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 5 448.87 2.71 2 2 73 71 31.09 0.07 3 2 76 74 25.14 0.62 4 2 127 125 23.78 0.15 5 2 128 126 23.77 0.15 6 2 131 129 23.60 0.15 7 3 6 3 479.25 0.38 8 3 7 4 473.23 3.39 9 4 7 3 488.61 4.29 10 4 8 4 473.23 3.39 11 5 8 3 475.86 2.08 12 5 9 4 473.24 3.39 13 6 9 3 473.25 3.40 14 6 10 4 469.89 1.72 15 6 124 118 47.46 0.60 16 6 127 121 45.66 0.29 17 7 10 3 472.98 1.07 18 7 11 4 469.84 1.76 19 7 73 66 46.61 0.76 20 7 74 67 48.50 0.19 21 8 11 3 475.97 0.81 22 8 12 4 473.47 0.01 23 9 12 3 482.08 0.18 24 9 13 4 476.83 1.69 25 9 120 111 61.45 0.06 26 9 121 112 61.29 0.07 27 9 124 115 61.27 0.06 28 10 13 3 476.85 1.69 29 10 14 4 476.85 1.68 30 10 70 60 61.24 0.04 31 10 124 114 61.31 0.06 32 10 125 115 61.27 0.06 33 10 128 118 61.16 0.04 34 11 14 3 476.86 1.68 35 11 15 4 476.85 1.68 36 11 70 59 61.28 0.04 37 11 73 62 61.28 0.05 38 12 15 3 486.86 1.99 39 12 16 4 476.86 1.68 40 13 16 3 483.34 1.61 41 13 17 4 476.84 1.67 42 13 113 100 70.82 0.82 43 13 121 108 62.12 0.24 44 13 125 112 62.00 0.22 45 14 17 3 475.80 2.17 46 14 18 4 475.67 2.23 47 14 21 7 413.02 4.03 48 14 63 49 67.83 0.66 49 14 66 52 61.94 0.28 50 14 67 53 61.94 0.28 51 14 70 56 61.94 0.28 52 14 109 95 70.78 0.81 53 15 18 3 476.71 1.70 54 16 113 97 87.75 0.87 55 16 116 100 72.48 0.12 56 17 20 3 487.97 3.44 57 17 21 4 445.80 4.49 58 17 24 7 412.53 4.27 59 17 109 92 70.88 0.81 60 18 21 3 502.08 1.81 61 20 23 3 479.54 1.94 62 20 24 4 466.78 1.62 63 21 24 3 483.87 0.23 64 21 25 4 466.78 1.62 65 21 63 42 90.67 0.59 66 22 25 3 478.64 2.40 67 22 26 4 466.79 1.62 68 22 60 38 97.19 1.49 69 22 63 41 96.87 1.33 70 23 26 3 478.64 2.40 71 23 27 4 466.82 1.60 72 24 27 3 468.30 2.33 73 24 28 4 468.29 2.34 74 24 108 84 120.45 1.40 75 24 109 85 122.78 0.03 76 24 112 88 128.16 0.35 77 25 28 3 478.67 0.27 78 25 29 4 468.29 2.34 79 25 59 34 118.23 0.40 80 26 29 3 479.43 0.65 81 26 30 4 469.37 2.88 82 26 55 29 127.49 0.16 83 26 56 30 124.15 1.32 84 26 59 33 118.38 0.39 85 27 30 3 476.64 0.75 86 27 31 4 462.94 2.02 87 27 108 81 129.53 0.21 88 27 112 85 131.25 1.02 89 28 31 3 471.06 2.91 90 28 32 4 462.95 2.02 91 28 101 73 128.44 0.26 92 28 104 76 128.44 0.25 93 28 105 77 128.44 0.25 94 28 108 80 129.53 0.21 95 29 32 3 469.42 2.08 96 29 33 4 464.21 1.40 97 29 55 26 130.35 0.64 98 29 58 29 130.00 0.47 99 29 59 30 129.50 0.22 100 29 101 72 129.49 0.23 101 30 33 3 469.41 2.08 102 30 34 4 463.72 0.76 103 30 50 20 131.28 1.00 104 31 34 3 478.58 0.54 105 31 35 4 458.41 3.41 106 31 104 73 130.98 0.93 107 31 107 76 131.15 0.98 108 31 108 77 131.20 1.00 109 31 111 80 131.34 1.04 110 32 35 3 471.34 3.05 111 32 36 4 442.03 0.95 112 32 39 7 319.24 3.33 113 32 100 68 130.94 0.90 114 32 101 69 130.97 0.92 115 32 104 72 131.03 0.93 116 33 37 4 442.12 0.99 117 33 39 6 306.66 2.96 118 33 40 7 293.42 3.66 119 33 43 10 299.32 0.71 120 33 48 15 131.32 0.98 121 33 55 22 131.27 0.99 122 34 37 3 491.03 0.96 123 36 39 3 498.69 4.28 124 36 100 64 130.98 0.89 125 36 103 67 131.31 1.03 126 36 104 68 131.31 1.03 127 37 40 3 487.53 1.73 128 38 41 3 492.72 0.86 129 39 42 3 498.81 2.14 130 39 43 4 489.93 0.09 131 39 97 58 130.98 0.92 132 39 100 61 131.21 0.99 133 40 43 3 490.03 0.04 134 40 44 4 485.85 1.95 135 40 48 8 135.64 0.62 136 41 44 3 500.98 0.28 137 42 45 3 650.18 0.62 138 42 93 51 130.72 0.83 139 42 94 52 131.13 1.00 140 42 97 55 131.19 1.01 141 43 46 3 487.65 1.25 142 43 48 5 408.89 7.52 143 43 58 15 131.55 1.07 144 45 54 9 134.97 1.16 145 46 54 8 134.97 1.16 146 46 58 12 134.93 1.18 147 47 52 5 151.21 2.00 148 47 54 7 134.99 1.16 149 47 55 8 134.99 1.16 150 48 55 7 134.97 1.15 151 49 52 3 487.34 1.73 152 51 56 5 462.40 3.60 153 52 55 3 476.45 0.56 154 52 56 4 467.57 1.01 155 53 56 3 477.22 3.81 156 53 57 4 467.61 1.02 157 54 57 3 475.94 1.99 158 54 58 4 472.30 1.32 159 55 58 3 474.75 2.54 160 55 59 4 472.50 1.22 161 56 59 3 479.28 2.16 162 56 60 4 472.53 1.22 163 57 60 3 480.88 2.02 164 57 61 4 472.56 1.19 165 58 61 3 478.46 3.40 166 58 62 4 472.56 1.18 167 59 62 3 482.60 1.33 168 59 63 4 473.26 0.80 169 60 63 3 479.45 2.11 170 60 64 4 472.51 1.10 171 61 64 3 483.92 0.12 172 61 65 4 472.50 1.10 173 62 65 3 483.93 0.13 174 62 66 4 472.47 1.09 175 62 101 39 140.50 0.84 176 63 66 3 480.28 1.96 177 63 67 4 475.96 4.12 178 64 67 3 475.95 4.12 179 64 68 4 476.24 3.98 180 65 68 3 483.73 0.09 181 65 69 4 476.20 3.95 182 65 80 15 145.98 0.15 183 65 83 18 142.43 1.89 184 66 69 3 476.21 3.96 185 66 70 4 476.20 3.95 186 66 105 39 162.33 2.47 187 66 132 66 142.69 1.81 188 67 70 3 476.20 3.95 189 67 71 4 476.20 3.96 190 68 71 3 477.89 3.10 191 68 72 4 468.20 0.04 192 68 79 11 171.90 8.18 193 68 80 12 154.07 3.85 194 69 72 3 474.61 3.15 195 69 73 4 449.60 2.69 196 69 76 7 233.66 22.71 197 69 80 11 175.00 6.62 198 69 128 59 181.87 3.27 199 69 132 63 177.20 5.52 200 70 73 3 473.38 3.49 201 70 128 58 181.88 3.27 202 72 75 3 484.35 1.99 203 72 76 4 446.54 10.89 204 72 79 7 278.14 4.79 205 73 76 3 477.05 3.35 206 75 78 3 497.99 0.83 207 75 79 4 463.55 2.41 208 76 79 3 471.73 1.69 209 76 80 4 447.99 0.97 210 76 128 52 268.12 5.80 211 76 131 55 267.29 5.55 212 76 132 56 265.31 4.66 213 76 135 59 264.31 4.50 214 77 81 4 437.76 3.14 215 77 135 58 264.39 4.46 216 78 81 3 472.69 3.52 217 80 83 3 479.86 4.48 218 80 84 4 466.12 2.35 219 80 132 52 270.42 5.66 220 80 135 55 269.19 5.91 221 80 136 56 269.19 5.91 222 81 84 3 466.16 2.37 223 81 85 4 470.22 4.38 224 81 139 58 269.23 5.91 225 82 85 3 477.34 3.41 226 82 86 4 474.78 2.10 227 83 86 3 474.78 2.10 228 83 87 4 474.78 2.10 229 83 136 53 272.01 5.96 230 84 87 3 477.47 0.77 231 84 88 4 474.78 2.10 232 84 135 51 272.11 6.02 233 84 136 52 272.00 5.97 234 84 138 54 272.01 5.97 235 84 139 55 271.93 5.94 236 85 88 3 481.18 5.30 237 85 89 4 466.41 2.08 238 85 139 54 271.95 5.95 239 86 90 4 423.60 8.03 240 86 91 5 375.24 4.67 241 87 91 4 349.94 5.42 242 87 92 5 312.88 4.48 243 87 98 11 276.04 6.46 244 87 136 49 272.19 6.04 245 87 140 53 271.92 5.96 246 88 92 4 319.68 7.20 247 88 139 51 272.01 5.97 248 88 140 52 271.81 5.98 249 89 92 3 486.01 0.87 250 89 139 50 272.10 6.01 251 93 97 4 481.49 1.03 252 93 98 5 473.39 1.48 253 93 140 47 272.36 6.05 254 94 97 3 493.91 0.40 255 95 98 3 493.57 0.58 256 95 137 42 272.67 6.04 257 95 140 45 272.64 6.04 258 96 99 3 491.93 0.94 259 96 100 4 481.55 0.99 260 97 100 3 489.21 4.83 261 97 101 4 483.91 2.18 262 98 101 3 489.19 4.84 263 98 102 4 473.19 1.44 264 98 133 35 273.12 6.05 265 98 136 38 273.14 6.06 266 98 137 39 273.13 6.06 267 98 140 42 273.13 6.06 268 99 102 3 484.56 1.85 269 99 103 4 472.97 1.52 270 100 103 3 486.00 1.13 271 100 104 4 479.09 4.59 272 101 104 3 481.43 3.43 273 101 105 4 474.76 4.29 274 102 105 3 478.93 2.21 275 102 106 4 474.75 4.29 276 102 129 27 273.77 6.11 277 102 133 31 273.66 6.06 278 103 106 3 478.97 2.20 279 103 107 4 474.75 4.30 280 104 107 3 478.97 2.20 281 104 108 4 475.47 3.95 282 105 108 3 479.00 2.19 283 105 109 4 479.00 2.19 284 105 129 24 273.99 6.12 285 106 109 3 482.13 3.71 286 106 110 4 479.04 2.17 287 106 117 11 274.87 6.25 288 106 122 16 274.44 6.26 289 106 125 19 274.44 6.27 290 106 126 20 274.36 6.29 291 106 129 23 273.99 6.13 292 107 110 3 479.08 2.15 293 107 111 4 479.06 2.16 294 108 111 3 483.57 0.10 295 108 112 4 475.58 0.41 296 109 112 3 483.19 2.20 297 109 113 4 462.18 6.29 298 109 125 16 274.57 6.27 299 110 113 3 484.69 1.45 300 110 117 7 274.89 6.25 301 113 116 3 468.69 2.78 302 113 117 4 322.97 8.66 303 116 121 5 456.19 0.84 304 117 121 4 456.20 0.83 305 117 122 5 445.62 4.46 306 117 125 8 426.86 13.84 307 118 121 3 469.31 0.77 308 118 122 4 459.56 0.71 309 119 122 3 472.24 6.96 310 119 123 4 463.44 1.20 311 120 123 3 473.57 1.18 312 120 124 4 464.36 0.79 313 121 124 3 466.75 1.85 314 121 125 4 464.36 0.80 315 122 125 3 481.62 2.88 316 122 126 4 469.88 1.88 317 123 126 3 478.22 2.27 318 123 127 4 469.91 1.88 319 124 127 3 472.48 0.59 320 124 128 4 469.91 1.89 321 125 128 3 477.24 0.24 322 125 129 4 472.14 0.77 323 126 129 3 475.72 1.01 324 126 130 4 472.39 0.89 325 127 130 3 482.61 2.43 326 127 131 4 472.08 0.74 327 128 131 3 489.81 6.03 328 128 132 4 472.38 0.89 329 129 132 3 482.61 2.43 330 129 133 4 465.51 2.53 331 130 133 3 470.99 1.30 332 130 134 4 465.51 2.52 333 131 134 3 472.35 0.90 334 131 135 4 465.51 2.52 335 132 135 3 469.91 0.32 336 132 136 4 471.38 1.48 337 133 136 3 472.44 0.96 338 133 137 4 471.38 1.48 339 134 137 3 476.73 0.13 340 134 138 4 475.66 0.67 341 135 138 3 476.75 0.14 342 136 140 4 496.15 2.48 343 137 140 3 481.41 2.66