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 62.03 1.16 2 18 46 28 62.08 1.13 3 18 47 29 62.09 1.13 4 18 48 30 50.84 2.62 5 18 49 31 55.80 0.17 6 18 53 35 49.48 1.94 7 19 46 27 62.40 1.10 8 19 47 28 62.10 1.12 9 20 47 27 64.95 0.29 10 20 48 28 62.50 1.05 11 20 60 40 62.13 1.10 12 20 70 50 62.09 1.12 13 20 71 51 62.44 0.97 14 20 72 52 63.55 0.83 15 21 24 3 352.31 2.79 16 21 25 4 331.33 3.75 17 21 47 26 65.58 0.06 18 21 71 50 64.64 0.48 19 22 25 3 340.50 0.08 20 22 26 4 280.47 29.13 21 22 69 47 65.44 0.09 22 22 70 48 65.53 0.07 23 22 71 49 65.66 0.07 24 23 26 3 355.17 7.52 25 23 35 12 65.67 0.06 26 23 37 14 65.80 0.11 27 23 69 46 65.62 0.04 28 23 71 48 65.80 0.11 29 23 101 78 70.22 0.10 30 23 104 81 70.25 0.10 31 23 105 82 69.45 0.45 32 23 108 85 93.89 11.93 33 24 71 47 68.69 0.84 34 24 101 77 70.11 0.15 35 24 108 84 99.33 13.68 36 26 69 43 70.09 0.14 37 26 108 82 134.25 4.67 38 27 30 3 367.44 3.12 39 27 31 4 334.89 2.44 40 27 69 42 530.75 2.33 41 28 31 3 361.06 0.07 42 28 108 80 186.30 21.25 43 32 112 80 455.00 1.53 44 33 112 79 455.00 1.53 45 33 113 80 455.00 1.53 46 33 211 178 39.54 0.30 47 34 113 79 455.00 1.53 48 34 115 81 454.99 1.53 49 34 207 173 80.29 0.55 50 34 211 177 39.55 0.31 51 35 112 77 530.73 4.22 52 35 113 78 461.09 0.21 53 35 114 79 455.00 1.53 54 35 115 80 455.00 1.53 55 36 115 79 455.00 1.53 56 36 116 80 454.99 1.53 57 36 117 81 454.99 1.53 58 36 203 167 102.56 0.58 59 37 115 78 456.04 1.63 60 37 116 79 455.00 1.53 61 37 117 80 455.00 1.53 62 38 117 79 455.01 1.53 63 38 118 80 454.99 1.53 64 38 119 81 455.00 1.53 65 38 147 109 312.01 1.17 66 39 117 78 455.62 1.52 67 39 118 79 455.00 1.53 68 39 119 80 455.00 1.53 69 39 122 83 367.92 0.21 70 39 125 86 367.61 0.06 71 40 119 79 455.01 1.53 72 40 122 82 368.24 0.38 73 41 119 78 455.24 1.44 74 41 120 79 455.01 1.53 75 42 121 79 455.01 1.53 76 44 119 75 455.89 1.54 77 51 119 68 454.96 1.53 78 51 147 96 311.04 1.18 79 51 191 140 112.61 0.71 80 51 192 141 112.20 0.82 81 51 195 144 107.45 0.35 82 54 195 141 107.42 0.34 83 54 196 142 107.38 0.34 84 55 147 92 311.04 1.19 85 55 195 140 107.41 0.34 86 55 200 145 107.06 0.28 87 55 203 148 106.55 0.38 88 58 196 138 107.35 0.33 89 58 200 142 107.08 0.29 90 58 204 146 103.34 0.18 91 59 115 56 455.14 1.48 92 59 203 144 102.64 0.61 93 59 204 145 101.94 0.29 94 62 204 142 101.84 0.38 95 63 204 141 101.84 0.38 96 63 207 144 82.30 0.42 97 63 208 145 80.43 0.51 98 73 125 52 367.61 0.06 99 77 121 44 454.96 1.52 100 77 122 45 449.35 0.52 101 77 125 48 367.70 0.09 102 79 121 42 454.98 1.51 103 80 121 41 455.37 1.49 104 81 121 40 455.53 1.56 105 83 121 38 455.35 1.48 106 84 121 37 455.35 1.48 107 84 182 98 175.32 3.73 108 85 182 97 184.81 0.97 109 87 151 64 304.66 1.41 110 88 124 36 449.52 0.77 111 88 128 40 367.72 0.04 112 88 131 43 367.42 0.10 113 88 132 44 366.84 0.34 114 88 151 63 297.70 1.22 115 89 121 32 455.04 1.53 116 89 124 35 394.31 1.33 117 89 151 62 297.73 1.21 118 90 121 31 455.00 1.55 119 90 125 35 368.12 0.12 120 94 125 31 367.62 0.06 121 95 125 30 367.61 0.06 122 95 128 33 361.45 0.67 123 95 129 34 336.24 3.64 124 95 132 37 321.39 0.13 125 98 125 27 367.61 0.06 126 98 126 28 366.82 0.35 127 98 129 31 321.51 0.17 128 99 129 30 328.73 3.77 129 99 133 34 313.36 1.24 130 102 114 12 529.80 2.29 131 102 116 14 455.25 1.43 132 102 129 27 328.74 3.77 133 102 133 31 313.36 1.25 134 102 137 35 313.14 1.28 135 102 141 39 312.95 1.32 136 103 137 34 313.14 1.28 137 105 114 9 460.50 3.21 138 106 137 31 313.10 1.26 139 106 140 34 312.94 1.30 140 109 112 3 454.99 1.53 141 110 140 30 312.93 1.31 142 111 211 100 39.63 0.33 143 112 211 99 39.61 0.34 144 113 142 29 312.73 1.28 145 113 207 94 80.28 0.55 146 113 210 97 42.23 0.24 147 113 211 98 39.59 0.33 148 114 137 23 313.20 1.29 149 114 140 26 312.93 1.31 150 114 141 27 312.83 1.30 151 114 142 28 312.82 1.30 152 115 141 26 312.90 1.32 153 115 142 27 312.85 1.31 154 115 143 28 312.58 1.34 155 115 203 88 102.63 0.60 156 115 207 92 82.45 0.52 157 116 130 14 321.39 0.15 158 116 141 25 312.95 1.32 159 116 143 27 312.82 1.31 160 116 144 28 312.36 1.31 161 116 145 29 312.34 1.31 162 116 203 87 105.12 0.62 163 117 144 27 312.69 1.37 164 117 145 28 312.35 1.31 165 118 122 4 368.25 0.37 166 118 123 5 367.69 0.10 167 118 145 27 312.73 1.36 168 118 146 28 312.32 1.32 169 118 147 29 311.19 1.14 170 119 122 3 373.08 1.62 171 119 123 4 368.28 0.35 172 119 147 28 311.12 1.18 173 119 188 69 113.64 0.65 174 119 189 70 113.59 0.63 175 119 191 72 112.63 0.71 176 120 123 3 373.90 1.16 177 120 124 4 369.50 0.22 178 120 147 27 312.62 1.37 179 120 148 28 311.16 1.12 180 120 150 30 302.76 2.44 181 120 188 68 113.77 0.68 182 121 124 3 368.66 0.21 183 121 125 4 368.64 0.21 184 121 150 29 298.94 0.58 185 122 125 3 368.38 0.07 186 122 126 4 368.37 0.07 187 123 126 3 368.66 0.21 188 123 127 4 368.37 0.07 189 123 146 23 312.64 1.36 190 123 147 24 312.58 1.36 191 123 149 26 298.92 0.57 192 124 127 3 368.32 0.09 193 124 128 4 368.03 0.24 194 124 149 25 303.69 1.67 195 124 150 26 293.21 1.03 196 124 151 27 292.64 0.89 197 125 128 3 371.88 2.12 198 125 129 4 363.17 1.97 199 126 129 3 364.24 1.44 200 126 130 4 360.18 3.33 201 126 146 20 312.64 1.36 202 127 130 3 364.29 1.46 203 127 131 4 354.76 0.61 204 127 149 22 299.07 0.65 205 127 159 32 219.91 0.69 206 128 131 3 369.41 1.10 207 128 132 4 354.92 0.69 208 129 132 3 367.50 1.40 209 129 133 4 351.38 1.54 210 130 133 3 354.76 0.61 211 130 138 8 313.22 1.29 212 130 141 11 313.20 1.30 213 130 144 14 312.94 1.31 214 130 159 29 219.90 0.68 215 130 162 32 219.66 0.74 216 131 138 7 313.50 1.24 217 131 160 29 219.88 0.68 218 131 161 30 219.80 0.69 219 133 137 4 336.81 2.17 220 133 138 5 314.42 0.82 221 133 141 8 314.38 0.83 222 134 137 3 381.97 0.03 223 134 138 4 339.03 5.07 224 135 138 3 356.89 8.14 225 135 139 4 327.44 0.72 226 136 140 4 360.18 6.52 227 137 140 3 380.69 3.74 228 137 141 4 377.86 2.33 229 138 141 3 383.71 2.23 230 138 161 23 219.78 0.69 231 138 162 24 219.59 0.75 232 139 166 27 218.47 0.71 233 141 144 3 413.50 0.52 234 141 162 21 219.61 0.77 235 141 166 25 218.01 0.91 236 142 166 24 217.96 0.93 237 142 206 64 84.00 0.20 238 142 207 65 82.80 0.35 239 142 210 68 76.46 0.44 240 143 162 19 219.65 0.77 241 143 166 23 217.97 0.93 242 143 202 59 107.12 0.31 243 143 203 60 105.47 0.45 244 143 206 63 86.70 1.03 245 144 159 15 219.91 0.69 246 144 162 18 219.64 0.79 247 144 166 22 218.47 0.72 248 144 167 23 217.88 0.96 249 144 168 24 217.88 0.96 250 144 203 59 106.54 0.50 251 145 168 23 217.86 0.95 252 145 170 25 217.82 0.93 253 145 199 54 107.28 0.27 254 145 202 57 107.26 0.29 255 145 203 58 106.75 0.49 256 146 149 3 374.29 0.96 257 146 159 13 219.92 0.69 258 146 167 21 218.59 0.78 259 146 168 22 217.96 0.94 260 146 169 23 217.83 0.94 261 146 170 24 217.80 0.95 262 147 170 23 217.73 0.93 263 147 191 44 112.64 0.71 264 147 194 47 112.28 0.79 265 147 195 48 112.48 0.68 266 147 199 52 112.14 0.84 267 148 170 22 217.88 0.94 268 148 171 23 217.72 0.94 269 148 175 27 217.43 1.12 270 148 177 29 217.00 1.03 271 148 178 30 216.72 1.04 272 148 188 40 113.64 0.65 273 148 191 43 112.95 0.58 274 149 152 3 372.65 1.95 275 149 155 6 327.92 8.29 276 149 157 8 220.30 0.54 277 149 158 9 220.31 0.55 278 149 169 20 218.41 0.71 279 149 171 22 217.83 0.94 280 149 178 29 213.78 0.39 281 150 154 4 383.38 2.14 282 150 177 27 216.66 1.06 283 150 182 32 180.07 1.42 284 151 154 3 375.10 0.46 285 151 155 4 356.64 6.07 286 152 155 3 376.80 0.39 287 152 156 4 343.87 0.31 288 152 157 5 232.18 4.93 289 152 169 17 219.19 0.71 290 152 171 19 218.61 0.59 291 152 178 26 216.37 1.22 292 153 156 3 369.86 0.55 293 153 178 25 217.78 0.93 294 153 179 26 215.80 1.51 295 153 180 27 212.84 0.04 296 154 180 26 212.75 0.00 297 155 158 3 370.62 2.68 298 155 160 5 236.06 8.44 299 157 169 12 219.15 0.69 300 158 162 4 361.30 6.07 301 158 163 5 247.78 3.38 302 158 164 6 219.90 0.91 303 159 162 3 373.15 0.18 304 159 167 8 219.25 0.69 305 162 166 4 368.21 2.86 306 162 167 5 315.28 1.41 307 163 166 3 377.13 1.60 308 163 167 4 349.32 12.30 309 164 167 3 376.82 1.45 310 165 202 37 107.32 0.26 311 165 206 41 104.04 0.20 312 166 202 36 107.29 0.26 313 167 202 35 107.31 0.26 314 168 202 34 107.32 0.26 315 170 191 21 112.78 0.78 316 170 194 24 112.38 0.83 317 170 198 28 112.29 0.83 318 170 199 29 112.22 0.82 319 171 191 20 114.72 0.88 320 172 187 15 119.21 1.64 321 172 190 18 119.27 1.68 322 172 191 19 117.28 2.10 323 173 187 14 133.69 0.38 324 174 185 11 158.00 0.89 325 174 187 13 133.69 0.39 326 175 187 12 126.61 2.25 327 175 188 13 126.50 2.22 328 175 191 16 126.51 2.21 329 176 181 5 482.19 3.70 330 176 183 7 357.97 11.86 331 176 185 9 169.50 6.66 332 177 181 4 398.84 1.08 333 177 182 5 380.30 0.70 334 177 183 6 334.70 0.64 335 177 188 11 130.84 0.17 336 184 188 4 342.61 0.47 337 184 189 5 349.81 0.09 338 185 188 3 387.26 0.89 339 186 189 3 387.27 0.89 340 186 190 4 387.26 0.88 341 187 190 3 387.27 0.89 342 187 191 4 388.55 0.24 343 188 191 3 419.70 0.68 344 190 193 3 445.34 5.75 345 191 194 3 380.43 0.54 346 191 195 4 336.30 0.39 347 192 195 3 359.57 6.02 348 192 196 4 353.57 9.02 349 193 196 3 358.38 6.62 350 193 197 4 353.56 9.03 351 193 198 5 353.55 9.03 352 194 197 3 381.50 3.30 353 194 198 4 336.42 0.48 354 194 199 5 336.38 0.48 355 194 200 6 336.42 0.48 356 195 199 4 336.40 0.48 357 195 200 5 336.41 0.49 358 196 200 4 340.89 2.73 359 197 200 3 376.50 1.35 360 197 201 4 340.87 2.75 361 198 201 3 349.68 1.66 362 198 202 4 344.19 4.48 363 199 202 3 362.19 4.62 364 199 203 4 344.78 4.19 365 200 203 3 362.12 4.58 366 200 204 4 336.32 0.04 367 201 204 3 377.26 0.62 368 201 205 4 337.42 0.51 369 202 205 3 371.42 0.10 370 202 206 4 353.80 8.71 371 203 206 3 371.43 0.10 372 203 207 4 339.00 2.14 373 204 207 3 360.17 3.00 374 204 208 4 338.17 2.53 375 205 208 3 361.24 7.12 376 205 209 4 335.73 1.30 377 206 209 3 365.34 5.92 378 206 210 4 365.34 5.92 379 207 210 3 381.45 3.05 380 207 211 4 338.15 2.52 381 208 211 3 363.73 6.37 382 208 212 4 286.13 23.86 383 208 213 5 183.77 24.87