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 5 456.30 8.33 2 2 73 71 31.36 0.21 3 2 76 74 25.92 0.37 4 2 127 125 23.15 1.03 5 2 128 126 23.12 1.04 6 2 131 129 23.12 1.03 7 3 6 3 476.99 1.50 8 3 7 4 474.18 2.90 9 4 7 3 489.84 4.93 10 4 8 4 470.39 1.40 11 5 8 3 475.34 3.48 12 5 9 4 470.47 1.44 13 6 9 3 472.98 2.10 14 6 10 4 471.06 1.15 15 6 124 118 45.51 0.35 16 6 127 121 45.48 0.34 17 7 10 3 479.23 2.62 18 7 11 4 471.07 1.15 19 7 73 66 47.72 0.20 20 7 74 67 47.73 0.20 21 8 11 3 476.95 0.98 22 8 12 4 471.08 1.15 23 9 12 3 478.93 0.60 24 9 13 4 474.45 2.85 25 9 121 112 54.23 0.66 26 9 124 115 52.43 1.56 27 10 13 3 474.19 3.00 28 10 14 4 461.69 9.22 29 10 70 60 51.66 1.19 30 10 124 114 54.29 0.64 31 10 125 115 51.67 1.19 32 10 128 118 51.66 1.19 33 11 15 4 465.78 3.46 34 11 70 59 53.59 0.23 35 11 73 62 54.75 0.81 36 12 15 3 477.88 1.12 37 12 16 4 469.50 5.30 38 13 16 3 477.88 1.12 39 13 17 4 477.88 1.12 40 13 113 100 77.91 1.49 41 13 121 108 66.75 5.54 42 13 125 112 56.81 0.62 43 14 17 3 474.29 2.91 44 14 18 4 473.73 3.19 45 14 21 7 412.36 5.82 46 14 63 49 76.10 1.16 47 14 66 52 56.81 0.62 48 14 67 53 56.81 0.62 49 14 70 56 56.81 0.63 50 14 109 95 77.89 1.50 51 15 18 3 477.96 1.07 52 16 113 97 91.17 2.08 53 16 116 100 81.07 2.94 54 17 20 3 489.57 2.64 55 17 21 4 440.64 9.19 56 17 24 7 414.72 7.15 57 17 109 92 80.94 3.01 58 17 113 96 93.89 0.75 59 18 21 3 503.33 1.19 60 20 23 3 478.01 1.18 61 20 24 4 465.84 3.35 62 21 24 3 480.46 2.73 63 21 25 4 468.04 2.27 64 21 63 42 93.97 0.75 65 22 25 3 469.85 1.37 66 22 26 4 468.06 2.27 67 22 60 38 98.43 0.88 68 22 63 41 98.03 0.68 69 23 26 3 474.95 0.11 70 23 27 4 468.11 2.25 71 24 27 3 473.99 3.35 72 24 28 4 468.11 2.25 73 24 108 84 117.04 0.65 74 24 112 88 132.27 1.17 75 25 28 3 474.67 3.02 76 25 29 4 468.11 2.25 77 25 59 34 115.42 0.33 78 25 63 38 113.73 0.41 79 26 29 3 478.98 0.67 80 26 30 4 470.62 3.50 81 26 55 29 126.86 2.83 82 26 56 30 126.85 2.83 83 26 59 33 116.56 0.84 84 27 30 3 473.47 2.08 85 27 31 4 462.06 1.62 86 27 108 81 132.69 1.08 87 27 112 85 133.52 0.78 88 28 31 3 470.02 2.39 89 28 32 4 461.89 1.71 90 28 101 73 132.55 1.05 91 28 104 76 132.58 1.04 92 28 105 77 132.53 1.04 93 28 108 80 132.72 1.09 94 29 32 3 467.50 1.13 95 29 33 4 466.75 0.76 96 29 55 26 132.72 1.09 97 29 58 29 132.72 1.09 98 29 59 30 132.68 1.07 99 29 101 72 132.68 1.06 100 30 33 3 468.94 1.84 101 30 34 4 464.64 0.29 102 30 50 20 133.56 0.84 103 31 34 3 479.83 1.16 104 31 35 4 463.82 0.70 105 31 104 73 133.17 0.83 106 31 107 76 133.49 0.76 107 31 108 77 133.52 0.75 108 31 111 80 133.74 0.74 109 32 35 3 475.26 4.00 110 32 36 4 448.61 2.27 111 32 39 7 323.02 1.32 112 32 100 68 133.17 0.83 113 32 101 69 133.16 0.83 114 32 104 72 133.43 0.74 115 33 37 4 434.56 1.59 116 33 39 6 334.85 4.59 117 33 40 7 300.88 3.41 118 33 43 10 307.06 9.29 119 33 48 15 133.82 0.76 120 33 55 22 133.75 0.77 121 34 37 3 492.28 0.34 122 36 39 3 499.94 3.65 123 36 100 64 133.22 0.82 124 36 103 67 133.54 0.77 125 36 104 68 133.54 0.77 126 37 40 3 488.63 1.03 127 38 41 3 487.75 1.47 128 39 42 3 496.05 1.72 129 39 43 4 487.28 1.24 130 39 97 58 133.19 0.81 131 39 100 61 133.50 0.74 132 40 43 3 491.18 0.71 133 40 44 4 487.10 1.32 134 40 48 8 135.66 1.07 135 41 44 3 497.29 1.07 136 42 93 51 133.16 0.73 137 42 94 52 133.35 0.70 138 42 97 55 133.52 0.73 139 43 46 3 482.62 0.96 140 43 48 5 411.43 2.72 141 43 58 15 133.90 0.81 142 45 54 9 135.82 1.06 143 46 54 8 135.82 1.06 144 46 58 12 135.81 1.06 145 47 52 5 151.94 0.26 146 47 54 7 135.82 1.06 147 47 55 8 135.82 1.06 148 48 55 7 135.81 1.04 149 49 52 3 475.67 4.00 150 51 56 5 450.49 2.32 151 52 55 3 474.44 0.45 152 52 56 4 463.67 2.02 153 53 56 3 479.19 2.83 154 53 57 4 463.69 2.00 155 54 57 3 473.82 0.14 156 54 58 4 465.70 3.00 157 55 58 3 475.79 2.03 158 55 59 4 465.03 2.67 159 56 59 3 473.40 0.74 160 56 60 4 473.35 0.74 161 57 60 3 475.19 1.61 162 57 61 4 473.35 0.74 163 58 61 3 473.31 0.79 164 58 62 4 472.56 1.15 165 59 62 3 480.50 2.83 166 59 63 4 467.53 1.37 167 60 63 3 472.54 1.16 168 60 64 4 467.50 1.35 169 61 64 3 472.68 0.96 170 61 65 4 467.53 1.34 171 62 65 3 478.33 2.93 172 62 66 4 467.54 1.33 173 63 66 3 477.49 3.35 174 63 67 4 463.78 0.56 175 64 67 3 477.17 3.52 176 64 68 4 464.98 1.54 177 65 68 3 478.24 2.93 178 65 69 4 473.00 5.55 179 65 80 15 166.81 4.25 180 65 83 18 151.83 1.57 181 66 69 3 476.50 3.80 182 66 70 4 473.00 5.55 183 66 105 39 184.23 2.04 184 66 129 63 177.56 0.51 185 66 132 66 167.43 4.19 186 67 70 3 475.75 4.18 187 67 71 4 457.85 5.09 188 68 71 3 474.14 3.38 189 68 72 4 460.18 3.92 190 68 79 11 172.45 1.91 191 68 80 12 167.55 4.41 192 69 72 3 466.91 7.00 193 69 73 4 443.56 4.53 194 69 76 7 276.94 39.73 195 69 80 11 178.81 0.06 196 69 128 59 204.28 3.15 197 69 132 63 178.83 0.06 198 70 73 3 441.08 3.29 199 70 128 58 204.31 3.16 200 72 75 3 473.25 1.21 201 72 76 4 436.38 5.82 202 72 79 7 316.96 19.75 203 73 76 3 475.53 1.43 204 73 128 55 267.31 0.74 205 75 78 3 495.31 0.51 206 75 79 4 466.44 2.23 207 76 79 3 479.35 1.08 208 76 80 4 466.44 2.23 209 76 128 52 275.64 1.68 210 76 131 55 274.26 1.94 211 76 132 56 272.83 1.70 212 76 135 59 272.82 1.70 213 77 80 3 486.94 1.12 214 77 81 4 466.44 2.23 215 77 135 58 272.82 1.70 216 78 81 3 470.88 4.44 217 80 83 3 479.80 2.52 218 80 84 4 466.41 2.21 219 80 132 52 276.37 1.54 220 80 135 55 276.04 1.54 221 80 136 56 276.04 1.54 222 81 84 3 478.48 2.88 223 81 85 4 460.34 5.23 224 81 139 58 275.93 1.52 225 82 85 3 473.30 1.27 226 82 86 4 461.50 4.65 227 83 86 3 473.29 1.27 228 83 87 4 466.87 1.95 229 83 136 53 276.43 1.54 230 84 87 3 474.90 2.01 231 84 88 4 457.26 2.52 232 84 135 51 276.56 1.58 233 84 136 52 276.43 1.54 234 84 139 55 276.24 1.52 235 85 88 3 474.80 2.06 236 85 89 4 447.87 2.17 237 85 139 54 276.36 1.58 238 86 90 4 404.11 2.88 239 86 91 5 404.11 2.88 240 87 91 4 301.43 1.31 241 87 92 5 298.88 2.56 242 87 93 6 280.25 1.89 243 87 98 11 280.15 1.89 244 87 140 53 276.43 1.55 245 88 92 4 318.75 2.90 246 88 139 51 276.55 1.59 247 88 140 52 276.26 1.52 248 89 92 3 483.11 0.58 249 89 139 50 276.58 1.58 250 92 140 48 276.58 1.58 251 93 97 4 482.78 0.37 252 93 98 5 473.86 1.74 253 93 140 47 276.72 1.54 254 94 97 3 492.03 1.44 255 95 98 3 494.36 0.28 256 95 137 42 276.92 1.52 257 95 140 45 276.88 1.50 258 96 99 3 493.31 0.38 259 96 100 4 482.79 0.37 260 97 100 3 477.63 0.70 261 97 101 4 480.56 3.85 262 98 101 3 482.81 2.73 263 98 102 4 472.73 1.67 264 98 133 35 277.32 1.60 265 98 136 38 277.35 1.60 266 98 137 39 277.32 1.60 267 98 140 42 277.32 1.60 268 99 102 3 480.56 3.85 269 99 103 4 471.44 2.28 270 100 103 3 482.68 2.79 271 100 104 4 477.57 5.35 272 101 104 3 480.20 1.56 273 101 105 4 476.00 3.66 274 102 105 3 476.99 3.17 275 102 106 4 476.00 3.66 276 102 129 27 277.54 1.54 277 102 133 31 277.48 1.57 278 103 106 3 466.75 1.95 279 103 107 4 465.77 1.46 280 104 107 3 478.45 4.88 281 104 108 4 469.98 3.56 282 105 108 3 482.66 2.77 283 105 109 4 469.97 3.56 284 105 129 24 277.86 1.71 285 106 109 3 480.48 4.54 286 106 110 4 472.07 5.65 287 106 117 11 278.95 1.76 288 106 122 16 278.28 1.83 289 106 125 19 278.28 1.83 290 106 126 20 278.27 1.83 291 106 129 23 278.23 1.85 292 107 110 3 477.38 3.00 293 107 111 4 472.05 5.66 294 108 111 3 480.30 1.57 295 108 112 4 462.94 1.12 296 109 112 3 475.93 3.71 297 109 113 4 453.61 0.99 298 109 125 16 278.51 1.74 299 110 113 3 480.25 1.55 300 110 117 7 278.94 1.77 301 113 116 3 467.26 4.75 302 113 117 4 438.00 0.79 303 116 121 5 445.12 3.42 304 117 121 4 453.07 3.22 305 117 122 5 445.10 3.43 306 117 125 8 407.70 15.26 307 118 121 3 472.30 0.53 308 118 122 4 472.30 0.52 309 119 122 3 479.98 4.33 310 119 123 4 465.51 2.89 311 120 123 3 472.97 0.83 312 120 124 4 468.31 1.51 313 121 124 3 468.32 1.51 314 121 125 4 468.31 1.51 315 122 125 3 473.70 1.19 316 122 126 4 468.31 1.52 317 123 126 3 468.31 1.51 318 123 127 4 473.74 1.20 319 124 127 3 471.62 2.53 320 124 128 4 471.37 2.65 321 125 128 3 477.21 0.27 322 125 129 4 471.37 2.66 323 126 129 3 485.19 2.97 324 126 130 4 471.31 2.42 325 127 130 3 476.92 0.42 326 127 131 4 469.11 4.33 327 128 131 3 477.22 0.28 328 128 132 4 477.21 0.27 329 129 132 3 472.51 2.07 330 129 133 4 463.69 2.34 331 130 133 3 469.17 0.39 332 130 134 4 463.69 2.36 333 131 134 3 468.16 1.19 334 131 135 4 464.45 1.99 335 132 135 3 473.50 1.49 336 132 136 4 464.94 1.74 337 133 136 3 473.68 1.58 338 133 137 4 464.94 1.74 339 134 137 3 474.73 2.12 340 134 138 4 460.76 1.17 341 135 138 3 477.39 0.18 342 136 140 4 494.06 3.52 343 137 140 3 486.87 0.07