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 6 4 464.94 1.02 2 2 7 5 450.09 8.46 3 2 73 71 28.59 0.88 4 2 127 125 24.87 1.52 5 2 128 126 23.58 2.03 6 2 131 129 18.23 0.58 7 3 6 3 473.75 2.52 8 3 7 4 467.87 0.42 9 4 7 3 475.57 1.79 10 4 8 4 470.34 0.82 11 5 8 3 475.56 1.79 12 5 9 4 471.80 2.20 13 6 9 3 474.38 0.92 14 6 10 4 471.18 1.89 15 6 124 118 48.76 0.89 16 6 127 121 50.09 0.22 17 7 10 3 481.94 0.30 18 7 11 4 471.16 1.92 19 7 73 66 50.38 0.25 20 7 74 67 50.40 0.24 21 8 11 3 475.58 2.89 22 8 12 4 474.11 3.62 23 9 12 3 476.20 2.57 24 9 13 4 474.11 3.62 25 9 121 112 63.75 1.92 26 9 124 115 63.74 1.90 27 10 13 3 479.80 0.78 28 10 14 4 479.35 1.00 29 10 70 60 63.83 1.90 30 10 73 63 63.88 1.88 31 10 124 114 63.82 1.90 32 10 125 115 63.80 1.90 33 10 128 118 63.73 1.91 34 11 14 3 478.41 0.09 35 11 15 4 476.24 0.55 36 11 70 59 63.93 1.85 37 11 71 60 64.28 1.69 38 11 73 62 63.93 1.85 39 12 15 3 478.41 0.09 40 12 16 4 476.25 0.55 41 13 16 3 483.69 3.19 42 13 17 4 476.25 0.55 43 13 121 108 64.43 1.65 44 13 125 112 64.40 1.64 45 14 17 3 481.60 3.22 46 14 21 7 366.52 15.14 47 14 66 52 64.43 1.65 48 14 67 53 64.43 1.65 49 14 70 56 64.42 1.66 50 14 109 95 77.93 3.19 51 15 18 3 489.83 0.90 52 16 113 97 84.20 1.11 53 16 116 100 83.95 1.06 54 17 20 3 475.31 0.20 55 17 21 4 428.67 0.03 56 17 24 7 417.23 5.75 57 17 109 92 84.14 1.14 58 17 113 96 98.91 1.53 59 20 23 3 470.76 0.88 60 20 24 4 470.75 0.89 61 21 24 3 476.86 2.17 62 21 25 4 470.75 0.89 63 21 63 42 100.60 0.68 64 21 67 46 100.52 0.61 65 22 25 3 472.25 1.63 66 22 26 4 470.75 0.89 67 22 59 37 103.73 0.68 68 22 60 38 102.62 0.29 69 22 63 41 100.84 0.57 70 23 26 3 475.79 0.12 71 23 27 4 470.74 0.88 72 24 27 3 471.10 1.65 73 24 28 4 465.60 1.03 74 24 108 84 118.45 0.52 75 24 109 85 122.73 1.64 76 24 112 88 136.69 1.44 77 25 28 3 474.94 0.29 78 25 29 4 466.60 1.54 79 25 59 34 118.22 0.60 80 25 105 80 133.81 7.82 81 26 29 3 474.89 2.60 82 26 30 4 464.66 2.52 83 26 55 29 140.03 3.87 84 26 56 30 139.63 4.05 85 26 59 33 122.98 2.93 86 27 30 3 476.53 3.42 87 27 31 4 464.67 2.50 88 27 108 81 142.06 4.04 89 27 112 85 142.49 3.74 90 28 31 3 481.15 2.99 91 28 32 4 467.42 3.88 92 28 101 73 142.27 4.17 93 28 104 76 142.12 4.09 94 28 105 77 142.12 4.09 95 28 108 80 142.11 4.06 96 29 32 3 474.60 0.29 97 29 33 4 467.41 3.88 98 29 55 26 150.28 8.17 99 29 58 29 141.54 3.79 100 29 59 30 141.18 3.62 101 29 62 33 140.97 3.50 102 29 101 72 142.40 4.21 103 30 33 3 488.55 0.71 104 30 34 4 467.34 3.92 105 30 50 20 151.17 7.83 106 31 34 3 489.67 0.15 107 31 35 4 461.53 1.04 108 31 104 73 142.78 3.90 109 31 107 76 142.72 3.85 110 31 108 77 142.93 3.73 111 31 111 80 143.05 3.67 112 32 35 3 472.65 2.37 113 32 36 4 455.55 1.95 114 32 39 7 315.44 4.39 115 32 100 68 142.91 3.97 116 32 101 69 142.91 3.97 117 32 104 72 142.82 3.91 118 33 37 4 421.25 4.18 119 33 39 6 315.44 4.40 120 33 40 7 269.20 9.38 121 33 43 10 261.72 5.64 122 33 48 15 163.23 13.76 123 33 55 22 159.12 11.76 124 34 37 3 480.38 0.67 125 36 39 3 489.91 0.29 126 36 100 64 143.00 4.01 127 36 103 67 143.28 3.88 128 36 104 68 143.27 3.86 129 37 40 3 480.43 1.45 130 38 41 3 495.35 0.01 131 39 42 3 503.31 0.32 132 39 97 58 143.13 4.06 133 39 100 61 143.32 3.97 134 40 43 3 485.29 2.89 135 40 48 8 231.90 0.35 136 41 44 3 478.42 1.65 137 42 91 49 143.46 4.28 138 42 92 50 143.52 4.25 139 42 93 51 143.51 4.25 140 42 94 52 143.56 4.23 141 42 97 55 143.74 4.09 142 43 46 3 476.83 2.48 143 43 48 5 348.03 16.29 144 43 58 15 231.55 0.58 145 45 54 9 234.81 1.25 146 46 54 8 234.79 1.24 147 46 58 12 234.62 1.32 148 47 52 5 252.94 4.11 149 47 54 7 234.82 1.25 150 47 55 8 235.00 1.16 151 48 55 7 253.25 3.96 152 49 52 3 476.81 4.03 153 51 56 5 458.12 3.27 154 52 55 3 479.40 3.08 155 52 56 4 458.56 3.24 156 53 56 3 480.84 2.36 157 53 57 4 469.14 2.05 158 54 57 3 475.80 0.32 159 54 58 4 466.82 0.89 160 55 58 3 475.09 1.00 161 55 59 4 469.06 2.01 162 56 59 3 475.51 0.98 163 56 60 4 469.26 2.14 164 57 60 3 479.30 2.88 165 57 61 4 469.27 2.14 166 58 61 3 474.29 0.58 167 58 62 4 469.03 2.02 168 59 62 3 468.31 1.61 169 59 63 4 468.05 1.53 170 60 63 3 468.75 1.40 171 60 64 4 465.53 2.80 172 61 64 3 473.98 1.42 173 61 65 4 467.20 1.97 174 62 65 3 473.98 1.42 175 62 66 4 472.05 0.46 176 63 66 3 472.95 2.23 177 63 67 4 470.69 1.15 178 64 67 3 466.09 1.38 179 64 68 4 465.87 1.26 180 65 68 3 467.78 1.74 181 65 69 4 472.91 2.27 182 65 83 18 152.38 0.13 183 66 69 3 471.42 3.02 184 66 70 4 471.41 3.03 185 66 105 39 179.58 13.76 186 66 128 62 178.91 14.03 187 66 129 63 178.66 14.11 188 66 132 66 161.21 5.51 189 67 70 3 477.11 0.18 190 67 71 4 474.06 1.71 191 68 71 3 474.06 1.71 192 68 72 4 474.06 1.71 193 69 72 3 476.88 0.30 194 69 73 4 474.05 1.71 195 69 76 7 302.48 3.17 196 69 80 11 182.05 4.92 197 69 128 59 179.05 14.01 198 69 132 63 173.36 11.55 199 70 73 3 478.43 0.45 200 70 128 58 179.09 14.02 201 72 75 3 488.03 0.88 202 72 76 4 441.25 5.51 203 72 79 7 306.01 1.41 204 73 76 3 490.81 0.52 205 73 128 55 180.71 14.83 206 75 78 3 482.44 4.07 207 75 79 4 475.44 5.00 208 76 79 3 480.88 2.27 209 76 80 4 475.44 5.00 210 76 131 55 180.38 15.04 211 76 132 56 180.34 15.03 212 76 135 59 179.84 15.27 213 77 80 3 479.88 2.77 214 77 81 4 455.64 6.05 215 77 135 58 179.84 15.27 216 78 81 3 482.53 3.10 217 80 83 3 474.22 0.24 218 80 84 4 463.31 0.40 219 80 132 52 180.87 15.30 220 80 135 55 178.72 16.18 221 80 136 56 178.87 16.29 222 81 84 3 474.01 0.85 223 81 85 4 463.32 0.39 224 81 139 58 176.00 17.18 225 82 85 3 474.81 1.35 226 82 86 4 463.32 0.39 227 83 86 3 474.81 1.35 228 83 87 4 464.11 0.79 229 83 136 53 176.59 17.46 230 84 87 3 482.14 2.06 231 84 88 4 463.23 0.39 232 84 135 51 177.56 16.96 233 84 136 52 176.44 17.52 234 84 139 55 174.31 18.38 235 85 88 3 482.14 2.06 236 85 89 4 461.14 0.63 237 85 90 5 461.06 0.59 238 85 139 54 174.33 18.37 239 86 90 4 393.88 12.61 240 86 91 5 381.63 7.75 241 87 91 4 381.62 7.75 242 87 92 5 379.75 6.82 243 87 93 6 341.79 25.75 244 87 98 11 270.08 1.06 245 87 136 49 176.44 17.55 246 88 92 4 350.93 21.21 247 88 139 51 174.50 18.46 248 88 140 52 174.45 18.46 249 89 92 3 481.66 3.89 250 89 139 50 174.52 18.48 251 92 140 48 173.28 19.14 252 93 97 4 472.50 1.91 253 93 98 5 470.00 2.25 254 93 140 47 173.03 19.27 255 94 97 3 482.06 2.03 256 95 98 3 485.84 0.89 257 95 99 4 477.15 0.41 258 95 137 42 174.77 18.56 259 96 99 3 483.91 1.85 260 96 100 4 477.14 0.41 261 97 100 3 478.56 0.30 262 97 101 4 466.53 1.02 263 98 101 3 478.95 0.51 264 98 102 4 464.08 0.21 265 98 133 35 177.19 17.61 266 98 136 38 175.61 18.43 267 98 137 39 175.03 18.70 268 99 102 3 476.81 2.30 269 99 103 4 464.07 0.21 270 100 103 3 474.44 0.32 271 100 104 4 464.07 0.21 272 101 104 3 464.08 0.21 273 101 105 4 464.07 0.21 274 102 105 3 472.77 3.39 275 102 106 4 462.52 0.98 276 102 129 27 183.30 14.86 277 102 133 31 177.47 17.71 278 103 106 3 481.93 0.96 279 103 107 4 459.81 0.36 280 104 107 3 471.47 6.19 281 104 108 4 459.81 0.36 282 105 108 3 468.71 4.08 283 105 109 4 459.75 0.40 284 105 129 24 184.10 14.68 285 106 109 3 477.54 0.32 286 106 110 4 459.76 0.41 287 106 117 11 246.76 7.82 288 106 122 16 200.91 6.52 289 106 125 19 187.38 13.29 290 106 126 20 187.34 13.27 291 106 129 23 187.35 13.29 292 107 110 3 472.29 2.30 293 107 111 4 463.30 2.19 294 108 111 3 473.91 3.10 295 108 112 4 464.38 1.66 296 109 112 3 484.22 0.91 297 109 113 4 460.26 0.17 298 109 117 8 278.88 5.34 299 109 125 16 197.89 8.38 300 110 114 4 421.66 6.44 301 110 117 7 256.51 2.94 302 111 114 3 497.75 5.46 303 113 116 3 476.05 0.43 304 113 117 4 466.51 0.66 305 114 117 3 477.62 1.22 306 115 118 3 514.40 3.83 307 116 121 5 452.06 1.38 308 117 121 4 452.07 1.39 309 117 122 5 441.34 3.98 310 117 125 8 422.24 12.85 311 118 121 3 466.51 1.49 312 118 122 4 454.51 2.59 313 119 122 3 465.38 2.40 314 119 123 4 461.14 0.76 315 120 123 3 467.12 0.96 316 120 124 4 461.42 0.62 317 121 124 3 469.86 3.60 318 121 125 4 461.60 0.71 319 122 125 3 473.88 1.58 320 122 126 4 461.94 0.58 321 123 126 3 464.52 0.71 322 123 127 4 464.51 0.71 323 124 127 3 467.66 1.80 324 124 128 4 468.26 2.60 325 125 128 3 468.27 2.60 326 125 129 4 468.26 2.60 327 126 129 3 475.17 0.85 328 126 130 4 468.23 2.62 329 127 130 3 471.81 0.83 330 127 131 4 468.22 2.62 331 128 131 3 470.81 0.10 332 128 132 4 466.97 2.01 333 129 132 3 468.66 1.18 334 129 133 4 468.04 1.49 335 130 133 3 473.88 1.56 336 130 134 4 468.29 1.60 337 131 134 3 479.31 1.15 338 131 135 4 468.30 1.59 339 132 135 3 483.13 0.76 340 132 136 4 470.42 2.20 341 133 136 3 477.30 1.23 342 133 137 4 470.43 2.20 343 134 137 3 476.53 4.64 344 134 138 4 457.45 4.46 345 135 138 3 470.61 2.12 346 137 140 3 499.70 2.75