 116 100 83.42 2.71 54 17 20 3 488.25 0.78 55 17 21 4 448.84 7.07 56 17 24 7 446.23 0.72 57 17 109 92 82.74 2.35 58 17 113 96 90.54 2.92 59 18 21 3 495.07 1.53 60 20 23 3 477.68 3.95 61 20 24 4 461.47 1.63 62 21 24 3 472.76 1.04 63 21 25 4 469.79 2.54 64 21 63 42 151.24 0.07 65 22 25 3 469.93 2.60 66 22 26 4 471.58 1.65 67 22 60 38 151.99 0.29 68 22 63 41 151.24 0.07 69 23 26 3 476.12 0.96 70 23 27 4 472.61 1.27 71 24 27 3 475.88 0.36 72 24 28 4 474.09 0.53 73 24 108 84 135.21 5.88 74 24 109 85 137.52 4.71 75 24 112 88 143.32 1.64 76 25 28 3 480.49 2.67 77 25 29 4 474.09 0.53 78 25 59 34 153.28 0.18 79 25 63 38 152.09 0.47 80 26 29 3 482.11 3.58 81 26 30 4 473.86 0.41 82 26 55 29 154.00 0.04 83 26 56 30 153.89 0.06 84 26 59 33 153.33 0.17 85 27 30 3 473.86 0.42 86 27 31 4 473.86 0.42 87 27 108 81 147.62 0.36 88 27 112 85 147.41 0.38 89 28 31 3 473.85 0.42 90 28 32 4 473.84 0.42 91 28 101 73 148.81 0.42 92 28 104 76 148.49 0.43 93 28 105 77 148.45 0.42 94 28 108 80 147.78 0.29 95 29 32 3 480.93 2.85 96 29 33 4 471.15 1.77 97 29 43 14 222.37 6.44 98 29 55 26 167.25 6.45 99 29 58 29 154.88 0.28 100 29 59 30 154.00 0.09 101 29 62 33 154.00 0.09 102 29 101 72 148.83 0.42 103 30 33 3 473.18 0.99 104 30 34 4 471.31 1.89 105 30 50 20 178.81 0.79 106 31 34 3 481.56 3.77 107 31 35 4 471.31 1.89 108 31 104 73 148.72 0.44 109 31 107 76 148.70 0.44 110 31 108 77 148.59 0.49 111 31 111 80 148.69 0.44 112 32 35 3 473.75 0.67 113 32 36 4 460.89 0.84 114 32 39 7 320.50 18.25 115 32 100 68 148.92 0.42 116 32 101 69 148.90 0.42 117 32 104 72 148.74 0.43 118 33 37 4 425.47 3.89 119 33 39 6 330.43 13.29 120 33 40 7 273.08 0.12 121 33 43 10 271.02 1.03 122 33 48 15 196.94 0.27 123 33 55 22 181.55 2.15 124 34 37 3 484.37 0.63 125 36 39 3 494.43 2.56 126 36 100 64 149.73 0.52 127 36 103 67 149.72 0.53 128 36 104 68 149.69 0.53 129 37 40 3 481.44 3.24 130 38 41 3 485.38 1.28 131 39 42 3 492.59 4.88 132 39 97 58 149.81 0.50 133 39 100 61 149.81 0.52 134 40 43 3 480.87 0.37 135 40 48 8 254.34 0.32 136 41 44 3 494.97 1.49 137 42 93 51 150.50 0.54 138 42 94 52 150.53 0.55 139 42 97 55 150.33 0.62 140 43 46 3 479.62 1.68 141 43 48 5 414.49 13.08 142 43 58 15 221.90 2.44 143 45 54 9 263.42 4.04 144 46 54 8 263.40 4.05 145 46 55 9 263.44 4.05 146 46 58 12 263.37 4.04 147 47 52 5 267.13 2.33 148 47 54 7 263.50 4.04 149 47 55 8 263.51 4.03 150 48 55 7 263.48 4.04 151 49 52 3 482.86 0.04 152 51 56 5 454.79 1.11 153 52 55 3 480.10 4.28 154 52 56 4 454.80 1.11 155 53 56 3 467.78 1.89 156 53 57 4 462.06 4.74 157 54 57 3 482.94 5.70 158 54 58 4 462.07 4.74 159 55 58 3 482.94 5.70 160 55 59 4 466.06 1.38 161 56 59 3 482.88 5.73 162 56 60 4 470.24 0.58 163 57 60 3 474.25 1.42 164 57 61 4 470.30 0.57 165 58 61 3 474.93 1.08 166 58 62 4 476.41 2.50 167 59 62 3 481.56 0.01 168 59 63 4 476.41 2.50 169 60 63 3 482.70 0.65 170 60 64 4 478.17 1.61 171 61 64 3 484.07 1.33 172 61 65 4 478.18 1.61 173 62 65 3 492.83 3.05 174 62 66 4 484.07 1.33 175 63 66 3 486.94 6.00 176 63 67 4 471.66 0.72 177 64 67 3 486.03 6.46 178 64 68 4 471.63 0.74 179 65 68 3 476.35 3.09 180 65 69 4 471.62 0.73 181 65 83 18 150.40 0.55 182 66 69 3 476.34 3.08 183 66 70 4 461.05 4.55 184 66 105 39 148.65 0.46 185 66 128 62 145.95 0.01 186 66 129 63 145.60 0.09 187 66 132 66 143.91 0.32 188 67 70 3 472.66 1.25 189 67 71 4 461.01 4.54 190 68 71 3 472.61 1.27 191 68 72 4 460.28 4.18 192 68 79 11 218.08 1.16 193 69 72 3 471.89 1.64 194 69 73 4 460.14 4.24 195 69 76 7 272.79 5.23 196 69 80 11 196.77 2.42 197 69 128 59 146.28 0.11 198 69 132 63 145.44 0.06 199 70 73 3 461.30 3.45 200 70 128 58 146.28 0.12 201 72 75 3 472.91 4.62 202 72 76 4 432.07 11.76 203 72 79 7 292.98 4.34 204 73 76 3 485.22 1.53 205 73 128 55 146.43 0.10 206 75 78 3 496.10 4.44 207 75 79 4 461.54 1.17 208 76 79 3 475.66 5.03 209 76 80 4 461.53 1.17 210 76 128 52 146.45 0.11 211 76 131 55 145.83 0.01 212 76 132 56 145.78 0.01 213 76 135 59 145.29 0.04 214 77 80 3 480.10 2.81 215 77 81 4 461.52 1.17 216 77 135 58 144.52 0.42 217 78 81 3 477.19 6.82 218 80 83 3 470.26 1.09 219 80 84 4 465.97 0.24 220 80 132 52 145.55 0.04 221 80 135 55 142.60 0.19 222 80 136 56 142.52 0.15 223 81 84 3 474.07 3.00 224 81 85 4 467.44 0.49 225 82 85 3 473.26 3.40 226 82 86 4 467.44 0.49 227 83 86 3 468.78 0.17 228 83 87 4 467.29 0.91 229 83 136 53 141.09 0.11 230 84 87 3 475.00 1.26 231 84 88 4 464.05 2.52 232 84 135 51 142.19 0.28 233 84 136 52 141.08 0.10 234 84 139 55 138.53 0.77 235 85 88 3 470.81 0.84 236 85 89 4 463.88 2.60 237 86 89 3 479.97 2.73 238 86 90 4 447.15 1.85 239 86 91 5 435.14 7.86 240 87 91 4 413.13 18.84 241 87 92 5 350.26 12.58 242 87 93 6 350.24 12.57 243 87 98 11 280.82 0.23 244 87 136 49 140.77 0.14 245 87 140 53 132.06 2.17 246 88 92 4 361.32 7.04 247 88 139 51 136.28 0.07 248 88 140 52 130.42 1.37 249 89 92 3 493.18 1.22 250 89 139 50 140.28 0.07 251 93 97 4 477.47 2.18 252 93 98 5 477.47 2.18 253 93 140 47 130.41 1.37 254 94 97 3 494.17 0.35 255 95 98 3 494.73 2.38 256 95 137 42 135.47 0.47 257 95 140 45 129.62 1.36 258 96 99 3 493.06 2.33 259 96 100 4 478.19 1.82 260 97 100 3 479.53 4.43 261 97 101 4 471.89 0.61 262 98 101 3 481.37 1.56 263 98 102 4 464.50 3.06 264 98 133 35 140.81 0.04 265 98 136 38 136.28 0.11 266 98 137 39 135.50 0.46 267 98 140 42 130.58 1.30 268 99 102 3 481.36 1.57 269 99 103 4 466.00 2.31 270 100 103 3 481.37 1.57 271 100 104 4 470.98 0.41 272 101 104 3 471.01 0.40 273 101 105 4 464.34 2.93 274 102 105 3 473.16 1.47 275 102 106 4 471.70 0.75 276 102 129 27 141.52 0.27 277 103 106 3 472.72 1.24 278 103 107 4 471.74 0.74 279 104 107 3 475.25 0.62 280 104 108 4 471.75 0.74 281 105 108 3 478.41 0.96 282 105 109 4 471.75 0.74 283 105 129 24 149.15 3.54 284 106 109 3 476.22 2.05 285 106 110 4 472.22 0.97 286 106 117 11 218.82 2.30 287 106 122 16 168.42 2.46 288 106 125 19 159.49 0.87 289 106 126 20 159.46 0.86 290 106 129 23 150.77 3.48 291 107 110 3 476.22 2.06 292 107 111 4 470.32 1.93 293 108 111 3 475.33 2.50 294 108 112 4 470.32 1.93 295 109 112 3 482.43 1.04 296 109 113 4 440.19 0.14 297 109 117 8 227.97 5.04 298 109 125 16 170.09 1.31 299 110 117 7 220.66 1.39 300 113 116 3 478.41 0.33 301 113 117 4 440.48 0.36 302 114 117 3 489.62 0.90 303 115 118 3 519.47 2.10 304 116 121 5 448.35 3.12 305 117 121 4 449.64 2.47 306 117 122 5 444.82 4.85 307 117 125 8 431.56 0.99 308 118 121 3 470.05 1.40 309 118 122 4 460.97 3.12 310 119 122 3 470.06 1.41 311 119 123 4 470.04 1.42 312 120 123 3 476.53 1.24 313 120 124 4 470.65 1.70 314 121 124 3 480.17 4.51 315 121 125 4 470.63 1.71 316 122 125 3 481.59 1.28 317 122 126 4 473.09 2.97 318 123 126 3 481.00 0.37 319 123 127 4 480.38 0.68 320 124 127 3 480.51 0.61 321 124 128 4 477.24 2.25 322 125 128 3 469.66 1.93 323 125 129 4 470.00 2.24 324 126 129 3 481.15 1.38 325 126 130 4 470.00 2.23 326 127 130 3 476.84 0.78 327 127 131 4 468.91 2.79 328 128 131 3 472.70 0.90 329 128 132 4 472.68 0.90 330 129 132 3 472.69 0.90 331 129 133 4 472.74 0.92 332 130 133 3 482.93 6.01 333 130 134 4 472.76 0.94 334 131 134 3 472.84 0.90 335 131 135 4 472.76 0.94 336 132 135 3 480.75 4.23 337 132 136 4 472.75 0.95 338 133 136 3 472.59 1.10 339 133 137 4 472.59 1.10 340 134 137 3 486.29 1.43 341 134 138 4 471.32 0.48 342 135 138 3 477.06 1.47 343 136 140 4 487.70 3.37 344 137 140 3 485.35 2.66