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 5 452.95 10.11 2 2 73 71 29.41 0.77 3 2 76 74 25.83 0.65 4 2 127 125 23.18 0.45 5 2 128 126 23.09 0.41 6 2 131 129 23.09 0.41 7 3 6 3 462.30 5.44 8 3 7 4 470.36 1.56 9 4 7 3 477.36 5.00 10 4 8 4 470.30 1.60 11 5 8 3 470.44 1.54 12 5 9 4 470.63 1.43 13 6 9 3 472.39 1.57 14 6 10 4 471.66 1.94 15 6 124 118 46.44 0.07 16 6 127 121 47.30 0.36 17 7 10 3 476.73 0.59 18 7 11 4 470.63 1.43 19 7 73 66 47.61 0.51 20 7 74 67 48.95 1.17 21 8 11 3 477.92 1.65 22 8 12 4 470.57 1.41 23 9 12 3 476.57 1.81 24 9 13 4 470.94 1.59 25 9 120 111 64.21 0.21 26 9 121 112 64.19 0.21 27 9 124 115 64.00 0.27 28 10 13 3 475.33 2.43 29 10 14 4 466.70 3.01 30 10 70 60 64.19 0.21 31 10 124 114 64.20 0.21 32 10 125 115 64.19 0.21 33 10 128 118 64.08 0.18 34 11 14 3 478.99 0.60 35 11 15 4 469.55 1.58 36 11 70 59 64.16 0.23 37 11 73 62 64.17 0.23 38 12 15 3 470.26 1.94 39 12 16 4 477.09 1.23 40 13 16 3 478.36 0.59 41 13 17 4 477.09 1.23 42 13 113 100 76.44 2.31 43 13 121 108 67.34 0.24 44 13 125 112 65.43 0.69 45 14 17 3 470.53 1.51 46 14 18 4 467.99 0.24 47 14 21 7 401.54 5.15 48 14 63 49 69.95 0.74 49 14 66 52 65.45 0.69 50 14 67 53 65.44 0.69 51 14 70 56 65.43 0.69 52 14 109 95 76.35 2.27 53 15 18 3 473.52 3.00 54 16 113 97 88.69 0.42 55 16 116 100 84.54 1.61 56 17 20 3 483.26 1.26 57 17 21 4 459.61 0.26 58 17 24 7 407.08 5.19 59 17 109 92 84.39 1.72 60 17 113 96 89.81 0.14 61 18 21 3 502.83 1.44 62 20 23 3 477.20 1.22 63 20 24 4 461.36 0.97 64 21 24 3 479.38 2.77 65 21 25 4 465.47 3.02 66 21 63 42 95.45 1.10 67 22 25 3 476.81 1.47 68 22 26 4 476.81 1.47 69 22 60 38 102.19 2.25 70 22 63 41 96.70 0.49 71 23 26 3 484.34 0.30 72 23 27 4 479.41 2.77 73 24 27 3 477.29 3.83 74 24 28 4 473.04 3.36 75 24 108 84 121.52 1.56 76 24 109 85 123.63 0.56 77 24 112 88 128.49 0.23 78 25 28 3 481.54 1.70 79 25 29 4 476.81 1.46 80 25 59 34 116.59 0.85 81 26 29 3 478.93 0.40 82 26 30 4 476.80 1.46 83 26 55 29 128.24 0.21 84 26 56 30 122.40 0.83 85 26 59 33 118.08 1.38 86 27 30 3 476.80 1.45 87 27 31 4 473.00 3.35 88 27 108 81 128.89 0.34 89 27 112 85 129.56 0.54 90 28 31 3 475.60 1.62 91 28 32 4 463.13 1.39 92 28 101 73 128.74 0.35 93 28 104 76 128.74 0.35 94 28 105 77 128.75 0.35 95 28 108 80 128.91 0.34 96 29 32 3 470.62 4.33 97 29 33 4 465.64 2.65 98 29 55 26 128.96 0.32 99 29 58 29 128.93 0.30 100 29 59 30 128.93 0.30 101 29 101 72 128.80 0.37 102 30 33 3 481.80 0.33 103 30 34 4 467.07 3.37 104 30 50 20 129.81 0.53 105 31 34 3 481.81 0.33 106 31 35 4 444.30 0.26 107 31 104 73 129.38 0.59 108 31 107 76 129.71 0.64 109 31 108 77 129.74 0.62 110 31 111 80 129.90 0.67 111 32 35 3 478.77 1.85 112 32 36 4 443.88 0.07 113 32 39 7 284.67 4.19 114 32 43 11 277.71 2.54 115 32 101 69 129.33 0.62 116 32 104 72 129.54 0.57 117 33 37 4 418.65 2.28 118 33 39 6 315.90 11.42 119 33 40 7 279.41 1.66 120 33 43 10 277.68 2.53 121 33 48 15 130.12 0.58 122 33 55 22 130.02 0.60 123 36 39 3 500.90 3.17 124 36 100 64 129.50 0.56 125 36 103 67 129.81 0.60 126 36 104 68 129.87 0.62 127 37 40 3 480.53 2.52 128 38 41 3 502.06 3.54 129 39 42 3 501.84 3.65 130 39 43 4 487.66 1.04 131 39 97 58 129.36 0.64 132 39 100 61 129.83 0.59 133 40 43 3 486.78 1.49 134 40 48 8 130.78 0.85 135 41 44 3 494.19 2.12 136 42 93 51 129.31 0.62 137 42 94 52 129.79 0.58 138 42 97 55 129.91 0.61 139 43 46 3 484.29 0.43 140 43 48 5 414.76 11.34 141 43 58 15 130.16 0.55 142 45 54 9 187.63 29.15 143 46 54 8 187.57 29.18 144 46 58 12 187.53 29.16 145 47 52 5 235.78 40.28 146 47 54 7 189.74 30.18 147 47 55 8 191.03 29.54 148 48 55 7 191.03 29.55 149 49 52 3 489.95 2.50 150 51 56 5 449.86 1.04 151 52 55 3 478.06 1.02 152 52 56 4 465.44 2.71 153 53 56 3 472.00 2.70 154 53 57 4 465.24 2.77 155 54 57 3 465.70 2.58 156 54 58 4 470.05 0.40 157 55 58 3 475.72 2.06 158 55 59 4 473.81 1.12 159 56 59 3 473.81 1.12 160 56 60 4 473.81 1.12 161 57 60 3 480.62 2.27 162 57 61 4 473.86 1.09 163 58 61 3 475.98 2.16 164 58 62 4 473.31 0.83 165 59 62 3 482.72 1.22 166 59 63 4 473.31 0.83 167 60 63 3 473.31 0.83 168 60 64 4 473.31 0.83 169 61 64 3 482.21 1.48 170 61 65 4 474.18 1.75 171 62 65 3 487.82 2.25 172 62 66 4 476.12 0.78 173 63 66 3 476.11 0.78 174 63 67 4 470.85 0.07 175 64 67 3 463.45 2.90 176 64 68 4 463.32 2.96 177 65 68 3 478.82 2.63 178 65 69 4 465.49 4.04 179 65 80 15 160.40 7.00 180 65 83 18 160.31 7.03 181 66 69 3 468.84 2.36 182 66 70 4 470.75 1.40 183 66 105 39 180.43 0.50 184 66 129 63 173.33 3.04 185 66 132 66 165.67 4.55 186 67 70 3 479.86 2.59 187 67 71 4 459.36 0.95 188 68 71 3 472.22 0.67 189 68 72 4 459.25 0.90 190 68 79 11 211.53 21.39 191 68 80 12 205.51 24.40 192 69 72 3 475.00 0.90 193 69 73 4 451.72 1.67 194 69 76 7 276.01 5.58 195 69 80 11 205.83 24.24 196 69 128 59 192.24 2.31 197 69 132 63 179.12 0.18 198 70 73 3 476.78 1.79 199 70 128 58 194.84 3.36 200 72 75 3 458.91 5.96 201 72 76 4 415.44 5.70 202 72 79 7 272.57 2.23 203 73 76 3 473.98 2.20 204 73 128 55 238.80 6.48 205 75 78 3 492.25 1.21 206 75 79 4 428.87 7.25 207 76 79 3 456.21 8.31 208 76 80 4 415.85 8.50 209 76 128 52 245.31 5.58 210 76 131 55 243.58 4.86 211 76 132 56 243.39 4.79 212 76 135 59 239.38 6.78 213 77 81 4 427.09 8.47 214 77 135 58 239.39 6.79 215 78 81 3 471.79 3.97 216 80 83 3 480.25 2.00 217 80 84 4 471.24 2.51 218 80 132 52 246.98 6.01 219 80 135 55 246.89 6.04 220 80 136 56 246.89 6.04 221 81 84 3 474.99 0.64 222 81 85 4 477.62 0.68 223 81 139 58 246.64 6.17 224 82 85 3 480.25 1.99 225 82 86 4 474.39 2.31 226 83 86 3 477.00 1.01 227 83 87 4 474.39 2.31 228 83 136 53 247.23 6.19 229 84 87 3 478.12 0.45 230 84 88 4 474.39 2.31 231 84 135 51 247.46 6.12 232 84 136 52 247.22 6.20 233 84 139 55 247.19 6.21 234 85 88 3 476.10 1.46 235 85 89 4 458.76 1.80 236 85 139 54 247.22 6.20 237 86 90 4 441.86 10.21 238 86 91 5 400.69 19.14 239 87 91 4 389.95 14.70 240 87 92 5 357.12 6.37 241 87 93 6 357.10 6.36 242 87 98 11 266.91 1.13 243 87 136 49 247.51 6.11 244 87 140 53 247.20 6.20 245 88 92 4 365.21 2.33 246 88 139 51 247.43 6.09 247 88 140 52 246.99 6.12 248 89 92 3 485.01 1.11 249 89 139 50 247.44 6.10 250 92 140 48 247.46 6.11 251 93 97 4 482.20 0.66 252 93 98 5 468.60 3.86 253 93 140 47 247.56 6.12 254 94 97 3 501.30 3.70 255 95 98 3 488.73 2.59 256 95 137 42 247.72 6.13 257 95 140 45 247.69 6.12 258 96 99 3 488.73 2.59 259 96 100 4 479.92 1.79 260 97 100 3 476.37 0.01 261 97 101 4 475.10 0.62 262 98 101 3 485.00 1.64 263 98 102 4 468.29 1.77 264 98 133 35 248.16 6.09 265 98 136 38 248.17 6.09 266 98 137 39 248.10 6.12 267 98 140 42 248.08 6.11 268 99 102 3 468.30 1.78 269 99 103 4 468.29 1.78 270 100 103 3 477.01 2.35 271 100 104 4 471.87 0.73 272 101 104 3 480.86 3.71 273 101 105 4 470.89 0.24 274 102 105 3 481.54 3.37 275 102 106 4 465.55 1.07 276 102 129 27 248.58 6.12 277 102 133 31 248.44 6.08 278 103 106 3 478.19 2.43 279 103 107 4 466.60 1.24 280 104 107 3 472.89 1.91 281 104 108 4 466.60 1.23 282 105 108 3 475.61 2.61 283 105 109 4 466.78 1.15 284 105 129 24 248.97 6.16 285 106 109 3 479.32 5.11 286 106 110 4 469.10 2.31 287 106 117 11 251.27 5.79 288 106 122 16 249.68 6.09 289 106 125 19 249.65 6.08 290 106 126 20 249.39 5.97 291 106 129 23 249.34 5.99 292 107 110 3 475.07 0.68 293 107 111 4 470.70 1.51 294 108 111 3 482.03 1.62 295 108 112 4 475.06 0.68 296 109 112 3 476.25 1.27 297 109 113 4 475.05 0.68 298 109 117 8 260.76 4.91 299 109 125 16 250.06 6.16 300 110 113 3 480.83 1.23 301 110 117 7 252.10 5.84 302 113 116 3 476.91 3.23 303 113 117 4 383.16 1.74 304 116 121 5 460.56 0.42 305 117 121 4 460.56 0.42 306 117 122 5 460.55 0.42 307 117 125 8 427.19 14.37 308 118 121 3 474.75 1.75 309 118 122 4 473.70 1.20 310 119 122 3 479.48 4.08 311 119 123 4 473.71 1.21 312 120 123 3 473.74 1.22 313 120 124 4 473.74 1.22 314 121 124 3 473.75 1.22 315 121 125 4 473.74 1.22 316 122 125 3 476.63 0.23 317 122 126 4 473.75 1.22 318 123 126 3 479.47 1.65 319 123 127 4 476.62 0.23 320 124 127 3 478.42 1.14 321 124 128 4 473.14 1.27 322 125 128 3 473.15 1.27 323 125 129 4 473.14 1.27 324 126 129 3 470.45 0.08 325 126 130 4 468.73 4.12 326 127 130 3 472.20 2.39 327 127 131 4 465.56 2.52 328 128 131 3 478.63 0.84 329 128 132 4 463.49 1.50 330 129 132 3 479.23 1.14 331 129 133 4 463.47 1.51 332 130 133 3 462.97 1.34 333 130 134 4 462.95 1.34 334 131 134 3 469.56 0.31 335 131 135 4 461.18 1.39 336 132 135 3 464.25 0.65 337 132 136 4 461.20 1.38 338 133 136 3 471.16 2.20 339 133 137 4 461.16 1.34 340 134 137 3 472.01 2.37 341 134 138 4 453.33 2.60 342 135 138 3 473.10 1.83 343 136 140 4 486.58 0.89 344 137 140 3 489.22 1.59