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 46 28 98.27 19.91 2 18 47 29 101.34 21.46 3 18 48 30 92.64 20.88 4 18 49 31 95.84 19.28 5 18 53 35 88.98 24.86 6 19 46 27 101.37 21.45 7 19 47 28 101.36 21.46 8 19 48 29 101.34 21.46 9 20 47 27 104.17 22.18 10 20 48 28 103.42 22.47 11 20 60 40 112.26 26.91 12 20 65 45 113.22 26.64 13 20 70 50 103.49 22.54 14 20 71 51 103.53 22.50 15 20 72 52 103.68 22.43 16 21 24 3 363.82 7.20 17 21 25 4 289.29 22.34 18 21 47 26 110.25 24.94 19 21 71 50 104.58 22.66 20 22 25 3 350.19 6.84 21 22 26 4 289.08 22.23 22 22 69 47 113.16 26.60 23 22 70 48 112.88 26.45 24 22 71 49 112.81 26.38 25 23 26 3 334.23 3.91 26 23 35 12 114.47 25.97 27 23 37 14 114.44 25.96 28 23 69 46 113.25 26.59 29 23 71 48 113.35 26.46 30 23 101 78 114.62 25.88 31 23 104 81 114.74 25.82 32 23 105 82 114.63 25.89 33 23 108 85 115.56 26.22 34 24 71 47 114.50 25.96 35 24 101 77 114.67 25.87 36 24 104 80 115.06 25.91 37 24 108 84 116.06 26.39 38 26 69 43 114.65 25.91 39 26 108 82 152.94 8.64 40 27 30 3 372.05 2.69 41 27 31 4 281.25 29.92 42 27 69 42 529.25 1.38 43 28 31 3 349.56 7.54 44 28 108 80 177.40 3.58 45 32 112 80 455.07 0.68 46 33 112 79 455.07 0.68 47 33 113 80 455.07 0.68 48 33 211 178 33.02 0.38 49 34 113 79 455.07 0.68 50 34 115 81 455.06 0.68 51 34 207 173 60.54 8.52 52 35 112 77 496.50 0.12 53 35 113 78 460.69 1.35 54 35 114 79 455.09 0.68 55 35 115 80 455.08 0.68 56 36 115 79 455.08 0.68 57 36 116 80 455.07 0.68 58 36 117 81 455.07 0.68 59 36 203 167 81.24 8.69 60 37 115 78 456.64 0.34 61 37 116 79 455.09 0.68 62 37 117 80 455.08 0.68 63 38 117 79 455.09 0.67 64 38 118 80 455.07 0.68 65 38 119 81 455.08 0.68 66 39 117 78 455.43 0.74 67 39 118 79 455.08 0.68 68 39 119 80 455.08 0.68 69 39 122 83 358.00 2.79 70 39 125 86 357.19 2.82 71 40 119 79 455.09 0.68 72 40 122 82 358.23 2.77 73 41 119 78 455.12 0.67 74 41 120 79 455.09 0.68 75 41 122 81 387.13 0.33 76 42 121 79 455.09 0.68 77 44 119 75 455.61 0.83 78 51 119 68 455.06 0.69 79 51 147 96 308.72 1.49 80 51 191 140 90.04 8.86 81 51 192 141 89.79 8.82 82 51 195 144 88.61 9.12 83 54 195 141 88.64 9.13 84 54 196 142 86.16 10.38 85 55 145 90 308.86 1.48 86 55 147 92 308.75 1.47 87 55 195 140 88.62 9.13 88 55 200 145 85.89 10.42 89 55 203 148 85.23 10.68 90 58 196 138 88.61 9.14 91 58 200 142 85.91 10.41 92 59 115 56 455.30 0.75 93 59 200 141 85.85 10.41 94 59 203 144 81.25 8.69 95 59 204 145 81.18 8.68 96 62 204 142 81.19 8.67 97 63 204 141 81.16 8.65 98 63 207 144 61.86 9.01 99 73 125 52 357.19 2.82 100 77 121 44 455.04 0.69 101 77 122 45 449.05 0.16 102 77 125 48 357.29 2.79 103 79 121 42 455.06 0.68 104 80 121 41 455.18 0.69 105 83 121 38 455.19 0.69 106 84 121 37 455.29 0.64 107 84 182 98 115.69 19.68 108 85 182 97 129.06 26.36 109 88 124 36 409.00 7.55 110 88 128 40 357.53 2.66 111 88 131 43 357.14 2.82 112 88 132 44 356.80 2.78 113 88 151 63 284.76 1.62 114 89 121 32 455.06 0.69 115 89 124 35 389.51 2.20 116 89 151 62 284.80 1.65 117 90 121 31 455.05 0.69 118 90 125 35 362.06 0.73 119 94 125 31 357.19 2.83 120 95 125 30 357.19 2.83 121 95 128 33 350.56 0.24 122 95 129 34 335.45 2.04 123 95 132 37 331.64 0.15 124 98 116 18 461.18 1.58 125 98 125 27 357.18 2.83 126 98 126 28 357.11 2.81 127 98 129 31 331.68 0.17 128 99 129 30 331.66 0.16 129 99 132 33 321.79 4.01 130 99 133 34 310.22 1.45 131 102 114 12 517.80 3.47 132 102 116 14 455.10 0.68 133 102 129 27 331.62 0.14 134 102 130 28 323.22 4.34 135 102 133 31 310.22 1.45 136 102 137 35 309.85 1.28 137 102 141 39 309.62 1.33 138 103 137 34 309.83 1.28 139 105 114 9 481.17 7.46 140 106 137 31 309.76 1.29 141 106 140 34 309.60 1.33 142 109 112 3 455.07 0.68 143 110 140 30 309.58 1.34 144 111 211 100 33.23 0.34 145 112 211 99 33.16 0.30 146 113 140 27 309.59 1.34 147 113 142 29 309.21 1.33 148 113 207 94 60.37 8.61 149 113 210 97 33.22 0.33 150 113 211 98 33.14 0.30 151 114 137 23 309.85 1.29 152 114 140 26 309.61 1.33 153 114 141 27 309.56 1.34 154 114 142 28 309.54 1.33 155 115 141 26 309.60 1.34 156 115 142 27 309.56 1.34 157 115 143 28 309.24 1.32 158 115 203 88 81.23 8.69 159 115 207 92 61.48 8.98 160 116 130 14 323.25 4.33 161 116 141 25 309.65 1.33 162 116 143 27 309.56 1.34 163 116 144 28 308.87 1.48 164 116 145 29 308.91 1.46 165 116 203 87 82.23 8.98 166 117 144 27 309.23 1.40 167 117 145 28 308.91 1.46 168 118 122 4 358.09 2.82 169 118 123 5 357.87 2.73 170 118 145 27 309.06 1.49 171 118 146 28 308.84 1.50 172 118 147 29 308.76 1.47 173 119 122 3 365.04 0.54 174 119 123 4 358.05 2.81 175 119 147 28 308.76 1.48 176 119 188 69 91.28 9.07 177 119 189 70 91.25 9.07 178 119 191 72 90.04 8.86 179 120 123 3 369.69 1.72 180 120 124 4 363.02 0.40 181 120 147 27 308.95 1.46 182 120 148 28 308.75 1.46 183 120 150 30 295.92 0.33 184 120 188 68 91.27 9.08 185 121 124 3 364.75 0.48 186 121 125 4 362.99 0.38 187 121 150 29 290.06 0.97 188 122 125 3 364.27 0.72 189 122 126 4 362.53 0.15 190 123 126 3 364.78 0.47 191 123 127 4 361.72 0.54 192 123 146 23 308.96 1.46 193 123 147 24 308.95 1.46 194 123 149 26 290.06 0.97 195 124 127 3 364.89 1.30 196 124 128 4 363.98 1.76 197 124 149 25 299.92 0.35 198 124 150 26 284.82 1.64 199 124 151 27 283.96 1.73 200 125 128 3 372.70 3.69 201 125 129 4 358.14 1.19 202 126 129 3 372.70 3.69 203 126 130 4 364.00 1.75 204 126 144 18 309.59 1.35 205 126 146 20 308.99 1.45 206 127 130 3 372.69 3.69 207 127 131 4 350.38 5.07 208 127 149 22 294.37 3.12 209 127 159 32 219.81 0.04 210 127 160 33 219.83 0.04 211 128 131 3 358.74 2.34 212 128 132 4 350.38 5.06 213 129 132 3 371.83 3.27 214 129 133 4 349.16 4.47 215 130 133 3 351.55 3.27 216 130 138 8 309.89 1.30 217 130 141 11 309.86 1.28 218 130 144 14 309.60 1.35 219 130 159 29 219.81 0.04 220 130 162 32 218.69 0.39 221 131 138 7 310.37 1.42 222 131 160 29 219.55 0.07 223 131 161 30 219.52 0.06 224 133 137 4 346.50 7.42 225 133 138 5 342.97 7.26 226 133 141 8 310.62 1.15 227 134 137 3 365.23 0.55 228 134 138 4 348.45 8.94 229 135 138 3 364.59 0.86 230 135 139 4 349.00 8.67 231 136 139 3 365.35 0.51 232 136 140 4 365.35 0.51 233 137 140 3 370.63 2.14 234 137 141 4 365.35 0.51 235 138 141 3 378.52 1.80 236 138 161 23 219.05 0.24 237 138 162 24 218.62 0.39 238 139 166 27 216.79 0.12 239 141 144 3 423.38 0.74 240 141 162 21 218.64 0.40 241 141 166 25 216.33 0.09 242 142 162 20 218.66 0.41 243 142 166 24 216.31 0.09 244 142 206 64 65.89 6.83 245 142 207 65 61.68 8.94 246 142 210 68 38.26 2.16 247 143 162 19 218.68 0.40 248 143 166 23 216.31 0.09 249 143 202 59 85.86 10.38 250 143 203 60 85.14 10.44 251 143 206 63 67.72 9.38 252 144 159 15 219.80 0.06 253 144 162 18 218.65 0.40 254 144 166 22 216.41 0.09 255 144 167 23 216.31 0.09 256 144 168 24 216.31 0.09 257 144 202 58 85.97 10.43 258 144 203 59 85.16 10.44 259 145 168 23 216.31 0.09 260 145 170 25 216.06 0.14 261 145 199 54 86.61 10.12 262 145 202 57 85.98 10.43 263 145 203 58 85.50 10.62 264 146 149 3 367.49 0.76 265 146 159 13 219.81 0.04 266 146 167 21 216.50 0.12 267 146 168 22 216.34 0.09 268 146 169 23 216.08 0.14 269 146 170 24 216.06 0.14 270 147 170 23 216.05 0.13 271 147 191 44 90.11 8.88 272 147 194 47 89.84 8.83 273 147 195 48 89.86 8.84 274 147 199 52 89.78 8.84 275 148 170 22 216.17 0.12 276 148 171 23 215.85 0.19 277 148 175 27 215.70 0.19 278 148 177 29 215.94 0.10 279 148 178 30 215.53 0.11 280 148 188 40 91.28 9.07 281 148 191 43 90.53 9.03 282 149 152 3 347.06 7.49 283 149 155 6 343.30 5.57 284 149 158 9 220.03 0.07 285 149 159 10 220.02 0.10 286 149 169 20 216.37 0.10 287 149 171 22 216.06 0.14 288 149 177 28 215.96 0.09 289 149 178 29 214.88 0.02 290 150 154 4 383.44 0.27 291 150 177 27 215.54 0.12 292 150 182 32 122.84 23.23 293 151 154 3 358.96 8.07 294 151 155 4 343.34 5.55 295 152 155 3 369.61 2.75 296 152 156 4 343.31 5.57 297 152 157 5 220.83 0.20 298 152 169 17 217.26 0.13 299 152 171 19 216.42 0.07 300 152 178 26 215.25 0.06 301 153 156 3 344.73 6.24 302 153 178 25 216.03 0.06 303 153 179 26 214.99 0.02 304 153 180 27 214.19 0.36 305 154 180 26 214.18 0.38 306 155 158 3 354.00 7.06 307 155 160 5 220.83 0.20 308 157 169 12 217.24 0.14 309 158 162 4 362.60 1.99 310 158 163 5 240.91 4.11 311 158 164 6 220.47 0.10 312 159 162 3 351.07 3.77 313 159 167 8 219.06 0.77 314 162 166 4 366.87 2.69 315 162 167 5 335.87 9.09 316 163 166 3 371.70 0.28 317 163 167 4 366.85 2.71 318 164 167 3 367.98 2.14 319 165 202 37 86.70 10.09 320 165 206 41 85.13 10.43 321 166 202 36 86.52 10.17 322 166 210 44 61.55 9.19 323 167 202 35 86.55 10.16 324 168 202 34 86.17 10.36 325 170 191 21 90.84 8.88 326 170 194 24 89.88 8.81 327 170 198 28 89.84 8.81 328 170 199 29 89.82 8.82 329 171 191 20 91.22 9.00 330 172 187 15 97.06 11.59 331 172 190 18 96.92 11.46 332 172 191 19 91.41 9.03 333 173 187 14 98.65 11.64 334 174 185 11 122.62 23.32 335 174 187 13 98.50 11.72 336 175 187 12 98.26 11.84 337 175 188 13 97.50 11.47 338 175 191 16 97.51 11.46 339 176 181 5 452.62 6.78 340 176 183 7 350.25 1.23 341 176 185 9 106.53 15.20 342 177 181 4 394.25 6.62 343 177 182 5 342.83 4.94 344 177 183 6 255.59 2.02 345 177 188 11 99.91 12.70 346 184 188 4 328.00 3.33 347 184 189 5 325.20 1.93 348 185 188 3 371.30 0.21 349 186 189 3 371.30 0.21 350 187 190 3 370.70 0.51 351 187 191 4 377.41 2.01 352 188 191 3 407.45 3.00 353 190 193 3 424.25 0.60 354 191 194 3 375.12 2.17 355 191 195 4 353.51 7.05 356 192 195 3 372.05 0.14 357 192 196 4 368.31 0.34 358 193 196 3 371.56 0.39 359 193 197 4 348.79 9.41 360 193 198 5 346.37 10.60 361 194 197 3 369.16 0.82 362 194 198 4 340.73 7.79 363 194 199 5 287.33 18.03 364 194 200 6 287.54 18.12 365 195 199 4 287.91 18.32 366 195 200 5 287.25 17.98 367 196 200 4 332.59 0.26 368 197 200 3 377.02 2.44 369 197 201 4 328.20 5.21 370 198 201 3 362.63 1.60 371 198 202 4 328.20 5.21 372 199 202 3 373.31 3.73 373 199 203 4 338.06 1.45 374 200 203 3 360.88 9.95 375 200 204 4 350.06 4.55 376 201 204 3 368.79 1.67 377 201 205 4 329.00 5.98 378 202 205 3 356.41 7.66 379 202 206 4 329.00 5.98 380 203 206 3 351.47 3.85 381 203 207 4 338.25 0.35 382 204 207 3 355.24 7.27 383 204 208 4 338.24 0.35 384 205 208 3 356.63 7.41 385 205 209 4 346.34 5.28 386 206 209 3 369.31 1.51 387 206 210 4 346.34 5.32 388 207 210 3 364.88 2.08 389 207 211 4 346.31 5.30 390 208 211 3 364.29 2.37 391 208 212 4 270.01 23.32 392 209 212 3 368.06 0.48