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 61.45 0.91 2 18 46 28 61.45 0.91 3 18 47 29 61.45 0.91 4 18 48 30 49.90 1.92 5 18 49 31 56.15 0.30 6 18 53 35 43.01 1.30 7 19 46 27 62.15 0.95 8 19 47 28 61.55 0.86 9 20 47 27 63.01 0.58 10 20 48 28 62.22 0.91 11 20 60 40 62.04 1.06 12 20 70 50 61.23 0.70 13 20 71 51 62.21 0.97 14 20 72 52 62.61 0.78 15 21 24 3 372.75 2.52 16 21 25 4 339.44 0.45 17 21 47 26 64.05 0.17 18 21 71 50 63.22 0.47 19 22 25 3 359.49 9.15 20 22 26 4 334.06 2.33 21 22 69 47 63.94 0.11 22 22 70 48 63.55 0.35 23 22 71 49 64.08 0.16 24 23 26 3 367.73 1.24 25 23 35 12 64.09 0.15 26 23 37 14 64.54 0.36 27 23 69 46 64.09 0.15 28 23 71 48 64.52 0.35 29 23 101 78 65.80 0.19 30 23 104 81 65.81 0.20 31 23 105 82 65.45 0.10 32 23 108 85 92.22 13.02 33 24 71 47 65.36 0.00 34 24 101 77 65.81 0.20 35 24 108 84 96.48 15.09 36 26 69 43 65.22 0.07 37 26 108 82 127.51 0.90 38 27 30 3 373.17 4.11 39 27 31 4 335.05 2.33 40 27 69 42 519.24 8.06 41 28 31 3 373.17 4.11 42 28 108 80 193.30 17.75 43 32 112 80 453.50 2.08 44 33 112 79 453.50 2.08 45 33 113 80 453.50 2.08 46 33 211 178 39.54 0.30 47 34 113 79 453.50 2.08 48 34 115 81 453.50 2.08 49 34 207 173 80.28 0.55 50 34 211 177 36.73 1.10 51 35 112 77 521.08 1.98 52 35 113 78 458.12 2.04 53 35 114 79 453.52 2.08 54 35 115 80 453.50 2.08 55 36 115 79 453.51 2.08 56 36 116 80 453.50 2.08 57 36 117 81 453.50 2.08 58 36 203 167 102.50 0.61 59 37 115 78 455.59 1.65 60 37 116 79 453.53 2.08 61 37 117 80 453.51 2.08 62 38 117 79 453.52 2.08 63 38 118 80 453.51 2.08 64 38 119 81 453.51 2.08 65 39 117 78 453.99 2.21 66 39 118 79 453.51 2.08 67 39 119 80 453.51 2.08 68 39 122 83 364.32 0.08 69 39 125 86 362.42 0.87 70 40 119 79 453.54 2.08 71 40 122 82 364.54 0.04 72 41 119 78 453.64 2.08 73 41 120 79 453.54 2.08 74 42 121 79 453.54 2.08 75 44 119 75 454.19 2.10 76 51 119 68 453.40 2.11 77 51 147 96 309.07 0.51 78 51 191 140 114.00 1.50 79 51 192 141 113.68 1.51 80 51 195 144 108.78 1.01 81 54 195 141 108.78 1.02 82 54 196 142 108.77 1.01 83 55 147 92 308.93 0.43 84 55 195 140 108.77 1.02 85 55 200 145 108.26 0.88 86 55 203 148 107.46 1.19 87 58 196 138 109.03 0.90 88 58 200 142 108.23 0.86 89 58 204 146 103.30 0.20 90 59 115 56 455.41 1.50 91 59 203 144 102.17 0.45 92 59 204 145 101.81 0.36 93 62 204 142 101.83 0.37 94 62 208 146 82.34 0.42 95 63 204 141 101.83 0.37 96 63 207 144 82.13 0.32 97 73 125 52 362.43 0.86 98 77 121 44 453.50 2.08 99 77 122 45 453.02 2.03 100 77 125 48 364.08 0.14 101 79 121 42 453.50 2.08 102 80 121 41 453.67 2.08 103 83 121 38 454.19 2.30 104 84 121 37 454.18 2.30 105 84 182 98 166.94 5.29 106 85 182 97 178.80 0.65 107 87 151 64 304.74 1.36 108 88 124 36 424.64 1.54 109 88 128 40 363.58 0.40 110 88 131 43 362.44 0.86 111 88 132 44 362.35 0.91 112 88 151 63 293.14 1.06 113 89 121 32 453.57 2.08 114 89 124 35 393.98 1.15 115 89 151 62 293.13 1.07 116 90 121 31 453.54 2.08 117 90 125 35 364.83 0.15 118 94 125 31 362.56 0.89 119 95 125 30 362.56 0.89 120 95 128 33 359.70 0.21 121 95 129 34 337.09 0.40 122 95 132 37 326.38 0.10 123 98 125 27 362.42 0.86 124 98 126 28 362.21 0.95 125 98 129 31 327.68 0.65 126 99 129 30 326.47 0.06 127 99 132 33 325.88 0.22 128 99 133 34 316.25 2.02 129 102 114 12 524.95 4.68 130 102 116 14 453.62 2.08 131 102 129 27 326.39 0.09 132 102 130 28 326.23 0.17 133 102 133 31 311.29 0.20 134 102 137 35 310.96 0.33 135 102 141 39 310.68 0.22 136 103 133 30 311.29 0.20 137 103 137 34 310.95 0.33 138 105 114 9 465.82 6.63 139 106 137 31 310.90 0.33 140 106 140 34 310.68 0.22 141 109 112 3 453.50 2.08 142 110 140 30 310.66 0.22 143 111 211 100 39.62 0.32 144 113 142 29 310.41 0.24 145 113 207 94 80.28 0.55 146 113 210 97 41.54 0.38 147 113 211 98 39.59 0.33 148 114 137 23 310.97 0.32 149 114 140 26 310.68 0.22 150 114 141 27 310.55 0.18 151 114 142 28 310.43 0.24 152 115 141 26 310.66 0.22 153 115 142 27 310.55 0.18 154 115 143 28 310.25 0.17 155 115 203 88 102.50 0.61 156 115 207 92 82.45 0.52 157 116 130 14 326.10 0.11 158 116 141 25 310.68 0.21 159 116 143 27 310.49 0.21 160 116 144 28 310.14 0.22 161 116 145 29 310.08 0.24 162 116 203 87 105.67 0.88 163 117 144 27 310.37 0.23 164 117 145 28 310.09 0.24 165 118 122 4 364.47 0.01 166 118 123 5 363.00 0.58 167 118 145 27 310.38 0.23 168 118 146 28 310.06 0.23 169 118 147 29 308.94 0.43 170 119 122 3 365.38 0.42 171 119 123 4 364.50 0.01 172 119 147 28 308.93 0.44 173 119 188 69 115.93 1.79 174 119 189 70 115.80 1.74 175 119 191 72 114.06 1.47 176 120 123 3 373.38 1.42 177 120 124 4 366.05 0.61 178 120 147 27 310.26 0.26 179 120 148 28 308.95 0.43 180 120 150 30 297.93 0.07 181 120 188 68 115.93 1.79 182 121 124 3 373.32 1.40 183 121 125 4 364.99 0.08 184 121 150 29 298.10 0.15 185 122 125 3 369.33 2.09 186 122 126 4 364.85 0.15 187 123 126 3 377.04 0.46 188 123 127 4 364.85 0.15 189 123 146 23 310.32 0.23 190 123 147 24 310.26 0.25 191 123 149 26 295.48 1.16 192 124 127 3 371.52 3.21 193 124 128 4 364.58 0.25 194 124 149 25 303.16 1.57 195 124 150 26 293.15 1.06 196 124 151 27 291.91 0.53 197 125 128 3 375.05 1.45 198 125 129 4 364.24 0.43 199 126 129 3 371.68 3.12 200 126 130 4 364.23 0.43 201 126 146 20 310.32 0.23 202 127 130 3 374.12 3.46 203 127 131 4 351.81 6.63 204 127 149 22 298.91 0.56 205 127 159 32 217.74 0.43 206 128 131 3 366.92 0.98 207 128 132 4 358.17 4.51 208 129 132 3 366.07 0.56 209 129 133 4 358.16 4.51 210 130 133 3 365.00 0.02 211 130 138 8 311.01 0.30 212 130 141 11 310.99 0.31 213 130 144 14 310.68 0.23 214 130 159 29 217.73 0.42 215 130 162 32 217.25 0.38 216 131 138 7 311.38 0.25 217 131 160 29 217.68 0.42 218 131 161 30 217.65 0.42 219 133 137 4 356.38 4.17 220 133 138 5 318.23 2.73 221 133 141 8 311.24 0.29 222 134 137 3 381.97 0.04 223 134 138 4 346.79 8.95 224 135 138 3 372.50 0.34 225 135 139 4 335.70 6.74 226 136 140 4 350.92 8.01 227 137 140 3 376.62 2.94 228 137 141 4 360.93 4.91 229 138 141 3 383.71 2.23 230 138 161 23 217.28 0.39 231 138 162 24 217.22 0.39 232 139 166 27 216.59 0.42 233 141 144 3 413.50 0.52 234 141 162 21 217.19 0.39 235 141 166 25 215.83 0.07 236 142 166 24 215.83 0.07 237 142 206 64 86.39 1.18 238 142 207 65 82.62 0.48 239 142 210 68 77.80 0.65 240 143 162 19 217.22 0.39 241 143 166 23 215.83 0.07 242 143 202 59 108.23 0.86 243 143 203 60 106.23 0.59 244 143 206 63 86.70 1.03 245 144 159 15 217.72 0.43 246 144 162 18 217.22 0.39 247 144 166 22 216.36 0.32 248 144 167 23 215.81 0.08 249 144 168 24 215.70 0.14 250 144 202 58 108.55 1.02 251 144 203 59 107.36 0.91 252 145 168 23 215.71 0.13 253 145 170 25 215.51 0.22 254 145 199 54 108.73 0.98 255 145 202 57 108.67 0.96 256 145 203 58 108.05 1.08 257 146 149 3 372.54 0.86 258 146 159 13 217.74 0.43 259 146 167 21 216.56 0.44 260 146 168 22 215.75 0.13 261 146 169 23 215.55 0.16 262 146 170 24 215.43 0.21 263 147 170 23 215.24 0.14 264 147 191 44 114.07 1.47 265 147 194 47 113.73 1.53 266 147 195 48 113.75 1.52 267 147 199 52 113.66 1.53 268 148 170 22 215.61 0.18 269 148 171 23 215.12 0.09 270 148 175 27 214.91 0.14 271 148 177 29 214.71 0.10 272 148 178 30 214.52 0.15 273 148 188 40 115.80 1.74 274 148 191 43 115.02 1.61 275 149 152 3 369.55 0.36 276 149 155 6 303.58 20.45 277 149 158 9 218.05 0.55 278 149 159 10 218.03 0.54 279 149 169 20 215.73 0.14 280 149 171 22 215.52 0.23 281 149 178 29 214.41 0.10 282 150 154 4 383.38 2.14 283 150 177 27 214.57 0.04 284 150 182 32 176.04 0.80 285 151 154 3 372.16 1.02 286 151 155 4 348.66 10.73 287 152 155 3 376.80 0.39 288 152 156 4 343.87 0.31 289 152 157 5 219.11 1.03 290 152 169 17 216.69 0.47 291 152 171 19 216.46 0.48 292 152 178 26 213.63 0.43 293 153 156 3 356.68 6.71 294 153 178 25 215.40 0.09 295 153 179 26 214.37 0.29 296 153 180 27 213.35 0.30 297 154 180 26 213.34 0.31 298 155 158 3 367.73 1.24 299 155 160 5 218.57 0.32 300 157 169 12 216.72 0.45 301 158 162 4 371.00 1.22 302 158 163 5 225.91 3.20 303 158 164 6 217.79 0.09 304 159 162 3 371.00 1.22 305 159 167 8 217.03 0.34 306 162 166 4 370.64 1.63 307 162 167 5 322.95 5.24 308 163 166 3 377.58 1.38 309 163 167 4 356.47 5.46 310 164 167 3 361.47 9.12 311 165 202 37 108.73 0.96 312 165 206 41 105.89 0.82 313 166 202 36 108.71 0.96 314 167 202 35 108.73 0.96 315 168 202 34 108.73 0.96 316 170 191 21 114.68 1.76 317 170 194 24 113.83 1.57 318 170 198 28 113.67 1.53 319 170 199 29 113.69 1.54 320 171 191 20 115.64 1.57 321 172 187 15 125.51 2.83 322 172 190 18 118.12 1.74 323 172 191 19 117.90 1.65 324 173 187 14 131.46 0.12 325 174 185 11 166.58 5.48 326 174 187 13 131.47 0.12 327 175 187 12 131.45 0.12 328 175 188 13 131.44 0.12 329 175 191 16 131.44 0.12 330 176 181 5 453.91 0.86 331 176 183 7 362.54 9.58 332 176 185 9 204.56 13.57 333 177 181 4 400.81 0.46 334 177 182 5 380.30 0.70 335 177 183 6 338.81 1.44 336 177 188 11 131.43 0.12 337 184 188 4 336.55 1.22 338 184 189 5 336.56 1.21 339 185 188 3 373.07 1.04 340 186 189 3 378.40 1.62 341 187 190 3 384.12 2.46 342 187 191 4 388.55 0.24 343 188 191 3 419.70 0.68 344 190 193 3 433.45 0.19 345 191 194 3 385.17 2.94 346 191 195 4 351.67 7.55 347 192 195 3 377.00 0.91 348 192 196 4 351.67 7.55 349 193 196 3 369.20 1.21 350 193 197 4 343.03 4.23 351 193 198 5 332.32 0.01 352 194 197 3 375.71 6.19 353 194 198 4 330.87 0.53 354 194 199 5 330.40 0.29 355 194 200 6 330.40 0.29 356 195 199 4 330.39 0.29 357 195 200 5 330.33 0.26 358 196 200 4 360.51 3.77 359 197 200 3 376.51 1.34 360 197 201 4 332.26 0.00 361 198 201 3 368.22 0.08 362 198 202 4 332.79 0.27 363 199 202 3 369.89 0.77 364 199 203 4 341.03 2.00 365 200 203 3 363.12 5.00 366 200 204 4 339.00 3.02 367 201 204 3 377.26 0.62 368 201 205 4 336.41 1.72 369 202 205 3 354.36 8.63 370 202 206 4 336.74 0.17 371 203 206 3 363.71 3.97 372 203 207 4 336.16 0.46 373 204 207 3 354.97 0.41 374 204 208 4 334.24 0.48 375 205 208 3 360.18 7.65 376 205 209 4 350.98 7.88 377 206 209 3 372.58 2.29 378 206 210 4 372.58 2.29 379 207 210 3 381.45 3.05 380 207 211 4 353.15 7.41 381 208 211 3 372.23 2.12 382 208 212 4 243.97 3.81