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 61.13 0.76 2 18 46 28 61.14 0.76 3 18 47 29 61.19 0.73 4 18 48 30 53.82 1.12 5 18 49 31 55.85 0.14 6 18 53 35 40.80 0.22 7 19 46 27 61.73 0.77 8 19 47 28 61.26 0.70 9 20 47 27 64.34 0.09 10 20 48 28 62.27 0.83 11 20 60 40 63.77 0.58 12 20 70 50 61.23 0.70 13 20 71 51 61.75 0.57 14 20 72 52 62.61 0.78 15 21 24 3 352.31 2.79 16 21 25 4 284.42 27.21 17 21 47 26 64.93 0.27 18 21 71 50 62.91 0.62 19 22 25 3 366.88 0.41 20 22 26 4 221.68 2.21 21 22 69 47 64.75 0.29 22 22 70 48 64.81 0.28 23 22 71 49 64.96 0.28 24 23 26 3 354.52 7.84 25 23 35 12 65.03 0.27 26 23 37 14 65.42 0.08 27 23 69 46 64.97 0.29 28 23 71 48 65.05 0.26 29 23 101 78 68.39 1.03 30 23 104 81 68.52 1.08 31 23 105 82 67.64 0.83 32 23 108 85 68.51 1.09 33 24 71 47 68.03 1.18 34 24 101 77 68.53 1.04 35 24 104 80 68.89 1.22 36 24 108 84 69.23 1.39 37 26 69 43 68.34 1.02 38 26 108 82 134.65 4.46 39 27 30 3 367.44 3.12 40 27 31 4 334.87 2.42 41 27 69 42 506.16 17.02 42 28 31 3 358.01 5.02 43 28 108 80 157.56 11.36 44 32 112 80 455.12 1.58 45 33 112 79 455.12 1.58 46 33 113 80 455.12 1.58 47 33 211 178 39.58 0.33 48 34 113 79 455.12 1.58 49 34 115 81 455.11 1.59 50 34 207 173 80.12 0.62 51 34 211 177 38.12 0.41 52 35 112 77 528.85 3.25 53 35 113 78 461.03 0.22 54 35 114 79 455.12 1.58 55 35 115 80 455.12 1.58 56 36 115 79 455.12 1.58 57 36 116 80 455.12 1.59 58 36 117 81 455.12 1.59 59 36 203 167 101.15 0.44 60 37 115 78 455.70 1.55 61 37 116 79 455.13 1.59 62 37 117 80 455.12 1.59 63 38 117 79 455.13 1.58 64 38 118 80 455.12 1.59 65 38 119 81 455.12 1.59 66 38 147 109 311.42 0.89 67 39 117 78 455.62 1.52 68 39 118 79 455.12 1.59 69 39 119 80 455.12 1.59 70 39 122 83 363.69 1.56 71 39 125 86 363.60 1.51 72 40 119 79 455.16 1.58 73 40 122 82 364.37 1.23 74 41 119 78 455.38 1.51 75 41 120 79 455.14 1.58 76 42 121 79 455.12 1.57 77 44 119 75 455.69 1.57 78 51 119 68 454.89 1.49 79 51 147 96 309.76 0.55 80 51 191 140 112.16 0.49 81 51 192 141 111.80 0.60 82 51 195 144 108.73 0.98 83 54 195 141 108.76 1.01 84 54 196 142 108.75 1.01 85 55 147 92 309.81 0.57 86 55 195 140 108.72 0.99 87 55 200 145 108.47 0.98 88 55 203 148 106.40 0.55 89 58 196 138 108.70 1.01 90 58 200 142 108.47 0.98 91 59 115 56 455.39 1.65 92 59 203 144 101.14 0.44 93 59 204 145 100.33 0.72 94 62 204 142 100.33 0.72 95 62 208 146 80.81 0.33 96 63 204 141 100.33 0.72 97 63 207 144 80.75 0.36 98 73 125 52 363.60 1.51 99 77 121 44 455.06 1.59 100 77 122 45 444.50 3.42 101 77 125 48 364.45 1.41 102 79 121 42 455.12 1.57 103 80 121 41 455.38 1.51 104 83 121 38 455.47 1.51 105 84 121 37 455.76 1.67 106 84 182 98 162.16 0.94 107 85 182 97 168.67 4.19 108 87 151 64 304.73 1.36 109 88 124 36 435.14 7.96 110 88 128 40 364.50 1.38 111 88 131 43 363.76 1.52 112 88 132 44 363.53 1.50 113 88 151 63 292.31 0.65 114 89 121 32 455.34 1.49 115 89 124 35 383.49 4.10 116 89 151 62 296.13 1.26 117 90 121 31 455.11 1.57 118 90 125 35 364.69 1.31 119 94 125 31 363.75 1.48 120 95 125 30 363.74 1.48 121 95 128 33 359.23 0.40 122 95 129 34 338.27 0.19 123 95 132 37 329.24 1.60 124 98 125 27 363.63 1.52 125 98 126 28 363.47 1.53 126 98 129 31 329.31 1.60 127 99 129 30 329.29 1.60 128 99 132 33 328.75 1.66 129 99 133 34 313.19 1.32 130 102 116 14 464.17 5.79 131 102 129 27 334.39 0.95 132 102 130 28 329.18 1.64 133 102 133 31 313.19 1.32 134 102 137 35 312.96 1.32 135 102 141 39 312.86 1.31 136 103 137 34 312.91 1.30 137 105 114 9 493.54 13.32 138 106 114 8 538.23 1.97 139 106 137 31 312.90 1.29 140 106 140 34 312.85 1.31 141 109 112 3 455.12 1.58 142 109 114 5 455.11 1.59 143 110 114 4 455.22 1.55 144 110 140 30 312.83 1.30 145 111 211 100 39.63 0.32 146 112 211 99 39.62 0.32 147 113 142 29 312.58 1.33 148 113 207 94 80.15 0.61 149 113 210 97 41.27 0.24 150 113 211 98 39.59 0.33 151 114 137 23 313.00 1.33 152 114 140 26 312.86 1.30 153 114 141 27 312.81 1.29 154 114 142 28 312.78 1.29 155 115 141 26 312.82 1.30 156 115 142 27 312.81 1.30 157 115 143 28 312.44 1.27 158 115 203 88 101.20 0.42 159 115 207 92 80.74 0.33 160 116 130 14 329.17 1.64 161 116 141 25 312.87 1.31 162 116 143 27 312.79 1.30 163 116 144 28 312.35 1.32 164 116 145 29 312.31 1.33 165 117 144 27 312.62 1.34 166 117 145 28 312.31 1.33 167 118 122 4 364.37 1.23 168 118 123 5 363.55 1.55 169 118 126 8 363.42 1.55 170 118 145 27 312.63 1.35 171 118 146 28 312.23 1.31 172 118 147 29 310.12 0.60 173 119 122 3 365.79 0.84 174 119 123 4 364.34 1.24 175 119 147 28 310.03 0.65 176 119 188 69 115.44 0.30 177 119 189 70 115.36 0.30 178 119 191 72 112.17 0.49 179 120 123 3 370.36 0.21 180 120 124 4 368.08 0.93 181 120 147 27 312.52 1.39 182 120 148 28 310.16 0.62 183 120 150 30 302.76 2.44 184 120 188 68 115.44 0.30 185 121 124 3 367.01 1.46 186 121 125 4 365.45 0.98 187 121 150 29 298.94 0.58 188 122 125 3 370.48 1.52 189 122 126 4 365.45 0.98 190 123 126 3 368.16 0.38 191 123 127 4 365.44 0.98 192 123 146 23 312.58 1.36 193 123 147 24 312.53 1.39 194 123 149 26 298.93 0.57 195 124 127 3 365.45 0.91 196 124 128 4 364.47 1.35 197 124 149 25 303.22 1.54 198 124 150 26 292.33 0.65 199 124 151 27 291.85 0.49 200 125 128 3 376.17 0.01 201 125 129 4 364.25 1.41 202 126 129 3 366.44 0.47 203 126 130 4 364.38 1.50 204 126 146 20 312.58 1.36 205 127 130 3 365.51 0.94 206 127 131 4 364.38 1.50 207 127 149 22 298.97 0.59 208 127 159 32 219.89 1.90 209 128 131 3 366.91 0.98 210 128 132 4 366.06 0.67 211 129 132 3 365.97 0.61 212 129 133 4 359.56 2.57 213 130 133 3 356.60 4.07 214 130 138 8 313.07 1.32 215 130 141 11 313.03 1.30 216 130 144 14 312.87 1.32 217 130 159 29 219.89 1.90 218 130 162 32 219.64 1.91 219 131 138 7 313.42 1.28 220 131 160 29 219.88 1.90 221 131 161 30 219.81 1.88 222 133 137 4 350.66 6.54 223 133 138 5 313.56 1.22 224 133 141 8 313.21 1.36 225 134 137 3 381.97 0.03 226 134 138 4 343.28 10.22 227 135 138 3 352.26 7.33 228 135 139 4 343.75 10.04 229 136 140 4 348.54 9.20 230 137 140 3 377.10 2.70 231 137 141 4 352.44 9.15 232 138 141 3 380.88 0.82 233 138 161 23 219.66 1.86 234 138 162 24 219.22 1.72 235 139 166 27 219.03 1.70 236 141 144 3 413.50 0.52 237 141 162 21 219.24 1.72 238 141 166 25 218.94 1.73 239 142 166 24 218.91 1.73 240 142 206 64 82.75 0.34 241 142 207 65 82.52 0.43 242 142 210 68 76.64 0.35 243 143 162 19 219.67 1.88 244 143 166 23 218.91 1.73 245 143 202 59 108.48 0.99 246 143 203 60 105.47 0.46 247 143 206 63 82.76 0.34 248 144 159 15 219.89 1.90 249 144 162 18 219.31 1.75 250 144 166 22 218.96 1.74 251 144 167 23 218.81 1.77 252 144 168 24 218.80 1.77 253 144 202 58 108.55 1.02 254 144 203 59 107.62 1.11 255 145 168 23 218.82 1.76 256 145 170 25 218.74 1.75 257 145 199 54 108.73 0.98 258 145 202 57 108.55 1.02 259 145 203 58 107.95 1.14 260 146 149 3 372.54 0.86 261 146 159 13 219.91 1.90 262 146 167 21 219.02 1.71 263 146 168 22 218.88 1.75 264 146 169 23 218.75 1.76 265 146 170 24 218.69 1.73 266 147 170 23 218.19 1.53 267 147 191 44 112.17 0.49 268 147 194 47 111.61 0.48 269 147 195 48 111.84 0.59 270 147 199 52 111.31 0.38 271 148 170 22 218.77 1.76 272 148 171 23 218.13 1.54 273 148 175 27 217.86 1.44 274 148 177 29 218.06 1.54 275 148 178 30 217.32 1.33 276 148 188 40 115.44 0.30 277 148 191 43 114.20 0.52 278 149 152 3 369.78 0.24 279 149 155 6 340.31 12.05 280 149 157 8 220.30 1.79 281 149 158 9 220.29 1.79 282 149 169 20 218.90 1.75 283 149 171 22 218.66 1.75 284 149 177 28 217.60 1.30 285 149 178 29 216.71 1.36 286 150 154 4 383.38 2.14 287 150 177 27 217.58 1.30 288 151 154 3 372.16 1.01 289 151 155 4 353.84 5.29 290 152 155 3 371.09 1.16 291 152 156 4 332.01 0.48 292 152 157 5 220.34 1.77 293 152 169 17 219.09 1.73 294 152 171 19 218.84 1.77 295 152 178 26 217.50 1.54 296 153 156 3 369.44 0.33 297 153 178 25 218.25 1.52 298 153 179 26 217.77 1.41 299 153 180 27 215.30 0.68 300 154 180 26 213.36 0.30 301 155 158 3 369.31 2.02 302 155 160 5 220.33 1.84 303 157 169 12 219.14 1.71 304 158 162 4 361.30 6.07 305 158 163 5 228.39 1.96 306 158 164 6 220.00 1.98 307 159 162 3 371.00 1.22 308 159 167 8 219.86 2.04 309 162 166 4 370.69 1.65 310 162 167 5 323.18 3.27 311 163 166 3 376.85 1.43 312 163 167 4 369.06 2.46 313 164 167 3 370.68 1.65 314 165 202 37 108.73 0.96 315 165 206 41 105.34 0.46 316 166 202 36 108.69 0.96 317 167 202 35 108.73 0.96 318 168 202 34 108.73 0.96 319 170 191 21 114.21 0.53 320 170 194 24 111.61 0.48 321 170 198 28 111.56 0.49 322 170 199 29 111.55 0.46 323 171 191 20 116.52 0.26 324 172 187 15 120.56 0.14 325 172 190 18 117.42 0.17 326 172 191 19 117.06 0.16 327 173 187 14 132.06 0.43 328 174 185 11 146.65 2.66 329 174 187 13 132.06 0.43 330 175 187 12 129.85 0.47 331 175 188 13 126.20 2.17 332 175 191 16 126.25 2.15 333 176 181 5 458.57 5.27 334 176 183 7 329.68 1.88 335 176 185 9 180.53 18.18 336 177 181 4 402.03 2.68 337 177 182 5 370.93 2.29 338 177 183 6 306.37 21.93 339 177 188 11 131.88 0.67 340 184 188 4 370.21 2.50 341 184 189 5 370.23 2.50 342 185 188 3 383.95 1.11 343 185 189 4 383.23 0.75 344 186 189 3 387.26 0.89 345 186 190 4 387.26 0.89 346 187 190 3 387.26 0.89 347 187 191 4 387.26 0.89 348 188 191 3 419.70 0.68 349 190 193 3 431.48 1.18 350 191 194 3 379.24 1.12 351 191 195 4 344.18 11.30 352 192 195 3 378.94 4.58 353 192 196 4 356.18 5.30 354 193 196 3 375.47 0.11 355 193 197 4 327.71 0.70 356 193 198 5 324.92 2.05 357 194 197 3 380.93 3.58 358 194 198 4 324.89 2.04 359 194 199 5 324.88 2.04 360 194 200 6 324.88 2.04 361 195 199 4 324.29 1.79 362 195 200 5 324.22 1.82 363 196 200 4 342.79 3.77 364 197 200 3 376.72 1.45 365 197 201 4 334.63 1.19 366 198 201 3 357.35 5.50 367 198 202 4 334.63 1.19 368 199 202 3 373.98 2.81 369 199 203 4 335.83 0.59 370 200 203 3 362.17 8.71 371 200 204 4 328.17 3.23 372 201 204 3 375.50 0.27 373 201 205 4 336.31 0.04 374 202 205 3 369.38 0.92 375 202 206 4 336.29 0.05 376 203 206 3 363.70 3.96 377 203 207 4 352.31 8.06 378 204 207 3 362.12 3.17 379 204 208 4 354.13 7.16 380 205 208 3 355.85 6.31 381 205 209 4 354.15 7.15 382 206 209 3 372.81 2.19 383 206 210 4 372.81 2.19 384 207 210 3 381.45 3.05 385 207 211 4 353.16 7.42 386 208 211 3 371.41 2.53 387 208 212 4 204.30 23.82