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 5 452.62 2.53 2 2 74 72 26.66 0.30 3 2 77 75 23.75 1.15 4 2 128 126 24.86 0.35 5 2 129 127 24.70 0.28 6 3 6 3 475.50 0.35 7 3 7 4 475.50 0.35 8 4 7 3 483.11 1.85 9 4 8 4 475.50 0.35 10 5 8 3 486.86 0.03 11 5 9 4 469.50 3.35 12 6 9 3 480.85 3.03 13 6 10 4 473.15 1.51 14 6 125 119 45.70 0.46 15 6 128 122 45.71 0.46 16 7 10 3 485.93 0.55 17 7 11 4 469.76 3.20 18 7 74 67 45.76 0.38 19 7 75 68 50.32 1.90 20 8 11 3 486.16 0.42 21 8 12 4 464.76 0.69 22 9 12 3 481.44 2.79 23 9 13 4 473.77 1.04 24 9 125 116 59.09 0.47 25 10 13 3 483.12 1.68 26 10 14 4 468.36 2.48 27 10 71 61 59.12 0.46 28 10 74 64 59.14 0.47 29 10 125 115 59.13 0.47 30 10 126 116 59.12 0.46 31 10 129 119 59.11 0.46 32 11 14 3 477.94 0.91 33 11 15 4 468.57 2.38 34 11 71 60 59.13 0.46 35 11 74 63 59.11 0.44 36 12 15 3 480.64 2.26 37 12 16 4 468.28 0.82 38 13 16 3 480.63 2.26 39 13 17 4 467.07 1.42 40 13 117 104 70.30 0.10 41 13 118 105 67.62 1.16 42 13 122 109 62.32 0.84 43 13 126 113 59.29 0.51 44 14 17 3 481.80 0.45 45 14 18 4 455.71 1.42 46 14 21 7 379.81 6.38 47 14 64 50 62.91 1.09 48 14 67 53 59.33 0.53 49 14 68 54 59.33 0.53 50 14 71 57 59.28 0.51 51 16 117 101 80.00 4.69 52 17 20 3 487.51 0.20 53 17 24 7 394.12 14.82 54 17 110 93 90.55 0.53 55 17 114 97 95.28 1.24 56 18 21 3 467.42 1.62 57 20 23 3 481.03 2.50 58 20 24 4 464.30 3.04 59 20 114 94 117.14 0.77 60 21 24 3 470.71 3.16 61 21 25 4 476.88 1.14 62 21 64 43 168.12 5.73 63 22 25 3 482.94 2.42 64 22 26 4 476.92 1.14 65 22 61 39 173.88 2.88 66 23 26 3 489.23 0.72 67 23 27 4 476.94 1.15 68 23 113 90 148.09 2.47 69 24 27 3 482.29 1.53 70 24 28 4 476.93 1.15 71 24 64 40 173.84 2.88 72 24 109 85 145.39 3.84 73 24 110 86 145.38 3.84 74 24 113 89 149.75 1.65 75 24 114 90 151.16 0.95 76 25 28 3 482.83 1.26 77 25 29 4 476.91 1.16 78 25 60 35 175.08 3.46 79 25 64 39 173.84 2.88 80 26 29 3 482.29 1.54 81 26 30 4 474.74 0.72 82 26 52 26 188.03 1.88 83 26 56 30 176.89 3.65 84 26 57 31 176.72 3.66 85 26 60 34 175.92 3.85 86 27 30 3 484.06 0.11 87 27 31 4 477.76 0.43 88 27 109 82 151.52 0.79 89 27 113 86 151.44 0.80 90 28 31 3 477.78 0.43 91 28 32 4 475.91 1.36 92 28 102 74 152.46 0.61 93 28 105 77 152.22 0.69 94 28 106 78 152.22 0.68 95 28 109 81 151.53 0.78 96 29 32 3 477.32 0.66 97 29 33 4 475.92 1.36 98 29 56 27 188.00 1.87 99 29 59 30 176.96 3.65 100 29 60 31 176.83 3.69 101 29 63 34 176.83 3.71 102 29 102 73 152.49 0.60 103 30 33 3 487.89 2.17 104 30 34 4 474.14 2.25 105 30 51 21 188.69 2.02 106 30 52 22 188.69 2.02 107 30 56 26 188.12 1.82 108 31 34 3 481.38 1.15 109 31 35 4 464.93 0.58 110 31 105 74 152.24 0.68 111 31 108 77 152.22 0.67 112 31 109 78 152.15 0.69 113 31 112 81 151.95 0.59 114 32 36 4 441.03 3.70 115 32 39 7 272.00 1.21 116 32 43 11 270.27 1.08 117 32 101 69 152.55 0.62 118 32 102 70 152.51 0.60 119 32 105 73 152.28 0.68 120 33 37 4 374.34 2.62 121 33 39 6 300.06 1.07 122 33 40 7 270.22 1.10 123 33 49 16 199.72 1.89 124 33 50 17 198.81 2.33 125 33 51 18 198.77 2.33 126 33 56 23 198.00 2.06 127 34 37 3 488.61 2.06 128 34 51 17 198.78 2.33 129 36 39 3 490.30 0.00 130 36 101 65 152.72 0.64 131 36 104 68 152.74 0.64 132 36 105 69 152.72 0.64 133 37 40 3 490.52 0.12 134 38 41 3 499.61 0.77 135 38 101 63 153.17 0.63 136 39 42 3 505.32 1.37 137 39 43 4 495.68 1.97 138 39 98 59 153.10 0.65 139 39 101 62 153.09 0.65 140 40 43 3 495.68 1.97 141 40 44 4 487.79 0.89 142 40 49 9 214.30 4.61 143 41 44 3 506.42 0.39 144 42 45 3 568.07 2.40 145 42 93 51 153.65 0.55 146 42 94 52 153.60 0.58 147 42 95 53 153.66 0.55 148 42 98 56 153.32 0.58 149 43 46 3 491.62 3.31 150 43 49 6 243.33 9.65 151 43 59 16 205.48 1.03 152 46 55 9 223.29 2.19 153 46 56 10 237.08 2.39 154 46 59 13 223.28 2.19 155 47 55 8 241.00 0.42 156 48 53 5 406.80 10.23 157 50 53 3 492.06 5.41 158 50 56 6 389.91 6.59 159 52 56 4 458.22 1.34 160 53 56 3 465.84 2.77 161 53 57 4 465.87 2.79 162 54 57 3 466.30 3.00 163 54 58 4 483.76 0.17 164 55 58 3 483.77 0.17 165 55 59 4 468.73 1.37 166 56 59 3 483.88 0.23 167 56 60 4 471.11 0.18 168 57 60 3 485.60 0.59 169 57 61 4 481.84 1.13 170 58 61 3 482.01 1.20 171 58 62 4 479.87 0.14 172 59 62 3 483.16 0.85 173 59 63 4 474.63 2.48 174 60 63 3 483.17 0.85 175 60 64 4 474.63 2.48 176 61 64 3 487.62 0.53 177 61 65 4 469.20 0.26 178 62 65 3 475.59 2.93 179 62 66 4 472.07 1.18 180 63 66 3 482.94 4.26 181 63 67 4 469.25 0.29 182 63 102 39 152.64 0.53 183 64 67 3 469.25 0.30 184 64 68 4 471.47 0.82 185 64 106 42 152.57 0.51 186 65 68 3 476.75 1.11 187 65 69 4 471.48 0.82 188 66 69 3 476.06 1.47 189 66 70 4 471.48 0.82 190 66 84 18 153.81 0.46 191 67 70 3 472.65 0.24 192 67 71 4 471.46 0.83 193 67 106 39 152.60 0.51 194 67 129 62 149.81 0.52 195 67 130 63 149.43 0.58 196 67 133 66 147.19 0.09 197 68 71 3 478.02 1.66 198 68 72 4 473.39 3.97 199 69 72 3 478.43 1.45 200 69 73 4 473.39 3.97 201 69 80 11 248.14 7.46 202 69 81 12 238.83 12.11 203 70 73 3 473.39 3.97 204 70 74 4 448.68 1.47 205 70 77 7 315.38 18.75 206 70 81 11 220.78 3.16 207 70 129 59 150.01 0.58 208 70 133 63 148.10 0.01 209 71 74 3 466.66 3.91 210 71 129 58 150.08 0.58 211 73 76 3 493.86 3.48 212 73 77 4 433.61 11.40 213 73 80 7 272.73 4.42 214 74 77 3 483.55 1.67 215 74 129 55 150.10 0.57 216 76 79 3 483.67 0.55 217 76 80 4 470.30 4.91 218 77 80 3 477.31 1.41 219 77 81 4 469.75 4.64 220 77 129 52 150.19 0.61 221 77 132 55 149.51 0.60 222 77 133 56 149.30 0.49 223 77 136 59 147.22 0.09 224 78 81 3 486.12 1.71 225 78 82 4 460.12 0.18 226 78 136 58 147.21 0.10 227 78 139 61 146.17 0.30 228 79 82 3 487.59 1.73 229 81 84 3 483.79 1.61 230 81 85 4 466.49 2.58 231 81 133 52 149.03 0.42 232 81 136 55 146.52 0.38 233 81 137 56 146.29 0.27 234 82 85 3 474.40 0.30 235 82 86 4 466.54 2.60 236 82 139 57 145.50 0.46 237 82 140 58 145.09 0.41 238 83 86 3 477.86 1.38 239 83 87 4 476.18 2.22 240 84 87 3 477.86 1.38 241 84 88 4 477.79 1.42 242 84 137 53 145.53 0.45 243 85 88 3 480.86 0.12 244 85 89 4 477.79 1.42 245 85 136 51 146.27 0.26 246 85 137 52 145.34 0.53 247 85 139 54 144.97 0.69 248 85 140 55 142.50 0.25 249 86 89 3 480.86 0.12 250 86 90 4 477.80 1.41 251 86 140 54 142.85 0.07 252 87 90 3 485.63 0.82 253 87 91 4 467.63 6.48 254 87 92 5 456.55 0.94 255 88 92 4 386.56 16.11 256 88 93 5 365.19 5.44 257 88 94 6 318.40 7.75 258 88 99 11 292.94 4.96 259 88 141 53 137.88 0.88 260 89 93 4 361.48 13.78 261 89 140 51 141.00 0.49 262 89 141 52 135.97 0.06 263 90 93 3 490.40 3.08 264 90 140 50 142.84 0.06 265 94 98 4 477.81 0.69 266 94 99 5 471.42 0.13 267 94 141 47 134.51 0.47 268 95 98 3 496.88 2.69 269 96 99 3 488.04 1.74 270 96 141 45 131.62 0.96 271 97 100 3 482.62 0.97 272 97 101 4 477.52 2.92 273 98 101 3 481.27 1.04 274 98 102 4 473.59 0.96 275 99 102 3 476.29 0.11 276 99 103 4 470.18 2.66 277 99 134 35 146.14 0.32 278 99 137 38 144.17 0.29 279 99 141 42 134.38 0.32 280 100 103 3 477.33 3.62 281 100 104 4 468.19 1.61 282 101 104 3 483.56 0.46 283 101 105 4 469.30 2.17 284 102 105 3 475.54 0.95 285 102 106 4 469.28 2.19 286 103 106 3 481.47 2.02 287 103 107 4 468.17 1.61 288 103 130 27 148.56 0.71 289 103 134 31 146.89 0.06 290 104 107 3 477.54 0.86 291 104 108 4 462.57 4.46 292 105 108 3 468.80 1.35 293 105 109 4 462.44 4.52 294 106 109 3 470.20 0.66 295 106 110 4 462.45 4.51 296 106 130 24 148.71 0.64 297 107 110 3 470.20 0.66 298 107 111 4 465.09 3.20 299 107 118 11 251.20 2.43 300 107 123 16 161.35 4.99 301 107 126 19 149.97 0.71 302 107 127 20 149.49 0.74 303 107 130 23 148.97 0.65 304 108 111 3 476.26 1.85 305 108 112 4 467.19 2.08 306 109 112 3 473.75 1.14 307 109 113 4 467.17 2.07 308 110 113 3 484.13 1.15 309 110 114 4 459.89 0.58 310 110 118 8 276.80 9.46 311 110 126 16 200.31 4.08 312 111 115 4 406.53 4.58 313 111 118 7 255.97 4.79 314 112 115 3 499.22 0.16 315 114 117 3 477.13 1.43 316 114 118 4 463.38 0.29 317 115 118 3 474.63 0.04 318 116 119 3 511.61 0.96 319 117 122 5 457.53 2.35 320 118 122 4 457.54 2.35 321 118 123 5 453.60 0.39 322 118 126 8 444.86 4.72 323 119 122 3 464.10 0.91 324 119 123 4 462.76 0.20 325 120 123 3 474.73 0.32 326 120 124 4 462.77 0.20 327 121 124 3 482.61 3.19 328 121 125 4 464.04 0.35 329 122 125 3 478.89 1.18 330 122 126 4 467.18 2.41 331 123 126 3 475.60 0.06 332 123 127 4 461.61 0.58 333 124 127 3 470.34 2.52 334 124 128 4 468.67 1.69 335 125 128 3 475.06 0.21 336 125 129 4 466.08 1.63 337 126 129 3 466.57 1.38 338 126 130 4 465.18 1.18 339 127 130 3 476.19 0.67 340 127 131 4 465.50 1.02 341 128 131 3 473.36 0.74 342 128 132 4 465.50 1.02 343 129 132 3 473.62 0.61 344 129 133 4 465.50 1.02 345 130 133 3 473.44 0.53 346 130 134 4 471.61 0.39 347 131 134 3 476.47 1.22 348 131 135 4 471.64 0.37 349 132 135 3 472.46 0.78 350 132 136 4 466.41 2.25 351 133 136 3 468.87 3.40 352 133 137 4 466.47 2.21 353 134 137 3 479.50 4.29 354 134 138 4 466.78 2.06 355 135 138 3 467.29 1.80 356 135 139 4 461.36 4.76 357 136 139 3 471.91 4.74 358 137 141 4 473.56 0.65 359 138 141 3 469.88 2.49