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 8 406.81 2.26 2 2 51 49 101.77 1.06 3 3 6 3 428.90 3.50 4 3 7 4 434.12 0.92 5 4 7 3 434.12 0.92 6 4 8 4 434.12 0.92 7 4 103 99 67.20 0.92 8 4 104 100 67.31 0.87 9 5 8 3 434.12 0.92 10 5 9 4 434.12 0.92 11 5 42 37 111.88 0.40 12 6 9 3 434.12 0.92 13 6 10 4 425.78 5.08 14 6 42 36 111.86 0.39 15 6 45 39 111.81 0.41 16 6 46 40 111.78 0.41 17 6 49 43 111.47 0.58 18 6 51 45 108.77 1.07 19 7 10 3 429.97 3.00 20 7 11 4 427.59 1.81 21 7 73 66 78.62 1.17 22 7 76 69 78.62 1.17 23 7 103 96 78.56 1.16 24 8 11 3 438.09 0.82 25 8 12 4 433.83 1.31 26 8 32 24 145.17 2.48 27 8 103 95 78.63 1.12 28 9 12 3 438.10 0.81 29 9 13 4 431.73 0.27 30 9 28 19 145.27 2.49 31 9 32 23 145.19 2.48 32 9 34 25 145.17 2.48 33 9 39 30 112.10 0.41 34 9 42 33 111.92 0.42 35 9 46 37 111.83 0.42 36 10 13 3 433.99 1.24 37 10 14 4 431.72 0.27 38 10 46 36 111.81 0.42 39 10 51 41 108.77 1.07 40 10 66 56 82.42 1.98 41 10 70 60 79.58 0.73 42 10 73 63 79.25 0.85 43 11 14 3 436.51 0.06 44 11 15 4 431.77 0.30 45 11 73 62 79.23 0.87 46 11 74 63 78.63 1.16 47 11 77 66 78.66 1.15 48 11 102 91 79.52 0.69 49 12 15 3 436.19 0.10 50 12 16 4 424.62 4.21 51 12 28 16 145.30 2.48 52 12 31 19 145.28 2.49 53 12 32 20 145.27 2.49 54 13 16 3 436.91 0.14 55 13 17 4 424.61 4.21 56 13 23 10 158.13 0.68 57 13 28 15 145.31 2.47 58 13 46 33 111.91 0.47 59 13 52 39 108.76 1.07 60 13 60 47 101.39 0.73 61 13 62 49 100.08 1.14 62 14 17 3 436.91 0.14 63 14 18 4 427.56 2.73 64 14 62 48 100.11 1.16 65 14 67 53 88.89 1.20 66 14 70 56 80.91 1.33 67 14 71 57 80.86 1.32 68 14 74 60 80.82 1.30 69 15 18 3 438.33 0.58 70 15 19 4 422.32 0.12 71 15 74 59 79.77 0.80 72 16 19 3 429.64 3.77 73 16 20 4 408.72 2.87 74 16 21 5 408.66 2.84 75 16 22 6 347.54 11.38 76 16 23 7 161.28 0.70 77 16 27 11 157.00 0.17 78 16 28 12 158.59 0.63 79 17 20 3 433.96 0.02 80 17 21 4 395.88 7.30 81 17 22 5 203.05 5.38 82 17 23 6 203.04 5.38 83 17 60 43 101.45 0.71 84 17 62 45 100.97 0.86 85 18 71 53 88.95 1.19 86 20 27 7 397.35 7.96 87 23 28 5 422.97 4.50 88 23 60 37 101.41 0.72 89 24 27 3 428.60 2.14 90 24 28 4 423.44 4.71 91 25 28 3 440.28 3.70 92 25 29 4 428.29 2.29 93 25 36 11 146.11 2.39 94 25 39 14 144.85 2.50 95 25 40 15 144.85 2.50 96 26 29 3 432.73 0.07 97 26 30 4 428.00 2.15 98 27 30 3 429.22 1.82 99 27 31 4 428.00 2.15 100 28 31 3 431.19 0.83 101 28 32 4 428.94 1.68 102 28 39 11 145.28 2.77 103 28 60 32 101.39 0.73 104 29 32 3 437.49 0.56 105 29 33 4 422.81 4.74 106 29 34 5 363.76 0.05 107 29 35 6 189.06 2.37 108 29 36 7 165.12 1.61 109 29 39 10 147.15 2.92 110 30 33 3 427.66 2.00 111 34 38 4 430.61 2.00 112 34 39 5 418.12 3.63 113 35 38 3 441.32 0.59 114 35 39 4 429.38 2.62 115 36 39 3 430.61 2.01 116 36 40 4 419.34 3.04 117 37 40 3 433.38 3.39 118 37 41 4 431.89 3.25 119 38 41 3 436.74 0.83 120 38 42 4 431.88 3.25 121 39 42 3 438.30 0.06 122 39 43 4 431.39 3.50 123 40 43 3 431.38 3.51 124 40 44 4 431.38 3.52 125 41 44 3 438.52 0.16 126 41 45 4 431.37 3.52 127 42 45 3 431.99 1.17 128 42 46 4 415.95 0.58 129 43 46 3 432.48 3.25 130 43 47 4 421.95 2.43 131 43 52 9 175.02 3.71 132 43 54 11 121.34 2.35 133 43 60 17 101.66 0.83 134 44 47 3 429.00 1.09 135 44 48 4 421.81 2.50 136 45 48 3 429.00 1.09 137 45 49 4 421.82 2.50 138 46 49 3 431.19 2.11 139 46 50 4 417.50 4.65 140 46 51 5 375.81 0.90 141 46 52 6 278.23 47.89 142 47 50 3 422.53 1.69 143 47 52 5 278.23 47.89 144 47 53 6 161.60 3.55 145 49 65 16 99.41 1.12 146 50 63 13 100.07 1.14 147 50 65 15 99.41 1.12 148 51 62 11 100.10 1.13 149 51 63 12 100.06 1.15 150 51 65 14 99.24 1.06 151 51 66 15 93.46 1.16 152 51 69 18 91.66 0.35 153 52 60 8 106.30 3.10 154 52 61 9 100.97 0.93 155 52 62 10 100.10 1.13 156 52 63 11 100.08 1.14 157 53 60 7 106.31 3.10 158 53 61 8 106.25 3.13 159 53 63 10 100.52 1.09 160 54 59 5 114.62 1.04 161 54 60 6 106.32 3.10 162 55 58 3 418.55 0.12 163 55 59 4 156.10 2.54 164 55 61 6 106.31 3.10 165 58 61 3 472.69 2.79 166 62 66 4 395.80 0.36 167 62 67 5 395.75 0.34 168 63 66 3 425.61 2.80 169 63 67 4 424.38 0.82 170 64 67 3 441.74 1.71 171 64 68 4 426.85 2.04 172 65 68 3 446.26 3.35 173 65 69 4 426.88 2.02 174 66 69 3 437.42 1.07 175 66 70 4 423.67 5.80 176 67 70 3 430.42 2.43 177 67 71 4 424.18 0.68 178 68 71 3 444.76 0.34 179 68 72 4 424.19 0.68 180 69 72 3 435.83 4.65 181 69 73 4 424.10 0.72 182 70 73 3 440.50 2.31 183 70 74 4 421.37 0.58 184 71 74 3 431.69 1.94 185 71 75 4 420.20 0.01 186 72 75 3 424.07 2.29 187 72 76 4 422.36 1.64 188 72 107 35 307.64 3.31 189 73 76 3 433.00 1.43 190 73 77 4 422.36 1.63 191 73 107 34 307.78 3.25 192 74 77 3 444.51 2.27 193 74 78 4 422.38 1.65 194 75 78 3 444.51 2.27 195 75 79 4 422.88 1.40 196 75 110 35 308.08 3.10 197 76 79 3 444.51 2.27 198 76 80 4 435.08 2.44 199 76 102 26 308.50 3.11 200 76 103 27 308.50 3.11 201 76 107 31 308.20 3.07 202 76 110 34 307.94 3.18 203 77 80 3 446.10 1.48 204 77 81 4 426.19 2.02 205 77 95 18 309.10 3.17 206 77 98 21 308.79 3.20 207 77 99 22 308.80 3.20 208 77 102 25 308.50 3.11 209 78 81 3 439.29 1.83 210 78 82 4 426.43 2.14 211 79 82 3 426.47 2.15 212 79 83 4 426.42 2.15 213 79 110 31 308.17 3.08 214 79 113 34 308.04 3.12 215 79 114 35 308.03 3.13 216 79 117 38 308.02 3.13 217 80 83 3 433.70 0.30 218 80 84 4 424.50 2.25 219 80 98 18 308.95 3.22 220 80 101 21 308.81 3.19 221 80 102 22 308.80 3.20 222 80 105 25 308.49 3.12 223 80 110 30 308.20 3.07 224 80 113 33 308.04 3.12 225 81 84 3 437.29 3.27 226 81 85 4 425.44 2.71 227 81 94 13 309.12 3.15 228 81 95 14 309.11 3.15 229 81 98 17 309.03 3.15 230 82 85 3 443.02 0.75 231 82 86 4 425.44 2.71 232 82 117 35 308.03 3.13 233 82 121 39 307.10 3.42 234 83 86 3 436.19 2.67 235 83 87 4 421.68 0.83 236 83 113 30 308.18 3.08 237 83 116 33 308.06 3.12 238 83 117 34 308.04 3.13 239 84 87 3 442.70 0.57 240 84 88 4 419.35 0.21 241 84 89 5 354.59 1.46 242 84 94 10 309.26 3.12 243 84 97 13 309.25 3.12 244 84 98 14 309.24 3.12 245 85 88 3 432.62 5.63 246 85 91 6 309.71 3.02 247 85 94 9 309.27 3.12 248 86 117 31 308.08 3.11 249 86 120 34 307.98 3.16 250 86 121 35 307.32 3.48 251 86 127 41 200.78 2.77 252 86 130 44 200.75 2.75 253 87 130 43 190.47 7.90 254 89 93 4 421.81 0.56 255 89 94 5 394.62 13.04 256 90 93 3 450.53 0.72 257 90 94 4 423.27 1.27 258 91 94 3 435.00 1.96 259 93 96 3 437.72 4.22 260 93 97 4 429.63 0.20 261 94 97 3 433.88 1.46 262 94 98 4 429.63 0.21 263 95 98 3 433.67 1.81 264 95 99 4 429.82 0.10 265 96 99 3 444.86 2.12 266 96 100 4 427.14 1.24 267 97 100 3 434.59 3.00 268 97 101 4 429.10 0.26 269 98 101 3 435.18 3.31 270 98 102 4 423.38 3.11 271 99 102 3 438.48 1.57 272 100 104 4 436.07 0.54 273 101 104 3 432.49 1.26 274 101 105 4 427.02 0.55 275 105 109 4 416.17 3.50 276 105 110 5 396.11 3.98 277 105 113 8 371.62 8.27 278 106 109 3 431.14 3.00 279 106 110 4 418.37 4.60 280 107 110 3 421.35 3.11 281 107 111 4 427.06 0.51 282 108 111 3 427.07 0.50 283 108 112 4 427.07 0.50 284 109 112 3 427.07 0.50 285 109 113 4 427.07 0.50 286 110 113 3 434.35 0.52 287 110 114 4 427.06 0.51 288 111 114 3 431.54 0.89 289 111 115 4 427.27 0.40 290 112 115 3 438.44 1.49 291 112 116 4 438.31 1.55 292 113 116 3 438.31 1.55 293 113 117 4 427.70 3.75 294 114 117 3 438.31 1.55 295 114 118 4 426.11 0.18 296 115 118 3 428.55 1.04 297 115 119 4 426.10 0.17 298 116 119 3 428.37 0.96 299 116 120 4 427.03 0.29 300 117 120 3 435.72 0.68 301 117 121 4 421.70 0.84 302 118 121 3 425.50 1.05 303 118 122 4 420.59 1.41 304 119 122 3 451.29 1.48 305 119 126 7 364.17 10.65 306 120 123 3 437.13 1.45 307 120 126 6 332.83 1.92 308 120 127 7 284.61 25.21 309 120 130 10 273.21 30.91 310 121 127 6 420.24 0.54 311 122 126 4 447.98 0.82 312 123 126 3 441.99 2.25 313 123 127 4 431.91 0.65 314 124 127 3 431.91 0.65 315 124 128 4 431.87 0.66 316 125 128 3 435.69 2.57 317 125 129 4 426.19 2.18 318 126 129 3 441.41 0.28 319 126 130 4 433.82 4.07 320 127 130 3 444.77 2.06 321 127 131 4 433.83 4.07 322 128 131 3 435.81 3.08 323 128 132 4 425.30 2.05 324 129 132 3 441.31 0.33 325 129 133 4 435.03 2.81 326 130 133 3 442.19 2.02 327 130 134 4 437.95 0.10 328 131 134 3 444.64 0.80 329 131 135 4 432.70 2.72 330 132 136 4 417.53 0.62 331 133 136 3 429.73 2.37