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 17 57 40 37.47 0.91 2 18 45 27 63.05 0.22 3 18 46 28 63.08 0.22 4 18 47 29 62.94 0.20 5 18 48 30 54.96 1.63 6 18 49 31 56.29 1.26 7 18 53 35 50.48 0.83 8 19 46 27 64.75 0.29 9 19 47 28 63.26 0.15 10 20 47 27 65.02 0.21 11 20 48 28 64.79 0.21 12 20 56 36 63.25 0.14 13 20 60 40 63.27 0.14 14 20 65 45 65.33 0.38 15 20 70 50 63.25 0.14 16 20 71 51 64.45 0.35 17 20 72 52 64.96 0.18 18 21 24 3 347.12 10.81 19 21 25 4 233.18 2.06 20 21 47 26 66.17 0.28 21 21 71 50 64.97 0.20 22 22 25 3 342.56 0.04 23 22 26 4 233.18 2.06 24 22 69 47 65.80 0.30 25 22 70 48 65.98 0.31 26 22 71 49 66.27 0.33 27 23 26 3 331.40 5.53 28 23 35 12 66.29 0.32 29 23 37 14 66.41 0.37 30 23 69 46 66.25 0.35 31 23 71 48 66.31 0.32 32 23 101 78 67.41 0.38 33 23 104 81 67.47 0.44 34 23 105 82 66.47 0.40 35 23 108 85 129.77 1.23 36 24 71 47 66.58 0.38 37 24 101 77 67.68 0.51 38 24 104 80 68.47 0.60 39 24 108 84 130.79 1.37 40 26 69 43 95.33 14.64 41 26 108 82 135.97 0.92 42 27 30 3 375.82 0.92 43 27 31 4 286.62 16.12 44 27 69 42 539.57 0.32 45 27 108 81 135.97 0.91 46 28 31 3 343.41 8.36 47 28 108 80 140.19 2.18 48 32 112 80 458.31 1.42 49 33 112 79 458.31 1.42 50 33 113 80 458.31 1.42 51 33 211 178 37.02 0.96 52 34 113 79 458.31 1.42 53 34 115 81 458.31 1.43 54 34 207 173 79.95 0.73 55 35 112 77 517.98 3.73 56 35 113 78 466.28 3.08 57 35 114 79 458.32 1.42 58 35 115 80 458.31 1.43 59 36 115 79 458.31 1.43 60 36 116 80 458.31 1.43 61 36 117 81 458.31 1.43 62 36 203 167 101.22 0.74 63 37 115 78 464.57 2.60 64 37 116 79 458.32 1.42 65 37 117 80 458.32 1.42 66 38 117 79 458.33 1.42 67 38 118 80 458.32 1.42 68 38 119 81 458.33 1.42 69 39 117 78 462.28 3.30 70 39 118 79 458.33 1.42 71 39 119 80 458.33 1.42 72 39 122 83 363.14 1.88 73 39 125 86 361.82 2.23 74 40 119 79 458.34 1.42 75 40 122 82 363.24 1.84 76 41 119 78 458.41 1.43 77 41 120 79 458.34 1.42 78 42 121 79 458.33 1.42 79 44 119 75 462.66 3.19 80 51 119 68 458.31 1.42 81 51 147 96 310.77 0.49 82 51 191 140 110.68 1.78 83 51 192 141 109.39 1.33 84 51 195 144 107.65 1.30 85 54 195 141 107.75 1.32 86 54 196 142 107.75 1.32 87 55 147 92 310.76 0.49 88 55 195 140 107.70 1.32 89 55 200 145 107.46 1.28 90 55 203 148 107.17 1.29 91 58 196 138 107.73 1.32 92 58 200 142 107.42 1.25 93 59 115 56 458.39 1.43 94 59 200 141 107.39 1.26 95 59 203 144 101.74 0.49 96 59 204 145 98.19 0.66 97 62 204 142 98.09 0.66 98 63 204 141 98.06 0.64 99 63 207 144 84.14 1.06 100 63 208 145 80.03 0.76 101 73 125 52 361.81 2.23 102 77 121 44 458.23 1.47 103 77 122 45 455.12 1.16 104 77 125 48 361.86 2.21 105 79 121 42 458.31 1.44 106 80 121 41 458.44 1.44 107 83 121 38 462.24 3.29 108 84 121 37 458.47 1.41 109 84 182 98 121.95 2.09 110 87 151 64 305.32 1.03 111 88 124 36 428.47 7.12 112 88 128 40 362.11 2.31 113 88 131 43 362.06 2.33 114 88 132 44 361.70 2.19 115 88 151 63 295.90 1.22 116 89 121 32 458.37 1.42 117 89 124 35 401.67 0.24 118 89 151 62 295.91 1.21 119 90 121 31 458.33 1.42 120 90 125 35 363.11 1.89 121 94 125 31 361.85 2.21 122 95 125 30 361.86 2.21 123 95 128 33 357.65 0.40 124 95 129 34 346.19 2.59 125 95 132 37 337.49 1.69 126 98 116 18 468.38 2.12 127 98 125 27 361.80 2.22 128 98 126 28 361.66 2.19 129 98 129 31 337.79 1.60 130 99 129 30 337.78 1.60 131 99 132 33 334.25 0.50 132 99 133 34 320.11 0.62 133 102 114 12 527.59 0.04 134 102 116 14 458.36 1.42 135 102 129 27 337.77 1.60 136 102 130 28 337.73 1.61 137 102 133 31 314.06 0.47 138 102 137 35 313.97 0.48 139 102 141 39 313.75 0.45 140 103 137 34 313.88 0.50 141 105 114 9 480.92 12.69 142 106 137 31 313.87 0.51 143 106 140 34 313.74 0.46 144 109 112 3 458.31 1.42 145 110 140 30 313.72 0.46 146 111 211 100 38.02 0.57 147 112 211 99 38.02 0.57 148 113 140 27 313.74 0.46 149 113 142 29 313.35 0.47 150 113 207 94 79.97 0.72 151 113 210 97 42.59 1.72 152 113 211 98 37.13 1.01 153 114 137 23 313.99 0.47 154 114 140 26 313.74 0.46 155 114 141 27 313.71 0.46 156 114 142 28 313.69 0.45 157 115 141 26 313.73 0.46 158 115 142 27 313.72 0.46 159 115 143 28 313.22 0.40 160 115 203 88 101.22 0.74 161 115 207 92 83.91 1.15 162 116 130 14 337.69 1.60 163 116 141 25 313.79 0.47 164 116 143 27 313.71 0.46 165 116 144 28 312.67 0.34 166 116 145 29 312.19 0.46 167 117 126 9 361.60 2.23 168 117 144 27 313.48 0.47 169 117 145 28 312.50 0.30 170 118 122 4 363.19 1.85 171 118 123 5 362.25 2.29 172 118 126 8 361.60 2.23 173 118 145 27 313.48 0.47 174 118 146 28 311.76 0.24 175 118 147 29 310.91 0.55 176 119 122 3 369.37 1.14 177 119 123 4 363.24 1.84 178 119 147 28 310.82 0.51 179 119 188 69 112.57 1.18 180 119 189 70 112.56 1.19 181 119 191 72 110.69 1.78 182 120 123 3 379.69 2.10 183 120 124 4 374.63 1.50 184 120 147 27 313.22 0.41 185 120 148 28 310.75 0.48 186 120 150 30 297.39 0.48 187 120 188 68 112.57 1.18 188 121 124 3 372.52 0.44 189 121 125 4 363.40 1.86 190 122 125 3 363.08 2.03 191 122 126 4 363.54 2.80 192 123 126 3 370.94 3.37 193 123 127 4 364.08 2.54 194 123 146 23 313.29 0.38 195 123 147 24 313.23 0.40 196 123 149 26 296.66 0.85 197 124 127 3 370.42 0.62 198 124 128 4 368.83 0.16 199 124 149 25 298.62 0.13 200 124 150 26 295.91 1.22 201 124 151 27 291.41 0.72 202 125 128 3 371.61 1.54 203 125 129 4 368.83 0.16 204 126 129 3 371.61 1.54 205 126 130 4 368.83 0.16 206 126 146 20 313.29 0.38 207 127 130 3 368.88 0.18 208 127 131 4 368.85 0.17 209 127 149 22 301.61 0.80 210 127 159 32 226.81 0.15 211 127 160 33 226.81 0.16 212 128 131 3 364.23 2.50 213 128 132 4 359.19 5.01 214 129 132 3 364.23 2.50 215 129 133 4 359.18 5.00 216 130 133 3 364.21 2.49 217 130 138 8 314.05 0.47 218 130 141 11 314.00 0.48 219 130 144 14 313.75 0.46 220 130 159 29 226.82 0.14 221 130 162 32 226.37 0.20 222 131 138 7 314.55 0.54 223 131 159 28 226.83 0.14 224 131 160 29 226.75 0.14 225 131 161 30 226.62 0.15 226 133 137 4 342.11 9.75 227 133 138 5 327.96 3.45 228 133 141 8 314.52 0.55 229 134 137 3 375.20 3.43 230 134 138 4 342.12 9.75 231 135 138 3 375.11 6.32 232 135 139 4 343.66 10.51 233 136 139 3 372.93 1.41 234 136 140 4 367.49 1.31 235 137 140 3 380.80 0.77 236 137 141 4 366.08 0.61 237 138 141 3 370.57 0.23 238 138 161 23 226.59 0.14 239 138 162 24 226.31 0.18 240 139 166 27 225.27 0.19 241 141 144 3 427.14 2.75 242 141 162 21 226.36 0.18 243 141 166 25 224.93 0.27 244 142 162 20 226.41 0.20 245 142 166 24 224.88 0.26 246 142 206 64 87.25 0.48 247 142 207 65 85.39 0.56 248 142 210 68 79.05 0.60 249 143 162 19 226.44 0.22 250 143 166 23 224.89 0.26 251 143 202 59 107.40 1.27 252 143 203 60 105.12 1.19 253 143 206 63 88.84 0.32 254 144 159 15 226.81 0.15 255 144 162 18 226.41 0.20 256 144 166 22 225.23 0.17 257 144 167 23 224.87 0.26 258 144 168 24 224.85 0.27 259 144 202 58 107.53 1.26 260 144 203 59 106.85 1.44 261 145 168 23 224.86 0.27 262 145 170 25 224.44 0.46 263 145 199 54 107.68 1.31 264 145 202 57 107.64 1.30 265 145 203 58 107.44 1.24 266 146 149 3 385.48 1.78 267 146 159 13 226.84 0.17 268 146 167 21 225.28 0.14 269 146 168 22 224.90 0.29 270 146 169 23 224.52 0.43 271 146 170 24 224.44 0.47 272 147 170 23 224.38 0.47 273 147 191 44 111.94 1.15 274 147 194 47 109.16 1.64 275 147 195 48 108.99 1.65 276 147 199 52 108.84 1.60 277 148 170 22 224.86 0.29 278 148 171 23 224.37 0.47 279 148 175 27 224.19 0.57 280 148 177 29 224.22 0.54 281 148 178 30 222.74 0.61 282 148 188 40 112.56 1.19 283 148 191 43 111.95 1.16 284 149 152 3 340.01 10.03 285 149 155 6 317.50 1.09 286 149 158 9 226.91 0.17 287 149 169 20 225.00 0.27 288 149 171 22 224.81 0.29 289 149 177 28 224.22 0.55 290 149 178 29 222.41 0.67 291 150 154 4 384.39 0.96 292 150 177 27 223.68 0.48 293 150 182 32 127.04 2.02 294 151 154 3 372.50 0.52 295 151 155 4 342.48 10.29 296 152 155 3 372.50 0.53 297 152 156 4 341.42 10.83 298 152 157 5 227.03 0.15 299 152 169 17 225.43 0.17 300 152 171 19 224.90 0.28 301 152 178 26 222.24 0.83 302 153 156 3 356.03 6.95 303 153 178 25 224.75 0.29 304 153 179 26 222.51 0.60 305 153 180 27 215.97 0.41 306 155 158 3 371.07 0.45 307 155 160 5 227.05 0.14 308 157 169 12 225.41 0.15 309 158 162 4 370.37 0.60 310 158 164 6 226.38 0.20 311 159 162 3 370.51 0.32 312 159 167 8 225.42 0.17 313 162 166 4 365.22 1.14 314 162 167 5 258.00 1.25 315 163 166 3 370.26 3.33 316 163 167 4 349.05 6.95 317 164 167 3 365.81 1.79 318 165 202 37 107.74 1.34 319 165 206 41 105.22 1.25 320 166 202 36 107.64 1.30 321 166 206 40 101.20 0.73 322 167 202 35 107.69 1.32 323 168 202 34 107.69 1.32 324 170 191 21 112.22 1.12 325 170 194 24 109.20 1.64 326 170 198 28 109.14 1.62 327 170 199 29 108.95 1.64 328 171 191 20 112.49 1.20 329 172 187 15 116.94 1.79 330 172 190 18 113.50 1.54 331 172 191 19 113.18 1.41 332 173 187 14 118.95 0.82 333 174 185 11 122.17 2.20 334 174 187 13 118.95 0.82 335 175 187 12 118.95 0.82 336 175 188 13 118.95 0.83 337 175 191 16 118.95 0.83 338 176 181 5 507.17 5.99 339 176 183 7 273.50 21.30 340 177 181 4 405.24 0.42 341 177 183 6 206.39 12.25 342 177 188 11 118.73 0.94 343 184 188 4 345.58 7.73 344 184 189 5 364.88 1.91 345 185 188 3 375.10 0.37 346 186 189 3 375.12 0.82 347 186 190 4 369.21 2.14 348 187 190 3 375.78 0.10 349 187 191 4 376.95 0.10 350 188 191 3 409.35 1.49 351 190 193 3 430.07 2.47 352 191 194 3 374.12 0.20 353 191 195 4 329.74 1.60 354 192 195 3 371.14 1.68 355 192 196 4 319.75 1.08 356 193 196 3 367.24 1.75 357 193 197 4 320.29 0.81 358 193 198 5 319.73 1.09 359 194 197 3 359.08 4.78 360 194 198 4 319.51 1.04 361 194 199 5 319.43 1.07 362 194 200 6 319.44 1.07 363 195 199 4 319.44 1.07 364 195 200 5 319.44 1.07 365 196 200 4 357.75 5.07 366 197 200 3 381.20 1.71 367 197 201 4 347.28 8.52 368 198 201 3 371.57 2.61 369 198 202 4 326.23 2.00 370 199 202 3 377.57 3.52 371 199 203 4 348.31 9.03 372 200 203 3 367.51 0.56 373 200 204 4 348.29 9.02 374 201 204 3 372.89 0.46 375 201 205 4 343.69 11.33 376 202 205 3 372.88 0.46 377 202 206 4 347.42 13.19 378 203 206 3 372.88 0.46 379 203 207 4 342.12 10.54 380 204 207 3 370.19 0.89 381 204 208 4 319.43 0.81 382 205 208 3 368.04 0.18 383 205 209 4 343.86 12.28 384 206 209 3 373.92 0.17 385 206 210 4 364.14 2.23 386 207 210 3 371.44 1.41 387 207 211 4 339.50 10.09 388 208 211 3 373.63 0.65 389 208 212 4 157.06 7.65