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 5 443.99 5.08 2 2 73 71 28.73 0.97 3 2 76 74 24.87 0.88 4 2 127 125 24.46 0.29 5 2 128 126 24.28 0.19 6 2 131 129 23.24 0.07 7 3 6 3 472.97 3.51 8 3 7 4 467.41 0.70 9 4 7 3 468.18 0.33 10 4 8 4 468.21 0.31 11 5 8 3 474.95 3.68 12 5 9 4 470.43 1.42 13 6 9 3 476.38 1.88 14 6 10 4 471.06 1.15 15 6 124 118 45.58 0.32 16 6 127 121 45.56 0.32 17 7 10 3 479.23 2.62 18 7 11 4 471.06 1.15 19 7 73 66 47.97 0.32 20 7 74 67 47.98 0.31 21 8 11 3 482.28 1.09 22 8 12 4 471.07 1.15 23 9 12 3 471.48 1.35 24 9 13 4 471.11 1.17 25 9 120 111 61.19 1.36 26 9 121 112 61.08 1.36 27 9 124 115 61.02 1.36 28 10 13 3 474.04 3.08 29 10 14 4 465.97 4.08 30 10 70 60 61.02 1.36 31 10 124 114 61.07 1.36 32 10 125 115 61.06 1.36 33 10 128 118 60.98 1.32 34 11 14 3 471.01 1.56 35 11 15 4 469.76 1.83 36 11 70 59 61.04 1.36 37 11 73 62 61.05 1.36 38 12 15 3 477.60 0.98 39 12 16 4 473.46 3.04 40 13 16 3 477.94 1.06 41 13 17 4 474.33 2.60 42 13 113 100 82.30 2.27 43 13 116 103 78.45 1.08 44 13 121 108 77.14 1.16 45 13 125 112 61.62 1.10 46 14 17 3 474.74 2.40 47 14 18 4 474.33 2.60 48 14 21 7 382.92 4.30 49 14 66 52 61.62 1.11 50 14 67 53 61.62 1.11 51 14 70 56 61.61 1.11 52 14 105 91 78.43 1.08 53 14 109 95 78.50 1.06 54 15 18 3 477.95 1.07 55 16 113 97 92.99 1.24 56 16 116 100 92.84 1.27 57 17 20 3 485.39 4.73 58 17 21 4 441.14 6.79 59 17 24 7 387.34 6.54 60 17 109 92 89.24 0.34 61 17 113 96 93.58 1.53 62 18 21 3 503.33 1.19 63 20 23 3 478.67 1.51 64 20 24 4 465.83 1.10 65 21 24 3 465.84 1.10 66 21 25 4 468.07 2.23 67 21 63 42 98.05 0.63 68 22 25 3 477.22 1.69 69 22 26 4 468.07 2.23 70 22 59 37 106.37 0.94 71 22 60 38 99.21 0.48 72 22 63 41 98.11 0.64 73 23 26 3 473.19 0.33 74 23 27 4 468.05 2.24 75 24 27 3 478.19 1.25 76 24 28 4 465.89 3.31 77 24 108 84 125.12 0.37 78 24 109 85 125.12 0.37 79 24 112 88 129.41 0.27 80 25 28 3 473.99 0.74 81 25 29 4 463.69 2.21 82 25 59 34 116.34 0.02 83 26 29 3 477.88 0.13 84 26 30 4 467.36 4.04 85 26 55 29 128.96 0.18 86 26 56 30 125.41 1.96 87 26 59 33 117.30 0.48 88 27 30 3 475.62 1.00 89 27 31 4 457.24 3.42 90 27 108 81 129.81 0.35 91 27 112 85 130.66 0.70 92 28 31 3 470.02 2.39 93 28 32 4 463.28 2.46 94 28 104 76 129.69 0.38 95 28 105 77 129.69 0.38 96 28 108 80 129.85 0.33 97 29 32 3 472.43 0.24 98 29 33 4 464.06 2.85 99 29 55 26 129.89 0.33 100 29 58 29 129.84 0.35 101 29 59 30 129.83 0.35 102 29 101 72 129.78 0.35 103 30 33 3 478.72 0.61 104 30 34 4 463.82 0.70 105 30 50 20 130.91 0.70 106 31 34 3 480.61 1.55 107 31 35 4 448.89 2.96 108 31 104 73 130.30 0.60 109 31 107 76 130.75 0.75 110 31 108 77 130.75 0.75 111 32 35 3 460.48 2.83 112 32 36 4 448.72 3.04 113 32 39 7 222.66 31.34 114 32 43 11 215.31 34.97 115 32 100 68 130.31 0.60 116 32 101 69 130.30 0.60 117 32 104 72 130.66 0.72 118 33 37 4 349.48 5.83 119 33 39 6 226.99 33.51 120 33 40 7 215.38 34.98 121 33 43 10 204.32 29.47 122 33 48 15 131.06 0.70 123 33 55 22 130.96 0.71 124 36 39 3 492.82 0.10 125 36 100 64 130.34 0.61 126 36 103 67 130.84 0.76 127 36 104 68 130.84 0.76 128 37 40 3 488.63 1.03 129 38 41 3 487.75 1.47 130 39 42 3 493.57 0.48 131 39 43 4 487.09 1.31 132 39 97 58 130.34 0.61 133 39 100 61 130.79 0.78 134 40 43 3 491.17 0.72 135 40 44 4 479.94 2.25 136 40 48 8 139.50 2.48 137 41 44 3 504.13 1.30 138 42 92 50 130.42 0.65 139 42 93 51 130.41 0.65 140 42 94 52 130.65 0.74 141 42 97 55 130.79 0.79 142 43 46 3 483.81 0.67 143 43 48 5 419.56 2.18 144 43 58 15 135.19 1.95 145 45 54 9 138.87 2.81 146 46 54 8 138.86 2.82 147 46 58 12 138.86 2.82 148 47 52 5 195.73 25.23 149 47 54 7 138.88 2.82 150 47 55 8 189.66 28.21 151 48 55 7 198.19 26.45 152 49 52 3 483.92 0.12 153 51 56 5 420.30 1.30 154 52 55 3 466.51 3.52 155 52 56 4 463.11 4.37 156 53 56 3 479.19 2.83 157 53 57 4 463.17 4.36 158 54 57 3 472.76 0.39 159 54 58 4 464.73 3.58 160 55 58 3 471.94 0.02 161 55 59 4 464.72 3.58 162 56 59 3 473.56 0.49 163 56 60 4 473.70 0.57 164 57 60 3 473.71 0.57 165 57 61 4 473.70 0.57 166 58 61 3 473.69 0.58 167 58 62 4 473.69 0.58 168 59 62 3 480.50 2.83 169 59 63 4 473.70 0.58 170 60 63 3 473.73 0.56 171 60 64 4 473.56 0.52 172 61 64 3 478.42 2.89 173 61 65 4 473.56 0.52 174 62 65 3 488.75 2.29 175 62 66 4 478.34 2.93 176 63 66 3 477.19 3.50 177 63 67 4 474.35 4.92 178 64 67 3 464.69 0.09 179 64 68 4 464.69 0.09 180 65 68 3 478.23 2.93 181 65 69 4 474.31 4.90 182 65 80 15 151.33 1.52 183 65 83 18 145.27 4.50 184 66 69 3 476.50 3.81 185 66 70 4 458.75 2.87 186 66 105 39 184.40 1.99 187 66 129 63 171.56 2.49 188 66 132 66 163.57 3.50 189 67 70 3 473.18 5.46 190 67 71 4 450.63 1.19 191 68 71 3 470.21 3.89 192 68 72 4 445.16 3.92 193 68 79 11 216.88 19.09 194 69 72 3 477.42 1.75 195 69 73 4 432.37 1.06 196 69 76 7 287.79 5.59 197 69 80 11 179.37 4.41 198 69 128 59 193.35 2.47 199 69 132 63 180.00 4.09 200 70 73 3 471.38 4.49 201 70 128 58 209.68 5.83 202 72 75 3 474.51 1.81 203 72 76 4 433.60 0.21 204 72 79 7 310.13 16.77 205 73 76 3 475.32 1.53 206 73 128 55 241.64 5.06 207 75 78 3 495.31 0.51 208 75 79 4 454.67 3.64 209 76 79 3 466.42 2.22 210 76 80 4 454.67 3.64 211 76 128 52 246.87 4.20 212 76 131 55 245.03 5.08 213 76 132 56 243.88 4.53 214 76 135 59 242.43 5.25 215 77 80 3 482.22 1.24 216 77 81 4 427.79 0.77 217 77 135 58 242.44 5.25 218 78 81 3 470.85 4.44 219 80 83 3 479.80 2.52 220 80 84 4 470.98 0.95 221 80 132 52 247.26 4.17 222 80 135 55 246.94 4.11 223 81 84 3 473.31 0.22 224 81 85 4 467.98 2.44 225 81 139 58 246.94 4.11 226 82 85 3 480.70 1.73 227 82 86 4 474.35 0.74 228 83 86 3 474.48 0.82 229 83 87 4 467.94 2.46 230 83 136 53 247.38 4.19 231 84 87 3 475.85 1.53 232 84 88 4 464.81 3.98 233 84 135 51 247.43 4.17 234 84 136 52 247.37 4.19 235 84 139 55 247.34 4.20 236 85 88 3 473.96 2.48 237 85 89 4 451.72 6.00 238 85 90 5 451.72 6.00 239 85 139 54 247.06 4.06 240 86 90 4 424.68 4.17 241 86 91 5 417.98 0.82 242 87 91 4 407.87 4.21 243 87 92 5 399.94 8.14 244 87 93 6 399.92 8.13 245 87 98 11 300.53 2.02 246 87 136 49 247.55 4.20 247 87 140 53 247.34 4.20 248 88 92 4 399.91 8.13 249 88 139 51 247.45 4.17 250 88 140 52 247.30 4.19 251 89 92 3 485.15 1.63 252 89 139 50 247.47 4.17 253 92 140 48 247.53 4.18 254 93 97 4 482.80 0.38 255 93 98 5 482.79 0.38 256 93 140 47 247.57 4.20 257 94 97 3 492.03 1.44 258 95 98 3 491.98 1.47 259 95 99 4 482.81 0.38 260 95 137 42 247.84 4.19 261 95 140 45 247.72 4.20 262 96 99 3 490.80 0.88 263 96 100 4 482.80 0.38 264 97 100 3 480.49 0.72 265 97 101 4 480.49 0.72 266 98 101 3 480.79 3.74 267 98 102 4 472.69 1.68 268 98 133 35 248.12 4.12 269 98 136 38 248.12 4.12 270 98 137 39 248.12 4.13 271 98 140 42 248.07 4.13 272 99 102 3 475.08 4.12 273 99 103 4 475.07 4.12 274 100 103 3 482.68 2.79 275 100 104 4 475.09 4.12 276 101 104 3 482.68 2.80 277 101 105 4 465.17 1.74 278 102 105 3 476.99 3.17 279 102 106 4 465.18 1.73 280 102 129 27 248.54 4.08 281 103 106 3 479.46 4.41 282 103 107 4 466.44 1.82 283 104 107 3 470.78 0.35 284 104 108 4 465.71 2.19 285 105 108 3 482.70 2.80 286 105 109 4 466.46 1.80 287 105 129 24 249.24 3.83 288 106 109 3 480.48 4.54 289 106 110 4 466.45 1.80 290 106 117 11 249.82 4.05 291 106 122 16 249.64 4.00 292 106 125 19 249.53 3.96 293 106 126 20 249.41 3.90 294 106 129 23 249.36 3.89 295 107 110 3 480.29 1.58 296 107 111 4 476.75 0.18 297 108 111 3 491.41 2.56 298 108 112 4 468.56 3.92 299 109 112 3 480.26 1.55 300 109 113 4 459.43 1.04 301 109 125 16 249.75 4.04 302 110 117 7 250.63 3.65 303 113 116 3 477.07 0.02 304 113 117 4 431.46 4.05 305 115 118 3 535.16 3.24 306 116 121 5 449.16 0.82 307 117 121 4 453.85 1.53 308 117 122 5 454.06 1.43 309 117 125 8 427.70 14.60 310 118 121 3 472.31 0.52 311 118 122 4 464.12 3.60 312 119 122 3 479.99 4.33 313 119 123 4 473.85 1.26 314 120 123 3 473.86 1.26 315 120 124 4 473.85 1.26 316 121 124 3 473.86 1.26 317 121 125 4 473.84 1.26 318 122 125 3 483.92 2.97 319 122 126 4 473.80 1.27 320 123 126 3 476.76 0.20 321 123 127 4 471.06 2.62 322 124 127 3 476.81 0.26 323 124 128 4 471.28 2.70 324 125 128 3 477.21 0.27 325 125 129 4 477.21 0.27 326 126 129 3 478.50 0.38 327 126 130 4 471.06 2.56 328 127 130 3 483.86 3.05 329 127 131 4 476.91 0.42 330 128 131 3 465.53 2.52 331 128 132 4 465.53 2.52 332 129 132 3 477.20 0.28 333 129 133 4 464.42 1.98 334 130 133 3 473.24 1.32 335 130 134 4 464.44 1.99 336 131 134 3 472.54 2.06 337 131 135 4 464.09 2.16 338 132 135 3 472.45 2.02 339 132 136 4 464.09 2.17 340 133 136 3 472.49 2.04 341 133 137 4 464.05 2.18 342 134 137 3 473.67 1.58 343 134 138 4 454.91 2.39 344 135 138 3 474.12 1.43 345 136 140 4 486.87 0.07 346 137 140 3 481.94 2.54