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 63.13 0.60 2 18 46 28 63.14 0.61 3 18 47 29 63.13 0.61 4 18 48 30 55.77 0.15 5 18 49 31 56.16 0.30 6 18 53 35 47.92 2.73 7 19 46 27 63.29 0.66 8 19 47 28 63.18 0.60 9 20 47 27 65.19 0.23 10 20 48 28 63.75 0.64 11 20 60 40 64.65 0.14 12 20 65 45 65.04 0.06 13 20 70 50 63.18 0.59 14 20 71 51 63.91 0.24 15 20 72 52 64.33 0.45 16 21 24 3 352.31 2.79 17 21 25 4 297.42 20.71 18 21 47 26 65.81 0.01 19 21 71 50 65.41 0.10 20 22 25 3 340.50 0.08 21 22 26 4 333.83 2.33 22 22 69 47 65.48 0.07 23 22 70 48 65.75 0.04 24 22 71 49 65.90 0.04 25 23 26 3 340.92 0.13 26 23 35 12 65.93 0.04 27 23 37 14 66.47 0.22 28 23 69 46 65.92 0.04 29 23 71 48 66.93 0.01 30 23 101 78 70.25 0.09 31 23 104 81 70.28 0.09 32 23 105 82 69.23 0.01 33 23 108 85 98.62 14.02 34 24 71 47 67.66 0.33 35 24 101 77 70.26 0.07 36 24 108 84 125.84 0.78 37 26 69 43 70.90 0.28 38 26 108 82 135.40 5.49 39 27 30 3 379.43 0.98 40 27 31 4 334.97 2.40 41 27 69 42 509.71 3.21 42 28 31 3 371.28 5.05 43 28 108 80 204.09 9.45 44 32 112 80 453.12 1.90 45 33 112 79 453.12 1.90 46 33 113 80 453.12 1.90 47 33 211 178 39.58 0.33 48 34 113 79 453.14 1.90 49 34 115 81 453.12 1.90 50 34 207 173 79.06 1.16 51 34 211 177 39.55 0.31 52 35 112 77 521.09 3.85 53 35 113 78 457.86 1.91 54 35 114 79 453.14 1.90 55 35 115 80 453.13 1.90 56 36 115 79 453.13 1.90 57 36 116 80 453.13 1.90 58 36 117 81 453.13 1.90 59 36 203 167 104.50 0.39 60 37 115 78 455.50 1.56 61 37 116 79 453.14 1.90 62 37 117 80 453.14 1.90 63 38 117 79 453.14 1.90 64 38 118 80 453.14 1.90 65 38 119 81 453.14 1.90 66 39 117 78 453.38 1.89 67 39 118 79 453.14 1.90 68 39 119 80 453.14 1.90 69 39 122 83 368.99 0.30 70 39 125 86 368.56 0.42 71 40 119 79 453.15 1.90 72 40 122 82 369.03 0.33 73 41 119 78 453.26 1.90 74 41 120 79 453.14 1.90 75 42 121 79 453.14 1.90 76 44 119 75 453.62 1.78 77 51 119 68 453.06 1.94 78 51 147 96 309.07 0.51 79 51 191 140 112.75 0.77 80 51 192 141 112.55 0.73 81 51 195 144 108.77 1.01 82 54 195 141 108.76 1.02 83 54 196 142 108.75 1.02 84 55 147 92 308.93 0.42 85 55 195 140 108.75 1.02 86 55 200 145 108.47 0.98 87 55 203 148 106.98 0.59 88 58 196 138 108.73 1.02 89 58 200 142 108.30 0.91 90 58 204 146 104.17 0.55 91 59 115 56 454.66 1.16 92 59 203 144 104.14 0.53 93 59 204 145 104.00 0.54 94 62 204 142 104.00 0.54 95 63 204 141 103.99 0.54 96 63 207 144 84.81 1.31 97 73 125 52 368.54 0.41 98 77 121 44 453.16 1.93 99 77 122 45 450.06 3.35 100 77 125 48 368.68 0.40 101 79 121 42 453.12 1.95 102 80 121 41 453.32 1.91 103 81 121 40 453.40 1.88 104 83 121 38 453.35 1.88 105 84 121 37 453.32 1.86 106 84 150 66 308.57 0.55 107 84 182 98 161.33 3.47 108 85 182 97 172.66 2.19 109 87 151 64 305.38 1.05 110 88 124 36 447.70 0.65 111 88 128 40 368.60 0.43 112 88 131 43 368.48 0.42 113 88 132 44 368.29 0.37 114 88 151 63 298.68 1.40 115 89 121 32 453.04 1.99 116 89 124 35 393.24 4.92 117 89 151 62 299.69 0.88 118 90 121 31 453.01 1.98 119 90 125 35 368.97 0.30 120 94 125 31 368.60 0.43 121 95 125 30 368.60 0.43 122 95 128 33 363.49 0.78 123 95 129 34 339.56 0.75 124 95 132 37 321.60 2.49 125 98 125 27 368.54 0.42 126 98 126 28 368.31 0.39 127 98 129 31 326.05 0.31 128 99 129 30 321.85 2.37 129 99 133 34 310.98 0.23 130 102 114 12 524.65 4.78 131 102 116 14 453.31 1.86 132 102 129 27 321.85 2.37 133 102 133 31 310.98 0.23 134 102 137 35 310.73 0.20 135 102 141 39 310.58 0.24 136 103 137 34 310.71 0.19 137 105 114 9 474.25 0.53 138 106 137 31 310.68 0.18 139 106 140 34 310.61 0.21 140 109 112 3 453.12 1.90 141 110 140 30 310.53 0.21 142 111 211 100 39.63 0.32 143 112 211 99 39.62 0.32 144 113 142 29 310.38 0.24 145 113 207 94 79.37 1.00 146 113 210 97 41.29 0.50 147 113 211 98 39.59 0.33 148 114 137 23 310.76 0.21 149 114 140 26 310.60 0.23 150 114 141 27 310.50 0.21 151 114 142 28 310.42 0.24 152 115 141 26 310.54 0.21 153 115 142 27 310.52 0.21 154 115 143 28 310.24 0.17 155 115 203 88 104.57 0.36 156 115 207 92 80.73 0.34 157 116 141 25 310.61 0.23 158 116 143 27 310.43 0.24 159 116 144 28 310.03 0.22 160 116 145 29 310.00 0.21 161 116 203 87 105.73 0.57 162 117 144 27 310.38 0.23 163 117 145 28 310.00 0.21 164 118 122 4 369.01 0.30 165 118 123 5 368.73 0.42 166 118 126 8 367.71 0.70 167 118 145 27 310.39 0.24 168 118 146 28 310.00 0.20 169 118 147 29 309.08 0.50 170 119 122 3 370.76 0.44 171 119 123 4 369.03 0.32 172 119 147 28 308.93 0.44 173 119 188 69 113.87 0.77 174 119 189 70 113.56 0.66 175 119 191 72 112.77 0.77 176 120 123 3 375.42 0.44 177 120 124 4 369.24 0.35 178 120 147 27 310.20 0.28 179 120 148 28 308.94 0.43 180 120 150 30 299.75 0.86 181 120 188 68 113.88 0.77 182 121 124 3 370.84 0.45 183 121 125 4 369.09 0.30 184 121 150 29 304.64 1.20 185 122 125 3 369.03 0.26 186 122 126 4 368.71 0.33 187 123 126 3 372.87 1.67 188 123 127 4 368.91 0.20 189 123 146 23 310.27 0.26 190 123 147 24 310.21 0.27 191 123 149 26 304.25 1.39 192 124 127 3 372.78 1.71 193 124 128 4 368.51 0.40 194 124 149 25 305.05 1.00 195 124 150 26 299.68 0.89 196 124 151 27 295.88 0.33 197 125 128 3 374.18 1.01 198 125 129 4 357.41 0.64 199 126 129 3 365.62 0.26 200 126 130 4 354.97 2.16 201 126 146 20 310.28 0.25 202 127 130 3 359.80 1.96 203 127 131 4 352.10 0.72 204 127 149 22 305.19 0.93 205 127 159 32 225.27 2.12 206 127 160 33 225.25 2.13 207 128 131 3 363.63 2.44 208 128 132 4 351.60 0.97 209 129 132 3 360.37 3.42 210 129 133 4 342.45 5.54 211 130 133 3 343.69 4.92 212 130 138 8 310.87 0.23 213 130 141 11 310.87 0.23 214 130 144 14 310.63 0.23 215 130 159 29 225.27 2.12 216 130 162 32 224.95 2.20 217 131 138 7 311.69 0.03 218 131 160 29 225.18 2.16 219 131 161 30 225.13 2.16 220 133 137 4 356.88 12.58 221 133 138 5 312.04 0.12 222 133 141 8 311.73 0.04 223 134 137 3 381.97 0.04 224 134 138 4 330.78 0.94 225 135 138 3 350.31 10.70 226 135 139 4 318.95 1.40 227 136 140 4 338.54 4.20 228 137 140 3 377.85 2.32 229 137 141 4 359.54 6.83 230 138 141 3 383.71 2.23 231 138 161 23 225.06 2.17 232 138 162 24 224.91 2.21 233 139 166 27 223.75 2.42 234 141 144 3 414.95 0.21 235 141 162 21 224.93 2.19 236 141 166 25 223.72 2.43 237 142 166 24 223.72 2.43 238 142 206 64 87.06 1.80 239 142 207 65 82.78 0.29 240 142 210 68 76.35 0.21 241 143 162 19 224.99 2.18 242 143 166 23 223.71 2.43 243 143 202 59 108.48 0.99 244 143 203 60 106.19 0.57 245 143 206 63 88.17 1.24 246 144 159 15 225.25 2.15 247 144 162 18 224.94 2.19 248 144 166 22 223.78 2.46 249 144 167 23 223.67 2.46 250 144 168 24 223.66 2.46 251 144 202 58 108.56 1.01 252 144 203 59 107.75 1.04 253 145 168 23 223.66 2.46 254 145 170 25 223.59 2.48 255 145 199 54 108.72 0.99 256 145 202 57 108.64 0.97 257 145 203 58 108.53 1.02 258 146 149 3 378.15 1.94 259 146 159 13 225.31 2.12 260 146 167 21 223.81 2.47 261 146 168 22 223.69 2.46 262 146 169 23 223.60 2.48 263 146 170 24 223.59 2.47 264 147 170 23 223.47 2.50 265 147 191 44 112.78 0.77 266 147 194 47 112.58 0.72 267 147 195 48 112.59 0.73 268 147 199 52 112.20 0.88 269 148 170 22 223.63 2.46 270 148 171 23 223.46 2.48 271 148 175 27 223.48 2.50 272 148 177 29 223.30 2.56 273 148 178 30 223.08 2.52 274 148 188 40 114.03 0.70 275 148 191 43 113.09 0.65 276 149 152 3 352.66 8.31 277 149 155 6 330.29 7.10 278 149 158 9 226.12 2.37 279 149 159 10 225.59 2.19 280 149 169 20 223.69 2.47 281 149 171 22 223.59 2.48 282 149 177 28 223.39 2.51 283 149 178 29 222.71 2.42 284 150 154 4 383.38 2.14 285 150 177 27 223.21 2.52 286 151 154 3 372.15 1.02 287 151 155 4 356.69 6.71 288 152 155 3 376.80 0.39 289 152 156 4 334.75 4.87 290 152 157 5 227.23 1.81 291 152 169 17 223.84 2.50 292 152 171 19 223.69 2.44 293 152 178 26 223.05 2.58 294 153 156 3 351.00 9.97 295 153 178 25 223.49 2.39 296 153 179 26 222.71 2.42 297 153 180 27 218.72 0.47 298 154 180 26 218.57 0.54 299 155 158 3 369.31 2.02 300 155 160 5 225.68 2.14 301 157 169 12 223.89 2.46 302 158 162 4 361.30 6.07 303 158 164 6 225.19 2.33 304 159 162 3 373.68 0.12 305 159 167 8 224.41 2.71 306 162 166 4 341.58 3.78 307 162 167 5 319.01 1.20 308 163 166 3 377.92 1.22 309 163 167 4 334.12 4.46 310 164 167 3 364.67 7.52 311 165 202 37 108.75 0.97 312 165 206 41 106.31 0.60 313 166 202 36 108.70 0.96 314 167 202 35 108.73 0.96 315 168 202 34 108.73 0.96 316 170 191 21 113.46 0.90 317 170 194 24 112.60 0.73 318 170 198 28 112.58 0.72 319 170 199 29 112.37 0.81 320 171 191 20 114.78 1.10 321 172 187 15 120.41 0.42 322 172 190 18 116.67 1.02 323 172 191 19 115.46 0.77 324 173 187 14 132.28 0.32 325 174 185 11 138.11 1.60 326 174 187 13 132.28 0.32 327 175 187 12 122.14 1.10 328 175 188 13 120.69 0.38 329 175 191 16 120.68 0.38 330 176 181 5 439.74 10.57 331 176 183 7 337.15 3.10 332 176 185 9 144.69 4.89 333 177 181 4 400.45 0.28 334 177 182 5 358.60 6.35 335 177 183 6 329.82 0.60 336 177 188 11 124.25 2.16 337 184 188 4 346.60 1.53 338 184 189 5 352.93 1.33 339 185 188 3 383.62 0.95 340 186 189 3 387.27 0.89 341 186 190 4 387.26 0.89 342 187 190 3 387.26 0.89 343 187 191 4 387.26 0.89 344 188 191 3 419.70 0.68 345 190 193 3 438.55 2.36 346 191 194 3 381.16 0.90 347 191 195 4 350.71 10.45 348 192 195 3 370.70 0.47 349 192 196 4 350.71 10.45 350 193 196 3 358.38 6.62 351 193 197 4 350.71 10.46 352 193 198 5 350.70 10.45 353 194 197 3 361.67 4.97 354 194 198 4 331.50 0.86 355 194 199 5 331.38 0.92 356 194 200 6 331.38 0.93 357 195 199 4 331.52 1.00 358 195 200 5 331.38 0.93 359 196 200 4 341.88 4.16 360 197 200 3 376.51 1.34 361 197 201 4 335.28 0.87 362 198 201 3 340.69 2.82 363 198 202 4 335.28 0.87 364 199 202 3 362.19 4.62 365 199 203 4 336.72 0.15 366 200 203 3 353.04 0.04 367 200 204 4 334.89 0.76 368 201 204 3 377.26 0.62 369 201 205 4 334.88 0.76 370 202 205 3 338.02 0.91 371 202 206 4 334.88 0.76 372 203 206 3 363.70 3.96 373 203 207 4 334.53 0.33 374 204 207 3 360.17 3.00 375 204 208 4 334.53 0.34 376 205 208 3 373.45 1.01 377 205 209 4 336.77 0.78 378 206 209 3 356.20 10.48 379 206 210 4 356.20 10.48 380 207 210 3 381.45 3.05 381 207 211 4 335.26 1.54 382 208 211 3 363.73 6.37 383 208 212 4 237.39 1.54 384 208 213 5 189.97 22.16