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 5 445.01 0.65 2 2 73 71 30.67 0.14 3 2 76 74 27.27 1.12 4 2 127 125 22.93 0.28 5 2 128 126 22.39 0.09 6 2 131 129 22.39 0.09 7 3 6 3 474.33 0.29 8 3 7 4 474.40 0.33 9 4 7 3 474.42 0.32 10 4 8 4 474.41 0.33 11 5 8 3 485.66 1.06 12 5 9 4 474.42 0.33 13 6 9 3 477.72 1.21 14 6 10 4 472.18 1.45 15 6 124 118 47.95 0.43 16 6 127 121 46.69 0.24 17 7 10 3 476.82 1.66 18 7 11 4 469.18 2.93 19 7 73 66 48.10 0.35 20 7 74 67 52.31 1.10 21 8 11 3 476.19 0.54 22 8 12 4 469.17 2.93 23 9 12 3 477.05 0.10 24 9 13 4 469.15 2.92 25 9 121 112 59.77 0.04 26 9 124 115 59.77 0.04 27 10 13 3 486.09 2.59 28 10 14 4 455.50 4.72 29 10 70 60 59.76 0.07 30 10 124 114 59.79 0.05 31 10 125 115 59.75 0.06 32 10 128 118 59.74 0.06 33 11 14 3 478.01 1.45 34 11 15 4 446.57 0.32 35 11 70 59 59.77 0.07 36 11 71 60 59.80 0.09 37 11 73 62 59.80 0.08 38 12 15 3 469.57 1.82 39 12 16 4 472.88 0.18 40 13 16 3 477.82 1.42 41 13 17 4 472.87 0.17 42 13 113 100 79.49 0.93 43 13 121 108 59.90 0.07 44 13 125 112 59.90 0.07 45 14 17 3 468.31 2.10 46 14 18 4 468.31 2.11 47 14 21 7 405.62 5.40 48 14 63 49 71.67 1.00 49 14 66 52 59.92 0.11 50 14 67 53 59.91 0.12 51 14 70 56 59.90 0.11 52 15 18 3 473.71 0.58 53 16 113 97 95.47 1.50 54 16 116 100 93.95 0.76 55 17 20 3 484.95 0.68 56 17 21 4 425.61 2.19 57 17 24 7 408.75 3.73 58 17 109 92 91.18 2.15 59 17 113 96 96.62 1.15 60 18 21 3 493.20 3.39 61 20 23 3 473.48 1.03 62 20 24 4 468.97 0.07 63 21 24 3 468.98 0.07 64 21 25 4 466.95 1.08 65 21 63 42 98.42 1.24 66 22 25 3 471.75 1.31 67 22 26 4 468.06 0.53 68 22 60 38 101.62 0.14 69 22 63 41 98.67 1.34 70 23 26 3 480.18 5.54 71 23 27 4 464.29 2.35 72 23 56 33 118.02 0.16 73 24 27 3 482.82 4.22 74 24 28 4 468.67 2.85 75 24 108 84 118.07 0.16 76 24 109 85 122.14 0.48 77 24 112 88 129.44 0.49 78 25 28 3 473.26 0.57 79 25 29 4 468.69 2.85 80 25 59 34 117.98 0.17 81 25 63 38 117.94 0.16 82 26 29 3 474.60 0.11 83 26 30 4 468.69 2.85 84 26 55 29 125.62 1.59 85 26 56 30 125.59 1.57 86 26 59 33 117.95 0.15 87 27 30 3 476.44 2.29 88 27 31 4 467.42 2.21 89 27 108 81 130.91 0.21 90 27 112 85 132.22 0.35 91 28 31 3 469.30 1.27 92 28 32 4 467.42 2.21 93 28 101 73 130.65 0.11 94 28 104 76 130.75 0.15 95 28 105 77 130.71 0.11 96 28 108 80 131.19 0.28 97 29 32 3 476.84 2.10 98 29 33 4 463.73 2.04 99 29 55 26 132.20 0.41 100 29 58 29 131.24 0.05 101 29 59 30 131.22 0.06 102 29 101 72 130.84 0.18 103 30 33 3 479.88 1.18 104 30 34 4 466.15 3.25 105 30 50 20 132.55 0.33 106 31 34 3 477.61 0.04 107 31 35 4 466.06 3.29 108 31 104 73 132.21 0.40 109 31 107 76 132.40 0.39 110 31 108 77 132.41 0.39 111 31 111 80 132.66 0.33 112 32 35 3 474.34 0.48 113 32 36 4 452.06 3.67 114 32 39 7 301.49 8.01 115 32 100 68 132.19 0.40 116 32 101 69 132.19 0.41 117 32 104 72 132.32 0.41 118 33 37 4 427.02 8.72 119 33 39 6 306.30 0.93 120 33 40 7 215.23 26.23 121 33 43 10 156.41 3.16 122 33 48 15 132.61 0.29 123 36 39 3 485.89 2.97 124 36 100 64 132.25 0.39 125 36 103 67 132.58 0.35 126 36 104 68 132.62 0.33 127 37 40 3 480.01 0.08 128 38 41 3 484.42 0.32 129 39 42 3 484.69 0.29 130 39 43 4 489.88 4.00 131 39 97 58 132.18 0.42 132 39 100 61 132.53 0.34 133 40 43 3 494.28 1.80 134 40 44 4 479.77 1.05 135 40 48 8 147.83 0.48 136 41 44 3 498.08 0.10 137 42 93 51 131.96 0.31 138 42 94 52 132.47 0.36 139 42 97 55 132.56 0.33 140 43 46 3 477.99 0.97 141 43 48 5 423.20 0.09 142 43 58 15 139.27 1.46 143 45 54 9 142.98 3.09 144 46 54 8 142.93 3.12 145 46 55 9 142.94 3.12 146 46 58 12 142.92 3.12 147 47 52 5 162.31 3.32 148 47 54 7 143.00 3.09 149 47 55 8 143.07 3.06 150 48 52 4 408.15 0.78 151 48 55 7 143.09 3.07 152 49 52 3 475.96 0.88 153 52 55 3 463.50 6.10 154 52 56 4 461.89 6.77 155 53 56 3 471.84 1.79 156 53 57 4 461.56 6.92 157 54 57 3 480.91 2.75 158 54 58 4 471.72 1.84 159 55 58 3 473.70 2.00 160 55 59 4 471.10 0.78 161 56 59 3 473.70 2.00 162 56 60 4 472.62 1.48 163 57 60 3 483.98 4.19 164 57 61 4 472.64 1.48 165 58 61 3 474.88 0.36 166 58 62 4 473.19 1.21 167 59 62 3 480.23 2.31 168 59 63 4 472.06 1.77 169 60 63 3 472.53 0.88 170 60 64 4 463.57 2.48 171 61 64 3 472.64 0.94 172 61 65 4 464.67 1.71 173 62 65 3 483.15 0.40 174 62 66 4 470.36 1.14 175 62 101 39 151.97 3.10 176 63 66 3 478.30 2.83 177 63 67 4 464.67 1.71 178 64 67 3 478.30 2.83 179 64 68 4 468.34 0.13 180 65 68 3 468.79 0.35 181 65 69 4 468.78 0.35 182 65 80 15 152.09 3.10 183 65 83 18 151.96 3.09 184 66 69 3 477.03 2.68 185 66 70 4 468.34 0.14 186 66 105 39 157.66 0.46 187 66 129 63 157.75 0.35 188 66 132 66 152.19 3.14 189 67 70 3 473.74 2.12 190 67 71 4 473.04 2.21 191 68 71 3 475.06 1.20 192 68 72 4 469.28 4.09 193 68 79 11 157.09 0.75 194 69 72 3 475.39 1.37 195 69 73 4 461.84 3.05 196 69 76 7 272.49 2.71 197 69 80 11 152.88 2.85 198 69 128 59 167.67 0.76 199 69 132 63 158.37 0.10 200 70 73 3 470.31 1.19 201 70 128 58 177.51 5.74 202 72 75 3 471.42 0.29 203 72 76 4 426.12 3.87 204 72 79 7 274.00 2.28 205 73 76 3 479.47 1.52 206 75 78 3 479.88 1.34 207 75 79 4 458.75 1.60 208 76 79 3 469.56 1.56 209 76 80 4 458.75 1.60 210 76 128 52 263.87 2.67 211 76 131 55 262.02 2.46 212 76 132 56 261.72 2.35 213 77 81 4 441.08 7.21 214 77 135 58 259.00 1.10 215 78 81 3 469.17 1.42 216 80 83 3 480.16 0.21 217 80 84 4 449.70 3.67 218 80 132 52 266.29 3.42 219 80 135 55 266.02 3.54 220 80 136 56 266.26 3.43 221 81 84 3 471.39 4.59 222 81 85 4 466.03 1.91 223 81 139 58 266.09 3.51 224 82 85 3 480.09 0.90 225 82 86 4 466.04 1.90 226 83 86 3 477.44 3.79 227 83 87 4 477.42 3.79 228 83 136 53 267.13 3.81 229 84 87 3 483.45 0.78 230 84 88 4 477.39 3.79 231 84 135 51 267.14 3.81 232 84 136 52 267.12 3.82 233 84 138 54 267.12 3.81 234 84 139 55 266.87 3.77 235 85 88 3 478.64 3.19 236 85 89 4 463.72 10.63 237 85 139 54 266.86 3.77 238 86 89 3 480.62 2.18 239 86 90 4 440.03 1.69 240 86 91 5 435.25 4.09 241 87 91 4 366.30 1.33 242 87 92 5 345.88 11.54 243 87 93 6 333.95 5.58 244 87 98 11 279.52 3.62 245 87 136 49 267.23 3.84 246 87 140 53 267.04 3.84 247 88 92 4 354.35 4.61 248 88 139 51 267.03 3.83 249 88 140 52 266.82 3.75 250 89 92 3 492.91 3.16 251 92 140 48 267.17 3.81 252 93 97 4 482.50 0.33 253 93 98 5 480.56 1.30 254 93 140 47 267.32 3.83 255 94 97 3 495.75 2.32 256 94 98 4 484.89 0.86 257 95 98 3 496.92 1.20 258 95 140 45 267.52 3.83 259 96 99 3 491.77 5.60 260 96 100 4 481.04 0.57 261 97 100 3 475.44 0.89 262 97 101 4 475.11 1.03 263 98 101 3 476.77 1.81 264 98 102 4 474.51 0.74 265 98 133 35 267.98 3.79 266 98 136 38 268.00 3.79 267 98 137 39 267.99 3.79 268 98 140 42 267.82 3.71 269 99 102 3 477.79 2.39 270 99 103 4 474.50 0.74 271 100 103 3 473.30 1.35 272 100 104 4 473.29 1.35 273 101 104 3 471.82 2.19 274 101 105 4 465.99 0.77 275 102 105 3 466.00 0.78 276 102 106 4 466.05 0.79 277 102 129 27 268.31 3.89 278 102 133 31 268.31 3.89 279 103 106 3 469.20 0.76 280 103 107 4 466.05 0.79 281 104 107 3 469.25 1.08 282 104 108 4 466.04 0.80 283 105 108 3 472.39 2.38 284 105 109 4 464.09 1.77 285 105 129 24 269.11 3.91 286 106 109 3 472.72 2.39 287 106 110 4 462.45 2.59 288 106 117 11 270.44 3.66 289 106 122 16 270.00 3.63 290 106 125 19 269.88 3.57 291 106 126 20 269.75 3.64 292 106 129 23 269.82 3.58 293 107 110 3 472.25 2.31 294 107 111 4 461.99 2.69 295 108 111 3 474.81 1.81 296 108 112 4 461.98 2.69 297 109 112 3 475.38 4.05 298 109 113 4 456.18 0.01 299 109 125 16 270.17 3.70 300 110 113 3 479.81 1.83 301 110 117 7 270.72 3.85 302 113 116 3 477.86 0.55 303 113 117 4 472.25 2.25 304 114 117 3 482.03 0.70 305 115 118 3 526.28 0.91 306 116 121 5 451.25 2.62 307 117 121 4 451.25 2.62 308 117 122 5 451.22 2.60 309 117 125 8 434.28 5.87 310 118 121 3 472.82 1.66 311 118 122 4 452.16 2.17 312 119 122 3 467.41 1.05 313 119 123 4 453.50 2.83 314 120 123 3 471.29 0.01 315 120 124 4 465.25 3.04 316 121 124 3 474.74 1.70 317 121 125 4 474.73 1.70 318 122 125 3 476.56 2.61 319 122 126 4 474.82 1.78 320 123 126 3 474.88 1.77 321 123 127 4 474.85 1.77 322 124 127 3 474.72 1.72 323 124 128 4 468.85 1.22 324 125 128 3 473.62 2.91 325 125 129 4 467.89 0.73 326 126 129 3 482.05 1.31 327 126 130 4 467.89 0.73 328 127 130 3 481.29 0.93 329 127 131 4 459.85 0.65 330 128 131 3 478.31 2.42 331 128 132 4 460.53 0.30 332 129 132 3 475.88 3.64 333 129 133 4 459.84 0.63 334 130 133 3 473.00 1.61 335 130 134 4 461.06 0.03 336 131 134 3 465.44 2.16 337 131 135 4 461.37 0.20 338 132 135 3 474.12 5.26 339 132 136 4 461.35 0.21 340 133 136 3 476.43 4.11 341 133 137 4 461.36 0.21 342 134 137 3 481.11 1.46 343 134 138 4 461.33 0.23 344 135 138 3 481.11 1.46 345 136 140 4 489.82 1.20 346 137 140 3 485.50 0.97