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 18 45 27 63.41 0.05 2 18 46 28 63.41 0.05 3 18 47 29 63.40 0.06 4 18 48 30 52.88 0.09 5 18 49 31 53.37 0.29 6 18 53 35 45.72 2.25 7 19 46 27 63.41 0.05 8 19 47 28 63.40 0.06 9 20 47 27 65.03 0.26 10 20 48 28 64.11 0.03 11 20 60 40 62.80 0.24 12 20 70 50 62.80 0.24 13 20 71 51 63.82 0.17 14 20 72 52 63.87 0.15 15 21 24 3 351.62 8.02 16 21 25 4 239.31 6.11 17 21 47 26 65.78 0.13 18 21 71 50 64.78 0.24 19 22 25 3 353.20 6.43 20 22 26 4 238.81 6.36 21 22 69 47 65.56 0.11 22 22 70 48 65.56 0.08 23 22 71 49 65.80 0.12 24 23 26 3 333.57 2.21 25 23 35 12 65.81 0.12 26 23 37 14 65.92 0.17 27 23 69 46 65.81 0.12 28 23 71 48 65.92 0.17 29 23 101 78 70.23 0.17 30 23 104 81 71.00 0.12 31 23 105 82 67.06 0.06 32 23 108 85 71.00 0.12 33 24 71 47 67.70 0.04 34 24 101 77 70.91 0.12 35 24 104 80 71.17 0.05 36 24 108 84 71.39 0.04 37 26 69 43 70.85 0.15 38 26 108 82 125.98 1.62 39 27 30 3 337.63 0.24 40 27 31 4 295.50 21.30 41 27 69 42 529.24 6.55 42 28 31 3 348.83 1.74 43 28 108 80 127.02 1.38 44 32 112 80 454.98 2.89 45 33 112 79 454.98 2.89 46 33 113 80 454.98 2.89 47 33 211 178 35.90 0.66 48 34 113 79 454.98 2.89 49 34 115 81 454.95 2.89 50 34 207 173 78.06 0.17 51 34 211 177 35.91 0.67 52 35 112 77 525.15 0.21 53 35 113 78 457.49 2.85 54 35 114 79 454.97 2.89 55 35 115 80 454.97 2.89 56 36 115 79 454.97 2.89 57 36 116 80 454.95 2.89 58 36 117 81 454.95 2.89 59 36 203 167 101.48 0.51 60 37 115 78 456.79 3.18 61 37 116 79 454.97 2.89 62 37 117 80 454.97 2.89 63 38 117 79 454.97 2.89 64 38 118 80 454.95 2.90 65 38 119 81 454.97 2.89 66 39 117 78 455.62 3.14 67 39 118 79 454.97 2.89 68 39 119 80 454.97 2.89 69 39 122 83 366.60 0.50 70 39 125 86 366.22 0.64 71 40 119 79 454.96 2.90 72 40 122 82 369.75 1.00 73 41 119 78 455.04 2.91 74 41 120 79 454.94 2.90 75 41 121 80 454.83 2.93 76 41 122 81 402.84 0.35 77 42 121 79 454.95 2.89 78 44 119 75 456.75 3.25 79 51 119 68 454.86 2.94 80 51 147 96 309.24 0.28 81 51 191 140 111.32 0.63 82 51 192 141 110.84 0.73 83 51 195 144 108.43 1.25 84 54 195 141 109.03 1.51 85 54 196 142 108.44 1.22 86 55 145 90 309.69 0.26 87 55 147 92 309.23 0.28 88 55 195 140 108.47 1.23 89 55 200 145 107.80 1.13 90 55 203 148 106.70 0.81 91 58 196 138 108.42 1.22 92 58 200 142 107.71 1.14 93 58 204 146 101.31 0.43 94 59 115 56 455.48 3.12 95 59 203 144 102.14 0.85 96 59 204 145 101.03 0.48 97 62 204 142 101.04 0.48 98 63 204 141 101.03 0.48 99 63 207 144 84.75 0.85 100 73 125 52 366.22 0.64 101 77 121 44 454.94 2.91 102 77 122 45 447.95 2.89 103 77 125 48 366.31 0.61 104 79 121 42 454.97 2.90 105 80 121 41 455.54 3.14 106 83 121 38 455.06 2.90 107 84 121 37 455.06 2.90 108 84 182 98 181.65 0.64 109 85 182 97 185.13 0.83 110 87 151 64 304.78 0.80 111 88 124 36 443.86 1.28 112 88 128 40 366.35 0.59 113 88 131 43 366.20 0.65 114 88 132 44 366.00 0.74 115 88 151 63 294.50 0.39 116 89 121 32 454.97 2.90 117 89 124 35 388.00 1.15 118 89 151 62 294.56 0.36 119 90 121 31 454.94 2.89 120 90 125 35 366.61 0.51 121 94 125 31 366.32 0.59 122 95 125 30 366.31 0.59 123 95 128 33 365.03 0.49 124 95 129 34 342.57 2.29 125 95 132 37 337.09 0.44 126 98 116 18 469.78 2.99 127 98 125 27 366.29 0.60 128 98 126 28 366.08 0.59 129 98 129 31 337.20 0.40 130 99 129 30 337.20 0.40 131 99 132 33 335.56 1.16 132 99 133 34 316.88 2.32 133 102 116 14 455.60 2.60 134 102 129 27 337.20 0.40 135 102 130 28 337.19 0.40 136 102 133 31 311.25 0.22 137 102 137 35 311.02 0.21 138 102 141 39 310.76 0.23 139 103 137 34 311.03 0.21 140 105 114 9 455.99 2.79 141 106 137 31 310.99 0.19 142 106 140 34 310.75 0.21 143 109 112 3 454.96 2.90 144 110 140 30 310.74 0.21 145 111 211 100 38.99 0.62 146 113 140 27 310.73 0.21 147 113 142 29 310.54 0.16 148 113 207 94 78.05 0.18 149 113 210 97 39.02 0.61 150 113 211 98 36.29 0.56 151 114 137 23 311.01 0.20 152 114 140 26 310.75 0.21 153 114 141 27 310.62 0.17 154 114 142 28 310.56 0.17 155 115 141 26 310.72 0.21 156 115 142 27 310.66 0.22 157 115 143 28 310.24 0.17 158 115 203 88 101.33 0.43 159 115 207 92 84.98 0.74 160 116 130 14 337.14 0.40 161 116 141 25 310.75 0.23 162 116 143 27 310.56 0.18 163 116 144 28 310.03 0.23 164 116 145 29 310.03 0.23 165 116 203 87 102.45 0.84 166 117 126 9 365.71 0.72 167 117 144 27 310.35 0.21 168 117 145 28 309.78 0.10 169 118 122 4 366.69 0.53 170 118 123 5 366.47 0.55 171 118 126 8 365.71 0.72 172 118 145 27 310.35 0.21 173 118 146 28 309.52 0.23 174 118 147 29 309.26 0.28 175 119 122 3 372.13 0.18 176 119 123 4 366.73 0.52 177 119 147 28 309.25 0.28 178 119 188 69 118.15 1.73 179 119 189 70 114.61 0.04 180 119 191 72 111.55 0.72 181 120 123 3 382.71 3.29 182 120 124 4 373.96 1.08 183 120 147 27 310.19 0.26 184 120 148 28 309.25 0.27 185 120 150 30 295.37 0.04 186 120 188 68 118.16 1.73 187 121 124 3 373.44 1.79 188 121 125 4 366.74 0.51 189 122 125 3 366.54 0.50 190 122 126 4 366.24 0.65 191 123 126 3 366.38 0.72 192 123 127 4 366.22 0.64 193 123 146 23 310.25 0.25 194 123 147 24 310.19 0.26 195 123 149 26 294.56 0.36 196 124 127 3 366.44 0.73 197 124 128 4 366.22 0.64 198 124 149 25 300.61 2.85 199 124 150 26 294.50 0.39 200 124 151 27 290.32 0.29 201 125 128 3 367.29 0.61 202 125 129 4 363.10 0.24 203 126 129 3 371.06 3.73 204 126 130 4 350.00 6.79 205 126 146 20 310.26 0.25 206 127 130 3 366.05 1.24 207 127 131 4 346.20 4.89 208 127 149 22 300.57 2.87 209 127 159 32 224.86 0.27 210 128 131 3 356.38 3.60 211 128 132 4 352.57 1.71 212 129 132 3 353.65 1.17 213 129 133 4 341.73 3.72 214 130 133 3 348.56 1.38 215 130 138 8 311.06 0.21 216 130 141 11 311.04 0.22 217 130 144 14 310.76 0.24 218 130 159 29 224.86 0.27 219 130 162 32 224.47 0.37 220 131 138 7 313.17 0.67 221 131 160 29 224.81 0.28 222 131 161 30 224.65 0.32 223 133 137 4 347.32 10.57 224 133 138 5 314.38 1.18 225 133 141 8 313.27 0.62 226 134 137 3 378.99 1.46 227 134 138 4 339.08 0.10 228 135 138 3 347.42 0.77 229 135 139 4 339.10 0.11 230 136 139 3 379.91 1.82 231 136 140 4 340.64 0.65 232 137 140 3 370.47 2.90 233 137 141 4 354.31 6.19 234 138 141 3 357.12 6.72 235 138 161 23 224.55 0.36 236 138 162 24 224.45 0.38 237 139 166 27 223.77 0.49 238 141 144 3 428.91 2.19 239 141 162 21 224.48 0.38 240 141 166 25 223.72 0.49 241 142 162 20 224.49 0.37 242 142 166 24 223.70 0.49 243 142 206 64 89.17 0.75 244 142 207 65 85.00 0.73 245 142 210 68 75.59 0.01 246 143 162 19 224.49 0.38 247 143 166 23 223.71 0.49 248 143 202 59 107.72 1.08 249 143 203 60 104.81 0.11 250 143 206 63 94.86 0.42 251 144 159 15 224.86 0.27 252 144 162 18 224.49 0.38 253 144 166 22 223.78 0.48 254 144 167 23 223.68 0.48 255 144 168 24 223.67 0.48 256 144 202 58 107.95 1.14 257 144 203 59 107.58 1.09 258 145 168 23 223.62 0.50 259 145 170 25 223.37 0.43 260 145 199 54 108.32 1.18 261 145 202 57 108.23 1.20 262 145 203 58 107.88 1.17 263 146 149 3 377.16 2.38 264 146 159 13 224.87 0.27 265 146 167 21 223.79 0.48 266 146 168 22 223.75 0.49 267 146 169 23 223.52 0.48 268 146 170 24 223.36 0.44 269 147 170 23 223.30 0.45 270 147 191 44 111.61 0.76 271 147 194 47 110.86 0.72 272 147 195 48 111.13 0.59 273 147 199 52 110.81 0.74 274 148 170 22 223.62 0.43 275 148 171 23 223.30 0.45 276 148 175 27 223.21 0.54 277 148 177 29 223.13 0.49 278 148 178 30 222.74 0.48 279 148 188 40 114.70 0.01 280 148 191 43 113.89 0.03 281 149 152 3 341.74 1.37 282 149 155 6 243.72 8.10 283 149 157 8 225.75 0.41 284 149 158 9 225.74 0.41 285 149 159 10 225.41 0.25 286 149 169 20 223.77 0.48 287 149 171 22 223.44 0.49 288 149 177 28 223.13 0.49 289 149 178 29 221.24 0.14 290 150 177 27 223.06 0.53 291 150 182 32 182.21 0.92 292 151 154 3 348.00 11.28 293 151 155 4 243.73 8.11 294 152 155 3 382.85 0.23 295 152 156 4 243.71 8.11 296 152 157 5 225.72 0.42 297 152 169 17 223.95 0.47 298 152 171 19 223.73 0.47 299 152 178 26 222.70 0.47 300 153 156 3 294.40 12.36 301 153 178 25 223.42 0.45 302 153 179 26 222.46 0.59 303 153 180 27 218.30 0.68 304 154 180 26 221.85 0.75 305 155 158 3 370.37 0.09 306 155 160 5 225.80 0.40 307 157 169 12 223.91 0.48 308 158 162 4 368.88 0.15 309 158 163 5 226.06 0.49 310 158 164 6 225.17 0.06 311 159 162 3 368.91 0.14 312 159 167 8 223.94 0.48 313 162 166 4 378.49 0.61 314 162 167 5 245.20 8.77 315 163 166 3 378.49 0.61 316 163 167 4 358.94 7.49 317 164 167 3 348.69 15.51 318 165 206 41 104.82 0.12 319 166 202 36 108.25 1.20 320 166 206 40 101.23 0.40 321 167 202 35 108.33 1.18 322 168 202 34 108.33 1.19 323 170 191 21 113.84 0.01 324 170 194 24 110.94 0.68 325 170 198 28 110.92 0.69 326 170 199 29 110.83 0.74 327 171 191 20 114.59 0.04 328 172 187 15 122.50 0.11 329 172 190 18 121.86 0.11 330 172 191 19 116.67 0.96 331 173 187 14 126.37 0.92 332 174 185 11 143.75 0.34 333 174 187 13 128.13 2.39 334 175 187 12 123.03 0.09 335 175 188 13 123.02 0.08 336 175 191 16 123.02 0.08 337 176 181 5 461.15 1.19 338 176 183 7 362.51 9.59 339 176 185 9 146.01 0.76 340 177 181 4 397.99 1.51 341 177 182 5 380.28 0.70 342 177 183 6 328.01 7.66 343 177 188 11 122.73 0.07 344 184 188 4 342.78 1.92 345 184 189 5 369.42 0.21 346 185 188 3 373.62 0.39 347 186 189 3 377.31 1.46 348 186 190 4 372.56 0.92 349 187 190 3 377.32 1.46 350 187 191 4 381.58 0.67 351 188 191 3 419.70 0.68 352 191 194 3 373.98 1.34 353 191 195 4 346.32 12.60 354 192 195 3 369.15 1.19 355 192 196 4 369.14 1.19 356 193 196 3 354.28 6.25 357 193 197 4 318.69 0.57 358 193 198 5 318.64 0.55 359 194 197 3 346.56 3.66 360 194 198 4 318.62 0.55 361 194 199 5 318.54 0.58 362 194 200 6 318.72 0.67 363 195 199 4 318.62 0.67 364 195 200 5 318.49 0.60 365 196 200 4 330.66 3.18 366 197 200 3 389.95 2.62 367 197 201 4 329.58 3.72 368 198 201 3 345.16 4.07 369 198 202 4 324.74 1.52 370 199 202 3 336.87 0.82 371 199 203 4 328.47 3.39 372 200 203 3 328.05 3.60 373 200 204 4 321.86 0.76 374 201 204 3 336.92 7.65 375 201 205 4 322.50 0.44 376 202 205 3 353.92 6.21 377 202 206 4 322.50 0.43 378 203 206 3 365.15 4.07 379 203 207 4 319.92 0.85 380 204 207 3 356.81 8.24 381 204 208 4 319.88 0.84 382 205 208 3 361.44 6.88 383 205 209 4 322.49 2.35 384 206 209 3 344.07 0.45 385 206 210 4 319.69 0.94 386 207 210 3 370.12 0.91 387 207 211 4 319.68 0.94 388 208 211 3 370.30 0.82 389 208 212 4 319.53 0.86 390 208 213 5 125.87 4.49 391 209 212 3 361.39 5.21