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 61.09 0.76 2 18 46 28 61.09 0.76 3 18 47 29 61.02 0.73 4 18 48 30 49.49 1.95 5 18 49 31 53.55 1.30 6 18 53 35 43.43 1.09 7 19 46 27 61.29 0.69 8 19 47 28 61.13 0.76 9 20 47 27 62.15 0.55 10 20 48 28 61.33 0.68 11 20 60 40 61.28 0.68 12 20 70 50 60.97 0.63 13 20 71 51 61.31 0.67 14 20 72 52 61.98 0.46 15 21 24 3 352.31 2.79 16 21 25 4 284.27 27.13 17 21 47 26 62.69 0.35 18 21 71 50 61.77 0.56 19 22 25 3 340.38 0.02 20 22 26 4 283.60 27.45 21 22 69 47 62.44 0.23 22 22 70 48 62.62 0.32 23 22 71 49 63.50 0.09 24 23 26 3 354.85 7.67 25 23 35 12 63.62 0.13 26 23 37 14 63.73 0.07 27 23 69 46 63.60 0.12 28 23 71 48 63.62 0.11 29 23 101 78 67.63 0.99 30 23 104 81 68.20 1.08 31 23 105 82 65.05 0.30 32 23 108 85 68.25 1.05 33 24 71 47 64.56 0.14 34 24 101 77 68.20 1.08 35 24 104 80 68.28 1.07 36 24 108 84 96.44 15.12 37 26 69 43 67.76 0.86 38 26 108 82 134.25 4.67 39 27 30 3 345.96 3.10 40 27 31 4 326.87 6.45 41 27 69 42 517.85 8.75 42 28 31 3 363.69 8.85 43 28 108 80 164.88 7.69 44 32 112 80 455.88 0.92 45 33 112 79 455.90 0.93 46 33 113 80 455.88 0.92 47 33 211 178 35.58 0.53 48 34 113 79 455.91 0.92 49 34 115 81 455.88 0.92 50 34 207 173 80.12 0.62 51 34 211 177 35.58 0.53 52 35 112 77 532.23 4.95 53 35 113 78 460.42 0.53 54 35 114 79 455.90 0.92 55 35 115 80 455.90 0.93 56 36 115 79 455.90 0.93 57 36 116 80 455.90 0.93 58 36 117 81 455.90 0.93 59 36 203 167 102.50 0.21 60 37 115 78 456.31 0.86 61 37 116 79 455.91 0.93 62 37 117 80 455.91 0.93 63 38 117 79 455.91 0.93 64 38 118 80 455.91 0.93 65 38 119 81 455.91 0.93 66 39 117 78 456.07 0.95 67 39 118 79 455.91 0.92 68 39 119 80 455.91 0.93 69 39 122 83 366.24 0.06 70 39 125 86 364.72 0.10 71 40 119 79 455.93 0.92 72 40 122 82 366.26 0.07 73 41 119 78 455.99 0.94 74 41 120 79 455.93 0.92 75 41 122 81 392.74 1.54 76 42 121 79 455.93 0.92 77 44 119 75 457.41 0.28 78 51 119 68 455.88 0.93 79 51 147 96 308.58 0.28 80 51 191 140 112.60 0.71 81 51 192 141 112.15 0.85 82 51 195 144 107.98 1.00 83 54 195 141 108.00 0.99 84 54 196 142 107.98 0.98 85 55 147 92 308.60 0.27 86 55 195 140 108.00 0.98 87 55 200 145 107.53 0.83 88 55 203 148 105.54 0.83 89 58 196 138 108.00 0.99 90 58 200 142 107.54 0.83 91 58 204 146 102.49 0.21 92 59 115 56 456.16 0.83 93 59 203 144 102.50 0.21 94 59 204 145 102.26 0.13 95 62 204 142 102.28 0.14 96 62 208 146 82.14 0.35 97 63 204 141 102.28 0.14 98 63 207 144 80.75 0.36 99 73 125 52 364.72 0.10 100 77 121 44 455.89 0.92 101 77 122 45 455.17 0.57 102 77 125 48 365.04 0.05 103 79 121 42 455.89 0.92 104 80 121 41 456.05 0.94 105 83 121 38 456.06 0.98 106 84 121 37 456.06 0.98 107 84 150 66 308.22 0.37 108 84 182 98 156.59 1.15 109 85 182 97 156.62 1.16 110 87 151 64 304.74 1.36 111 88 124 36 434.22 8.42 112 88 128 40 365.09 0.01 113 88 131 43 364.79 0.10 114 88 132 44 364.60 0.12 115 88 151 63 291.78 0.40 116 89 121 32 455.98 0.95 117 89 124 35 403.04 3.39 118 89 151 62 291.25 0.14 119 90 121 31 455.89 0.91 120 90 125 35 366.21 0.04 121 94 125 31 365.04 0.06 122 95 125 30 365.04 0.06 123 95 128 33 362.29 0.18 124 95 129 34 339.48 0.80 125 95 132 37 332.66 0.30 126 98 125 27 364.76 0.08 127 98 126 28 364.56 0.12 128 98 129 31 332.61 0.45 129 99 129 30 332.61 0.46 130 99 132 33 330.85 0.39 131 99 133 34 311.95 0.14 132 102 114 12 535.04 0.31 133 102 116 14 456.03 0.94 134 102 129 27 334.00 1.15 135 102 130 28 332.51 0.46 136 102 133 31 311.28 0.20 137 102 137 35 310.80 0.25 138 102 141 39 310.55 0.26 139 103 133 30 311.29 0.20 140 103 137 34 310.79 0.24 141 105 114 9 486.81 10.99 142 106 137 31 310.69 0.23 143 106 140 34 310.54 0.27 144 109 112 3 455.89 0.93 145 110 140 30 310.53 0.26 146 111 211 100 39.52 0.29 147 113 142 29 310.41 0.24 148 113 207 94 80.15 0.61 149 113 210 97 39.60 0.33 150 113 211 98 36.73 1.10 151 114 137 23 310.81 0.25 152 114 140 26 310.55 0.28 153 114 141 27 310.43 0.24 154 114 142 28 310.42 0.25 155 115 141 26 310.52 0.27 156 115 142 27 310.44 0.26 157 115 143 28 310.10 0.23 158 115 203 88 104.34 0.69 159 115 207 92 82.39 0.49 160 116 130 14 332.51 0.46 161 116 141 25 310.56 0.27 162 116 143 27 310.43 0.25 163 116 144 28 310.00 0.18 164 116 145 29 309.57 0.00 165 116 203 87 104.83 0.47 166 117 144 27 310.26 0.29 167 117 145 28 308.91 0.14 168 118 122 4 366.24 0.06 169 118 123 5 365.56 0.03 170 118 126 8 364.57 0.12 171 118 145 27 310.30 0.28 172 118 146 28 308.64 0.28 173 118 147 29 308.62 0.28 174 119 122 3 371.14 1.88 175 119 123 4 366.24 0.06 176 119 147 28 308.60 0.29 177 119 188 69 114.55 1.10 178 119 189 70 113.60 0.65 179 119 191 72 112.62 0.72 180 120 123 3 368.18 0.84 181 120 124 4 366.97 0.23 182 120 147 27 310.22 0.28 183 120 148 28 308.58 0.29 184 120 150 30 302.76 2.44 185 120 188 68 114.55 1.10 186 121 124 3 373.25 2.92 187 121 125 4 366.96 0.23 188 122 125 3 366.94 0.23 189 122 126 4 364.99 0.04 190 123 126 3 366.17 0.61 191 123 127 4 364.73 0.12 192 123 146 23 310.22 0.28 193 123 147 24 310.21 0.28 194 123 149 26 294.41 1.69 195 124 127 3 366.93 0.95 196 124 128 4 364.74 0.12 197 124 150 26 290.87 0.06 198 124 151 27 290.53 0.15 199 125 128 3 363.87 0.58 200 125 129 4 363.81 0.59 201 126 129 3 360.43 2.29 202 126 130 4 352.33 6.33 203 126 146 20 310.26 0.29 204 127 130 3 370.56 2.79 205 127 131 4 364.01 0.47 206 127 149 22 298.89 0.56 207 127 159 32 221.16 0.11 208 128 131 3 366.08 0.56 209 128 132 4 358.30 2.39 210 129 132 3 366.07 0.57 211 129 133 4 351.80 1.31 212 130 133 3 353.99 0.23 213 130 138 8 310.81 0.25 214 130 141 11 310.82 0.27 215 130 144 14 310.54 0.27 216 130 159 29 221.16 0.11 217 130 162 32 220.86 0.15 218 131 138 7 311.21 0.30 219 131 160 29 221.07 0.11 220 131 161 30 220.97 0.12 221 133 137 4 335.66 0.96 222 133 138 5 311.38 0.38 223 133 141 8 311.05 0.35 224 134 137 3 377.03 2.44 225 134 138 4 325.22 5.29 226 135 138 3 352.26 7.33 227 135 139 4 324.19 4.77 228 136 140 4 359.03 3.95 229 137 140 3 380.69 3.74 230 137 141 4 362.17 5.52 231 138 141 3 383.71 2.23 232 138 161 23 220.92 0.12 233 138 162 24 220.76 0.13 234 139 166 27 219.60 0.17 235 141 144 3 408.45 2.00 236 141 162 21 220.81 0.13 237 141 166 25 219.46 0.24 238 142 166 24 219.44 0.24 239 142 206 64 83.30 0.11 240 142 207 65 82.84 0.32 241 142 210 68 76.64 0.35 242 143 162 19 220.89 0.14 243 143 166 23 219.44 0.24 244 143 202 59 107.54 0.83 245 143 203 60 105.52 0.43 246 143 206 63 86.69 1.03 247 144 159 15 221.15 0.10 248 144 162 18 220.88 0.14 249 144 166 22 219.55 0.27 250 144 167 23 219.30 0.27 251 144 168 24 219.27 0.27 252 144 202 58 107.83 0.97 253 144 203 59 106.11 0.72 254 145 168 23 219.28 0.28 255 145 170 25 219.21 0.26 256 145 199 54 107.88 0.95 257 145 202 57 107.89 0.98 258 145 203 58 107.75 0.95 259 146 149 3 372.54 0.86 260 146 159 13 221.19 0.11 261 146 167 21 219.59 0.29 262 146 168 22 219.37 0.28 263 146 169 23 219.25 0.27 264 146 170 24 219.22 0.26 265 147 170 23 219.15 0.29 266 147 191 44 112.62 0.72 267 147 194 47 112.20 0.83 268 147 195 48 112.45 0.69 269 147 199 52 112.12 0.83 270 148 170 22 219.33 0.30 271 148 171 23 219.12 0.29 272 148 175 27 219.16 0.27 273 148 177 29 219.08 0.29 274 148 178 30 218.82 0.40 275 148 188 40 114.55 1.10 276 148 191 43 112.65 0.73 277 149 152 3 357.67 6.30 278 149 155 6 289.64 14.77 279 149 157 8 221.50 0.14 280 149 158 9 221.50 0.14 281 149 169 20 219.39 0.32 282 149 171 22 219.22 0.26 283 149 177 28 219.03 0.32 284 149 178 29 218.74 0.43 285 150 154 4 382.62 2.52 286 150 177 27 219.02 0.32 287 151 154 3 372.15 1.02 288 151 155 4 341.80 14.16 289 152 155 3 376.80 0.39 290 152 156 4 315.38 1.90 291 152 157 5 222.03 0.12 292 152 169 17 219.88 0.30 293 152 171 19 219.43 0.29 294 152 178 26 218.78 0.44 295 153 156 3 338.04 3.50 296 153 178 25 219.19 0.24 297 153 179 26 218.78 0.44 298 153 180 27 218.12 0.14 299 154 180 26 218.09 0.15 300 155 158 3 369.32 2.02 301 155 160 5 221.86 0.24 302 157 169 12 219.88 0.29 303 158 162 4 371.00 1.22 304 158 163 5 248.64 2.94 305 158 164 6 221.34 0.14 306 159 162 3 368.87 0.15 307 159 167 8 220.50 0.55 308 162 166 4 356.46 5.46 309 162 167 5 290.96 13.56 310 163 166 3 376.81 1.45 311 163 167 4 346.95 10.21 312 164 167 3 364.67 7.52 313 165 206 41 106.08 0.71 314 166 202 36 107.91 0.97 315 167 202 35 107.94 0.96 316 168 202 34 107.94 0.96 317 170 191 21 112.66 0.74 318 170 194 24 112.27 0.86 319 170 198 28 112.20 0.83 320 170 199 29 112.17 0.84 321 171 191 20 115.09 1.07 322 172 187 15 120.58 0.48 323 172 190 18 118.45 1.57 324 172 191 19 118.36 1.54 325 173 187 14 130.28 0.68 326 174 185 11 139.84 0.74 327 174 187 13 130.27 0.68 328 175 187 12 126.31 2.23 329 175 188 13 120.83 0.52 330 175 191 16 120.85 0.51 331 176 181 5 438.75 8.30 332 176 183 7 325.31 0.32 333 176 185 9 139.75 0.70 334 177 181 4 400.04 1.68 335 177 182 5 362.91 6.33 336 177 183 6 331.26 2.67 337 177 188 11 120.78 0.49 338 184 188 4 344.62 2.82 339 184 189 5 350.14 0.06 340 185 188 3 383.95 1.11 341 186 189 3 383.00 3.02 342 186 190 4 379.07 4.98 343 187 190 3 387.25 0.89 344 187 191 4 387.25 0.89 345 188 191 3 415.70 2.68 346 190 193 3 438.55 2.36 347 191 194 3 379.30 1.09 348 191 195 4 327.11 0.38 349 192 195 3 370.67 0.45 350 192 196 4 327.11 0.38 351 193 196 3 349.72 10.93 352 193 197 4 327.10 0.37 353 193 198 5 327.09 0.37 354 194 197 3 380.93 3.58 355 194 198 4 324.33 1.01 356 194 199 5 319.25 0.86 357 194 200 6 319.31 0.89 358 195 199 4 319.25 0.86 359 195 200 5 319.25 0.86 360 196 200 4 334.63 1.19 361 197 200 3 376.51 1.34 362 197 201 4 322.31 0.22 363 198 201 3 339.30 3.52 364 198 202 4 324.36 1.25 365 199 202 3 369.48 0.97 366 199 203 4 335.83 0.59 367 200 203 3 353.04 0.04 368 200 204 4 331.55 2.33 369 201 204 3 361.32 4.94 370 201 205 4 336.31 0.04 371 202 205 3 337.40 0.51 372 202 206 4 336.31 0.04 373 203 206 3 346.08 4.84 374 203 207 4 336.81 0.80 375 204 207 3 367.30 0.56 376 204 208 4 335.70 0.24 377 205 208 3 353.39 7.50 378 205 209 4 336.78 0.79 379 206 209 3 372.79 2.19 380 206 210 4 372.58 2.30 381 207 210 3 380.34 2.50 382 207 211 4 341.34 12.70 383 208 211 3 372.23 2.12 384 208 212 4 278.85 21.24