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 1 116 115 27.07 0.44 2 2 5 3 447.42 2.58 3 2 6 4 447.24 0.42 4 2 67 65 27.14 0.41 5 2 73 71 27.07 0.44 6 2 116 114 27.14 0.41 7 2 119 117 27.12 0.41 8 2 120 118 27.12 0.42 9 2 123 121 27.07 0.44 10 3 6 3 462.13 2.25 11 3 7 4 447.25 0.40 12 3 68 65 28.32 0.17 13 4 7 3 448.88 1.21 14 4 8 4 444.14 1.16 15 5 8 3 453.64 1.18 16 5 9 4 448.92 3.54 17 5 115 110 37.02 0.13 18 5 116 111 37.02 0.13 19 5 120 115 36.95 0.16 20 6 9 3 454.38 0.82 21 6 10 4 454.25 0.88 22 6 64 58 86.92 25.14 23 6 67 61 80.30 21.82 24 6 68 62 80.32 21.78 25 6 120 114 37.02 0.13 26 7 10 3 454.37 0.82 27 7 11 4 454.25 0.88 28 8 11 3 457.52 2.39 29 8 12 4 454.37 0.82 30 8 16 8 398.86 2.67 31 8 115 107 61.73 2.18 32 9 12 3 459.09 2.19 33 9 13 4 437.52 1.64 34 9 16 7 398.85 2.67 35 9 64 55 98.54 20.59 36 9 108 99 65.82 0.18 37 9 115 106 63.80 1.18 38 9 120 111 63.67 1.22 39 10 13 3 445.88 3.29 40 10 64 54 105.44 24.04 41 10 65 55 110.41 26.52 42 10 68 58 98.55 20.59 43 12 15 3 463.90 0.54 44 12 16 4 447.40 0.29 45 13 16 3 460.44 0.92 46 13 17 4 447.38 0.28 47 13 57 44 137.09 25.75 48 13 60 47 133.04 27.41 49 13 61 48 132.96 27.44 50 13 64 51 132.78 27.49 51 14 17 3 460.48 0.93 52 14 18 4 446.50 0.73 53 14 53 39 142.27 23.87 54 14 54 40 149.44 20.29 55 14 57 43 140.59 24.04 56 15 18 3 464.03 0.59 57 15 19 4 455.14 3.60 58 16 19 3 462.62 0.13 59 16 20 4 445.55 0.26 60 16 107 91 107.12 5.03 61 16 113 97 112.39 2.06 62 16 115 99 111.05 2.65 63 17 20 3 462.60 0.12 64 17 21 4 446.33 1.27 65 17 56 39 149.16 20.12 66 17 57 40 148.99 19.91 67 17 60 43 141.62 23.54 68 18 21 3 447.93 0.48 69 18 22 4 446.43 1.22 70 18 47 29 153.90 20.94 71 18 52 34 150.06 20.18 72 18 53 35 149.87 20.12 73 18 56 38 149.48 20.15 74 19 22 3 450.44 0.97 75 19 23 4 449.04 2.52 76 19 47 28 154.47 21.05 77 19 107 88 113.52 1.83 78 20 23 3 450.54 1.77 79 20 24 4 450.55 1.76 80 20 60 40 149.75 19.98 81 20 104 84 113.45 1.88 82 20 107 87 113.52 1.83 83 21 24 3 450.55 1.76 84 21 25 4 450.55 1.76 85 21 35 14 248.03 2.79 86 21 38 17 229.45 2.66 87 21 52 31 153.97 20.82 88 21 56 35 149.84 20.02 89 21 60 39 149.79 20.00 90 22 25 3 450.56 1.75 91 22 26 4 450.56 1.75 92 22 43 21 159.33 23.38 93 22 46 24 154.59 21.01 94 22 47 25 154.59 21.00 95 22 52 30 154.03 20.87 96 23 26 3 457.50 1.80 97 23 27 4 447.59 0.49 98 24 27 3 458.02 0.35 99 24 28 4 443.56 1.25 100 24 31 7 406.98 4.14 101 24 99 75 114.05 1.72 102 24 100 76 114.28 1.65 103 24 103 79 113.93 1.65 104 25 28 3 456.08 0.61 105 25 29 4 436.25 2.39 106 25 31 6 399.03 8.12 107 25 32 7 354.02 4.83 108 25 35 10 354.01 4.83 109 25 38 13 243.99 0.36 110 26 29 3 456.07 0.61 111 26 32 6 415.19 0.04 112 26 43 17 218.74 2.19 113 27 102 75 115.10 1.42 114 27 103 76 115.04 1.39 115 27 106 79 114.95 1.31 116 28 31 3 461.50 0.79 117 28 99 71 114.94 1.51 118 28 102 74 115.13 1.42 119 28 103 75 115.12 1.41 120 29 32 3 464.45 0.69 121 30 33 3 471.99 1.45 122 31 34 3 471.99 1.46 123 31 35 4 465.76 1.66 124 31 96 65 115.05 1.56 125 31 99 68 115.14 1.42 126 32 35 3 466.57 2.53 127 32 38 6 391.32 15.46 128 32 39 7 298.81 20.12 129 32 41 9 298.83 20.11 130 32 46 14 244.43 7.06 131 34 92 58 115.23 1.56 132 34 96 62 115.28 1.49 133 35 38 3 462.97 2.89 134 35 39 4 460.42 2.35 135 36 39 3 464.97 1.89 136 37 41 4 465.39 0.14 137 37 49 12 240.64 0.70 138 38 41 3 469.31 1.81 139 38 46 8 282.44 10.48 140 38 52 14 207.26 1.94 141 38 55 17 207.24 1.96 142 41 45 4 439.47 2.58 143 41 46 5 438.49 2.99 144 41 49 8 392.57 7.40 145 42 45 3 447.38 3.75 146 42 46 4 442.47 1.18 147 43 46 3 459.18 2.16 148 43 47 4 442.47 1.18 149 44 47 3 448.77 0.57 150 44 48 4 446.72 0.95 151 45 48 3 454.15 2.77 152 45 49 4 446.72 0.95 153 46 49 3 450.73 6.27 154 46 52 6 397.49 6.66 155 47 52 5 406.63 3.93 156 49 52 3 461.88 0.49 157 49 53 4 455.59 2.65 158 50 53 3 461.88 0.49 159 50 54 4 450.12 0.42 160 51 54 3 458.05 1.42 161 51 55 4 449.46 0.09 162 52 55 3 460.03 1.61 163 52 56 4 455.24 2.80 164 53 56 3 460.50 1.38 165 53 57 4 449.42 0.10 166 54 57 3 460.04 1.61 167 54 58 4 450.06 0.42 168 55 58 3 451.14 0.48 169 55 59 4 450.03 0.50 170 56 59 3 453.03 0.99 171 56 60 4 450.14 0.57 172 57 60 3 453.16 0.93 173 57 61 4 442.00 1.70 174 58 61 3 452.99 1.40 175 58 62 4 447.14 0.87 176 59 62 3 454.94 3.00 177 59 63 4 450.08 0.60 178 60 63 3 450.98 5.52 179 60 64 4 444.39 2.23 180 60 104 44 128.24 5.23 181 61 64 3 452.68 1.48 182 61 65 4 449.19 0.19 183 62 65 3 452.13 1.67 184 62 66 4 444.29 2.25 185 62 83 21 126.88 4.19 186 62 86 24 126.89 4.20 187 63 66 3 452.69 1.82 188 63 67 4 447.75 0.91 189 63 100 37 128.31 5.15 190 63 101 38 129.12 5.56 191 63 104 41 129.68 5.87 192 64 67 3 447.75 0.91 193 64 68 4 442.37 3.60 194 64 120 56 143.43 13.28 195 65 68 3 443.40 1.27 196 65 69 4 436.27 0.54 197 66 69 3 447.89 5.30 198 66 70 4 445.37 5.08 199 66 75 9 192.27 2.48 200 66 79 13 129.34 5.36 201 66 123 57 143.50 13.31 202 67 70 3 451.86 7.29 203 67 120 53 143.50 13.31 204 67 123 56 143.37 13.38 205 69 76 7 193.79 1.91 206 69 79 10 192.23 2.56 207 70 73 3 447.62 2.48 208 70 74 4 264.08 6.71 209 70 75 5 217.25 9.89 210 70 123 53 148.88 15.97 211 71 74 3 446.30 2.44 212 72 122 50 149.62 16.34 213 73 119 46 149.63 16.33 214 73 122 49 149.61 16.34 215 73 123 50 149.53 16.30 216 73 126 53 149.49 16.32 217 74 126 52 149.12 16.52 218 75 123 48 149.62 16.34 219 75 126 51 149.18 16.55 220 75 127 52 148.03 17.12 221 75 130 55 139.24 21.46 222 76 79 3 446.94 3.39 223 76 80 4 446.95 3.38 224 77 80 3 460.35 3.31 225 77 81 4 446.97 3.38 226 78 81 3 449.67 2.04 227 78 82 4 447.97 2.88 228 79 82 3 448.89 3.29 229 79 83 4 448.03 2.87 230 80 83 3 453.54 0.10 231 80 84 4 448.03 2.86 232 80 130 50 138.22 22.43 233 80 131 51 136.81 23.14 234 80 134 54 136.06 23.51 235 81 84 3 448.00 2.87 236 81 85 4 441.88 0.18 237 81 134 53 136.05 23.50 238 82 85 3 459.06 1.81 239 82 86 4 441.90 0.21 240 83 86 3 457.19 0.86 241 83 89 6 316.69 16.84 242 83 127 44 145.00 19.16 243 83 131 48 136.83 23.14 244 84 131 47 136.71 23.20 245 84 134 50 136.31 23.40 246 84 136 52 129.40 26.85 247 86 89 3 445.41 1.52 248 86 90 4 435.48 3.44 249 87 90 3 441.95 0.21 250 89 92 3 448.62 1.43 251 89 97 8 371.77 17.52 252 92 96 4 450.22 2.51 253 92 97 5 449.23 2.01 254 92 136 44 122.33 30.96 255 93 96 3 468.91 3.75 256 93 97 4 460.01 0.70 257 93 136 43 119.76 32.25 258 93 137 44 119.49 32.30 259 94 97 3 460.01 0.70 260 94 98 4 458.31 1.54 261 94 128 34 140.10 22.12 262 94 131 37 139.56 22.39 263 94 132 38 137.28 23.52 264 94 136 42 119.77 32.26 265 94 137 43 119.69 32.27 266 95 98 3 460.64 1.94 267 95 99 4 449.43 2.10 268 96 99 3 464.58 0.04 269 96 100 4 449.56 2.04 270 97 100 3 455.99 0.41 271 97 101 4 449.44 2.10 272 97 128 31 140.21 22.17 273 97 131 34 137.49 23.53 274 97 136 39 120.24 32.12 275 98 101 3 451.78 1.41 276 98 102 4 448.50 2.56 277 98 128 30 140.80 21.91 278 99 102 3 453.66 0.03 279 99 103 4 448.42 2.52 280 100 103 3 454.93 0.68 281 100 104 4 445.86 1.20 282 101 104 3 448.95 0.36 283 101 105 4 442.11 0.68 284 101 123 22 150.87 17.41 285 101 124 23 149.50 17.71 286 101 127 26 147.50 18.77 287 102 105 3 445.55 2.09 288 102 106 4 445.24 2.25 289 103 106 3 452.20 1.24 290 103 107 4 445.92 1.91 291 104 107 3 449.35 2.07 292 104 108 4 445.91 1.91 293 104 120 16 158.30 14.47 294 105 108 3 450.55 2.30 295 105 109 4 445.91 1.90 296 105 117 12 158.37 14.46 297 105 120 15 157.91 14.28 298 105 121 16 157.85 14.29 299 106 109 3 452.22 0.14 300 106 110 4 442.38 0.14 301 107 110 3 450.71 0.61 302 107 111 4 441.66 0.50 303 108 111 3 448.04 0.73 304 108 115 7 158.87 14.62 305 108 117 9 158.79 14.62 306 108 120 12 158.79 14.62 307 109 117 8 158.81 14.61 308 111 115 4 469.43 1.62 309 116 119 3 463.56 4.84 310 116 120 4 444.62 1.82 311 117 120 3 460.75 6.24 312 117 121 4 435.36 2.50 313 118 121 3 445.60 0.28 314 118 122 4 435.74 2.69 315 119 122 3 444.09 1.48 316 119 123 4 435.72 2.69 317 120 123 3 439.72 0.70 318 120 124 4 439.70 0.70 319 121 124 3 448.36 1.10 320 121 125 4 439.69 0.70 321 122 125 3 448.17 1.20 322 122 126 4 438.12 0.69 323 123 126 3 447.76 0.20 324 123 127 4 439.94 0.24 325 124 127 3 444.36 1.97 326 124 128 4 437.12 1.65 327 125 128 3 450.62 0.18 328 125 129 4 432.32 0.75 329 126 129 3 447.21 1.24 330 126 130 4 437.38 3.28 331 127 130 3 458.20 3.98 332 127 131 4 442.35 5.76 333 128 131 3 452.05 0.91 334 128 132 4 433.08 0.01 335 129 132 3 451.04 1.42 336 129 133 4 438.61 2.77 337 130 133 3 450.13 0.96 338 130 134 4 438.60 2.77 339 131 134 3 449.09 2.48 340 131 135 4 440.43 1.85 341 131 136 5 384.63 1.09 342 132 135 3 451.12 1.46 343 132 136 4 405.29 11.38