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 53 36 38.37 0.48 2 18 45 27 61.13 0.76 3 18 46 28 61.15 0.75 4 18 47 29 61.14 0.75 5 18 48 30 53.56 0.10 6 18 49 31 54.66 0.45 7 18 53 35 41.24 0.01 8 19 46 27 61.15 0.75 9 19 47 28 61.15 0.76 10 20 47 27 62.61 0.78 11 20 48 28 61.33 0.68 12 20 60 40 61.31 0.67 13 20 70 50 61.23 0.70 14 20 71 51 61.33 0.67 15 20 72 52 62.23 0.90 16 21 24 3 356.08 4.67 17 21 25 4 288.82 24.96 18 21 47 26 63.15 0.60 19 21 71 50 62.43 0.86 20 22 25 3 341.28 0.47 21 22 26 4 241.75 48.49 22 22 69 47 63.03 0.57 23 22 70 48 63.08 0.58 24 22 71 49 63.40 0.49 25 23 26 3 369.32 0.44 26 23 35 12 63.42 0.48 27 23 37 14 64.06 0.17 28 23 69 46 64.05 0.18 29 23 71 48 64.06 0.17 30 23 101 78 65.77 0.18 31 23 104 81 65.91 0.14 32 23 105 82 65.50 0.07 33 23 108 85 91.92 12.89 34 24 71 47 65.07 0.12 35 24 101 77 65.89 0.15 36 24 104 80 66.40 0.04 37 24 108 84 92.05 12.86 38 26 69 43 65.53 0.08 39 26 108 82 125.82 0.83 40 27 30 3 353.30 3.95 41 27 31 4 334.47 2.65 42 27 69 42 536.87 2.35 43 28 31 3 353.30 3.94 44 28 108 80 125.87 0.88 45 32 112 80 459.38 0.55 46 33 112 79 459.38 0.55 47 33 113 80 459.38 0.55 48 33 211 178 35.41 0.49 49 34 113 79 459.39 0.55 50 34 115 81 459.38 0.55 51 34 207 173 80.09 0.64 52 34 211 177 35.46 0.48 53 35 112 77 503.49 9.43 54 35 113 78 462.02 0.66 55 35 114 79 459.40 0.55 56 35 115 80 459.39 0.55 57 36 115 79 459.41 0.55 58 36 116 80 459.39 0.55 59 36 117 81 459.39 0.55 60 36 203 167 102.14 0.43 61 37 115 78 460.75 0.73 62 37 116 79 459.41 0.55 63 37 117 80 459.41 0.55 64 38 117 79 459.41 0.55 65 38 118 80 459.40 0.55 66 38 119 81 459.41 0.55 67 39 117 78 460.68 0.70 68 39 118 79 459.41 0.55 69 39 119 80 459.41 0.55 70 39 122 83 363.79 0.88 71 39 125 86 362.62 0.95 72 40 119 79 459.41 0.55 73 40 122 82 363.84 0.90 74 41 119 78 459.49 0.56 75 41 120 79 459.42 0.55 76 42 121 79 459.42 0.55 77 44 119 75 461.26 0.42 78 51 119 68 459.33 0.59 79 51 147 96 309.21 0.29 80 51 191 140 112.35 0.73 81 51 192 141 111.86 0.91 82 51 195 144 108.70 0.97 83 54 195 141 109.89 0.39 84 54 196 142 108.70 0.98 85 55 147 92 309.21 0.29 86 55 195 140 108.70 0.98 87 55 200 145 108.25 0.89 88 55 203 148 106.95 0.58 89 58 196 138 108.68 0.98 90 58 200 142 108.27 0.89 91 58 204 146 102.09 0.42 92 59 115 56 460.16 0.73 93 59 203 144 102.56 0.65 94 59 204 145 101.81 0.36 95 62 204 142 101.84 0.38 96 62 208 146 82.13 0.34 97 63 204 141 101.95 0.43 98 63 207 144 81.86 0.19 99 73 125 52 362.69 0.95 100 77 121 44 459.37 0.53 101 77 122 45 457.75 0.50 102 77 125 48 363.12 0.74 103 79 121 42 459.39 0.52 104 80 121 41 460.41 0.80 105 81 121 40 460.49 0.77 106 83 121 38 460.49 0.69 107 84 120 36 461.53 0.58 108 84 121 37 459.38 0.52 109 84 150 66 309.82 0.43 110 84 177 93 223.34 2.48 111 84 182 98 182.40 0.84 112 84 183 99 182.40 0.84 113 84 184 100 182.39 0.84 114 85 182 97 182.40 0.84 115 87 151 64 305.32 1.07 116 88 124 36 453.16 1.05 117 88 128 40 362.99 1.03 118 88 131 43 362.63 0.95 119 88 132 44 362.44 0.96 120 88 151 63 296.95 0.84 121 89 121 32 459.37 0.52 122 89 124 35 388.93 7.08 123 89 151 62 296.96 0.84 124 90 121 31 459.37 0.52 125 90 125 35 364.08 1.01 126 94 125 31 362.73 0.94 127 95 125 30 362.73 0.94 128 95 128 33 359.82 0.27 129 95 129 34 341.19 3.02 130 95 132 37 332.46 0.47 131 98 125 27 362.66 0.96 132 98 126 28 362.35 1.01 133 98 129 31 332.58 0.43 134 99 129 30 332.61 0.42 135 99 132 33 331.32 0.63 136 99 133 34 311.90 0.17 137 102 114 12 534.15 0.10 138 102 116 14 460.80 1.21 139 102 129 27 332.58 0.43 140 102 130 28 332.56 0.44 141 102 133 31 311.22 0.18 142 102 137 35 310.95 0.21 143 102 141 39 310.70 0.23 144 103 137 34 310.84 0.27 145 105 114 9 469.25 2.81 146 106 137 31 310.83 0.26 147 106 140 34 310.71 0.23 148 109 112 3 459.38 0.55 149 110 140 30 310.68 0.24 150 111 211 100 39.62 0.32 151 113 142 29 310.37 0.23 152 113 207 94 80.11 0.61 153 113 210 97 40.84 0.93 154 113 211 98 35.81 0.65 155 114 137 23 310.95 0.22 156 114 140 26 310.70 0.23 157 114 141 27 310.53 0.21 158 114 142 28 310.53 0.21 159 115 141 26 310.68 0.23 160 115 142 27 310.56 0.20 161 115 143 28 310.26 0.18 162 115 203 88 102.16 0.43 163 115 207 92 82.45 0.52 164 116 130 14 332.50 0.46 165 116 141 25 310.71 0.23 166 116 143 27 310.50 0.20 167 116 144 28 310.10 0.20 168 116 145 29 310.07 0.24 169 116 203 87 105.29 0.70 170 117 144 27 310.38 0.23 171 117 145 28 310.07 0.24 172 118 122 4 363.80 0.89 173 118 123 5 363.76 0.88 174 118 126 8 362.32 1.01 175 118 145 27 310.38 0.23 176 118 146 28 310.04 0.21 177 118 147 29 309.36 0.23 178 119 122 3 370.74 0.45 179 119 123 4 364.83 0.37 180 119 147 28 309.23 0.29 181 119 188 69 113.86 0.77 182 119 189 70 113.45 0.68 183 119 191 72 112.40 0.73 184 120 123 3 373.07 0.67 185 120 124 4 366.82 0.30 186 120 147 27 310.25 0.25 187 120 148 28 309.18 0.32 188 120 150 30 298.96 0.54 189 120 188 68 113.62 0.64 190 121 124 3 370.48 1.52 191 121 125 4 370.45 1.53 192 121 150 29 298.94 0.54 193 122 125 3 370.47 1.53 194 122 126 4 370.45 1.53 195 123 126 3 371.80 2.19 196 123 127 4 365.74 0.83 197 123 146 23 310.32 0.23 198 123 147 24 310.20 0.28 199 123 149 26 298.89 0.56 200 124 127 3 371.79 2.21 201 124 128 4 365.09 0.52 202 124 150 26 295.08 0.10 203 124 151 27 291.73 0.44 204 125 128 3 372.56 1.79 205 125 129 4 360.73 2.70 206 126 129 3 367.56 0.71 207 126 130 4 359.82 3.15 208 126 146 20 310.32 0.23 209 127 130 3 375.03 3.26 210 127 131 4 342.92 2.79 211 127 149 22 305.08 0.96 212 127 159 32 225.24 2.12 213 128 131 3 368.69 0.09 214 128 132 4 352.71 1.79 215 129 132 3 373.04 0.71 216 129 133 4 356.60 4.07 217 130 133 3 359.58 2.58 218 130 138 8 310.99 0.23 219 130 141 11 310.95 0.23 220 130 144 14 310.73 0.25 221 130 159 29 225.24 2.13 222 130 162 32 225.01 2.15 223 131 138 7 311.42 0.20 224 131 160 29 225.20 2.15 225 131 161 30 225.09 2.12 226 133 137 4 350.63 6.52 227 133 138 5 311.57 0.24 228 133 141 8 311.31 0.37 229 134 137 3 381.97 0.03 230 134 138 4 339.28 12.31 231 135 138 3 367.88 1.97 232 135 139 4 343.80 10.07 233 136 140 4 349.06 7.45 234 137 140 3 380.69 3.74 235 137 141 4 357.29 6.73 236 138 141 3 374.72 3.90 237 138 161 23 225.02 2.15 238 138 162 24 224.94 2.19 239 139 166 27 224.13 2.23 240 141 144 3 412.60 1.39 241 141 162 21 224.93 2.19 242 141 166 25 224.09 2.25 243 142 166 24 223.99 2.29 244 142 206 64 82.83 0.37 245 142 207 65 82.56 0.46 246 142 210 68 76.64 0.35 247 143 162 19 224.98 2.17 248 143 166 23 224.08 2.25 249 143 202 59 108.53 1.02 250 143 203 60 106.18 0.58 251 143 206 63 86.98 1.18 252 144 159 15 225.23 2.14 253 144 162 18 224.98 2.17 254 144 166 22 224.17 2.26 255 144 167 23 223.99 2.29 256 144 168 24 223.98 2.29 257 144 202 58 108.54 1.02 258 144 203 59 107.29 0.94 259 145 168 23 223.94 2.31 260 145 170 25 223.79 2.38 261 145 199 54 108.70 0.97 262 145 202 57 108.58 1.00 263 145 203 58 108.21 0.86 264 146 149 3 372.54 0.86 265 146 159 13 225.28 2.15 266 146 167 21 224.20 2.27 267 146 168 22 224.07 2.28 268 146 169 23 223.81 2.37 269 146 170 24 223.64 2.46 270 147 170 23 223.59 2.47 271 147 191 44 112.40 0.73 272 147 194 47 111.97 0.83 273 147 195 48 111.91 0.91 274 147 199 52 111.78 0.91 275 148 170 22 223.87 2.35 276 148 171 23 223.52 2.44 277 148 175 27 223.62 2.46 278 148 177 29 223.41 2.46 279 148 178 30 222.83 2.38 280 148 188 40 113.87 0.78 281 148 191 43 112.48 0.73 282 149 152 3 366.66 1.04 283 149 155 6 291.78 13.70 284 149 157 8 226.16 2.35 285 149 158 9 226.16 2.35 286 149 159 10 225.80 2.19 287 149 169 20 224.08 2.28 288 149 171 22 223.84 2.35 289 149 177 28 223.45 2.48 290 149 178 29 222.65 2.29 291 150 154 4 382.62 2.52 292 150 177 27 223.34 2.48 293 150 182 32 182.40 0.84 294 151 154 3 372.15 1.02 295 151 155 4 340.29 12.04 296 152 155 3 376.80 0.39 297 152 156 4 340.23 12.07 298 152 157 5 236.09 2.61 299 152 169 17 224.31 2.29 300 152 171 19 224.08 2.25 301 152 178 26 222.81 2.37 302 153 156 3 347.71 8.33 303 153 178 25 223.62 2.41 304 153 179 26 222.64 2.28 305 153 180 27 222.51 2.30 306 154 180 26 222.50 2.31 307 155 158 3 367.73 1.23 308 155 160 5 237.42 7.99 309 157 169 12 224.44 2.21 310 158 162 4 361.30 6.07 311 158 163 5 247.77 3.38 312 158 164 6 225.16 2.21 313 159 162 3 361.02 5.93 314 159 167 8 224.49 2.19 315 162 166 4 372.27 3.72 316 162 167 5 315.28 1.40 317 163 166 3 376.19 2.08 318 163 167 4 340.33 11.90 319 164 167 3 367.60 6.05 320 165 202 37 108.73 0.96 321 165 206 41 105.44 0.47 322 166 202 36 108.70 0.96 323 167 202 35 108.72 0.96 324 168 202 34 108.73 0.96 325 170 191 21 112.59 0.76 326 170 194 24 111.98 0.83 327 170 198 28 111.88 0.88 328 170 199 29 111.84 0.90 329 171 191 20 114.31 1.07 330 172 187 15 120.28 2.19 331 172 190 18 120.00 2.34 332 172 191 19 119.35 2.08 333 173 187 14 132.32 0.30 334 174 185 11 202.63 9.51 335 174 187 13 138.60 2.83 336 175 187 12 132.32 0.30 337 175 188 13 132.31 0.30 338 175 191 16 128.32 1.67 339 176 181 5 443.98 0.24 340 176 183 7 378.60 1.55 341 176 185 9 182.06 0.99 342 177 181 4 399.08 0.96 343 177 182 5 374.22 2.34 344 177 183 6 349.72 12.89 345 177 188 11 134.64 4.87 346 184 188 4 352.03 6.53 347 184 189 5 337.94 0.52 348 185 188 3 372.97 0.29 349 186 189 3 378.23 3.62 350 186 190 4 387.26 0.89 351 187 190 3 387.26 0.89 352 187 191 4 387.26 0.89 353 188 191 3 419.70 0.68 354 190 193 3 438.55 2.36 355 191 194 3 376.95 3.00 356 191 195 4 343.80 11.49 357 192 195 3 360.00 4.88 358 192 196 4 343.81 11.48 359 193 196 3 347.69 1.27 360 193 197 4 332.00 2.44 361 193 198 5 321.31 0.24 362 194 197 3 375.72 6.19 363 194 198 4 318.88 0.97 364 194 199 5 317.78 1.51 365 194 200 6 317.80 1.51 366 195 199 4 317.78 1.51 367 195 200 5 317.77 1.52 368 196 200 4 350.17 8.96 369 197 200 3 376.50 1.35 370 197 201 4 347.97 10.06 371 198 201 3 368.24 0.07 372 198 202 4 347.96 10.05 373 199 202 3 369.89 0.77 374 199 203 4 334.27 0.48 375 200 203 3 360.54 3.79 376 200 204 4 324.32 1.31 377 201 204 3 365.81 6.34 378 201 205 4 334.87 0.77 379 202 205 3 357.46 7.08 380 202 206 4 336.74 0.18 381 203 206 3 369.18 1.23 382 203 207 4 335.13 4.08 383 204 207 3 361.15 3.50 384 204 208 4 335.13 4.07 385 205 208 3 367.57 0.42 386 205 209 4 339.24 2.02 387 206 209 3 372.58 2.29 388 206 210 4 372.58 2.29 389 207 210 3 380.35 2.50 390 207 211 4 324.18 1.42 391 208 211 3 372.22 2.12 392 208 212 4 283.75 21.63