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 64.95 0.29 2 18 46 28 64.95 0.29 3 18 47 29 64.95 0.29 4 18 48 30 56.14 0.33 5 18 49 31 61.79 0.01 6 18 53 35 52.48 0.45 7 19 46 27 65.08 0.24 8 19 47 28 64.96 0.29 9 20 47 27 65.72 0.10 10 20 48 28 65.44 0.10 11 20 56 36 64.95 0.30 12 20 60 40 64.97 0.29 13 20 65 45 65.34 0.07 14 20 70 50 64.92 0.28 15 20 71 51 65.00 0.31 16 20 72 52 65.53 0.13 17 21 24 3 372.75 2.52 18 21 25 4 333.99 2.30 19 21 47 26 65.92 0.07 20 21 71 50 65.72 0.06 21 22 25 3 359.49 9.15 22 22 26 4 333.98 2.30 23 22 69 47 65.80 0.10 24 22 70 48 65.84 0.07 25 22 71 49 65.93 0.06 26 23 26 3 339.87 0.24 27 23 35 12 66.08 0.12 28 23 37 14 67.08 0.61 29 23 69 46 66.08 0.12 30 23 71 48 66.38 0.27 31 23 101 78 70.25 0.09 32 23 104 81 70.28 0.09 33 23 105 82 69.18 0.58 34 23 108 85 70.48 0.20 35 24 71 47 68.44 0.06 36 24 101 77 70.24 0.07 37 24 108 84 94.92 11.41 38 26 69 43 69.80 0.27 39 26 108 82 177.25 25.77 40 27 30 3 363.86 8.76 41 27 31 4 335.03 2.44 42 27 69 42 532.35 5.00 43 28 31 3 374.72 3.33 44 28 108 80 187.69 20.66 45 32 112 80 460.15 0.30 46 33 112 79 460.15 0.30 47 33 113 80 460.14 0.30 48 33 211 178 39.61 0.34 49 34 113 79 460.16 0.30 50 34 115 81 460.13 0.30 51 34 207 173 80.29 0.55 52 34 211 177 39.61 0.34 53 35 112 77 534.59 2.30 54 35 113 78 462.09 0.62 55 35 114 79 460.15 0.29 56 35 115 80 460.14 0.30 57 36 115 79 460.15 0.29 58 36 116 80 460.14 0.30 59 36 117 81 460.14 0.30 60 36 203 167 104.00 0.14 61 37 115 78 461.38 0.40 62 37 116 79 460.16 0.29 63 37 117 80 460.16 0.29 64 38 117 79 460.16 0.29 65 38 118 80 460.15 0.29 66 38 119 81 460.16 0.29 67 39 117 78 460.92 0.51 68 39 118 79 460.15 0.30 69 39 119 80 460.16 0.29 70 39 122 83 364.38 0.48 71 39 125 86 360.96 1.99 72 40 119 79 460.17 0.30 73 40 122 82 364.39 0.49 74 41 119 78 460.23 0.30 75 41 120 79 460.17 0.29 76 42 121 79 460.17 0.30 77 44 119 75 461.19 0.38 78 51 119 68 460.07 0.28 79 51 147 96 309.37 0.36 80 51 191 140 112.71 0.90 81 51 192 141 112.43 0.91 82 51 195 144 108.78 1.01 83 54 195 141 108.77 1.01 84 54 196 142 108.77 1.01 85 55 147 92 309.22 0.29 86 55 195 140 108.80 1.00 87 55 200 145 108.29 0.90 88 55 203 148 107.73 0.97 89 58 196 138 108.74 1.02 90 58 200 142 108.29 0.90 91 58 204 146 103.41 0.17 92 59 115 56 460.65 0.48 93 59 203 144 104.42 0.28 94 59 204 145 103.12 0.29 95 62 204 142 103.13 0.29 96 62 208 146 82.33 0.43 97 63 204 141 103.14 0.29 98 63 207 144 83.57 0.41 99 73 125 52 361.83 1.55 100 77 121 44 460.15 0.31 101 77 122 45 448.50 2.62 102 77 125 48 362.62 1.25 103 79 121 42 460.16 0.30 104 80 121 41 460.89 0.55 105 81 121 40 461.00 0.49 106 83 121 38 460.85 0.51 107 84 121 37 460.84 0.52 108 84 182 98 148.55 3.70 109 85 182 97 169.99 7.03 110 87 151 64 308.81 0.67 111 88 124 36 439.39 5.83 112 88 128 40 362.07 1.53 113 88 131 43 361.94 1.57 114 88 132 44 361.00 2.02 115 88 151 63 293.17 1.05 116 89 121 32 460.16 0.32 117 89 124 35 409.69 8.77 118 89 151 62 293.13 1.07 119 90 121 31 460.15 0.30 120 90 125 35 364.53 0.58 121 94 125 31 361.93 1.59 122 95 125 30 361.94 1.59 123 95 128 33 359.85 1.88 124 95 129 34 338.10 0.10 125 95 132 37 324.14 1.22 126 98 125 27 361.88 1.57 127 98 126 28 360.85 2.00 128 98 129 31 324.34 1.25 129 99 129 30 324.32 1.27 130 99 132 33 323.67 1.09 131 99 133 34 311.99 0.12 132 102 114 12 527.59 3.35 133 102 116 14 460.25 0.30 134 102 129 27 324.19 1.20 135 102 133 31 311.14 0.30 136 102 137 35 310.97 0.32 137 102 141 39 310.74 0.32 138 103 137 34 310.96 0.32 139 105 114 9 461.23 0.25 140 106 137 31 310.94 0.30 141 106 140 34 310.75 0.32 142 109 112 3 460.14 0.30 143 110 140 30 310.73 0.32 144 111 211 100 39.63 0.33 145 112 211 99 39.63 0.33 146 113 142 29 310.50 0.29 147 113 207 94 80.28 0.55 148 113 210 97 39.88 0.45 149 113 211 98 39.59 0.33 150 114 137 23 310.99 0.33 151 114 140 26 310.75 0.31 152 114 141 27 310.69 0.30 153 114 142 28 310.61 0.34 154 115 141 26 310.73 0.32 155 115 142 27 310.69 0.29 156 115 143 28 310.43 0.26 157 115 203 88 104.64 0.41 158 115 207 92 82.53 0.47 159 116 130 14 324.00 1.16 160 116 141 25 310.75 0.31 161 116 143 27 310.60 0.34 162 116 144 28 310.13 0.23 163 116 145 29 310.04 0.21 164 116 203 87 105.77 0.55 165 117 144 27 310.47 0.28 166 117 145 28 310.02 0.21 167 118 122 4 364.38 0.48 168 118 123 5 364.12 0.41 169 118 145 27 310.45 0.29 170 118 146 28 310.01 0.20 171 118 147 29 309.41 0.35 172 119 122 3 367.72 1.06 173 119 123 4 364.50 0.55 174 119 147 28 309.23 0.29 175 119 188 69 115.68 1.12 176 119 189 70 115.50 1.20 177 119 191 72 112.81 0.92 178 120 123 3 373.12 1.59 179 120 124 4 367.87 0.99 180 120 147 27 310.25 0.30 181 120 148 28 309.17 0.31 182 120 150 30 302.76 2.44 183 120 188 68 116.08 1.32 184 121 124 3 369.74 0.39 185 121 125 4 366.52 0.37 186 121 150 29 297.93 0.07 187 122 125 3 370.38 1.56 188 122 126 4 364.94 0.38 189 123 126 3 366.56 0.40 190 123 127 4 364.98 0.40 191 123 146 23 310.36 0.30 192 123 147 24 310.24 0.29 193 123 149 26 294.46 1.66 194 124 127 3 371.44 3.25 195 124 128 4 364.58 0.53 196 124 149 25 302.72 2.15 197 124 150 26 293.14 1.05 198 124 151 27 292.94 1.05 199 125 128 3 370.57 0.80 200 125 129 4 364.54 0.49 201 126 129 3 372.50 4.28 202 126 130 4 367.03 0.94 203 126 146 20 310.42 0.28 204 127 130 3 373.41 2.25 205 127 131 4 359.04 4.92 206 127 149 22 298.90 0.56 207 127 159 32 222.27 1.02 208 128 131 3 367.37 0.78 209 128 132 4 359.05 4.93 210 129 132 3 373.37 0.55 211 129 133 4 356.54 3.68 212 130 133 3 367.75 0.57 213 130 138 8 311.01 0.30 214 130 141 11 311.01 0.30 215 130 144 14 310.75 0.32 216 130 159 29 222.27 1.02 217 130 162 32 221.75 1.04 218 131 138 7 311.50 0.24 219 131 160 29 222.20 1.03 220 131 161 30 222.05 1.02 221 133 137 4 340.66 3.69 222 133 138 5 312.53 0.13 223 133 141 8 311.55 0.24 224 134 137 3 381.97 0.03 225 134 138 4 344.58 11.18 226 135 138 3 351.05 11.07 227 135 139 4 323.92 4.70 228 136 140 4 374.73 0.76 229 137 140 3 380.69 3.73 230 137 141 4 368.80 2.21 231 138 141 3 383.71 2.23 232 138 161 23 221.81 1.04 233 138 162 24 221.67 1.04 234 139 166 27 221.01 0.98 235 141 144 3 414.95 0.21 236 141 162 21 221.69 1.04 237 141 166 25 220.97 0.99 238 142 166 24 220.95 0.99 239 142 206 64 86.49 1.48 240 142 207 65 82.58 0.46 241 142 210 68 79.56 0.62 242 143 162 19 221.91 0.95 243 143 166 23 220.93 1.00 244 143 202 59 108.30 0.90 245 143 203 60 106.23 0.56 246 143 206 63 87.04 1.20 247 144 159 15 222.29 1.02 248 144 162 18 221.91 0.95 249 144 166 22 221.00 1.00 250 144 167 23 220.87 1.02 251 144 168 24 220.83 1.03 252 144 202 58 108.56 1.01 253 144 203 59 107.44 0.86 254 145 168 23 220.81 1.04 255 145 170 25 220.73 1.02 256 145 199 54 108.78 0.98 257 145 202 57 108.67 0.96 258 145 203 58 108.35 0.93 259 146 149 3 372.54 0.86 260 146 159 13 222.30 1.02 261 146 167 21 221.24 1.14 262 146 168 22 220.88 1.04 263 146 169 23 220.78 1.03 264 146 170 24 220.71 1.03 265 147 170 23 220.59 0.98 266 147 191 44 112.81 0.92 267 147 194 47 112.49 0.89 268 147 195 48 112.45 0.88 269 147 199 52 112.34 0.89 270 148 170 22 220.83 1.06 271 148 171 23 220.52 1.02 272 148 175 27 220.52 1.04 273 148 177 29 220.43 1.11 274 148 178 30 220.24 1.03 275 148 188 40 115.69 1.12 276 148 191 43 114.10 1.16 277 149 152 3 373.15 1.44 278 149 155 6 292.80 14.12 279 149 158 9 222.76 1.00 280 149 169 20 220.90 1.06 281 149 171 22 220.75 1.05 282 149 177 28 220.37 1.08 283 149 178 29 220.09 1.10 284 150 154 4 383.38 2.14 285 150 177 27 220.33 1.10 286 150 182 32 170.00 7.03 287 151 154 3 372.15 1.02 288 151 155 4 353.88 7.45 289 152 155 3 376.80 0.39 290 152 156 4 350.34 7.42 291 152 157 5 222.83 1.03 292 152 169 17 221.40 1.16 293 152 171 19 221.15 1.17 294 152 178 26 220.27 1.05 295 153 156 3 353.90 7.44 296 153 178 25 220.69 0.99 297 153 179 26 220.09 1.10 298 153 180 27 220.00 1.10 299 154 180 26 219.92 1.15 300 155 158 3 367.73 1.23 301 155 160 5 222.84 1.04 302 157 169 12 221.42 1.15 303 158 162 4 361.30 6.07 304 158 164 6 221.91 1.12 305 159 162 3 372.83 0.03 306 159 167 8 221.47 1.17 307 162 166 4 366.23 0.58 308 162 167 5 290.48 15.42 309 163 166 3 376.81 1.45 310 163 167 4 343.19 10.94 311 164 167 3 372.39 3.66 312 165 202 37 108.77 0.97 313 165 206 41 106.53 0.49 314 166 202 36 108.74 0.97 315 167 202 35 108.76 0.97 316 168 202 34 108.76 0.97 317 170 191 21 114.14 1.53 318 170 194 24 112.50 0.89 319 170 198 28 112.44 0.91 320 170 199 29 112.37 0.89 321 171 191 20 115.66 1.10 322 172 187 15 118.85 1.50 323 172 190 18 117.58 1.09 324 172 191 19 116.73 0.72 325 173 187 14 132.52 0.78 326 174 185 11 147.79 3.35 327 174 187 13 132.53 0.79 328 175 187 12 126.33 2.31 329 175 188 13 125.05 2.94 330 175 191 16 123.34 3.69 331 176 181 5 446.25 0.90 332 176 183 7 338.38 2.48 333 176 185 9 147.79 3.35 334 177 181 4 393.87 3.02 335 177 182 5 357.19 6.17 336 177 183 6 329.68 1.88 337 177 188 11 130.17 0.24 338 184 188 4 344.62 2.82 339 184 189 5 354.83 2.29 340 185 188 3 378.44 1.64 341 186 189 3 386.88 1.08 342 186 190 4 382.11 3.46 343 187 190 3 387.26 0.89 344 187 191 4 387.27 0.89 345 188 191 3 419.70 0.68 346 190 193 3 431.19 1.32 347 191 194 3 381.12 0.92 348 191 195 4 351.95 7.42 349 192 195 3 372.44 1.33 350 192 196 4 352.78 7.83 351 193 196 3 372.06 1.80 352 193 197 4 352.78 7.83 353 193 198 5 335.50 0.81 354 194 197 3 378.26 4.92 355 194 198 4 335.44 0.83 356 194 199 5 326.75 2.43 357 194 200 6 326.75 2.43 358 195 199 4 326.71 2.43 359 195 200 5 334.28 1.36 360 196 200 4 351.58 8.23 361 197 200 3 379.31 2.75 362 197 201 4 336.16 0.53 363 198 201 3 351.58 8.23 364 198 202 4 336.15 0.53 365 199 202 3 362.19 4.62 366 199 203 4 340.56 2.89 367 200 203 3 359.28 3.16 368 200 204 4 334.85 0.78 369 201 204 3 375.50 0.26 370 201 205 4 353.80 8.71 371 202 205 3 371.42 0.10 372 202 206 4 353.80 8.71 373 203 206 3 371.43 0.10 374 203 207 4 352.97 9.12 375 204 207 3 360.18 3.01 376 204 208 4 334.53 0.35 377 205 208 3 367.48 0.46 378 205 209 4 337.50 1.14 379 206 209 3 365.34 5.92 380 206 210 4 372.23 2.12 381 207 210 3 381.45 3.05 382 207 211 4 350.97 7.88 383 208 211 3 363.73 6.37 384 208 212 4 194.43 20.97 385 208 213 5 194.42 20.97