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 5 454.12 0.07 2 2 73 71 31.43 0.01 3 2 76 74 25.87 0.42 4 2 127 125 22.84 0.33 5 2 128 126 22.12 0.04 6 3 6 3 475.94 0.52 7 3 7 4 469.14 2.33 8 4 7 3 471.81 1.01 9 4 8 4 469.14 2.33 10 5 8 3 474.09 4.72 11 5 9 4 474.44 0.34 12 6 9 3 477.72 1.21 13 6 10 4 465.34 4.90 14 6 124 118 46.61 0.20 15 6 127 121 45.94 0.14 16 7 10 3 476.95 1.59 17 7 11 4 469.24 2.94 18 7 73 66 48.75 0.68 19 7 74 67 50.73 0.32 20 8 11 3 474.70 0.21 21 8 12 4 469.22 2.95 22 9 12 3 475.56 0.64 23 9 13 4 469.22 2.95 24 9 121 112 57.54 2.00 25 9 124 115 57.52 2.00 26 10 13 3 486.09 2.59 27 10 14 4 464.19 0.43 28 10 70 60 57.58 2.02 29 10 124 114 57.54 2.00 30 10 125 115 57.51 1.99 31 10 128 118 57.47 1.99 32 11 14 3 477.62 1.65 33 11 15 4 464.17 0.42 34 11 70 59 57.65 2.05 35 11 71 60 57.93 2.19 36 11 73 62 57.76 2.10 37 12 15 3 473.50 0.17 38 12 16 4 471.25 0.96 39 13 16 3 477.82 1.42 40 13 17 4 467.29 1.01 41 13 113 100 82.36 0.25 42 13 121 108 60.41 0.97 43 13 125 112 58.60 1.85 44 14 17 3 474.42 2.54 45 14 18 4 467.31 1.00 46 14 21 7 414.36 3.38 47 14 63 49 71.83 4.72 48 14 66 52 58.63 1.86 49 14 67 53 58.63 1.86 50 14 70 56 58.62 1.85 51 15 18 3 476.32 1.90 52 16 113 97 95.49 1.49 53 16 116 100 93.92 0.71 54 17 20 3 484.95 0.68 55 17 21 4 442.84 0.19 56 17 24 7 438.43 3.17 57 17 109 92 93.34 0.99 58 17 113 96 99.01 0.01 59 18 21 3 493.21 3.39 60 20 23 3 477.96 1.21 61 20 24 4 467.03 0.90 62 21 24 3 465.00 0.12 63 21 25 4 464.99 0.12 64 21 63 42 100.44 0.46 65 22 25 3 468.92 0.05 66 22 26 4 469.57 2.41 67 22 59 37 106.77 0.35 68 22 60 38 103.42 1.02 69 22 63 41 103.45 1.01 70 23 26 3 482.84 4.21 71 23 27 4 466.81 3.79 72 24 27 3 482.82 4.22 73 24 28 4 466.58 0.57 74 24 108 84 122.56 0.34 75 24 109 85 121.52 0.86 76 24 112 88 127.48 0.61 77 25 28 3 473.26 0.56 78 25 29 4 469.91 2.23 79 25 59 34 117.23 0.54 80 25 63 38 116.56 0.84 81 26 29 3 474.60 0.11 82 26 30 4 469.92 2.23 83 26 55 29 127.03 0.93 84 26 56 30 127.08 0.95 85 26 59 33 122.50 3.17 86 27 30 3 467.61 1.05 87 27 31 4 465.35 1.23 88 27 108 81 127.73 0.65 89 27 112 85 128.28 0.64 90 28 31 3 465.72 1.04 91 28 32 4 472.65 2.43 92 28 101 73 127.67 0.67 93 28 104 76 127.69 0.67 94 28 105 77 127.69 0.67 95 28 108 80 127.74 0.65 96 29 32 3 470.97 3.27 97 29 33 4 459.05 0.04 98 29 55 26 127.77 0.67 99 29 58 29 127.77 0.67 100 29 59 30 127.75 0.66 101 29 101 72 127.71 0.66 102 30 33 3 479.88 1.18 103 30 34 4 459.05 0.04 104 30 50 20 128.28 0.66 105 31 34 3 478.25 0.38 106 31 35 4 455.47 1.74 107 31 104 73 128.06 0.73 108 31 107 76 128.25 0.67 109 31 108 77 128.25 0.67 110 32 35 3 472.97 0.17 111 32 36 4 455.45 1.74 112 32 39 7 242.93 30.12 113 32 100 68 128.03 0.74 114 32 101 69 128.03 0.74 115 32 104 72 128.18 0.70 116 33 37 4 394.86 5.91 117 33 39 6 250.90 29.72 118 33 40 7 169.73 6.46 119 33 43 10 164.03 9.30 120 33 48 15 128.34 0.68 121 36 39 3 483.94 3.95 122 36 100 64 128.11 0.73 123 36 103 67 128.44 0.71 124 36 104 68 128.44 0.71 125 37 40 3 480.00 0.09 126 38 41 3 488.05 1.38 127 39 42 3 488.15 1.43 128 39 43 4 494.28 1.80 129 39 97 58 128.07 0.74 130 39 100 61 128.37 0.68 131 40 43 3 494.28 1.80 132 40 48 8 149.46 0.26 133 41 44 3 498.08 0.10 134 42 93 51 127.98 0.70 135 42 94 52 128.22 0.71 136 42 97 55 128.41 0.70 137 43 46 3 478.38 0.77 138 43 48 5 452.62 0.68 139 43 58 15 130.71 0.35 140 45 54 9 175.65 13.20 141 46 54 8 175.63 13.20 142 46 55 9 175.66 13.21 143 46 58 12 152.22 1.52 144 47 52 5 180.72 10.68 145 47 54 7 175.75 13.15 146 47 55 8 178.87 11.60 147 48 52 4 406.35 13.22 148 48 55 7 175.66 13.20 149 49 52 3 467.99 3.12 150 51 56 5 455.45 0.42 151 52 55 3 469.69 2.29 152 52 56 4 468.34 3.52 153 53 56 3 470.25 2.56 154 53 57 4 468.35 3.52 155 54 57 3 471.77 1.82 156 54 58 4 471.78 1.82 157 55 58 3 472.92 2.39 158 55 59 4 472.49 1.47 159 56 59 3 474.35 1.68 160 56 60 4 472.52 1.48 161 57 60 3 483.92 4.22 162 57 61 4 472.52 1.48 163 58 61 3 474.82 0.33 164 58 62 4 472.52 1.49 165 59 62 3 474.84 0.34 166 59 63 4 471.92 1.79 167 60 63 3 471.93 1.79 168 60 64 4 471.93 1.79 169 61 64 3 478.94 1.71 170 61 65 4 474.07 0.72 171 62 65 3 483.15 0.40 172 62 66 4 474.07 0.72 173 62 101 39 141.18 6.27 174 63 66 3 475.68 1.52 175 63 67 4 466.54 4.50 176 64 67 3 470.36 1.14 177 64 68 4 462.81 2.64 178 65 68 3 466.45 0.85 179 65 69 4 462.82 2.65 180 65 83 18 129.81 0.69 181 66 69 3 475.27 3.56 182 66 70 4 461.97 3.08 183 66 105 39 165.74 0.78 184 66 129 63 173.03 8.00 185 66 132 66 148.82 2.48 186 67 70 3 474.18 1.90 187 67 71 4 470.42 1.15 188 68 71 3 475.34 1.32 189 68 72 4 470.42 1.15 190 68 79 11 173.52 7.75 191 69 72 3 475.42 1.35 192 69 73 4 470.31 1.19 193 69 76 7 218.38 30.08 194 69 80 11 166.46 11.29 195 69 128 59 206.84 8.88 196 69 132 63 172.91 8.06 197 70 73 3 470.31 1.19 198 70 128 58 206.83 8.86 199 72 75 3 471.40 0.30 200 72 76 4 428.86 16.59 201 72 79 7 296.25 2.54 202 73 76 3 477.25 2.62 203 75 78 3 479.88 1.34 204 75 79 4 465.38 1.70 205 76 79 3 469.97 0.59 206 76 80 4 465.36 1.71 207 76 128 52 271.48 0.90 208 76 131 55 268.88 0.88 209 76 132 56 265.30 0.42 210 76 135 59 265.30 0.42 211 77 80 3 472.18 0.32 212 77 81 4 462.07 0.07 213 77 135 58 265.30 0.42 214 78 81 3 472.38 0.18 215 80 83 3 481.44 0.28 216 80 84 4 469.53 6.25 217 80 132 52 273.86 0.29 218 80 135 55 273.78 0.25 219 80 136 56 273.78 0.25 220 81 84 3 478.93 1.54 221 81 85 4 469.54 6.25 222 81 139 58 273.81 0.23 223 82 85 3 480.16 0.94 224 82 86 4 478.93 1.55 225 83 86 3 478.93 1.55 226 83 87 4 469.51 6.25 227 83 136 53 274.51 0.01 228 84 88 4 455.98 3.06 229 84 135 51 274.54 0.04 230 84 136 52 274.50 0.02 231 84 138 54 274.49 0.03 232 84 139 55 274.43 0.03 233 85 88 3 470.24 2.79 234 85 89 4 455.98 3.06 235 85 139 54 274.44 0.07 236 86 89 3 483.51 0.73 237 86 90 4 415.90 9.09 238 86 91 5 415.89 9.09 239 87 91 4 383.75 6.13 240 87 92 5 381.13 7.38 241 87 93 6 381.11 7.38 242 87 98 11 281.64 1.11 243 87 136 49 274.61 0.04 244 87 140 53 274.47 0.03 245 88 92 4 381.19 7.40 246 88 139 51 274.50 0.04 247 88 140 52 274.36 0.08 248 89 92 3 490.06 1.74 249 92 140 48 274.58 0.04 250 93 97 4 480.31 0.93 251 93 98 5 471.75 2.24 252 93 140 47 274.62 0.03 253 94 97 3 495.75 2.32 254 95 98 3 487.62 0.51 255 95 140 45 274.68 0.04 256 96 99 3 492.31 5.33 257 96 100 4 484.05 2.08 258 97 100 3 484.06 2.08 259 97 101 4 476.76 0.28 260 98 101 3 485.39 1.42 261 98 102 4 473.30 1.35 262 98 133 35 275.19 0.01 263 98 136 38 275.20 0.02 264 98 137 39 275.19 0.02 265 98 140 42 275.18 0.03 266 99 102 3 473.95 1.68 267 99 103 4 473.30 1.35 268 100 103 3 473.30 1.35 269 100 104 4 473.30 1.35 270 101 104 3 473.29 1.35 271 101 105 4 464.30 1.61 272 102 105 3 474.92 0.65 273 102 106 4 466.00 0.78 274 102 129 27 275.55 0.04 275 102 133 31 275.28 0.01 276 103 106 3 471.25 0.07 277 103 107 4 466.07 0.81 278 104 107 3 477.20 3.05 279 104 108 4 465.10 1.27 280 105 108 3 472.39 2.38 281 105 109 4 465.10 1.27 282 105 129 24 276.34 0.30 283 106 109 3 472.57 2.46 284 106 110 4 465.09 1.27 285 106 117 11 277.12 0.41 286 106 122 16 276.60 0.40 287 106 125 19 276.37 0.29 288 106 126 20 276.34 0.29 289 106 129 23 276.31 0.28 290 107 110 3 472.23 2.32 291 107 111 4 464.12 1.73 292 108 111 3 474.69 3.66 293 108 112 4 464.01 1.68 294 109 112 3 479.81 1.83 295 109 113 4 452.66 0.18 296 109 125 16 276.92 0.33 297 110 117 7 277.12 0.40 298 113 116 3 477.86 0.55 299 113 117 4 472.25 2.25 300 114 117 3 478.08 0.66 301 115 118 3 526.28 0.91 302 116 121 5 463.89 3.71 303 117 121 4 465.74 2.79 304 117 122 5 452.72 1.88 305 117 125 8 423.99 0.69 306 118 121 3 468.31 1.51 307 118 122 4 465.25 3.04 308 119 122 3 468.31 1.51 309 119 123 4 465.73 2.80 310 120 123 3 481.19 1.02 311 120 124 4 465.74 2.79 312 121 124 3 474.73 1.70 313 121 125 4 466.05 2.62 314 122 125 3 474.84 1.79 315 122 126 4 470.09 4.04 316 123 126 3 472.78 2.81 317 123 127 4 463.05 1.11 318 124 127 3 472.66 2.75 319 124 128 4 465.84 0.29 320 125 128 3 473.78 2.83 321 125 129 4 467.89 0.73 322 126 129 3 482.05 1.31 323 126 130 4 467.89 0.73 324 127 130 3 481.29 0.93 325 127 131 4 467.28 0.42 326 128 131 3 478.31 2.42 327 128 132 4 465.79 2.00 328 129 132 3 478.04 4.71 329 129 133 4 464.94 1.57 330 130 133 3 476.79 3.50 331 130 134 4 463.38 1.13 332 131 134 3 473.21 1.72 333 131 135 4 464.15 1.51 334 132 135 3 480.23 2.21 335 132 136 4 464.16 1.51 336 133 136 3 476.43 4.11 337 133 137 4 462.55 1.56 338 134 137 3 475.47 1.36 339 134 138 4 460.50 0.54 340 135 138 3 474.62 1.79 341 136 140 4 489.82 1.20 342 137 140 3 485.50 0.97