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 73 71 25.17 0.34 2 2 132 130 23.12 0.52 3 2 133 131 23.09 0.49 4 2 136 134 23.11 0.51 5 3 6 3 489.50 1.13 6 3 7 4 474.38 5.56 7 4 7 3 493.53 3.14 8 4 8 4 482.70 1.40 9 5 8 3 500.19 0.20 10 5 9 4 489.39 1.95 11 6 9 3 489.40 1.95 12 6 10 4 500.22 0.24 13 6 128 122 48.96 0.47 14 6 129 123 46.16 0.29 15 6 132 126 46.16 0.29 16 7 10 3 502.51 1.38 17 7 11 4 500.25 0.24 18 7 73 66 48.33 0.79 19 7 74 67 48.33 0.79 20 8 11 3 500.25 0.24 21 8 12 4 500.24 0.24 22 9 12 3 500.25 0.24 23 9 13 4 492.07 4.33 24 9 125 116 63.66 1.22 25 9 126 117 61.09 0.05 26 9 129 120 60.90 0.06 27 10 13 3 508.66 3.38 28 10 14 4 493.57 3.58 29 10 70 60 60.84 0.06 30 10 73 63 60.88 0.07 31 10 129 119 61.08 0.05 32 10 130 120 60.95 0.06 33 10 133 123 60.90 0.04 34 11 14 3 500.17 0.23 35 11 15 4 479.81 3.29 36 11 70 59 60.87 0.04 37 12 15 3 505.67 0.55 38 12 16 4 500.17 0.24 39 13 17 4 475.96 3.76 40 13 118 105 79.92 2.04 41 13 126 113 69.58 1.19 42 13 130 117 69.53 1.19 43 14 18 4 427.36 4.34 44 14 22 8 74.12 2.18 45 14 63 49 69.58 1.18 46 14 64 50 69.67 1.23 47 14 66 52 69.56 1.18 48 14 67 53 69.56 1.18 49 14 70 56 69.54 1.19 50 14 130 116 69.59 1.19 51 15 19 4 413.29 11.37 52 16 19 3 482.74 4.92 53 16 117 101 80.42 2.23 54 16 118 102 80.42 2.23 55 17 21 4 482.78 7.87 56 17 26 9 80.19 2.17 57 17 114 97 80.30 2.23 58 17 117 100 80.41 2.23 59 17 118 101 80.45 2.24 60 17 122 105 80.45 2.23 61 17 130 113 80.31 2.23 62 18 21 3 481.38 8.56 63 18 22 4 173.17 0.10 64 18 23 5 121.14 22.65 65 21 24 3 461.75 0.57 66 21 117 96 122.56 0.01 67 22 63 41 80.88 2.21 68 22 64 42 80.61 2.26 69 23 26 3 486.94 1.86 70 23 27 4 486.94 1.86 71 23 60 37 86.21 0.40 72 23 63 40 80.91 2.19 73 24 28 4 487.83 1.42 74 24 60 36 105.39 1.48 75 25 28 3 509.80 2.43 76 25 29 4 487.72 1.48 77 26 29 3 512.00 1.33 78 26 30 4 475.62 4.33 79 26 63 37 122.50 0.02 80 26 110 84 122.56 0.03 81 26 113 87 124.36 0.89 82 26 114 88 122.59 0.01 83 27 30 3 486.11 0.67 84 27 31 4 475.22 4.13 85 27 59 32 122.52 0.03 86 27 60 33 122.55 0.03 87 27 63 36 122.52 0.02 88 28 32 4 484.56 0.00 89 28 55 27 130.43 1.58 90 28 56 28 124.92 1.11 91 28 59 31 122.62 0.03 92 29 32 3 501.48 1.52 93 29 33 4 501.48 1.52 94 29 113 84 136.56 0.54 95 29 114 85 136.75 0.56 96 29 116 87 136.94 0.53 97 30 33 3 494.31 2.06 98 30 34 4 493.79 1.80 99 30 106 76 136.47 0.57 100 30 109 79 136.51 0.56 101 30 110 80 136.45 0.57 102 30 113 83 136.72 0.56 103 31 34 3 493.79 1.80 104 31 35 4 488.39 0.90 105 31 45 14 153.72 4.67 106 31 55 24 136.98 0.53 107 31 58 27 136.92 0.52 108 31 59 28 136.88 0.52 109 31 62 31 136.91 0.52 110 31 106 75 136.51 0.56 111 32 35 3 497.98 3.26 112 32 36 4 486.39 0.11 113 32 50 18 137.10 0.49 114 32 55 23 136.96 0.52 115 33 36 3 496.00 4.32 116 33 37 4 475.35 5.40 117 34 37 3 488.70 1.05 118 34 38 4 468.16 8.37 119 34 41 7 419.55 10.30 120 34 45 11 323.68 5.88 121 34 102 68 136.44 0.55 122 34 105 71 136.67 0.59 123 34 106 72 136.50 0.56 124 35 38 3 486.85 0.08 125 35 39 4 468.13 8.38 126 35 41 6 407.63 4.41 127 35 42 7 367.12 15.84 128 35 45 10 242.46 32.28 129 35 47 12 151.39 3.52 130 35 55 20 137.13 0.55 131 36 39 3 505.86 0.71 132 36 50 14 137.25 0.52 133 38 41 3 509.92 0.77 134 39 42 3 508.65 1.12 135 40 44 4 486.97 6.80 136 40 102 62 136.94 0.51 137 41 44 3 485.66 7.46 138 41 45 4 476.53 2.89 139 41 97 56 136.31 0.57 140 41 102 61 136.82 0.54 141 42 45 3 497.69 3.47 142 42 46 4 467.88 1.44 143 42 47 5 372.64 4.18 144 43 46 3 482.94 6.09 145 43 95 52 135.72 0.83 146 44 95 51 135.65 0.81 147 44 97 53 136.09 0.66 148 44 98 54 136.11 0.67 149 45 58 13 137.24 0.56 150 47 52 5 235.08 34.54 151 47 54 7 137.99 0.58 152 47 55 8 137.97 0.57 153 47 58 11 137.97 0.57 154 48 52 4 482.62 3.75 155 49 52 3 514.87 1.44 156 52 55 3 510.97 3.38 157 53 56 3 501.56 2.02 158 53 57 4 492.16 2.69 159 54 57 3 492.16 2.69 160 54 58 4 485.01 6.25 161 55 58 3 494.31 1.60 162 55 59 4 471.81 1.83 163 56 60 4 473.95 0.75 164 57 60 3 484.75 1.29 165 57 61 4 484.68 1.34 166 58 61 3 489.22 0.93 167 58 62 4 486.64 0.35 168 59 62 3 490.60 1.62 169 59 63 4 486.69 0.33 170 60 63 3 503.18 1.42 171 60 64 4 499.94 3.04 172 61 64 3 505.03 0.51 173 61 65 4 503.18 1.43 174 62 65 3 503.20 1.42 175 62 66 4 498.86 0.74 176 63 66 3 496.45 1.28 177 63 67 4 495.63 0.87 178 63 110 47 155.55 1.31 179 63 114 51 157.27 0.95 180 63 134 71 155.37 1.18 181 64 67 3 495.63 0.87 182 64 68 4 495.62 0.87 183 65 68 3 501.88 3.83 184 65 69 4 489.91 1.99 185 65 82 17 154.83 1.02 186 65 83 18 153.74 1.42 187 65 86 21 153.00 1.04 188 66 69 3 488.02 1.03 189 66 70 4 488.00 1.03 190 66 110 44 157.27 0.96 191 66 134 68 155.41 1.20 192 66 137 71 155.07 1.07 193 67 70 3 486.44 1.82 194 67 71 4 493.34 1.63 195 68 71 3 509.01 0.80 196 68 82 14 155.38 1.23 197 69 72 3 504.47 2.39 198 69 73 4 496.30 2.08 199 69 79 10 154.94 0.97 200 69 83 14 155.07 1.07 201 69 137 68 155.53 1.23 202 70 73 3 505.93 2.35 203 72 75 3 479.15 3.99 204 72 79 7 157.00 0.89 205 73 79 6 276.57 47.02 206 73 133 60 182.70 7.17 207 75 79 4 498.50 3.17 208 76 79 3 517.46 4.72 209 76 80 4 463.63 1.15 210 78 81 3 493.51 0.67 211 78 82 4 497.65 0.15 212 79 82 3 509.77 1.75 213 79 83 4 493.35 2.30 214 80 83 3 500.25 0.68 215 80 84 4 493.35 2.30 216 80 140 60 289.56 1.57 217 81 84 3 502.04 2.35 218 81 85 4 497.07 0.43 219 82 85 3 501.50 2.62 220 82 86 4 497.10 0.42 221 83 86 3 501.70 1.89 222 83 87 4 501.50 2.62 223 83 137 54 292.70 0.77 224 83 140 57 292.67 0.76 225 83 141 58 292.63 0.75 226 84 87 3 509.80 5.26 227 84 88 4 497.12 0.43 228 84 140 56 292.69 0.76 229 84 141 57 292.64 0.75 230 84 143 59 292.63 0.74 231 84 144 60 292.61 0.75 232 85 88 3 509.51 5.40 233 85 89 4 500.78 1.39 234 86 89 3 501.14 1.21 235 86 90 4 500.78 1.39 236 86 141 55 292.69 0.74 237 87 90 3 501.50 2.61 238 87 91 4 495.38 1.30 239 87 141 54 292.69 0.74 240 87 144 57 292.66 0.75 241 87 145 58 292.58 0.73 242 88 91 3 499.75 3.49 243 88 144 56 292.64 0.74 244 88 145 57 292.63 0.76 245 88 147 59 292.04 0.97 246 89 92 3 511.15 2.21 247 89 93 4 486.98 2.23 248 90 93 3 491.70 0.14 249 90 98 8 292.74 0.74 250 90 145 55 292.67 0.75 251 91 146 55 292.65 0.74 252 91 147 56 292.60 0.73 253 93 96 3 490.35 3.52 254 93 98 5 416.49 5.03 255 95 98 3 550.16 1.11 256 98 103 5 493.49 1.54 257 98 145 47 293.33 0.78 258 99 102 3 519.00 0.15 259 99 103 4 500.41 1.93 260 99 145 46 293.54 0.88 261 100 103 3 500.42 1.92 262 100 142 42 293.64 0.85 263 100 145 45 293.56 0.89 264 101 105 4 500.41 1.93 265 102 105 3 502.34 0.96 266 102 106 4 484.17 1.39 267 103 106 3 492.14 2.58 268 103 107 4 484.17 1.39 269 103 138 35 293.87 0.84 270 103 141 38 293.87 0.83 271 103 142 39 293.83 0.83 272 103 145 42 293.83 0.83 273 104 107 3 493.10 3.07 274 104 108 4 493.10 3.07 275 105 108 3 497.57 0.83 276 105 109 4 493.59 1.89 277 106 109 3 504.14 0.77 278 106 110 4 493.59 1.89 279 107 110 3 502.55 1.56 280 107 111 4 502.56 1.55 281 108 111 3 502.57 1.55 282 108 112 4 502.56 1.55 283 109 112 3 502.56 1.55 284 109 113 4 502.56 1.55 285 110 113 3 509.92 2.13 286 110 114 4 502.55 1.55 287 110 134 24 294.92 0.72 288 111 114 3 504.38 0.63 289 111 122 11 297.15 0.37 290 111 127 16 295.07 0.69 291 111 130 19 295.07 0.70 292 111 131 20 295.08 0.70 293 112 115 3 511.28 0.94 294 112 116 4 506.51 1.45 295 113 116 3 505.56 1.85 296 114 117 3 505.55 1.85 297 114 118 4 488.81 0.12 298 114 122 8 297.19 0.37 299 114 130 16 295.84 0.54 300 114 134 20 295.67 0.52 301 115 118 3 485.45 1.46 302 115 119 4 422.66 7.23 303 115 122 7 297.19 0.37 304 118 121 3 485.85 4.04 305 118 122 4 373.34 24.59 306 122 126 4 448.39 13.86 307 122 127 5 455.86 10.12 308 122 130 8 436.51 8.33 309 123 126 3 490.06 5.92 310 123 127 4 485.91 2.90 311 124 127 3 497.80 2.40 312 124 128 4 477.30 1.80 313 125 128 3 485.91 2.90 314 125 129 4 481.84 2.83 315 126 129 3 503.56 1.22 316 126 130 4 489.62 1.04 317 127 130 3 489.73 0.99 318 127 131 4 481.85 2.83 319 128 131 3 482.71 2.51 320 128 132 4 484.81 3.56 321 129 132 3 505.36 4.92 322 129 133 4 482.45 4.74 323 130 133 3 480.93 5.50 324 130 134 4 475.22 4.19 325 131 135 4 478.26 2.67 326 132 135 3 492.36 2.64 327 133 136 3 489.54 0.62 328 133 137 4 485.33 0.87 329 134 137 3 483.69 1.69 330 134 138 4 462.86 0.45 331 135 138 3 501.47 3.10 332 135 139 4 447.12 3.58 333 136 140 4 470.81 15.44 334 137 140 3 496.45 2.62 335 137 141 4 496.45 2.62 336 138 141 3 496.47 2.62 337 138 142 4 496.45 2.62 338 139 142 3 500.03 0.83 339 140 143 3 511.74 1.76 340 141 144 3 511.34 0.91 341 141 145 4 468.62 7.51 342 142 145 3 483.74 1.19 343 142 146 4 483.74 1.19 344 144 147 3 504.23 3.04