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 5 440.85 2.75 2 2 73 71 31.81 0.18 3 2 76 74 25.21 0.66 4 2 127 125 22.48 0.08 5 2 128 126 22.48 0.08 6 2 131 129 22.18 0.07 7 3 6 3 474.37 0.27 8 3 7 4 469.13 2.35 9 4 7 3 474.48 0.33 10 4 8 4 474.48 0.33 11 5 8 3 481.84 0.84 12 5 9 4 474.47 0.33 13 6 9 3 477.72 1.21 14 6 10 4 474.47 0.33 15 6 124 118 46.65 0.22 16 6 127 121 46.67 0.21 17 7 10 3 476.95 1.58 18 7 11 4 469.21 2.95 19 7 73 66 48.67 0.64 20 7 74 67 49.56 0.27 21 8 11 3 474.67 0.20 22 8 12 4 469.19 2.92 23 9 12 3 475.56 0.64 24 9 13 4 472.09 1.46 25 9 121 112 59.47 0.11 26 9 124 115 58.98 0.35 27 10 13 3 486.09 2.59 28 10 14 4 464.20 0.42 29 10 70 60 59.62 0.01 30 10 124 114 59.47 0.11 31 10 125 115 59.46 0.10 32 10 128 118 59.00 0.34 33 11 14 3 477.62 1.65 34 11 15 4 456.28 4.38 35 11 70 59 59.74 0.06 36 11 71 60 60.22 0.29 37 11 73 62 60.12 0.24 38 12 15 3 477.06 1.93 39 12 16 4 471.18 1.02 40 13 16 3 477.82 1.42 41 13 17 4 471.18 1.02 42 13 113 100 81.97 0.01 43 13 121 108 60.70 0.21 44 13 125 112 60.66 0.23 45 14 17 3 467.06 1.04 46 14 18 4 467.06 1.04 47 14 21 7 417.43 1.42 48 14 63 49 68.50 1.65 49 14 66 52 60.66 0.24 50 14 67 53 60.66 0.24 51 14 70 56 60.66 0.23 52 15 18 3 476.01 1.75 53 16 113 97 90.83 3.82 54 16 116 100 89.26 3.04 55 17 20 3 482.35 0.62 56 17 21 4 427.39 6.01 57 17 24 7 421.83 8.79 58 17 109 92 89.16 3.08 59 17 113 96 91.46 3.76 60 18 21 3 492.73 3.63 61 20 23 3 470.12 0.65 62 20 24 4 461.34 3.97 63 21 24 3 469.06 0.12 64 21 25 4 461.91 3.69 65 21 63 42 98.14 1.46 66 22 25 3 468.13 0.58 67 22 26 4 468.13 0.57 68 22 60 38 103.62 1.24 69 22 63 41 98.23 1.46 70 23 26 3 480.27 5.50 71 23 27 4 464.27 2.50 72 23 56 33 118.02 0.18 73 24 27 3 482.84 4.21 74 24 28 4 464.26 2.50 75 24 108 84 119.83 1.03 76 24 109 85 126.75 1.87 77 24 112 88 128.56 1.16 78 25 28 3 474.39 0.00 79 25 29 4 470.66 1.85 80 25 59 34 118.00 0.18 81 25 63 38 117.97 0.18 82 26 29 3 475.79 0.70 83 26 30 4 470.66 1.86 84 26 55 29 125.62 1.60 85 26 56 30 125.05 1.31 86 26 59 33 118.00 0.17 87 27 30 3 469.39 1.23 88 27 31 4 469.38 1.23 89 27 108 81 128.92 1.25 90 27 112 85 129.50 1.25 91 28 31 3 469.39 1.23 92 28 32 4 467.42 2.20 93 28 101 73 128.68 1.21 94 28 104 76 128.69 1.21 95 28 105 77 128.72 1.23 96 28 108 80 128.97 1.27 97 29 32 3 474.68 1.42 98 29 33 4 467.43 2.20 99 29 55 26 129.10 1.33 100 29 58 29 129.09 1.34 101 29 59 30 128.97 1.29 102 29 101 72 128.83 1.28 103 30 33 3 477.77 2.23 104 30 34 4 461.07 0.97 105 30 50 20 129.39 1.25 106 31 34 3 468.91 1.86 107 31 35 4 458.38 2.31 108 31 104 73 129.14 1.29 109 31 107 76 129.38 1.27 110 31 108 77 129.47 1.23 111 32 35 3 473.35 0.02 112 32 36 4 445.91 6.52 113 32 39 7 305.87 1.15 114 32 101 69 129.11 1.28 115 32 104 72 129.32 1.28 116 33 37 4 406.11 11.01 117 33 39 6 327.66 12.04 118 33 40 7 305.87 1.15 119 33 43 10 305.84 1.16 120 33 48 15 129.58 1.25 121 34 37 3 482.88 0.90 122 36 39 3 491.22 5.69 123 36 100 64 129.15 1.29 124 36 103 67 129.47 1.24 125 36 104 68 129.48 1.23 126 37 40 3 480.06 0.06 127 38 41 3 492.08 0.69 128 39 42 3 486.45 0.97 129 39 43 4 489.88 4.00 130 39 97 58 129.13 1.28 131 39 100 61 129.47 1.24 132 40 43 3 489.88 4.00 133 40 44 4 480.91 0.48 134 40 48 8 247.77 1.72 135 41 44 3 498.08 0.10 136 42 93 51 128.97 1.31 137 42 94 52 129.34 1.23 138 42 97 55 129.49 1.25 139 43 46 3 477.87 1.02 140 43 48 5 445.66 2.81 141 43 58 15 244.15 3.06 142 45 54 9 248.99 2.20 143 46 54 8 247.93 1.67 144 46 55 9 248.99 2.20 145 46 58 12 247.89 1.69 146 47 52 5 249.01 2.19 147 47 54 7 249.00 2.21 148 47 55 8 249.00 2.21 149 48 52 4 388.97 10.62 150 48 55 7 249.00 2.20 151 49 52 3 475.96 0.88 152 52 55 3 470.41 2.65 153 52 56 4 465.88 4.79 154 53 56 3 472.53 1.48 155 53 57 4 472.52 1.48 156 54 57 3 480.94 2.74 157 54 58 4 472.53 1.48 158 55 58 3 472.53 1.48 159 55 59 4 472.53 1.48 160 56 59 3 474.35 1.68 161 56 60 4 472.58 1.50 162 57 60 3 483.97 4.19 163 57 61 4 472.58 1.51 164 58 61 3 474.88 0.36 165 58 62 4 472.57 1.52 166 59 62 3 481.25 1.80 167 59 63 4 471.95 1.83 168 60 63 3 472.95 2.35 169 60 64 4 471.94 1.84 170 61 64 3 472.52 1.52 171 61 65 4 471.88 1.82 172 62 65 3 483.15 0.40 173 62 66 4 462.79 2.59 174 62 101 39 150.45 3.73 175 63 66 3 475.68 1.52 176 63 67 4 464.62 1.73 177 64 67 3 476.70 3.62 178 64 68 4 466.43 0.84 179 65 68 3 466.43 0.84 180 65 69 4 466.43 0.83 181 65 80 15 153.25 2.35 182 65 83 18 151.10 1.28 183 66 69 3 479.93 1.23 184 66 70 4 466.43 0.84 185 66 105 39 166.28 0.34 186 66 129 63 161.06 1.56 187 66 132 66 153.25 2.35 188 67 70 3 471.37 3.31 189 67 71 4 475.07 1.19 190 68 71 3 475.09 1.19 191 68 72 4 475.06 1.20 192 68 79 11 162.44 2.84 193 69 72 3 475.42 1.35 194 69 73 4 461.99 2.98 195 69 76 7 248.72 6.18 196 69 80 11 153.40 2.39 197 69 128 59 183.02 3.00 198 69 132 63 159.16 0.87 199 70 73 3 470.31 1.19 200 70 128 58 179.81 1.33 201 72 75 3 468.81 1.59 202 72 76 4 423.38 5.24 203 72 79 7 277.90 1.26 204 73 76 3 481.89 0.34 205 75 78 3 475.12 1.03 206 75 79 4 448.41 0.70 207 76 79 3 455.48 3.88 208 76 80 4 436.82 5.09 209 76 128 52 225.06 1.57 210 76 131 55 224.94 1.62 211 76 132 56 223.26 2.48 212 76 135 59 223.25 2.47 213 77 81 4 454.81 3.56 214 77 135 58 223.26 2.47 215 78 81 3 469.17 1.42 216 80 83 3 480.16 0.21 217 80 84 4 464.40 0.98 218 80 132 52 226.33 1.98 219 80 135 55 225.35 1.54 220 81 84 3 477.11 1.73 221 81 85 4 464.41 0.98 222 81 139 58 225.68 1.73 223 82 85 3 479.44 0.57 224 82 86 4 475.69 4.66 225 83 86 3 474.43 5.29 226 83 87 4 468.99 8.01 227 83 136 53 226.38 1.99 228 84 87 3 476.26 4.38 229 84 88 4 459.77 3.38 230 84 135 51 226.41 1.97 231 84 136 52 226.38 1.99 232 84 138 54 226.37 1.99 233 84 139 55 226.28 2.00 234 85 88 3 478.64 3.19 235 85 89 4 455.31 1.16 236 85 139 54 226.30 1.99 237 86 89 3 485.32 0.17 238 86 90 4 454.91 0.97 239 86 91 5 410.38 8.35 240 87 91 4 405.30 10.89 241 87 92 5 351.54 14.96 242 87 93 6 324.36 1.38 243 87 98 11 293.85 0.66 244 87 136 49 226.49 1.97 245 87 140 53 226.30 1.99 246 88 92 4 391.99 5.26 247 88 139 51 226.34 2.00 248 88 140 52 226.27 1.98 249 89 92 3 490.06 1.74 250 92 140 48 226.39 1.98 251 93 97 4 482.50 0.33 252 93 98 5 475.51 3.56 253 93 140 47 226.50 1.98 254 94 97 3 495.75 2.32 255 94 98 4 484.89 0.86 256 95 98 3 496.92 1.20 257 96 99 3 494.80 4.09 258 96 100 4 484.06 2.08 259 97 100 3 484.06 2.08 260 97 101 4 479.62 1.22 261 98 101 3 485.38 1.42 262 98 102 4 474.46 0.77 263 98 133 35 227.28 2.19 264 98 136 38 227.38 2.14 265 98 137 39 227.27 2.19 266 98 140 42 227.25 2.18 267 99 102 3 476.77 1.81 268 99 103 4 474.45 0.77 269 100 103 3 474.45 0.77 270 100 104 4 474.45 0.77 271 101 104 3 469.04 0.78 272 101 105 4 463.32 0.82 273 102 105 3 469.43 3.16 274 102 106 4 461.35 0.17 275 102 129 27 227.84 2.31 276 102 133 31 227.85 2.31 277 103 106 3 468.98 0.65 278 103 107 4 461.75 0.38 279 104 107 3 476.98 3.17 280 104 108 4 466.63 2.01 281 105 108 3 480.23 1.54 282 105 109 4 466.63 2.01 283 105 129 24 228.43 2.37 284 106 109 3 472.74 2.38 285 106 110 4 464.00 1.68 286 106 117 11 244.30 4.95 287 106 122 16 229.05 2.35 288 106 125 19 228.63 2.30 289 106 126 20 228.62 2.31 290 106 129 23 228.52 2.35 291 107 110 3 472.11 2.38 292 107 111 4 461.43 2.96 293 108 111 3 476.59 2.71 294 108 112 4 461.44 2.96 295 109 112 3 470.17 1.45 296 109 113 4 450.79 2.36 297 109 125 16 229.31 2.37 298 110 113 3 479.81 1.83 299 110 117 7 244.44 4.89 300 113 116 3 477.86 0.55 301 113 117 4 446.12 1.43 302 114 117 3 480.09 1.67 303 115 118 3 526.28 0.91 304 116 121 5 449.01 3.73 305 117 121 4 451.70 2.39 306 117 122 5 440.93 7.78 307 117 125 8 424.35 0.56 308 118 121 3 467.34 4.40 309 118 122 4 461.91 1.69 310 119 122 3 465.25 0.02 311 119 123 4 468.48 4.97 312 120 123 3 474.81 1.80 313 120 124 4 468.48 4.98 314 121 124 3 474.87 1.78 315 121 125 4 467.75 5.33 316 122 125 3 474.86 1.78 317 122 126 4 474.82 1.78 318 123 126 3 474.84 1.78 319 123 127 4 474.83 1.78 320 124 127 3 474.84 1.78 321 124 128 4 474.71 1.72 322 125 128 3 475.36 2.04 323 125 129 4 467.89 0.73 324 126 129 3 482.05 1.31 325 126 130 4 468.89 1.24 326 127 130 3 474.79 4.18 327 127 131 4 466.42 2.48 328 128 131 3 478.31 2.42 329 128 132 4 466.42 2.48 330 129 132 3 475.88 3.64 331 129 133 4 464.81 1.64 332 130 133 3 473.00 1.61 333 130 134 4 464.67 1.43 334 131 134 3 466.19 2.17 335 131 135 4 464.50 1.34 336 132 135 3 475.73 4.46 337 132 136 4 465.55 0.98 338 133 136 3 476.43 4.11 339 133 137 4 465.50 0.07 340 134 137 3 481.44 1.29 341 134 138 4 461.45 0.19 342 135 138 3 481.12 1.46 343 136 140 4 491.44 0.39 344 137 140 3 485.50 0.97