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 5 442.00 0.61 2 2 73 71 30.28 0.88 3 2 76 74 25.25 0.31 4 2 127 125 22.80 0.12 5 2 128 126 22.05 0.26 6 2 131 129 21.80 0.13 7 3 6 3 476.94 1.02 8 3 7 4 464.88 5.44 9 4 7 3 475.97 0.10 10 4 8 4 464.88 5.44 11 5 8 3 478.05 1.04 12 5 9 4 475.42 0.17 13 6 9 3 478.72 0.70 14 6 10 4 467.34 3.89 15 6 124 118 47.12 0.18 16 6 127 121 47.12 0.18 17 7 10 3 475.32 0.10 18 7 11 4 470.25 2.44 19 7 73 66 47.34 0.21 20 7 74 67 49.67 1.14 21 8 11 3 475.32 0.10 22 8 12 4 470.24 2.44 23 9 12 3 478.05 0.60 24 9 13 4 470.22 2.45 25 9 121 112 59.98 0.83 26 9 124 115 59.95 0.83 27 10 13 3 479.00 1.96 28 10 14 4 470.09 2.43 29 10 70 60 60.23 0.70 30 10 124 114 59.98 0.83 31 10 125 115 59.98 0.83 32 10 128 118 59.91 0.80 33 11 14 3 478.93 2.00 34 11 15 4 459.78 2.59 35 11 70 59 60.26 0.68 36 11 71 60 60.28 0.68 37 11 73 62 60.28 0.68 38 12 15 3 473.12 3.77 39 12 16 4 469.38 1.90 40 13 16 3 478.82 0.92 41 13 17 4 465.24 0.17 42 13 121 108 60.59 0.58 43 13 125 112 60.58 0.58 44 14 17 3 467.66 1.38 45 14 18 4 465.38 0.25 46 14 21 7 398.96 6.41 47 14 66 52 60.77 0.47 48 14 67 53 60.58 0.57 49 14 70 56 60.58 0.56 50 14 109 95 78.65 0.55 51 15 18 3 464.36 3.10 52 16 113 97 94.85 1.17 53 16 116 100 91.82 0.32 54 17 20 3 485.95 0.18 55 17 21 4 443.26 1.93 56 17 24 7 425.76 1.26 57 17 109 92 91.84 0.26 58 17 113 96 94.94 1.20 59 18 21 3 496.86 2.56 60 20 23 3 474.48 0.54 61 20 24 4 467.89 1.56 62 21 24 3 467.89 1.56 63 21 25 4 465.13 2.94 64 21 63 42 96.33 0.73 65 22 25 3 469.04 1.02 66 22 26 4 469.04 1.02 67 22 60 38 99.22 1.96 68 22 63 41 99.23 1.96 69 23 26 3 481.18 5.04 70 23 27 4 465.18 2.96 71 23 56 33 117.55 0.40 72 24 27 3 482.81 4.23 73 24 28 4 463.04 1.74 74 24 108 84 119.81 0.52 75 24 109 85 119.85 0.14 76 24 112 88 124.91 1.78 77 24 113 89 124.91 1.78 78 25 28 3 470.27 0.94 79 25 29 4 465.07 0.72 80 25 59 34 117.63 0.34 81 25 63 38 117.56 0.35 82 26 29 3 471.60 0.07 83 26 30 4 465.02 0.70 84 26 55 29 123.42 2.29 85 26 56 30 122.62 2.83 86 26 59 33 117.61 0.33 87 27 30 3 469.45 1.51 88 27 31 4 465.03 0.70 89 27 108 81 125.09 1.76 90 27 112 85 125.44 1.79 91 28 31 3 471.83 0.32 92 28 32 4 467.06 2.08 93 28 101 73 124.93 1.78 94 28 104 76 124.95 1.78 95 28 105 77 124.94 1.78 96 28 108 80 125.17 1.78 97 29 32 3 469.30 1.25 98 29 33 4 462.98 1.74 99 29 55 26 125.30 1.84 100 29 58 29 125.14 1.78 101 29 59 30 125.14 1.78 102 29 101 72 125.01 1.78 103 30 33 3 485.35 0.56 104 30 34 4 462.94 1.75 105 30 50 20 125.47 1.82 106 31 34 3 480.92 2.77 107 31 35 4 461.92 1.49 108 31 104 73 125.11 1.75 109 31 107 76 125.27 1.76 110 31 108 77 125.37 1.80 111 32 35 3 473.53 0.89 112 32 36 4 456.44 1.26 113 32 39 7 338.45 17.01 114 32 101 69 125.08 1.75 115 32 104 72 125.22 1.75 116 33 37 4 385.61 3.60 117 33 39 6 299.46 2.49 118 33 40 7 166.57 8.05 119 33 43 10 166.58 8.05 120 33 48 15 125.56 1.80 121 36 39 3 491.24 1.12 122 36 100 64 125.15 1.73 123 36 103 67 125.48 1.79 124 36 104 68 125.49 1.79 125 37 40 3 483.18 1.50 126 38 41 3 485.42 0.82 127 39 42 3 488.75 1.12 128 39 43 4 483.82 1.18 129 39 97 58 125.14 1.72 130 39 100 61 125.41 1.82 131 40 43 3 482.95 0.54 132 40 44 4 476.10 0.01 133 40 48 8 146.46 0.28 134 41 44 3 495.29 2.30 135 42 93 51 124.84 1.80 136 42 94 52 125.01 1.79 137 42 97 55 125.30 1.78 138 43 46 3 478.87 1.53 139 43 48 5 430.28 10.10 140 43 58 15 125.72 1.79 141 45 54 9 135.66 5.71 142 46 54 8 135.51 5.76 143 46 58 12 135.46 5.78 144 47 52 5 160.66 6.75 145 47 54 7 139.21 3.94 146 47 55 8 135.67 5.71 147 48 52 4 403.87 5.35 148 48 55 7 138.79 4.15 149 49 52 3 475.93 0.90 150 52 55 3 471.41 2.15 151 52 56 4 469.69 2.87 152 53 56 3 471.30 2.08 153 53 57 4 472.80 1.33 154 54 57 3 472.81 1.33 155 54 58 4 472.81 1.33 156 55 58 3 474.25 0.62 157 55 59 4 473.53 0.98 158 56 59 3 474.26 0.64 159 56 60 4 473.55 0.99 160 57 60 3 479.94 2.19 161 57 61 4 473.55 0.99 162 58 61 3 473.76 0.89 163 58 62 4 473.54 0.99 164 59 62 3 481.20 2.83 165 59 63 4 462.33 3.98 166 60 63 3 473.97 1.84 167 60 64 4 462.33 3.98 168 61 64 3 473.00 0.76 169 61 65 4 462.31 3.98 170 62 65 3 479.29 2.33 171 62 66 4 468.38 3.12 172 62 101 39 155.16 1.51 173 63 66 3 476.68 1.02 174 63 67 4 468.37 3.12 175 64 67 3 466.00 1.04 176 64 68 4 463.50 0.20 177 65 68 3 469.72 0.88 178 65 69 4 465.98 1.03 179 65 80 15 154.50 1.84 180 65 83 18 154.50 1.84 181 66 69 3 470.22 1.08 182 66 70 4 465.98 1.03 183 66 105 39 162.58 1.72 184 66 128 62 177.65 5.69 185 66 129 63 159.44 0.48 186 66 132 66 158.63 0.09 187 67 70 3 475.18 1.40 188 67 71 4 471.37 1.66 189 68 71 3 476.32 0.83 190 68 72 4 471.37 1.66 191 68 79 11 159.41 0.39 192 69 72 3 476.41 0.86 193 69 73 4 457.66 5.14 194 69 76 7 280.12 1.32 195 69 80 11 159.40 0.39 196 69 128 59 187.13 1.03 197 69 132 63 159.59 0.41 198 70 73 3 471.31 1.69 199 70 128 58 187.07 1.01 200 72 75 3 472.78 0.39 201 72 76 4 417.87 0.39 202 72 79 7 284.69 0.88 203 73 76 3 478.25 3.12 204 75 78 3 481.41 1.23 205 75 79 4 459.23 4.78 206 76 79 3 470.97 1.09 207 76 80 4 456.65 6.06 208 76 128 52 265.09 2.30 209 76 131 55 263.50 2.50 210 76 132 56 261.83 1.91 211 77 80 3 477.75 3.10 212 77 81 4 445.72 4.92 213 77 135 58 261.13 1.57 214 78 81 3 469.93 0.81 215 80 83 3 481.16 0.70 216 80 84 4 461.41 7.21 217 80 132 52 267.08 3.08 218 80 135 55 267.08 3.08 219 80 136 56 267.08 3.08 220 81 84 3 479.86 2.01 221 81 85 4 479.88 2.02 222 81 139 58 266.92 3.21 223 82 85 3 481.11 1.41 224 82 86 4 479.87 2.02 225 83 86 3 479.88 2.02 226 83 87 4 479.88 2.02 227 83 136 53 267.62 3.33 228 84 87 3 484.45 0.27 229 84 88 4 461.12 0.60 230 84 135 51 267.61 3.33 231 84 136 52 267.60 3.33 232 84 138 54 267.59 3.33 233 84 139 55 267.55 3.33 234 85 88 3 479.63 2.68 235 85 89 4 458.51 1.90 236 85 139 54 267.54 3.34 237 86 89 3 484.52 0.23 238 86 90 4 449.82 3.77 239 86 91 5 447.99 4.66 240 87 91 4 440.88 8.21 241 87 92 5 360.33 4.42 242 87 93 6 338.87 15.14 243 87 98 11 280.36 3.03 244 87 136 49 267.66 3.33 245 87 140 53 267.54 3.34 246 88 92 4 396.81 13.81 247 88 139 51 267.60 3.33 248 88 140 52 267.53 3.33 249 89 92 3 493.91 3.66 250 92 140 48 267.64 3.33 251 93 97 4 478.35 0.06 252 93 98 5 472.75 2.74 253 93 140 47 267.68 3.33 254 94 97 3 488.44 0.93 255 95 98 3 481.85 0.99 256 95 140 45 267.80 3.28 257 96 99 3 485.05 2.58 258 96 100 4 470.12 3.58 259 97 100 3 475.38 1.54 260 97 101 4 465.23 1.12 261 98 101 3 477.43 2.56 262 98 102 4 465.24 1.12 263 98 133 35 268.06 3.35 264 98 136 38 268.05 3.35 265 98 137 39 268.01 3.34 266 98 140 42 268.01 3.34 267 99 102 3 475.41 0.29 268 99 103 4 471.19 1.82 269 100 103 3 475.41 0.29 270 100 104 4 473.42 1.28 271 101 104 3 471.26 1.79 272 101 105 4 465.31 1.12 273 102 105 3 472.72 2.52 274 102 106 4 467.06 0.32 275 102 129 27 268.57 3.49 276 102 133 31 268.41 3.41 277 103 106 3 470.04 1.79 278 103 107 4 467.06 0.32 279 104 107 3 467.01 0.29 280 104 108 4 465.36 1.12 281 105 108 3 467.58 0.03 282 105 109 4 465.37 1.13 283 105 129 24 269.56 3.58 284 106 109 3 473.57 2.96 285 106 110 4 467.57 0.03 286 106 117 11 270.43 3.66 287 106 122 16 269.78 3.62 288 106 125 19 269.72 3.66 289 106 126 20 269.71 3.66 290 106 129 23 269.67 3.62 291 107 110 3 475.82 4.09 292 107 111 4 467.57 0.03 293 108 111 3 477.60 3.21 294 108 112 4 477.60 3.21 295 109 112 3 483.75 0.13 296 109 113 4 458.17 1.51 297 109 125 16 269.98 3.53 298 110 113 3 480.81 1.33 299 110 117 7 270.47 3.65 300 113 116 3 478.85 0.06 301 113 117 4 463.35 2.21 302 114 117 3 481.09 1.17 303 115 118 3 525.59 0.56 304 116 121 5 451.52 1.91 305 117 121 4 451.54 1.92 306 117 122 5 450.47 2.43 307 117 125 8 421.20 10.13 308 118 121 3 465.57 2.82 309 118 122 4 456.69 0.67 310 119 122 3 466.19 2.51 311 119 123 4 462.86 2.50 312 120 123 3 469.84 0.69 313 120 124 4 464.51 1.67 314 121 124 3 465.82 2.32 315 121 125 4 469.12 5.50 316 122 125 3 475.83 2.27 317 122 126 4 463.56 1.19 318 123 126 3 477.67 1.35 319 123 127 4 466.25 2.51 320 124 127 3 475.71 2.21 321 124 128 4 469.84 0.71 322 125 128 3 471.62 0.18 323 125 129 4 468.88 0.24 324 126 129 3 485.62 0.12 325 126 130 4 468.89 0.23 326 127 130 3 477.48 4.19 327 127 131 4 469.89 0.73 328 128 131 3 477.48 4.19 329 128 132 4 466.02 2.67 330 129 132 3 476.88 3.14 331 129 133 4 464.45 1.82 332 130 133 3 471.99 3.12 333 130 134 4 463.43 1.16 334 131 134 3 466.47 1.65 335 131 135 4 465.15 1.01 336 132 135 3 475.12 4.76 337 132 136 4 465.15 1.02 338 133 136 3 470.36 0.07 339 133 137 4 459.13 2.54 340 134 137 3 473.18 5.42 341 134 138 4 457.83 1.88 342 135 138 3 480.28 1.88 343 136 140 4 490.83 0.70 344 137 140 3 487.25 1.09