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 61.11 0.77 2 18 46 28 61.11 0.77 3 18 47 29 61.10 0.77 4 18 48 30 49.68 2.04 5 18 49 31 53.90 1.08 6 18 53 35 43.93 0.84 7 19 46 27 61.77 0.76 8 19 47 28 61.55 0.86 9 20 47 27 63.02 0.57 10 20 48 28 62.39 0.82 11 20 60 40 61.28 0.69 12 20 70 50 61.22 0.66 13 20 71 51 62.45 0.85 14 20 72 52 62.54 0.74 15 21 24 3 367.74 0.03 16 21 25 4 333.97 2.41 17 21 47 26 63.59 0.38 18 21 71 50 62.60 0.78 19 22 25 3 340.50 0.08 20 22 26 4 333.97 2.41 21 22 69 47 63.34 0.42 22 22 70 48 63.55 0.35 23 22 71 49 63.56 0.35 24 23 26 3 354.89 7.66 25 23 35 12 63.63 0.38 26 23 37 14 64.31 0.48 27 23 69 46 63.62 0.39 28 23 71 48 64.28 0.47 29 23 101 78 65.72 0.15 30 23 104 81 65.81 0.20 31 23 105 82 65.45 0.10 32 23 108 85 65.81 0.20 33 24 71 47 64.97 0.22 34 24 101 77 65.83 0.21 35 24 108 84 66.18 0.08 36 26 69 43 65.43 0.03 37 26 108 82 176.47 26.16 38 27 30 3 356.67 2.26 39 27 31 4 334.89 2.44 40 27 69 42 528.66 5.77 41 28 31 3 354.87 4.73 42 28 108 80 176.49 26.17 43 32 112 80 458.92 1.09 44 33 112 79 458.92 1.09 45 33 113 80 458.91 1.09 46 33 211 178 35.54 0.51 47 34 113 79 458.91 1.09 48 34 115 81 458.91 1.09 49 34 207 173 80.29 0.55 50 34 211 177 36.73 1.10 51 35 112 77 530.75 4.21 52 35 113 78 461.04 1.12 53 35 114 79 458.92 1.09 54 35 115 80 458.92 1.09 55 36 115 79 458.92 1.09 56 36 116 80 458.92 1.09 57 36 117 81 458.92 1.09 58 36 203 167 102.15 0.39 59 37 115 78 460.01 1.06 60 37 116 79 458.93 1.09 61 37 117 80 458.92 1.09 62 38 117 79 458.94 1.08 63 38 118 80 458.92 1.09 64 38 119 81 458.93 1.09 65 39 117 78 459.53 1.18 66 39 118 79 458.93 1.09 67 39 119 80 458.93 1.09 68 39 122 83 362.72 1.00 69 39 125 86 362.62 0.95 70 40 119 79 458.94 1.09 71 40 122 82 363.14 0.79 72 41 119 78 459.00 1.10 73 41 120 79 458.93 1.09 74 42 121 79 458.95 1.08 75 44 119 75 459.75 1.09 76 51 119 68 458.91 1.09 77 51 147 96 309.67 0.51 78 51 191 140 115.00 1.91 79 51 192 141 114.45 1.97 80 51 195 144 108.77 1.01 81 54 195 141 108.75 1.01 82 54 196 142 108.75 1.01 83 55 147 92 309.67 0.52 84 55 195 140 108.72 1.01 85 55 200 145 108.25 0.90 86 55 203 148 107.33 1.18 87 58 196 138 108.72 1.02 88 58 200 142 108.28 0.90 89 58 204 146 102.11 0.37 90 59 115 56 459.66 1.03 91 59 203 144 102.15 0.39 92 59 204 145 101.81 0.36 93 62 204 142 101.78 0.39 94 62 208 146 82.31 0.44 95 63 204 141 101.82 0.37 96 63 207 144 82.34 0.42 97 73 125 52 362.62 0.95 98 77 121 44 458.97 1.07 99 77 122 45 457.05 0.79 100 77 125 48 363.04 0.79 101 79 121 42 458.97 1.07 102 80 121 41 459.78 0.95 103 83 121 38 459.47 1.20 104 84 121 37 459.41 1.23 105 84 182 98 160.46 2.25 106 85 182 97 171.02 3.02 107 87 151 64 304.74 1.36 108 88 124 36 423.53 2.10 109 88 128 40 362.80 0.94 110 88 131 43 362.74 0.92 111 88 132 44 362.62 0.88 112 88 151 63 292.30 0.65 113 89 121 32 459.03 1.05 114 89 124 35 394.28 3.85 115 89 151 62 292.29 0.67 116 90 121 31 458.95 1.08 117 90 125 35 363.39 0.67 118 94 125 31 362.74 0.94 119 95 125 30 362.75 0.93 120 95 128 33 359.65 0.18 121 95 129 34 331.96 1.12 122 95 132 37 326.56 0.01 123 98 125 27 362.67 0.96 124 98 126 28 362.32 1.01 125 98 129 31 327.84 0.57 126 99 129 30 327.84 0.57 127 99 132 33 325.86 0.21 128 99 133 34 315.16 0.34 129 102 114 12 525.50 4.41 130 102 116 14 459.01 1.08 131 102 129 27 327.06 0.17 132 102 130 28 326.55 0.01 133 102 133 31 312.37 0.74 134 102 137 35 312.13 0.77 135 102 141 39 311.94 0.83 136 103 137 34 312.12 0.76 137 105 114 9 460.24 1.55 138 106 137 31 312.10 0.76 139 106 140 34 311.95 0.82 140 109 112 3 458.91 1.09 141 110 140 30 311.92 0.83 142 111 211 100 39.63 0.33 143 113 142 29 311.80 0.83 144 113 207 94 80.28 0.55 145 113 210 97 56.37 8.05 146 113 211 98 39.59 0.33 147 114 137 23 312.14 0.77 148 114 140 26 311.94 0.83 149 114 141 27 311.85 0.82 150 114 142 28 311.85 0.82 151 115 141 26 311.91 0.83 152 115 142 27 311.86 0.82 153 115 143 28 311.66 0.87 154 115 203 88 104.23 0.60 155 115 207 92 82.45 0.53 156 116 130 14 326.11 0.12 157 116 141 25 311.94 0.82 158 116 143 27 311.85 0.83 159 116 144 28 311.43 0.88 160 116 145 29 311.39 0.89 161 117 144 27 311.71 0.88 162 117 145 28 311.38 0.90 163 118 122 4 362.73 1.00 164 118 123 5 362.72 0.99 165 118 145 27 311.69 0.87 166 118 146 28 311.18 0.79 167 118 147 29 309.66 0.51 168 119 122 3 370.74 0.45 169 119 123 4 363.11 1.02 170 119 147 28 309.66 0.51 171 119 188 69 117.50 2.07 172 119 189 70 117.48 2.08 173 119 191 72 115.00 1.91 174 120 123 3 370.81 0.47 175 120 124 4 366.99 1.44 176 120 147 27 311.59 0.91 177 120 148 28 309.62 0.54 178 120 150 30 302.76 2.44 179 120 188 68 117.52 2.08 180 121 124 3 369.41 1.17 181 121 125 4 364.50 0.33 182 121 150 29 298.13 0.14 183 122 125 3 364.94 1.07 184 122 126 4 363.64 0.43 185 123 126 3 363.95 0.58 186 123 127 4 363.61 0.39 187 123 146 23 311.64 0.89 188 123 147 24 311.58 0.92 189 123 149 26 295.48 1.16 190 124 127 3 371.37 3.29 191 124 128 4 363.81 0.49 192 124 149 25 303.51 1.75 193 124 150 26 292.32 0.64 194 124 151 27 291.83 0.49 195 125 128 3 371.69 3.12 196 125 129 4 362.04 1.38 197 126 129 3 373.01 4.03 198 126 130 4 348.63 1.29 199 126 146 20 311.65 0.90 200 127 130 3 372.56 1.79 201 127 131 4 354.76 0.61 202 127 149 22 303.52 1.75 203 127 159 32 223.34 1.18 204 128 131 3 366.39 1.24 205 128 132 4 359.82 1.93 206 129 132 3 365.96 0.62 207 129 133 4 359.17 2.37 208 130 133 3 354.70 5.00 209 130 138 8 312.17 0.78 210 130 141 11 312.16 0.79 211 130 144 14 311.93 0.84 212 130 159 29 223.34 1.18 213 130 162 32 223.02 1.12 214 131 138 7 312.81 0.83 215 131 160 29 223.31 1.19 216 131 161 30 223.24 1.18 217 133 137 4 364.39 0.34 218 133 138 5 313.26 0.83 219 133 141 8 312.81 0.83 220 134 137 3 381.97 0.04 221 134 138 4 348.85 8.10 222 135 138 3 377.61 2.21 223 135 139 4 350.44 7.29 224 136 140 4 369.31 1.95 225 137 140 3 377.86 2.32 226 137 141 4 369.31 1.95 227 138 141 3 380.83 3.67 228 138 161 23 223.08 1.12 229 138 162 24 222.81 1.14 230 139 166 27 221.92 1.50 231 141 144 3 414.95 0.21 232 141 162 21 222.86 1.15 233 141 166 25 221.78 1.44 234 142 166 24 221.74 1.44 235 142 206 64 83.95 0.21 236 142 207 65 82.57 0.46 237 142 210 68 79.08 0.86 238 143 162 19 223.02 1.11 239 143 166 23 221.75 1.44 240 143 202 59 108.28 0.89 241 143 203 60 105.70 0.34 242 143 206 63 87.75 1.56 243 144 159 15 223.33 1.17 244 144 162 18 222.94 1.13 245 144 166 22 221.78 1.44 246 144 167 23 221.68 1.46 247 144 168 24 221.66 1.46 248 144 202 58 108.53 1.02 249 144 203 59 107.70 1.07 250 145 168 23 221.65 1.46 251 145 170 25 221.59 1.47 252 145 199 54 108.72 0.99 253 145 202 57 108.56 1.01 254 145 203 58 108.28 0.89 255 146 149 3 372.54 0.86 256 146 159 13 223.35 1.18 257 146 167 21 221.78 1.44 258 146 168 22 221.69 1.46 259 146 169 23 221.63 1.47 260 146 170 24 221.53 1.50 261 147 170 23 221.36 1.42 262 147 191 44 115.00 1.91 263 147 194 47 114.73 1.87 264 147 195 48 114.88 1.90 265 147 199 52 114.42 1.94 266 148 170 22 221.64 1.46 267 148 171 23 221.36 1.43 268 148 175 27 221.28 1.47 269 148 177 29 221.28 1.45 270 148 178 30 220.84 1.40 271 148 188 40 117.53 2.08 272 148 191 43 115.36 1.80 273 149 152 3 369.55 0.36 274 149 155 6 313.53 25.41 275 149 158 9 223.94 1.27 276 149 159 10 223.62 1.12 277 149 169 20 221.69 1.46 278 149 171 22 221.47 1.41 279 149 177 28 221.28 1.45 280 149 178 29 220.09 1.10 281 150 154 4 382.62 2.52 282 150 177 27 220.98 1.42 283 150 182 32 160.56 2.25 284 151 154 3 375.10 0.46 285 151 155 4 347.67 8.35 286 152 155 3 376.80 0.39 287 152 156 4 347.71 8.33 288 152 157 5 225.03 1.55 289 152 169 17 222.00 1.48 290 152 171 19 221.72 1.46 291 152 178 26 220.77 1.44 292 153 156 3 366.57 1.10 293 153 178 25 221.30 1.29 294 153 179 26 220.62 1.36 295 153 180 27 220.03 1.10 296 154 180 26 219.91 1.06 297 155 158 3 370.62 2.68 298 155 160 5 223.94 1.02 299 157 169 12 222.02 1.48 300 158 162 4 361.30 6.07 301 158 163 5 285.36 22.91 302 158 164 6 222.98 1.11 303 159 162 3 373.22 0.35 304 159 167 8 222.03 1.47 305 162 166 4 366.31 0.54 306 162 167 5 315.26 1.39 307 163 166 3 376.81 1.45 308 163 167 4 351.20 8.10 309 164 167 3 368.00 0.30 310 165 202 37 108.75 0.97 311 165 206 41 105.34 0.46 312 166 202 36 108.71 0.96 313 167 202 35 108.73 0.96 314 168 202 34 108.73 0.96 315 170 191 21 116.02 1.47 316 170 194 24 114.61 2.00 317 170 198 28 114.50 1.96 318 170 199 29 114.45 1.94 319 171 191 20 117.57 2.07 320 172 187 15 121.05 0.73 321 172 190 18 118.61 1.62 322 172 191 19 118.49 1.62 323 173 187 14 132.22 0.64 324 174 185 11 186.90 17.38 325 174 187 13 131.92 0.49 326 175 187 12 122.52 0.83 327 175 188 13 122.52 0.83 328 175 191 16 122.52 0.83 329 176 181 5 422.43 6.02 330 176 183 7 362.51 9.59 331 176 185 9 191.18 18.34 332 177 181 4 401.06 0.04 333 177 182 5 374.22 2.34 334 177 183 6 326.05 3.69 335 177 188 11 126.90 1.36 336 184 188 4 375.34 5.07 337 184 189 5 357.61 3.81 338 185 188 3 384.97 0.60 339 186 189 3 381.66 1.92 340 186 190 4 377.36 4.07 341 187 190 3 387.26 0.88 342 187 191 4 388.55 0.24 343 188 191 3 419.70 0.68 344 190 193 3 439.36 1.96 345 191 194 3 385.53 1.29 346 191 195 4 369.20 1.21 347 192 195 3 385.53 1.29 348 192 196 4 369.20 1.21 349 193 196 3 358.38 6.62 350 193 197 4 353.08 9.27 351 193 198 5 351.25 10.18 352 194 197 3 375.72 6.19 353 194 198 4 331.99 0.55 354 194 199 5 324.98 4.03 355 194 200 6 324.98 4.02 356 195 199 4 325.00 4.03 357 195 200 5 324.98 4.02 358 196 200 4 365.27 1.41 359 197 200 3 376.50 1.35 360 197 201 4 356.56 5.76 361 198 201 3 368.24 0.07 362 198 202 4 356.55 5.75 363 199 202 3 369.89 0.77 364 199 203 4 345.69 0.33 365 200 203 3 360.53 3.79 366 200 204 4 337.30 0.45 367 201 204 3 374.86 1.82 368 201 205 4 339.04 0.41 369 202 205 3 353.04 7.25 370 202 206 4 337.39 0.50 371 203 206 3 369.18 1.23 372 203 207 4 349.70 8.52 373 204 207 3 360.45 3.15 374 204 208 4 349.72 8.53 375 205 208 3 371.94 1.77 376 205 209 4 349.75 8.54 377 206 209 3 372.79 2.19 378 206 210 4 372.58 2.29 379 207 210 3 381.45 3.05 380 207 211 4 349.52 8.67 381 208 211 3 371.41 2.53 382 208 212 4 301.49 32.67 383 208 213 5 277.81 21.77