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 73 71 36.77 0.08 2 2 127 125 27.25 0.15 3 2 128 126 26.71 0.41 4 3 6 3 476.26 0.34 5 3 7 4 473.38 0.32 6 4 7 3 477.74 1.23 7 4 8 4 473.38 0.32 8 5 8 3 475.50 0.73 9 5 9 4 469.37 1.69 10 6 9 3 468.50 1.05 11 6 10 4 472.20 0.81 12 6 124 118 55.82 1.03 13 6 127 121 53.72 0.05 14 7 10 3 478.31 3.89 15 7 11 4 472.09 0.88 16 7 73 66 56.22 1.16 17 7 74 67 60.47 0.72 18 8 11 3 478.41 2.12 19 8 12 4 470.82 1.50 20 9 12 3 473.84 0.16 21 9 13 4 470.81 1.50 22 9 121 112 68.31 1.34 23 9 124 115 68.25 1.35 24 10 13 3 483.30 1.65 25 10 14 4 470.99 0.65 26 10 70 60 68.31 1.33 27 10 124 114 68.29 1.35 28 10 125 115 68.28 1.35 29 10 128 118 68.22 1.33 30 11 14 3 478.15 1.27 31 11 15 4 471.25 0.51 32 11 70 59 68.34 1.33 33 11 73 62 68.34 1.33 34 12 15 3 478.54 0.73 35 12 16 4 473.47 0.62 36 13 16 3 480.12 2.69 37 13 17 4 474.64 1.30 38 13 113 100 91.37 1.60 39 13 121 108 68.81 1.21 40 13 125 112 68.41 1.34 41 14 17 3 474.64 1.30 42 14 18 4 474.63 1.30 43 14 21 7 389.35 11.43 44 14 66 52 68.39 1.34 45 14 67 53 68.40 1.34 46 14 70 56 68.40 1.34 47 15 18 3 476.69 0.28 48 16 113 97 100.95 0.14 49 16 116 100 95.20 2.98 50 17 20 3 490.55 1.07 51 17 21 4 452.27 1.93 52 17 24 7 427.01 10.68 53 17 109 92 97.81 1.39 54 17 113 96 100.98 0.13 55 18 21 3 493.75 2.19 56 20 23 3 490.59 2.00 57 20 24 4 470.34 4.41 58 21 24 3 481.09 2.75 59 21 25 4 473.34 2.92 60 21 63 42 106.90 0.74 61 22 25 3 486.24 0.18 62 22 26 4 482.55 1.69 63 22 59 37 111.96 0.48 64 22 60 38 109.80 0.39 65 22 63 41 109.76 0.42 66 23 26 3 482.55 1.69 67 23 27 4 482.55 1.69 68 24 27 3 481.24 2.34 69 24 28 4 480.29 2.82 70 24 108 84 127.54 0.29 71 24 109 85 130.22 0.90 72 24 112 88 146.25 0.23 73 25 28 3 482.78 1.57 74 25 29 4 480.28 2.83 75 25 59 34 125.91 0.46 76 26 29 3 483.75 1.09 77 26 30 4 472.20 0.54 78 26 55 29 148.63 1.20 79 26 56 30 148.64 1.20 80 26 59 33 124.56 0.23 81 27 30 3 477.42 2.07 82 27 31 4 477.36 2.10 83 27 108 81 152.99 2.31 84 27 112 85 152.99 2.27 85 28 31 3 479.42 1.07 86 28 32 4 477.38 2.10 87 28 101 73 152.96 2.33 88 28 104 76 152.98 2.32 89 28 105 77 152.91 2.30 90 28 108 80 153.00 2.31 91 29 32 3 477.38 2.10 92 29 33 4 477.38 2.10 93 29 55 26 156.45 3.75 94 29 58 29 150.74 0.90 95 29 59 30 150.41 1.00 96 29 62 33 150.29 0.95 97 29 101 72 153.14 2.39 98 30 33 3 480.67 0.46 99 30 34 4 473.11 0.04 100 30 50 20 173.16 12.00 101 30 55 25 156.58 3.75 102 31 34 3 480.82 2.77 103 31 35 4 473.11 0.04 104 31 104 73 153.63 2.27 105 31 107 76 153.69 2.25 106 31 108 77 153.67 2.23 107 31 111 80 153.69 2.23 108 32 35 3 474.33 0.57 109 32 36 4 464.95 4.25 110 32 39 7 434.16 4.84 111 32 100 68 153.74 2.33 112 32 101 69 153.69 2.29 113 32 104 72 153.68 2.28 114 33 36 3 477.56 1.10 115 33 37 4 461.17 4.50 116 33 39 6 434.16 4.84 117 33 40 7 332.99 6.87 118 33 43 10 279.65 4.62 119 33 48 15 173.64 12.11 120 34 37 3 499.19 5.36 121 36 39 3 493.55 1.65 122 36 100 64 153.78 2.31 123 36 103 67 153.84 2.30 124 36 104 68 153.81 2.29 125 37 40 3 487.76 3.13 126 38 41 3 496.57 1.28 127 39 42 3 506.74 1.95 128 39 97 58 153.93 2.40 129 39 100 61 154.00 2.37 130 40 43 3 489.00 2.03 131 40 48 8 244.64 1.15 132 41 44 3 493.62 3.52 133 42 92 50 154.27 2.56 134 42 93 51 154.25 2.56 135 42 94 52 154.30 2.52 136 42 97 55 154.24 2.47 137 43 46 3 484.70 4.68 138 43 48 5 424.49 0.83 139 43 58 15 226.59 3.24 140 45 54 9 245.05 1.06 141 46 54 8 245.03 1.07 142 46 58 12 244.97 1.08 143 47 52 5 286.16 14.75 144 47 54 7 245.28 1.19 145 47 55 8 248.25 2.67 146 48 55 7 251.93 2.36 147 49 52 3 470.43 1.75 148 51 56 5 459.32 1.29 149 52 55 3 485.31 5.17 150 52 56 4 478.88 8.38 151 53 56 3 488.98 3.34 152 53 57 4 479.19 8.22 153 54 57 3 481.25 7.19 154 54 58 4 481.20 7.21 155 55 58 3 487.75 3.95 156 55 59 4 481.22 7.21 157 56 59 3 478.10 0.89 158 56 60 4 467.95 0.56 159 57 60 3 490.17 0.35 160 57 61 4 471.82 0.25 161 58 61 3 481.79 4.54 162 58 62 4 471.82 0.25 163 59 62 3 479.97 4.33 164 59 63 4 471.92 0.21 165 60 63 3 474.50 1.49 166 60 64 4 474.55 1.47 167 61 64 3 479.26 0.81 168 61 65 4 474.68 1.53 169 62 65 3 487.28 3.15 170 62 66 4 474.69 1.53 171 63 66 3 484.76 1.89 172 63 67 4 474.69 1.54 173 64 67 3 480.28 0.27 174 64 68 4 475.69 2.02 175 65 68 3 480.09 4.22 176 65 69 4 475.64 2.06 177 65 80 15 177.24 12.21 178 65 83 18 165.90 6.56 179 66 69 3 474.50 2.62 180 66 70 4 476.38 0.95 181 66 105 39 162.99 1.45 182 66 129 63 161.68 2.02 183 66 132 66 161.19 1.86 184 67 70 3 481.21 0.72 185 67 71 4 476.39 0.94 186 68 71 3 478.85 0.29 187 68 72 4 476.18 0.83 188 68 79 11 235.02 10.53 189 69 72 3 476.18 0.84 190 69 73 4 432.70 2.46 191 69 76 7 253.08 0.92 192 69 80 11 213.49 2.92 193 69 128 59 179.33 10.39 194 69 132 63 161.22 1.85 195 70 73 3 460.82 5.34 196 70 128 58 179.36 10.38 197 72 75 3 483.71 3.16 198 72 76 4 440.67 11.46 199 72 79 7 292.55 4.25 200 73 76 3 478.06 2.98 201 73 128 55 183.16 12.27 202 75 78 3 483.20 0.24 203 75 79 4 447.51 7.24 204 76 79 3 467.66 0.35 205 76 80 4 433.94 3.19 206 76 128 52 183.69 12.55 207 76 131 55 182.90 12.62 208 76 132 56 182.78 12.63 209 77 80 3 471.12 0.61 210 77 81 4 430.75 1.58 211 77 135 58 181.30 13.38 212 78 81 3 463.56 0.79 213 80 83 3 490.38 0.21 214 80 84 4 474.48 3.15 215 80 132 52 183.19 12.86 216 80 135 55 180.59 14.09 217 80 136 56 180.54 14.10 218 81 84 3 474.49 3.15 219 81 85 4 474.49 3.15 220 82 85 3 489.73 1.41 221 82 86 4 474.48 3.14 222 83 86 3 483.90 1.58 223 83 87 4 465.19 0.74 224 83 136 53 179.79 14.49 225 84 87 3 480.53 4.83 226 84 88 4 464.43 1.10 227 84 135 51 180.48 14.31 228 84 136 52 179.75 14.50 229 85 88 3 490.37 1.65 230 85 89 4 431.49 2.01 231 85 90 5 431.50 2.02 232 86 90 4 408.31 0.07 233 86 91 5 400.43 3.87 234 87 91 4 355.41 18.65 235 87 92 5 335.41 8.69 236 87 93 6 285.83 0.11 237 87 98 11 276.56 1.21 238 87 136 49 180.09 14.68 239 88 136 48 180.09 14.68 240 88 137 49 179.77 14.54 241 88 139 51 175.60 16.52 242 88 140 52 174.75 16.73 243 89 92 3 490.34 0.22 244 89 139 50 178.41 15.49 245 92 140 48 174.22 17.60 246 93 97 4 484.07 1.47 247 93 98 5 477.64 1.94 248 93 140 47 174.23 17.62 249 94 97 3 490.56 3.98 250 95 98 3 499.84 1.21 251 95 137 42 176.40 16.62 252 95 140 45 170.81 19.48 253 96 99 3 497.00 5.00 254 96 100 4 485.50 0.75 255 97 100 3 485.50 0.74 256 97 101 4 482.75 0.62 257 98 101 3 490.70 3.23 258 98 102 4 479.30 2.46 259 98 133 35 180.28 14.77 260 98 136 38 179.41 15.23 261 98 137 39 176.48 16.67 262 99 102 3 487.85 1.81 263 99 103 4 480.18 2.02 264 100 103 3 487.86 1.81 265 100 104 4 480.19 2.02 266 101 104 3 487.85 1.81 267 101 105 4 480.17 2.02 268 102 105 3 487.84 1.82 269 102 106 4 482.75 0.72 270 102 129 27 181.16 14.69 271 103 106 3 489.81 0.08 272 103 107 4 482.76 0.71 273 104 107 3 482.76 0.71 274 104 108 4 482.71 0.69 275 105 108 3 474.72 3.33 276 105 109 4 471.05 1.50 277 105 129 24 181.34 14.77 278 106 109 3 476.05 1.02 279 106 110 4 476.05 1.02 280 106 117 11 202.42 4.67 281 106 122 16 181.68 14.80 282 106 125 19 181.59 14.83 283 106 126 20 181.58 14.83 284 106 129 23 181.52 14.86 285 107 110 3 480.52 0.46 286 107 111 4 476.03 1.03 287 108 111 3 479.77 0.84 288 108 112 4 475.98 1.05 289 109 112 3 478.74 0.33 290 109 113 4 465.26 6.40 291 109 125 16 186.91 12.39 292 110 117 7 257.69 17.57 293 113 116 3 483.64 0.42 294 113 117 4 438.27 9.41 295 115 118 3 531.83 1.57 296 116 121 5 418.81 0.73 297 117 122 5 430.87 5.32 298 117 125 8 411.37 4.21 299 118 121 3 471.29 5.95 300 118 122 4 461.94 1.24 301 119 122 3 465.93 3.22 302 119 123 4 469.41 4.96 303 120 123 3 479.35 0.01 304 120 124 4 470.30 4.51 305 121 124 3 470.30 4.51 306 121 125 4 470.30 4.52 307 122 125 3 473.91 2.71 308 122 126 4 470.30 4.51 309 123 126 3 486.30 0.67 310 123 127 4 476.01 1.65 311 124 127 3 471.07 0.83 312 124 128 4 474.23 5.36 313 125 128 3 478.54 3.21 314 125 129 4 474.22 5.37 315 126 129 3 479.77 2.59 316 126 130 4 474.22 5.37 317 127 130 3 483.05 0.95 318 127 131 4 471.54 6.71 319 128 131 3 471.56 0.22 320 128 132 4 467.87 2.06 321 129 132 3 477.07 2.54 322 129 133 4 467.87 2.06 323 130 133 3 480.80 4.49 324 130 134 4 475.60 1.89 325 131 134 3 476.99 2.58 326 131 135 4 475.74 1.96 327 132 135 3 482.22 1.28 328 132 136 4 474.73 2.46 329 133 136 3 480.76 0.56 330 133 137 4 474.33 2.66 331 134 137 3 480.95 0.46 332 134 138 4 461.26 3.87 333 135 138 3 468.38 0.66 334 137 140 3 464.65 2.39 335 137 141 4 463.62 2.58 336 138 141 3 459.13 0.32