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 10 8 429.21 1.31 2 2 73 71 24.00 1.77 3 2 127 125 23.86 2.19 4 2 128 126 18.30 0.58 5 2 131 129 18.28 0.59 6 3 6 3 485.66 1.35 7 3 7 4 466.00 0.15 8 4 7 3 479.41 4.48 9 4 8 4 466.00 0.15 10 5 8 3 482.81 3.41 11 5 9 4 461.56 2.38 12 6 9 3 467.95 3.27 13 6 10 4 459.84 1.52 14 6 124 118 46.30 0.61 15 6 127 121 46.37 0.58 16 7 10 3 477.17 0.60 17 7 11 4 465.40 7.96 18 7 73 66 46.81 0.81 19 7 74 67 47.70 0.38 20 8 11 3 484.90 1.27 21 8 12 4 468.79 6.28 22 9 12 3 484.90 1.27 23 9 13 4 471.58 4.89 24 9 121 112 53.69 2.35 25 9 124 115 53.59 2.31 26 10 13 3 485.98 2.30 27 10 14 4 473.41 3.98 28 10 70 60 53.65 2.33 29 10 73 63 53.65 2.33 30 10 125 115 53.64 2.33 31 10 128 118 53.62 2.33 32 11 14 3 485.98 2.31 33 11 15 4 474.42 3.47 34 11 70 59 53.64 2.33 35 11 73 62 53.65 2.33 36 12 15 3 484.57 3.00 37 12 16 4 473.03 2.77 38 13 16 3 477.50 0.10 39 13 17 4 465.36 1.06 40 13 121 108 54.85 2.32 41 13 125 112 54.01 2.25 42 14 17 3 471.60 1.21 43 14 18 4 465.50 0.99 44 14 21 7 390.68 16.32 45 14 66 52 60.55 1.02 46 14 67 53 60.56 1.01 47 14 70 56 54.01 2.26 48 14 109 95 79.32 0.57 49 15 18 3 471.21 1.41 50 16 113 97 93.66 0.26 51 16 116 100 91.78 0.62 52 17 20 3 483.34 3.81 53 17 21 4 437.42 0.12 54 17 24 7 371.13 15.99 55 17 109 92 91.63 0.72 56 17 113 96 97.02 0.44 57 18 21 3 490.33 0.32 58 20 23 3 478.04 5.83 59 20 24 4 462.65 4.12 60 20 113 93 114.79 0.26 61 21 24 3 460.06 5.42 62 21 25 4 468.64 1.15 63 21 63 42 98.70 0.33 64 22 25 3 472.07 2.86 65 22 26 4 468.65 1.15 66 22 59 37 100.21 0.39 67 22 60 38 98.73 0.34 68 22 63 41 98.73 0.33 69 23 26 3 478.00 2.10 70 23 27 4 472.88 2.46 71 24 27 3 472.92 2.44 72 24 28 4 472.92 2.44 73 24 108 84 116.93 0.92 74 24 109 85 125.84 1.30 75 24 112 88 131.28 0.84 76 24 113 89 131.38 0.79 77 25 28 3 479.66 3.53 78 25 29 4 469.50 0.73 79 25 59 34 114.99 0.14 80 26 29 3 480.47 3.33 81 26 30 4 463.78 2.12 82 26 55 29 126.66 1.37 83 26 56 30 126.53 1.30 84 26 59 33 116.60 0.10 85 27 30 3 466.10 2.08 86 27 31 4 463.75 2.12 87 27 108 81 131.56 0.77 88 27 112 85 131.94 0.68 89 28 31 3 478.57 4.28 90 28 32 4 468.16 0.15 91 28 101 73 131.38 0.80 92 28 104 76 131.47 0.78 93 28 105 77 131.39 0.79 94 28 108 80 131.59 0.77 95 29 32 3 472.92 2.42 96 29 33 4 468.16 0.15 97 29 55 26 131.65 0.81 98 29 58 29 131.52 0.76 99 29 59 30 131.52 0.77 100 29 101 72 131.44 0.76 101 30 33 3 484.11 3.18 102 30 34 4 472.79 2.48 103 30 50 20 132.44 0.66 104 30 51 21 132.40 0.67 105 31 34 3 484.11 3.18 106 31 35 4 467.87 0.03 107 31 104 73 131.55 0.77 108 31 107 76 132.06 0.61 109 31 108 77 132.06 0.61 110 32 35 3 489.64 0.42 111 32 36 4 442.69 3.62 112 32 39 7 343.36 5.58 113 32 100 68 131.55 0.74 114 32 101 69 131.48 0.78 115 32 104 72 131.62 0.76 116 33 37 4 435.29 0.03 117 33 39 6 343.36 5.57 118 33 40 7 248.78 41.72 119 33 43 10 140.91 0.77 120 33 48 15 132.53 0.70 121 33 55 22 132.40 0.67 122 34 37 3 484.77 2.86 123 36 39 3 490.68 1.37 124 36 100 64 131.60 0.77 125 36 103 67 132.12 0.62 126 36 104 68 132.12 0.62 127 37 40 3 486.39 0.56 128 38 41 3 487.96 1.33 129 39 42 3 490.88 0.12 130 39 97 58 131.60 0.77 131 39 100 61 132.06 0.60 132 40 43 3 476.60 0.51 133 40 48 8 132.83 0.63 134 41 44 3 490.37 0.37 135 42 92 50 131.53 0.79 136 42 93 51 131.55 0.80 137 42 94 52 131.91 0.64 138 42 97 55 132.07 0.61 139 43 46 3 480.55 0.86 140 43 48 5 390.08 4.49 141 43 58 15 132.71 0.65 142 46 54 8 133.26 0.61 143 46 55 9 133.38 0.62 144 46 58 12 133.30 0.59 145 47 52 5 206.40 33.28 146 47 54 7 134.19 0.22 147 47 55 8 134.20 0.22 148 48 55 7 134.22 0.24 149 49 52 3 477.36 0.12 150 52 55 3 473.32 1.65 151 52 56 4 452.18 0.55 152 53 56 3 467.34 4.63 153 53 57 4 463.75 0.67 154 54 57 3 471.17 3.04 155 54 58 4 463.75 0.66 156 55 58 3 474.69 1.28 157 55 59 4 463.75 0.66 158 56 59 3 474.69 1.28 159 56 60 4 470.09 1.03 160 57 60 3 472.34 2.15 161 57 61 4 476.01 0.30 162 58 61 3 482.39 3.50 163 58 62 4 472.32 2.15 164 59 62 3 473.69 1.71 165 59 63 4 472.33 2.15 166 60 63 3 475.49 0.85 167 60 64 4 466.23 0.88 168 61 64 3 472.31 1.45 169 61 65 4 468.46 0.27 170 62 65 3 476.81 1.61 171 62 66 4 466.08 0.88 172 63 66 3 470.99 0.99 173 63 67 4 464.57 1.64 174 64 67 3 466.28 0.78 175 64 68 4 464.57 1.64 176 65 68 3 464.56 1.62 177 65 69 4 463.61 2.10 178 65 83 18 145.81 4.98 179 66 69 3 466.09 2.53 180 66 70 4 462.85 0.92 181 66 105 39 208.28 0.30 182 66 128 62 209.18 0.88 183 66 129 63 190.33 8.52 184 66 132 66 173.30 5.91 185 67 70 3 462.86 0.93 186 67 71 4 462.85 0.93 187 68 71 3 472.86 2.59 188 68 72 4 464.35 0.18 189 68 79 11 176.50 4.16 190 69 72 3 467.04 0.65 191 69 73 4 462.78 0.96 192 69 76 7 254.15 41.65 193 69 80 11 170.13 0.98 194 69 128 59 212.65 0.71 195 69 132 63 190.28 8.48 196 70 73 3 482.07 2.31 197 70 128 58 230.74 9.51 198 72 75 3 474.70 2.20 199 72 76 4 434.90 1.66 200 72 79 7 289.84 3.29 201 73 76 3 485.30 1.26 202 73 128 55 265.85 3.62 203 75 78 3 486.19 3.95 204 75 79 4 461.29 0.14 205 76 79 3 461.38 0.18 206 76 80 4 454.27 3.37 207 76 128 52 266.88 3.33 208 76 131 55 266.22 3.66 209 76 132 56 266.05 3.62 210 76 135 59 266.02 3.60 211 77 80 3 481.73 1.84 212 77 81 4 446.81 2.90 213 77 135 58 266.03 3.61 214 78 81 3 478.76 3.33 215 80 83 3 468.87 3.69 216 80 84 4 468.96 2.20 217 80 132 52 268.68 3.67 218 80 135 55 268.08 3.73 219 80 136 56 268.61 3.71 220 81 84 3 475.06 0.12 221 81 85 4 469.00 2.21 222 82 85 3 478.76 0.40 223 82 86 4 469.00 2.21 224 83 86 3 476.66 0.67 225 83 87 4 469.81 1.81 226 83 136 53 269.19 3.93 227 84 87 3 481.52 1.47 228 84 88 4 454.40 4.83 229 84 135 51 269.19 3.93 230 84 136 52 269.19 3.93 231 84 139 55 269.00 3.87 232 85 89 4 387.51 14.89 233 85 90 5 383.50 16.89 234 86 90 4 382.60 17.32 235 86 91 5 382.59 17.32 236 87 91 4 382.58 17.33 237 87 92 5 382.56 17.32 238 87 93 6 322.95 12.44 239 87 98 11 274.64 3.04 240 87 136 49 269.35 3.98 241 88 92 4 382.54 17.33 242 88 136 48 269.38 3.96 243 88 137 49 269.19 3.93 244 88 139 51 269.18 3.92 245 88 140 52 269.01 3.86 246 89 92 3 480.14 0.14 247 89 139 50 269.17 3.93 248 89 140 51 269.08 3.91 249 89 141 52 268.98 3.86 250 92 140 48 269.23 3.92 251 92 141 49 269.32 3.97 252 93 97 4 470.14 2.21 253 93 98 5 468.29 3.14 254 93 140 47 269.39 3.97 255 94 97 3 475.90 0.53 256 95 98 3 483.78 1.94 257 95 99 4 481.98 1.04 258 95 137 42 269.51 3.96 259 95 140 45 269.49 3.95 260 96 99 3 484.78 1.44 261 96 100 4 470.14 2.21 262 97 100 3 471.74 1.38 263 97 101 4 469.09 2.71 264 98 101 3 473.36 0.57 265 98 102 4 469.09 2.68 266 98 133 35 270.18 3.89 267 98 136 38 270.19 3.90 268 98 137 39 270.16 3.89 269 99 102 3 471.30 1.56 270 99 103 4 467.37 1.82 271 100 103 3 470.49 0.27 272 100 104 4 467.38 1.82 273 101 104 3 472.29 0.65 274 101 105 4 467.35 1.82 275 102 105 3 470.18 3.34 276 102 106 4 463.66 0.08 277 102 129 27 270.51 3.92 278 103 106 3 466.31 1.40 279 103 107 4 462.54 0.81 280 104 107 3 462.54 0.81 281 104 108 4 462.40 0.88 282 105 108 3 471.35 3.02 283 105 109 4 462.03 0.69 284 105 129 24 271.08 3.73 285 106 109 3 472.95 4.40 286 106 110 4 461.11 0.23 287 106 117 11 274.80 4.46 288 106 122 16 271.97 3.85 289 106 125 19 271.87 3.86 290 106 126 20 271.85 3.87 291 106 129 23 271.81 3.86 292 107 110 3 471.04 0.24 293 107 111 4 457.50 1.46 294 108 111 3 474.45 1.47 295 108 112 4 457.52 1.45 296 109 112 3 472.60 0.55 297 109 113 4 456.64 1.16 298 109 117 8 277.20 3.52 299 109 125 16 271.99 3.85 300 110 113 3 463.55 0.04 301 110 114 4 402.26 5.23 302 110 117 7 274.79 4.47 303 113 116 3 464.50 3.02 304 113 117 4 452.33 2.44 305 114 117 3 462.58 3.40 306 117 122 5 425.56 0.66 307 117 125 8 395.56 9.88 308 118 121 3 471.79 5.33 309 118 122 4 464.88 4.21 310 119 122 3 473.03 0.14 311 119 123 4 464.89 4.21 312 120 123 3 473.21 0.06 313 120 124 4 464.88 4.21 314 121 124 3 469.48 1.92 315 121 125 4 462.55 3.06 316 122 125 3 470.44 0.39 317 122 126 4 459.23 4.71 318 123 126 3 459.94 4.37 319 123 127 4 460.43 4.12 320 124 127 3 475.41 0.13 321 124 128 4 460.44 4.12 322 125 128 3 460.44 4.12 323 125 129 4 460.44 4.12 324 126 129 3 470.43 0.86 325 126 130 4 458.50 5.08 326 127 130 3 461.30 2.43 327 127 131 4 452.39 1.95 328 128 131 3 464.57 0.45 329 128 132 4 456.08 3.79 330 129 132 3 468.63 2.06 331 129 133 4 470.34 3.34 332 130 133 3 474.89 1.06 333 130 134 4 470.20 3.41 334 131 134 3 474.89 1.06 335 131 135 4 472.00 2.51 336 132 135 3 474.89 1.07 337 132 136 4 472.00 2.51 338 133 136 3 470.90 1.96 339 133 137 4 463.04 1.97 340 134 137 3 477.99 3.92 341 134 138 4 467.48 0.25 342 135 138 3 475.06 0.10 343 137 140 3 502.80 1.21