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 75 74 250.93 0.38 2 2 74 72 251.21 0.27 3 2 75 73 251.20 0.27 4 2 76 74 251.18 0.26 5 2 77 75 251.17 0.26 6 3 77 74 251.17 0.26 7 4 33 29 251.19 0.27 8 4 69 65 251.22 0.27 9 4 76 72 251.22 0.27 10 4 77 73 251.19 0.26 11 4 78 74 251.18 0.26 12 4 79 75 251.17 0.26 13 5 33 28 251.20 0.26 14 5 34 29 251.19 0.27 15 5 79 74 251.18 0.26 16 6 32 26 251.19 0.26 17 6 33 27 251.21 0.26 18 6 78 72 251.22 0.27 19 6 79 73 251.20 0.26 20 6 80 74 251.18 0.26 21 6 81 75 251.18 0.26 22 7 31 24 251.21 0.27 23 7 32 25 251.22 0.27 24 7 40 33 251.20 0.27 25 7 43 36 251.21 0.27 26 7 44 37 251.18 0.26 27 7 80 73 251.20 0.26 28 7 81 74 251.18 0.26 29 7 83 76 251.17 0.26 30 8 30 22 251.21 0.27 31 8 31 23 251.22 0.27 32 8 44 36 251.19 0.27 33 8 48 40 251.21 0.27 34 8 81 73 251.21 0.27 35 8 82 74 251.18 0.26 36 8 83 75 251.18 0.26 37 8 85 77 251.16 0.26 38 9 29 20 251.24 0.27 39 9 30 21 251.24 0.27 40 9 48 39 251.22 0.27 41 9 82 73 251.21 0.26 42 9 83 74 251.18 0.26 43 9 85 76 251.04 0.21 44 10 17 7 251.27 0.26 45 10 29 19 251.25 0.27 46 10 62 52 251.22 0.26 47 10 83 73 251.22 0.27 48 10 84 74 251.17 0.26 49 10 85 75 251.16 0.26 50 10 121 111 54.02 0.20 51 10 122 112 53.68 0.08 52 10 125 115 45.31 0.43 53 11 17 6 268.22 8.17 54 11 18 7 251.25 0.27 55 11 48 37 251.25 0.27 56 11 54 43 251.25 0.27 57 11 55 44 251.25 0.27 58 11 56 45 251.22 0.27 59 11 85 74 251.17 0.26 60 11 86 75 251.15 0.25 61 11 87 76 250.93 0.26 62 11 103 92 135.49 0.70 63 12 16 4 322.95 0.10 64 12 17 5 268.24 8.15 65 12 84 72 251.23 0.27 66 12 85 73 251.19 0.26 67 12 86 74 251.16 0.26 68 12 87 75 251.14 0.26 69 12 106 94 128.28 0.09 70 12 122 110 54.30 0.32 71 12 125 113 53.34 0.17 72 12 126 114 52.99 0.21 73 12 129 117 39.91 1.09 74 13 16 3 415.12 2.08 75 13 87 74 251.11 0.24 76 13 103 90 135.55 0.73 77 15 105 90 135.28 0.80 78 15 106 91 135.06 0.77 79 16 103 87 135.50 0.71 80 16 104 88 135.26 0.80 81 16 105 89 131.96 0.21 82 16 106 90 130.21 0.12 83 17 29 12 293.63 1.72 84 17 103 86 135.48 0.70 85 17 104 87 135.16 0.82 86 17 109 92 104.41 1.56 87 17 122 105 54.30 0.32 88 18 30 12 293.61 1.73 89 18 48 30 263.69 2.57 90 18 52 34 263.69 2.57 91 18 54 36 258.25 0.48 92 18 92 74 136.71 0.52 93 18 102 84 135.55 0.73 94 18 103 85 135.21 0.79 95 19 27 8 294.47 1.65 96 19 28 9 294.37 1.69 97 19 29 10 293.63 1.72 98 19 30 11 293.62 1.73 99 19 101 82 135.60 0.72 100 19 102 83 135.55 0.73 101 19 104 85 135.03 0.76 102 19 109 90 79.39 3.20 103 19 112 93 55.01 0.07 104 19 113 94 54.94 0.04 105 20 27 7 298.03 0.12 106 20 28 8 294.48 1.65 107 20 29 9 293.98 1.88 108 20 30 10 293.63 1.72 109 20 51 31 264.37 2.83 110 20 52 32 264.26 2.83 111 20 98 78 136.31 0.53 112 20 100 80 135.72 0.74 113 20 101 81 135.56 0.74 114 21 25 4 347.69 0.03 115 21 26 5 318.19 2.79 116 21 27 6 310.08 5.91 117 21 98 77 136.31 0.53 118 21 99 78 136.29 0.53 119 21 100 79 135.75 0.74 120 22 25 3 414.66 1.79 121 22 26 4 327.57 1.90 122 22 28 6 317.42 2.44 123 22 99 77 136.30 0.53 124 23 97 74 136.41 0.52 125 23 99 76 136.31 0.53 126 25 99 74 136.29 0.53 127 26 114 88 54.94 0.07 128 26 115 89 54.95 0.07 129 27 100 73 136.26 0.53 130 27 102 75 135.58 0.74 131 27 104 77 135.31 0.83 132 27 112 85 54.83 0.06 133 27 113 86 54.84 0.07 134 28 113 85 54.75 0.10 135 28 118 90 54.10 0.24 136 29 82 53 251.23 0.26 137 29 113 84 54.80 0.07 138 29 118 89 54.03 0.20 139 29 121 92 54.02 0.20 140 29 122 93 53.72 0.12 141 30 48 18 264.31 2.83 142 30 51 21 264.39 2.83 143 30 52 22 264.37 2.81 144 31 47 16 264.51 2.83 145 31 51 20 264.56 2.81 146 31 67 36 251.66 0.27 147 31 78 47 251.59 0.28 148 31 80 49 251.29 0.24 149 31 82 51 251.24 0.26 150 32 43 11 265.39 2.85 151 32 47 15 264.88 2.66 152 33 43 10 276.13 8.21 153 33 46 13 265.42 2.85 154 33 47 14 265.27 2.79 155 33 78 45 251.56 0.29 156 34 38 4 386.78 5.76 157 34 43 9 276.13 8.21 158 35 38 3 431.44 1.44 159 35 46 11 314.35 4.58 160 38 42 4 410.13 0.37 161 38 43 5 409.75 2.41 162 38 46 8 393.77 2.81 163 39 42 3 433.06 1.50 164 39 43 4 420.01 2.66 165 40 43 3 427.70 1.18 166 40 44 4 421.12 0.23 167 40 81 41 251.44 0.24 168 40 83 43 251.39 0.23 169 41 44 3 431.88 1.25 170 41 45 4 432.05 1.17 171 41 58 17 263.94 2.40 172 41 83 42 251.41 0.23 173 42 45 3 434.09 0.14 174 42 46 4 431.63 1.08 175 43 46 3 436.03 1.11 176 43 47 4 429.59 0.06 177 44 47 3 436.10 1.15 178 44 48 4 423.24 0.86 179 44 58 14 263.95 2.40 180 44 83 39 251.28 0.24 181 44 85 41 251.18 0.26 182 45 48 3 438.07 2.18 183 45 49 4 422.16 2.11 184 45 55 10 316.82 0.62 185 45 56 11 288.94 9.14 186 45 58 13 264.06 2.45 187 45 85 40 251.18 0.27 188 46 49 3 431.93 3.21 189 46 50 4 419.17 0.69 190 47 50 3 432.98 2.69 191 47 51 4 419.16 0.69 192 48 51 3 422.09 1.82 193 48 52 4 412.20 2.79 194 48 53 5 412.17 2.79 195 48 54 6 385.14 2.56 196 48 85 37 251.16 0.26 197 49 52 3 428.20 0.72 198 49 53 4 402.73 3.50 199 49 54 5 361.57 4.96 200 49 55 6 349.14 0.59 201 50 95 45 136.28 0.57 202 51 94 43 136.33 0.56 203 51 95 44 136.28 0.56 204 51 98 47 136.23 0.56 205 52 91 39 145.76 4.75 206 52 92 40 136.53 0.51 207 52 93 41 136.35 0.56 208 52 101 49 135.56 0.74 209 53 90 37 159.50 2.06 210 53 91 38 145.81 4.76 211 54 87 33 247.85 1.49 212 54 89 35 174.67 1.85 213 54 90 36 150.53 2.43 214 54 91 37 145.77 4.75 215 54 92 38 137.08 0.42 216 54 103 49 135.58 0.73 217 55 88 33 184.16 0.03 218 55 89 34 171.26 1.52 219 56 86 30 251.08 0.31 220 56 88 32 192.18 3.01 221 57 85 28 251.25 0.25 222 57 86 29 251.19 0.26 223 57 88 31 246.55 0.01 224 58 83 25 251.41 0.23 225 58 84 26 251.31 0.25 226 58 85 27 251.22 0.27 227 59 84 25 251.41 0.23 228 59 85 26 251.31 0.25 229 59 86 27 251.30 0.25 230 59 132 73 19.80 0.17 231 60 83 23 251.60 0.27 232 60 84 24 251.46 0.21 233 60 128 68 37.53 0.30 234 60 132 72 22.35 1.36 235 61 81 20 251.85 0.25 236 61 82 21 251.72 0.29 237 61 83 22 251.60 0.27 238 61 128 67 37.53 0.30 239 62 82 20 251.72 0.29 240 62 83 21 251.66 0.27 241 62 84 22 251.65 0.27 242 62 121 59 53.74 0.10 243 62 124 62 45.33 0.43 244 62 125 63 45.30 0.42 245 62 128 66 36.18 0.38 246 63 81 18 251.96 0.28 247 63 82 19 251.80 0.25 248 63 121 58 53.68 0.10 249 63 124 61 45.33 0.43 250 64 79 15 252.43 0.21 251 64 80 16 252.26 0.17 252 64 81 17 251.99 0.27 253 64 121 57 53.65 0.10 254 65 79 14 252.44 0.21 255 65 80 15 252.38 0.21 256 65 82 17 252.26 0.17 257 65 117 52 53.41 0.22 258 65 118 53 53.49 0.20 259 65 121 56 53.45 0.18 260 66 77 11 300.26 2.73 261 66 78 12 252.78 0.14 262 66 79 13 252.47 0.20 263 67 77 10 300.45 2.69 264 67 78 11 274.11 10.33 265 68 75 7 306.78 0.36 266 68 76 8 301.35 3.00 267 68 77 9 300.47 2.69 268 69 75 6 310.44 1.46 269 69 76 7 301.44 2.97 270 69 78 9 301.35 3.01 271 70 73 3 439.30 2.28 272 70 74 4 377.09 3.31 273 70 75 5 332.81 2.10 274 71 74 3 428.12 1.39 275 71 76 5 351.88 11.60 276 82 121 39 53.66 0.10 277 84 125 41 45.30 0.42 278 84 128 44 36.20 0.38 279 84 129 45 36.18 0.38 280 84 132 48 22.12 1.25 281 87 91 4 477.13 1.02 282 87 103 16 135.52 0.71 283 92 101 9 135.71 0.70 284 92 102 10 135.66 0.70 285 92 103 11 135.62 0.71 286 93 101 8 135.74 0.71 287 94 98 4 360.45 1.72 288 94 99 5 343.32 10.28 289 94 100 6 217.41 41.55 290 94 101 7 135.67 0.75 291 95 98 3 433.85 1.18 292 104 108 4 415.53 1.29 293 104 109 5 404.19 0.32 294 104 112 8 360.58 1.28 295 105 108 3 428.41 1.31 296 105 109 4 422.10 1.97 297 106 109 3 428.87 1.08 298 106 110 4 422.44 2.14 299 106 122 16 54.88 0.08 300 106 126 20 53.84 0.10 301 106 129 23 51.01 0.29 302 107 110 3 428.88 1.08 303 107 111 4 422.45 2.13 304 108 111 3 443.41 5.32 305 108 112 4 422.82 1.95 306 109 112 3 435.31 1.27 307 109 113 4 421.02 2.85 308 109 122 13 54.90 0.08 309 110 122 12 167.52 56.22 310 110 126 16 54.56 0.09 311 113 118 5 398.74 2.25 312 113 119 6 363.20 0.12 313 113 122 9 342.13 2.41 314 114 119 5 408.39 2.46 315 115 118 3 434.98 2.78 316 115 119 4 411.03 1.18 317 116 119 3 430.79 2.53 318 116 120 4 413.07 0.16 319 117 120 3 427.57 0.92 320 117 121 4 413.07 0.15 321 118 121 3 420.86 3.06 322 118 122 4 413.03 0.12 323 119 122 3 431.68 2.52 324 119 123 4 414.19 6.40 325 120 123 3 431.68 2.52 326 120 124 4 420.06 3.46 327 121 124 3 431.82 1.42 328 121 125 4 420.05 3.46 329 122 125 3 431.82 1.42 330 122 126 4 416.89 5.03 331 123 126 3 430.56 2.06 332 123 127 4 426.70 0.12 333 124 127 3 430.57 2.06 334 124 128 4 424.19 1.11 335 125 128 3 430.55 2.06 336 125 129 4 430.54 2.07 337 126 129 3 430.55 2.06 338 126 130 4 430.56 2.06 339 127 130 3 433.98 0.81 340 127 131 4 425.75 0.35 341 128 131 3 427.06 0.32 342 128 132 4 425.75 0.33 343 129 132 3 433.39 1.06 344 129 133 4 425.73 0.33