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 5 467.25 1.86 2 2 73 71 28.62 0.57 3 2 76 74 28.45 0.48 4 2 127 125 26.96 0.27 5 2 128 126 25.34 0.54 6 2 131 129 25.34 0.54 7 3 6 3 467.95 1.56 8 3 7 4 467.34 1.88 9 4 7 3 475.22 2.06 10 4 8 4 467.86 1.61 11 5 8 3 471.80 3.45 12 5 9 4 467.91 1.57 13 6 9 3 472.60 2.21 14 6 10 4 469.60 0.70 15 6 124 118 46.36 0.59 16 6 127 121 46.38 0.60 17 7 10 3 488.14 2.04 18 7 11 4 472.63 2.23 19 7 73 66 47.27 0.40 20 7 74 67 47.72 0.61 21 8 11 3 477.52 0.21 22 8 12 4 472.30 2.40 23 9 12 3 476.35 0.38 24 9 13 4 471.42 2.83 25 9 120 111 62.95 0.69 26 9 121 112 62.82 0.65 27 9 124 115 62.60 0.55 28 10 13 3 475.38 2.83 29 10 14 4 471.10 2.99 30 10 70 60 62.54 0.58 31 10 124 114 62.81 0.65 32 10 125 115 62.71 0.60 33 10 128 118 62.69 0.60 34 11 14 3 479.89 2.15 35 11 15 4 465.08 1.05 36 11 70 59 62.65 0.63 37 11 73 62 62.70 0.61 38 12 15 3 479.61 1.60 39 12 16 4 474.97 6.00 40 13 16 3 481.69 2.65 41 13 17 4 475.02 5.98 42 13 113 100 69.85 0.10 43 13 121 108 63.09 0.73 44 13 125 112 62.92 0.69 45 14 17 3 476.47 5.25 46 14 18 4 471.43 2.91 47 14 21 7 416.27 16.07 48 14 66 52 62.81 0.64 49 14 67 53 62.77 0.62 50 14 70 56 62.77 0.62 51 14 109 95 69.84 0.10 52 15 18 3 476.30 5.34 53 16 116 100 74.26 2.15 54 17 20 3 493.97 2.08 55 17 21 4 453.39 2.48 56 17 24 7 398.15 14.28 57 17 109 92 75.70 1.22 58 17 113 96 86.47 4.94 59 18 21 3 495.07 1.53 60 20 23 3 476.83 4.37 61 20 24 4 473.11 2.50 62 21 24 3 474.39 1.86 63 21 25 4 471.62 3.25 64 21 63 42 86.89 4.75 65 22 25 3 479.50 0.66 66 22 26 4 473.19 2.46 67 22 60 38 92.59 2.01 68 22 63 41 92.59 2.01 69 23 26 3 479.17 2.49 70 23 27 4 473.19 2.45 71 24 27 3 480.12 0.97 72 24 28 4 474.09 0.53 73 24 108 84 128.85 0.53 74 24 109 85 129.17 1.83 75 24 112 88 132.32 0.58 76 24 113 89 132.32 0.58 77 25 28 3 482.00 1.92 78 25 29 4 474.10 0.53 79 25 59 34 125.53 1.78 80 25 105 80 126.23 1.81 81 26 29 3 480.05 2.45 82 26 30 4 474.09 0.53 83 26 55 29 128.74 0.47 84 26 56 30 128.75 0.48 85 26 59 33 125.92 1.84 86 27 30 3 477.54 1.20 87 27 31 4 473.95 0.46 88 27 108 81 132.89 0.53 89 27 112 85 133.35 0.68 90 28 31 3 476.53 0.04 91 28 32 4 471.26 1.80 92 28 101 73 132.72 0.52 93 28 104 76 132.78 0.49 94 28 105 77 132.71 0.51 95 28 108 80 133.15 0.64 96 29 32 3 481.55 2.55 97 29 33 4 471.41 1.88 98 29 43 14 133.57 0.94 99 29 55 26 133.25 0.79 100 29 58 29 133.22 0.80 101 29 62 33 132.71 0.56 102 29 101 72 132.85 0.52 103 30 33 3 474.14 3.25 104 30 34 4 474.13 3.25 105 30 50 20 133.69 0.80 106 31 34 3 484.90 5.44 107 31 35 4 471.10 2.00 108 31 104 73 133.56 0.71 109 31 107 76 133.68 0.73 110 31 108 77 133.62 0.71 111 31 111 80 133.84 0.73 112 32 35 3 476.52 2.06 113 32 36 4 469.88 2.60 114 32 39 7 284.35 1.13 115 32 100 68 133.55 0.72 116 32 101 69 133.56 0.72 117 32 104 72 133.59 0.71 118 33 37 4 435.30 19.87 119 33 39 6 293.92 5.90 120 33 40 7 266.50 3.22 121 33 43 10 202.76 35.08 122 33 48 15 133.90 0.73 123 33 55 22 133.85 0.74 124 36 39 3 491.89 3.83 125 36 100 64 133.60 0.74 126 36 103 67 133.81 0.76 127 36 104 68 133.81 0.76 128 37 40 3 486.71 0.60 129 38 41 3 486.44 1.81 130 39 42 3 501.22 0.57 131 39 97 58 133.55 0.71 132 39 100 61 133.74 0.75 133 40 43 3 480.31 0.65 134 40 48 8 134.62 0.45 135 41 44 3 493.28 2.33 136 42 93 51 133.45 0.82 137 42 94 52 133.69 0.73 138 42 97 55 133.80 0.77 139 43 46 3 487.19 5.46 140 43 48 5 439.99 3.64 141 43 58 15 134.43 0.58 142 46 54 8 135.31 0.70 143 46 55 9 202.88 33.09 144 46 58 12 202.80 33.05 145 47 52 5 284.45 7.15 146 47 54 7 202.90 33.09 147 47 55 8 202.91 33.10 148 48 55 7 202.91 33.10 149 49 52 3 482.86 0.04 150 51 56 5 461.35 2.25 151 52 55 3 474.19 1.31 152 52 56 4 469.00 1.28 153 53 56 3 471.48 0.04 154 53 57 4 464.21 3.68 155 54 57 3 482.95 5.70 156 54 58 4 482.95 5.69 157 55 58 3 482.95 5.69 158 55 59 4 467.44 2.06 159 56 59 3 482.95 5.69 160 56 60 4 469.01 1.22 161 57 60 3 469.09 1.25 162 57 61 4 467.70 0.56 163 58 61 3 474.05 0.64 164 58 62 4 473.99 3.71 165 59 62 3 481.56 0.01 166 59 63 4 467.53 1.16 167 60 63 3 482.80 0.60 168 60 64 4 478.18 1.61 169 61 64 3 484.94 0.89 170 61 65 4 478.26 1.66 171 62 65 3 492.83 3.05 172 62 66 4 484.07 1.33 173 62 101 39 146.75 0.65 174 63 66 3 486.94 6.00 175 63 67 4 471.56 0.84 176 64 67 3 486.09 6.42 177 64 68 4 471.23 1.01 178 65 68 3 474.59 0.86 179 65 69 4 471.23 1.01 180 65 80 15 163.27 9.87 181 65 83 18 143.81 0.44 182 66 69 3 471.24 1.01 183 66 70 4 469.31 1.97 184 66 105 39 192.28 3.65 185 66 129 63 174.37 4.44 186 66 132 66 164.31 9.38 187 67 70 3 471.24 1.00 188 67 71 4 469.28 1.98 189 68 71 3 466.16 0.11 190 68 72 4 458.10 3.01 191 68 79 11 168.90 7.21 192 69 72 3 467.23 6.44 193 69 73 4 451.26 0.34 194 69 76 7 276.36 3.45 195 69 80 11 191.33 4.04 196 69 128 59 220.00 0.48 197 69 132 63 191.35 4.01 198 70 73 3 459.06 2.32 199 70 128 58 220.05 0.53 200 72 75 3 472.93 4.62 201 72 76 4 442.04 6.78 202 72 79 7 308.49 6.46 203 73 76 3 485.22 1.53 204 73 128 55 251.01 0.10 205 75 78 3 487.76 0.27 206 75 79 4 462.82 0.33 207 76 79 3 477.09 4.32 208 76 80 4 452.01 0.69 209 76 128 52 251.78 0.27 210 76 131 55 251.40 0.09 211 76 132 56 251.28 0.06 212 76 135 59 251.19 0.06 213 77 80 3 481.66 2.03 214 77 81 4 450.81 0.12 215 77 135 58 251.22 0.06 216 78 81 3 475.44 7.70 217 80 83 3 472.95 0.25 218 80 84 4 460.62 1.78 219 80 132 52 251.98 0.26 220 80 135 55 251.71 0.24 221 80 136 56 251.70 0.25 222 81 84 3 474.54 2.71 223 81 85 4 468.77 0.18 224 81 139 58 251.67 0.26 225 82 85 3 476.75 1.65 226 82 86 4 468.78 0.17 227 83 86 3 471.23 0.64 228 83 87 4 468.78 0.17 229 83 136 53 251.91 0.29 230 84 87 3 483.23 1.06 231 84 88 4 462.16 0.85 232 84 135 51 252.02 0.26 233 84 136 52 251.90 0.29 234 84 139 55 251.71 0.27 235 85 88 3 470.79 0.85 236 85 89 4 457.90 2.04 237 85 139 54 251.78 0.24 238 86 89 3 481.57 1.93 239 86 90 4 441.70 6.02 240 86 91 5 423.17 15.26 241 87 91 4 392.19 8.45 242 87 92 5 359.78 2.47 243 87 93 6 332.20 16.25 244 87 98 11 282.11 0.86 245 87 140 53 251.93 0.27 246 88 92 4 418.25 4.58 247 88 139 51 251.99 0.28 248 88 140 52 251.72 0.29 249 89 92 3 493.18 1.22 250 89 139 50 252.03 0.27 251 93 97 4 474.45 0.66 252 93 98 5 474.42 0.66 253 93 140 47 252.09 0.26 254 94 97 3 494.17 0.35 255 95 98 3 492.01 1.79 256 95 137 42 252.61 0.44 257 95 140 45 252.59 0.45 258 96 99 3 493.05 2.33 259 96 100 4 478.20 1.81 260 97 100 3 479.05 4.67 261 97 101 4 469.48 5.12 262 98 101 3 487.09 4.42 263 98 102 4 464.79 2.49 264 98 133 35 253.02 0.33 265 98 136 38 253.04 0.34 266 98 137 39 253.02 0.34 267 98 140 42 253.00 0.33 268 99 102 3 481.36 1.57 269 99 103 4 464.93 2.46 270 100 103 3 481.37 1.57 271 100 104 4 465.71 2.17 272 101 104 3 473.23 1.69 273 101 105 4 464.97 2.48 274 102 105 3 475.69 2.83 275 102 106 4 471.63 0.80 276 102 129 27 253.28 0.33 277 103 106 3 472.63 1.28 278 103 107 4 472.05 0.98 279 104 107 3 475.25 0.61 280 104 108 4 471.64 0.81 281 105 108 3 474.88 0.80 282 105 109 4 471.68 0.79 283 105 129 24 254.24 0.21 284 106 109 3 476.22 2.05 285 106 110 4 476.22 2.06 286 106 117 11 255.88 0.22 287 106 122 16 254.91 0.35 288 106 125 19 254.67 0.30 289 106 126 20 254.61 0.32 290 106 129 23 254.58 0.30 291 107 110 3 476.22 2.06 292 107 111 4 472.16 1.03 293 108 111 3 475.33 2.50 294 108 112 4 472.72 1.31 295 109 112 3 475.30 2.52 296 109 113 4 468.50 2.83 297 109 117 8 256.11 0.12 298 109 125 16 255.39 0.32 299 110 113 3 474.40 2.07 300 110 117 7 256.09 0.12 301 113 116 3 478.41 0.33 302 113 117 4 438.12 4.40 303 114 117 3 489.46 0.82 304 115 118 3 515.33 1.60 305 116 121 5 430.19 7.11 306 117 122 5 419.38 1.72 307 117 125 8 409.99 2.59 308 118 121 3 470.03 1.39 309 118 122 4 460.16 3.54 310 119 122 3 470.06 1.41 311 119 123 4 472.40 0.82 312 120 123 3 476.54 1.24 313 120 124 4 472.43 0.82 314 121 124 3 472.88 0.87 315 121 125 4 472.44 0.80 316 122 125 3 486.67 1.27 317 122 126 4 474.94 2.05 318 123 126 3 481.00 0.36 319 123 127 4 480.38 0.68 320 124 127 3 477.88 1.93 321 124 128 4 471.85 4.94 322 125 128 3 469.88 1.81 323 125 129 4 469.50 1.62 324 126 129 3 481.15 1.38 325 126 130 4 470.37 2.06 326 127 130 3 474.63 1.88 327 127 131 4 470.93 1.78 328 128 131 3 482.30 6.33 329 128 132 4 470.95 1.77 330 129 132 3 470.88 1.71 331 129 133 4 470.54 1.54 332 130 133 3 481.22 6.87 333 130 134 4 464.92 1.29 334 131 134 3 473.53 0.28 335 131 135 4 464.93 1.28 336 132 135 3 484.64 2.29 337 132 136 4 469.87 1.19 338 133 136 3 472.75 1.02 339 133 137 4 471.33 0.48 340 134 137 3 486.29 1.43 341 134 138 4 471.65 0.64 342 135 138 3 477.23 1.39 343 136 140 4 496.19 0.88 344 137 140 3 485.64 2.51