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 63.50 0.44 2 18 46 28 63.51 0.44 3 18 47 29 63.48 0.43 4 18 48 30 55.12 0.70 5 18 49 31 58.00 1.92 6 18 53 35 49.49 1.94 7 19 46 27 63.80 0.40 8 19 47 28 63.55 0.42 9 20 47 27 65.30 0.12 10 20 48 28 64.47 0.40 11 20 56 36 63.50 0.44 12 20 60 40 64.65 0.14 13 20 65 45 65.40 0.07 14 20 70 50 63.54 0.41 15 20 71 51 64.28 0.43 16 20 72 52 64.92 0.17 17 21 24 3 362.79 2.45 18 21 25 4 339.48 0.43 19 21 47 26 65.88 0.04 20 21 71 50 65.41 0.10 21 22 25 3 340.50 0.08 22 22 26 4 185.34 20.79 23 22 69 47 65.48 0.07 24 22 70 48 65.75 0.04 25 22 71 49 65.89 0.05 26 23 26 3 354.82 7.69 27 23 35 12 65.92 0.05 28 23 37 14 66.50 0.23 29 23 69 46 65.92 0.04 30 23 71 48 66.50 0.23 31 23 101 78 70.22 0.12 32 23 104 81 70.39 0.07 33 23 105 82 69.54 0.41 34 23 108 85 94.26 12.00 35 24 71 47 69.39 0.49 36 24 101 77 70.45 0.10 37 24 104 80 71.19 0.10 38 24 108 84 99.73 13.88 39 26 69 43 70.92 0.27 40 26 108 82 201.62 10.70 41 27 30 3 374.95 0.64 42 27 31 4 340.47 0.35 43 27 69 42 522.99 9.29 44 28 31 3 374.72 3.33 45 28 108 80 204.09 9.46 46 32 112 80 459.39 0.68 47 33 112 79 459.39 0.68 48 33 113 80 459.39 0.68 49 33 211 178 39.59 0.33 50 34 113 79 459.39 0.68 51 34 115 81 459.38 0.67 52 34 207 173 80.27 0.56 53 34 211 177 39.57 0.29 54 35 112 77 526.00 6.59 55 35 113 78 462.11 0.61 56 35 114 79 459.39 0.68 57 35 115 80 459.39 0.68 58 36 115 79 459.39 0.68 59 36 116 80 459.39 0.68 60 36 117 81 459.39 0.68 61 36 203 167 102.26 0.35 62 37 115 78 460.48 0.80 63 37 116 79 459.40 0.68 64 37 117 80 459.40 0.68 65 38 117 79 459.41 0.68 66 38 118 80 459.38 0.68 67 38 119 81 459.39 0.68 68 38 147 109 311.38 0.90 69 39 117 78 460.28 0.81 70 39 118 79 459.39 0.68 71 39 119 80 459.39 0.68 72 39 122 83 366.22 0.64 73 39 125 86 365.78 0.42 74 40 119 79 459.41 0.68 75 40 122 82 366.70 0.40 76 41 119 78 459.48 0.68 77 41 120 79 459.41 0.68 78 42 121 79 459.41 0.68 79 44 119 75 460.48 0.91 80 51 119 68 459.38 0.67 81 51 147 96 309.76 0.55 82 51 191 140 112.11 0.52 83 51 192 141 111.41 0.48 84 51 195 144 108.76 1.02 85 54 195 141 108.75 1.02 86 54 196 142 108.73 1.02 87 55 147 92 309.70 0.52 88 55 195 140 108.73 1.01 89 55 200 145 108.20 0.85 90 55 203 148 105.75 0.88 91 58 196 138 108.71 1.02 92 58 200 142 108.20 0.85 93 58 204 146 103.31 0.19 94 59 115 56 460.44 0.89 95 59 203 144 103.80 0.03 96 59 204 145 101.94 0.43 97 62 204 142 101.95 0.48 98 62 208 146 84.47 1.49 99 63 204 141 101.94 0.43 100 63 207 144 84.48 1.49 101 73 125 52 365.78 0.42 102 77 121 44 459.38 0.70 103 77 122 45 456.29 0.41 104 77 125 48 366.58 0.32 105 79 121 42 459.44 0.68 106 80 121 41 459.55 0.65 107 83 121 38 460.05 0.89 108 84 121 37 459.51 0.68 109 84 182 98 169.25 2.60 110 85 182 97 185.41 0.68 111 87 151 64 305.32 1.07 112 88 124 36 445.12 1.94 113 88 128 40 366.17 0.54 114 88 131 43 365.88 0.40 115 88 132 44 365.57 0.25 116 88 151 63 297.98 1.29 117 89 121 32 459.44 0.67 118 89 124 35 390.93 3.77 119 89 151 62 298.12 1.23 120 90 121 31 459.38 0.65 121 90 125 35 366.67 0.35 122 94 125 31 365.82 0.45 123 95 125 30 365.81 0.44 124 95 128 33 360.69 0.70 125 95 129 34 339.49 0.80 126 95 132 37 332.70 0.58 127 98 125 27 365.78 0.43 128 98 126 28 365.67 0.43 129 98 129 31 332.88 0.56 130 99 129 30 332.83 0.57 131 99 132 33 327.79 1.14 132 99 133 34 315.68 2.31 133 102 114 12 529.49 2.45 134 102 116 14 459.47 0.68 135 102 129 27 332.82 0.56 136 102 130 28 332.81 0.56 137 102 133 31 312.46 0.70 138 102 137 35 312.10 0.80 139 102 141 39 311.92 0.83 140 103 133 30 312.46 0.70 141 103 137 34 312.05 0.78 142 105 114 9 488.94 13.04 143 106 137 31 311.97 0.82 144 106 140 34 311.94 0.83 145 109 112 3 459.39 0.68 146 110 140 30 311.92 0.83 147 111 211 100 39.63 0.32 148 112 211 99 39.63 0.32 149 113 142 29 311.80 0.84 150 113 207 94 80.28 0.55 151 113 210 97 40.86 0.92 152 113 211 98 39.59 0.33 153 114 137 23 312.12 0.80 154 114 140 26 311.93 0.83 155 114 141 27 311.85 0.82 156 114 142 28 311.84 0.83 157 115 141 26 311.90 0.83 158 115 142 27 311.88 0.83 159 115 143 28 311.69 0.89 160 115 203 88 103.36 0.19 161 115 207 92 81.53 0.06 162 116 130 14 332.75 0.58 163 116 141 25 311.93 0.83 164 116 143 27 311.88 0.84 165 116 144 28 311.44 0.88 166 116 145 29 311.39 0.89 167 116 203 87 105.44 0.71 168 117 144 27 311.70 0.89 169 117 145 28 311.42 0.88 170 118 122 4 366.22 0.64 171 118 123 5 366.12 0.59 172 118 145 27 311.72 0.88 173 118 146 28 311.32 0.86 174 118 147 29 310.22 0.59 175 119 122 3 367.88 0.98 176 119 123 4 366.70 0.39 177 119 147 28 310.01 0.66 178 119 188 69 113.67 0.63 179 119 189 70 113.59 0.64 180 119 191 72 112.10 0.53 181 120 123 3 368.08 0.93 182 120 124 4 368.04 0.91 183 120 147 27 311.58 0.91 184 120 148 28 310.06 0.67 185 120 150 30 299.20 0.70 186 120 188 68 113.67 0.63 187 121 124 3 372.10 0.23 188 121 125 4 366.73 0.38 189 121 150 29 299.19 0.70 190 122 125 3 370.36 1.57 191 122 126 4 366.43 0.21 192 123 126 3 371.07 2.53 193 123 127 4 366.44 0.21 194 123 146 23 311.67 0.88 195 123 147 24 311.64 0.89 196 123 149 26 299.19 0.70 197 124 127 3 367.93 0.53 198 124 128 4 366.45 0.20 199 124 149 25 304.60 1.21 200 124 150 26 297.98 1.29 201 124 151 27 292.84 1.00 202 125 128 3 372.41 2.77 203 125 129 4 361.75 2.16 204 126 129 3 367.90 0.54 205 126 130 4 357.28 4.39 206 126 146 20 311.70 0.92 207 127 130 3 366.62 0.29 208 127 131 4 360.99 2.52 209 127 149 22 299.99 1.09 210 127 159 32 221.63 0.15 211 128 131 3 369.75 1.28 212 128 132 4 354.75 0.61 213 129 132 3 363.18 2.85 214 129 133 4 351.81 1.31 215 130 133 3 354.75 0.61 216 130 138 8 312.13 0.80 217 130 141 11 312.11 0.82 218 130 144 14 311.93 0.84 219 130 159 29 221.63 0.15 220 130 162 32 221.38 0.16 221 131 138 7 312.74 0.86 222 131 160 29 221.62 0.16 223 131 161 30 221.55 0.19 224 133 137 4 351.87 7.14 225 133 138 5 312.72 1.09 226 133 141 8 312.47 0.98 227 134 137 3 381.97 0.03 228 134 138 4 327.26 2.22 229 135 138 3 352.66 10.27 230 135 139 4 325.15 0.73 231 136 140 4 351.67 10.77 232 137 140 3 377.86 2.32 233 137 141 4 362.16 5.53 234 138 141 3 380.88 0.82 235 138 161 23 221.43 0.14 236 138 162 24 221.28 0.13 237 139 166 27 220.35 0.22 238 141 144 3 414.95 0.21 239 141 162 21 221.28 0.13 240 141 166 25 220.28 0.24 241 142 166 24 220.22 0.21 242 142 206 64 83.99 0.20 243 142 207 65 82.56 0.46 244 142 210 68 79.45 0.68 245 143 162 19 221.34 0.10 246 143 166 23 220.22 0.21 247 143 202 59 108.54 1.02 248 143 203 60 105.66 0.49 249 143 206 63 87.76 1.56 250 144 159 15 221.62 0.15 251 144 162 18 221.32 0.09 252 144 166 22 220.34 0.22 253 144 167 23 220.19 0.20 254 144 168 24 220.18 0.20 255 144 202 58 108.56 1.01 256 144 203 59 106.92 1.12 257 145 168 23 220.16 0.21 258 145 170 25 219.88 0.12 259 145 199 54 108.70 1.00 260 145 202 57 108.59 1.00 261 145 203 58 108.36 0.93 262 146 149 3 372.54 0.86 263 146 159 13 221.63 0.15 264 146 167 21 220.41 0.24 265 146 168 22 220.26 0.24 266 146 169 23 220.06 0.21 267 146 170 24 219.75 0.18 268 147 170 23 219.54 0.24 269 147 191 44 112.12 0.52 270 147 194 47 111.80 0.62 271 147 195 48 111.77 0.64 272 147 199 52 111.17 0.36 273 148 170 22 220.14 0.18 274 148 171 23 219.52 0.23 275 148 175 27 219.59 0.19 276 148 177 29 218.66 0.04 277 148 178 30 218.42 0.02 278 148 188 40 113.67 0.63 279 148 191 43 112.14 0.52 280 149 152 3 369.55 0.36 281 149 155 6 316.35 1.42 282 149 158 9 221.72 0.17 283 149 169 20 220.29 0.23 284 149 171 22 220.01 0.24 285 149 177 28 218.67 0.04 286 149 178 29 217.88 0.09 287 150 154 4 383.38 2.14 288 150 177 27 218.49 0.04 289 150 182 32 174.05 5.00 290 151 154 3 372.15 1.02 291 151 155 4 369.44 0.34 292 152 155 3 372.41 1.81 293 152 156 4 327.58 5.75 294 152 157 5 222.92 0.12 295 152 169 17 220.87 0.19 296 152 171 19 220.27 0.24 297 152 178 26 218.23 0.05 298 153 156 3 351.28 9.42 299 153 178 25 220.00 0.28 300 153 179 26 218.28 0.08 301 153 180 27 215.50 1.28 302 154 180 26 212.87 0.06 303 155 158 3 371.07 1.15 304 155 160 5 223.09 0.22 305 157 169 12 220.86 0.20 306 158 162 4 358.84 7.29 307 158 163 5 247.69 3.42 308 158 164 6 222.04 0.21 309 159 162 3 371.27 1.08 310 159 167 8 221.44 0.07 311 162 166 4 370.65 1.63 312 162 167 5 288.86 14.61 313 163 166 3 379.18 0.58 314 163 167 4 342.69 12.35 315 164 167 3 374.16 2.77 316 165 202 37 108.73 0.96 317 165 206 41 105.67 0.49 318 166 202 36 108.70 0.96 319 167 202 35 108.72 0.96 320 168 202 34 108.72 0.96 321 170 191 21 112.13 0.52 322 170 194 24 111.81 0.62 323 170 198 28 111.79 0.62 324 170 199 29 111.39 0.47 325 171 191 20 114.60 1.05 326 172 187 15 119.39 1.76 327 172 190 18 118.39 1.54 328 172 191 19 114.84 0.95 329 173 187 14 132.30 0.34 330 174 185 11 157.14 0.66 331 174 187 13 133.88 1.14 332 175 187 12 131.93 0.53 333 175 188 13 130.95 0.04 334 175 191 16 130.90 0.01 335 176 181 5 461.79 6.88 336 176 183 7 362.51 9.59 337 176 185 9 205.81 18.80 338 177 181 4 398.84 1.08 339 177 182 5 353.81 13.94 340 177 183 6 333.81 3.94 341 177 188 11 130.94 0.04 342 184 188 4 335.08 1.95 343 184 189 5 335.10 1.95 344 185 188 3 379.35 1.19 345 186 189 3 381.26 1.72 346 187 190 3 387.25 0.89 347 187 191 4 387.25 0.89 348 188 191 3 412.86 2.75 349 191 194 3 365.17 5.00 350 191 195 4 351.57 7.61 351 192 195 3 355.68 5.55 352 192 196 4 351.56 7.61 353 193 196 3 362.74 6.25 354 193 197 4 335.00 3.38 355 193 198 5 331.84 2.25 356 194 197 3 381.63 3.23 357 194 198 4 331.80 2.25 358 194 199 5 321.98 0.45 359 194 200 6 321.99 0.45 360 195 199 4 321.91 0.48 361 195 200 5 321.89 0.49 362 196 200 4 351.67 8.21 363 197 200 3 376.72 1.45 364 197 201 4 348.27 9.91 365 198 201 3 368.24 0.07 366 198 202 4 345.12 11.63 367 199 202 3 373.99 2.80 368 199 203 4 357.36 5.51 369 200 203 3 376.36 1.62 370 200 204 4 324.81 1.52 371 201 204 3 377.28 1.15 372 201 205 4 329.08 3.66 373 202 205 3 373.09 0.94 374 202 206 4 329.06 3.67 375 203 206 3 363.70 3.96 376 203 207 4 334.04 1.09 377 204 207 3 360.17 3.00 378 204 208 4 334.23 1.18 379 205 208 3 353.89 7.05 380 205 209 4 353.16 7.42 381 206 209 3 372.58 2.29 382 206 210 4 372.58 2.29 383 207 210 3 380.35 2.50 384 207 211 4 353.16 7.42 385 208 211 3 363.73 6.37 386 208 212 4 275.18 23.08