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 62.93 0.51 2 18 46 28 62.93 0.51 3 18 47 29 62.93 0.51 4 18 48 30 53.78 1.10 5 18 49 31 54.20 1.27 6 18 53 35 49.49 1.94 7 19 46 27 62.99 0.51 8 19 47 28 62.96 0.53 9 20 47 27 64.45 0.14 10 20 48 28 63.32 0.42 11 20 60 40 64.55 0.19 12 20 65 45 64.56 0.19 13 20 70 50 63.06 0.55 14 20 71 51 63.08 0.54 15 20 72 52 63.58 0.29 16 21 24 3 349.53 4.17 17 21 25 4 297.26 20.64 18 21 47 26 64.99 0.24 19 21 71 50 64.59 0.21 20 22 25 3 354.18 6.76 21 22 26 4 148.99 2.12 22 22 69 47 64.70 0.26 23 22 70 48 64.89 0.26 24 22 71 49 64.97 0.29 25 23 26 3 354.97 7.62 26 23 35 12 65.03 0.27 27 23 37 14 65.42 0.08 28 23 69 46 64.97 0.29 29 23 71 48 65.41 0.09 30 23 101 78 68.30 1.06 31 23 104 81 68.40 1.03 32 23 105 82 67.41 0.88 33 23 108 85 96.12 14.96 34 24 71 47 66.66 0.48 35 24 101 77 68.36 1.01 36 24 108 84 96.79 15.17 37 26 69 43 68.03 1.16 38 26 108 82 131.30 1.79 39 27 30 3 360.55 10.42 40 27 31 4 334.87 2.42 41 27 69 42 528.66 5.77 42 28 31 3 371.28 5.05 43 28 108 80 148.35 2.40 44 32 112 80 457.49 0.28 45 33 112 79 457.49 0.28 46 33 113 80 457.49 0.28 47 33 211 178 36.73 1.10 48 34 113 79 457.50 0.28 49 34 115 81 457.48 0.28 50 34 207 173 80.14 0.61 51 34 211 177 35.59 0.54 52 35 112 77 522.47 4.27 53 35 113 78 461.11 0.20 54 35 114 79 457.50 0.28 55 35 115 80 457.49 0.28 56 36 115 79 457.50 0.28 57 36 116 80 457.49 0.28 58 36 117 81 457.49 0.28 59 36 203 167 103.35 0.20 60 37 115 78 458.05 0.38 61 37 116 79 457.49 0.28 62 37 117 80 457.49 0.28 63 38 117 79 457.50 0.28 64 38 118 80 457.49 0.28 65 38 119 81 457.49 0.28 66 38 147 109 315.10 0.42 67 39 117 78 458.19 0.55 68 39 118 79 457.49 0.28 69 39 119 80 457.49 0.28 70 39 122 83 366.11 0.28 71 39 125 86 365.60 0.38 72 40 119 79 457.49 0.28 73 40 122 82 366.23 0.22 74 41 119 78 457.55 0.28 75 41 120 79 457.50 0.28 76 42 121 79 457.49 0.27 77 44 119 75 457.91 0.38 78 51 119 68 457.38 0.28 79 51 147 96 313.62 0.07 80 51 191 140 111.17 1.33 81 51 192 141 110.73 1.18 82 51 195 144 108.89 1.06 83 54 195 141 108.92 1.05 84 54 196 142 108.91 1.05 85 55 147 92 313.59 0.09 86 55 195 140 108.92 1.05 87 55 200 145 108.28 0.89 88 55 203 148 107.48 1.08 89 58 196 138 108.92 1.05 90 58 200 142 108.47 0.98 91 59 115 56 457.82 0.42 92 59 203 144 103.80 0.03 93 59 204 145 103.11 0.29 94 62 204 142 103.13 0.28 95 62 208 146 84.44 1.50 96 63 204 141 103.14 0.28 97 63 207 144 84.47 1.49 98 73 125 52 365.63 0.40 99 77 121 44 457.47 0.27 100 77 122 45 455.88 0.20 101 77 125 48 365.90 0.37 102 79 121 42 457.47 0.27 103 80 121 41 457.67 0.30 104 83 121 38 457.67 0.29 105 84 121 37 457.67 0.29 106 84 182 98 157.41 0.73 107 85 182 97 161.47 1.29 108 87 151 64 305.94 0.77 109 88 124 36 438.05 9.42 110 88 128 40 365.86 0.33 111 88 131 43 365.77 0.35 112 88 132 44 365.61 0.30 113 88 151 63 293.15 1.06 114 89 121 32 457.56 0.28 115 89 124 35 401.64 0.17 116 89 151 62 296.96 0.84 117 90 121 31 457.51 0.27 118 90 125 35 366.55 0.21 119 94 125 31 365.80 0.33 120 95 125 30 365.80 0.33 121 95 128 33 363.12 0.24 122 95 129 34 339.87 0.98 123 95 132 37 332.72 0.59 124 98 125 27 365.60 0.38 125 98 126 28 365.43 0.42 126 98 129 31 332.94 0.59 127 99 129 30 332.86 0.55 128 99 132 33 330.84 0.39 129 99 133 34 316.76 0.08 130 102 114 12 524.67 4.82 131 102 116 14 457.54 0.28 132 102 129 27 332.85 0.55 133 102 130 28 332.80 0.56 134 102 133 31 316.41 0.26 135 102 137 35 316.29 0.29 136 102 141 39 316.12 0.27 137 103 137 34 316.23 0.27 138 105 114 9 463.01 1.95 139 106 137 31 316.14 0.26 140 106 140 34 316.11 0.27 141 109 112 3 457.49 0.28 142 110 140 30 316.08 0.27 143 111 211 100 39.60 0.33 144 113 142 29 315.75 0.29 145 113 207 94 80.16 0.61 146 113 210 97 39.61 0.33 147 113 211 98 36.73 1.10 148 114 137 23 316.35 0.28 149 114 140 26 316.11 0.28 150 114 141 27 316.00 0.28 151 114 142 28 315.92 0.24 152 115 141 26 316.10 0.28 153 115 142 27 316.01 0.28 154 115 143 28 315.74 0.24 155 115 203 88 103.36 0.20 156 115 207 92 82.44 0.52 157 116 130 14 332.76 0.58 158 116 141 25 316.14 0.28 159 116 143 27 316.04 0.27 160 116 144 28 315.41 0.21 161 116 145 29 315.39 0.21 162 116 203 87 106.23 0.59 163 117 144 27 315.86 0.24 164 117 145 28 315.39 0.21 165 118 122 4 366.38 0.29 166 118 123 5 366.03 0.25 167 118 126 8 365.10 0.39 168 118 145 27 315.88 0.21 169 118 146 28 315.25 0.14 170 118 147 29 313.70 0.07 171 119 122 3 366.57 0.24 172 119 123 4 366.41 0.29 173 119 147 28 313.66 0.06 174 119 188 69 115.48 1.62 175 119 189 70 115.08 1.42 176 119 191 72 111.55 1.14 177 120 123 3 373.04 1.58 178 120 124 4 368.45 0.70 179 120 147 27 315.75 0.23 180 120 148 28 313.64 0.05 181 120 150 30 302.76 2.44 182 120 188 68 115.48 1.62 183 121 124 3 373.18 2.96 184 121 125 4 366.50 0.25 185 121 150 29 298.91 0.56 186 122 125 3 366.43 0.21 187 122 126 4 366.36 0.19 188 123 126 3 366.23 0.07 189 123 127 4 366.16 0.09 190 123 146 23 315.80 0.23 191 123 147 24 315.75 0.23 192 123 149 26 298.91 0.56 193 124 127 3 366.17 0.10 194 124 128 4 366.13 0.10 195 124 149 25 303.54 1.74 196 124 150 26 293.17 1.05 197 124 151 27 293.03 1.09 198 125 128 3 372.56 1.79 199 125 129 4 365.30 0.11 200 126 129 3 370.57 0.79 201 126 130 4 362.14 1.43 202 126 146 20 315.83 0.24 203 127 130 3 360.54 3.33 204 127 131 4 348.81 0.15 205 127 149 22 298.93 0.57 206 127 159 32 218.40 0.77 207 128 131 3 361.20 3.83 208 128 132 4 351.01 1.26 209 129 132 3 366.30 1.29 210 129 133 4 351.00 1.27 211 130 133 3 359.25 2.86 212 130 138 8 316.39 0.25 213 130 141 11 316.32 0.26 214 130 144 14 316.10 0.27 215 130 159 29 218.40 0.77 216 130 162 32 218.12 0.67 217 131 138 7 316.66 0.34 218 131 160 29 218.40 0.75 219 131 161 30 218.34 0.72 220 133 137 4 340.88 12.27 221 133 138 5 316.76 0.29 222 133 141 8 316.60 0.30 223 134 137 3 376.87 2.52 224 134 138 4 323.68 0.01 225 135 138 3 372.50 0.34 226 135 139 4 336.44 6.39 227 136 140 4 351.68 10.77 228 137 140 3 377.86 2.32 229 137 141 4 377.86 2.33 230 138 141 3 380.69 3.73 231 138 161 23 218.16 0.65 232 138 162 24 217.94 0.60 233 139 166 27 217.64 0.65 234 141 144 3 411.14 0.67 235 141 162 21 217.97 0.59 236 141 166 25 217.06 0.88 237 142 166 24 217.06 0.88 238 142 206 64 82.85 0.38 239 142 207 65 82.60 0.48 240 142 210 68 76.64 0.35 241 143 162 19 218.12 0.65 242 143 166 23 217.05 0.88 243 143 202 59 108.48 0.98 244 143 203 60 106.25 0.59 245 143 206 63 86.69 1.03 246 144 159 15 218.47 0.80 247 144 162 18 218.00 0.58 248 144 166 22 217.28 0.77 249 144 167 23 217.01 0.86 250 144 168 24 217.00 0.87 251 144 202 58 108.56 1.01 252 144 203 59 108.17 0.84 253 145 168 23 216.98 0.87 254 145 170 25 216.88 0.89 255 145 199 54 108.73 0.96 256 145 202 57 108.67 0.96 257 145 203 58 108.53 1.02 258 146 149 3 372.54 0.86 259 146 159 13 218.50 0.80 260 146 167 21 217.34 0.74 261 146 168 22 217.01 0.87 262 146 169 23 216.94 0.85 263 146 170 24 216.83 0.85 264 147 170 23 216.37 0.91 265 147 191 44 111.64 1.18 266 147 194 47 110.75 1.16 267 147 195 48 110.78 1.18 268 147 199 52 110.67 1.17 269 148 170 22 216.96 0.86 270 148 171 23 216.38 0.91 271 148 175 27 216.03 1.05 272 148 177 29 215.95 1.08 273 148 178 30 215.41 1.24 274 148 188 40 115.09 1.43 275 148 191 43 113.62 1.37 276 149 152 3 359.69 5.29 277 149 155 6 255.36 3.66 278 149 157 8 218.93 0.94 279 149 158 9 218.91 0.95 280 149 169 20 217.00 0.88 281 149 171 22 216.68 0.92 282 149 178 29 214.73 1.30 283 150 154 4 382.62 2.52 284 150 177 27 215.04 1.34 285 151 154 3 372.15 1.02 286 151 155 4 297.69 18.91 287 152 155 3 372.39 1.81 288 152 156 4 290.94 14.12 289 152 157 5 219.15 0.82 290 152 169 17 217.43 0.72 291 152 171 19 217.02 0.89 292 152 178 26 215.65 1.11 293 153 156 3 335.03 1.99 294 153 178 25 216.34 1.19 295 153 179 26 215.65 1.11 296 153 180 27 214.33 1.14 297 154 180 26 212.34 0.14 298 155 158 3 369.49 0.35 299 155 160 5 219.16 0.83 300 157 169 12 217.47 0.73 301 158 162 4 361.30 6.07 302 158 163 5 226.60 2.85 303 158 164 6 218.21 0.65 304 159 162 3 370.23 0.57 305 159 167 8 217.66 0.66 306 162 166 4 370.65 1.63 307 162 167 5 252.81 5.53 308 163 166 3 377.12 1.61 309 163 167 4 315.63 25.88 310 164 167 3 353.12 13.29 311 165 202 37 108.74 0.96 312 165 206 41 106.53 0.49 313 166 202 36 108.73 0.95 314 167 202 35 108.73 0.96 315 168 202 34 108.73 0.95 316 170 191 21 114.44 1.40 317 170 194 24 110.79 1.13 318 170 198 28 110.78 1.17 319 170 199 29 110.70 1.17 320 171 191 20 116.70 0.73 321 172 187 15 119.84 1.96 322 172 190 18 119.82 1.96 323 172 191 19 119.58 1.97 324 172 194 22 114.84 1.53 325 173 187 14 128.78 1.46 326 174 185 11 149.80 4.22 327 174 187 13 131.30 0.21 328 175 187 12 128.77 1.46 329 175 188 13 127.48 1.65 330 175 191 16 127.48 1.65 331 176 181 5 442.29 2.88 332 176 183 7 335.23 4.79 333 176 185 9 193.72 18.99 334 177 181 4 399.08 0.96 335 177 182 5 347.54 1.35 336 177 183 6 334.73 5.03 337 177 188 11 129.67 0.56 338 178 191 13 120.12 2.04 339 184 188 4 376.63 4.05 340 184 189 5 374.12 0.55 341 185 188 3 383.24 0.76 342 185 189 4 386.90 1.07 343 186 189 3 387.27 0.89 344 186 190 4 387.26 0.89 345 187 190 3 387.27 0.89 346 187 191 4 388.56 0.24 347 188 191 3 412.85 2.75 348 190 193 3 433.45 0.19 349 191 194 3 379.24 1.12 350 191 195 4 332.16 2.17 351 192 195 3 370.67 0.45 352 192 196 4 332.17 2.17 353 193 196 3 360.42 7.63 354 193 197 4 324.04 1.46 355 193 198 5 324.03 1.46 356 194 197 3 360.22 7.74 357 194 198 4 323.98 1.46 358 194 199 5 323.87 1.42 359 194 200 6 323.97 1.46 360 195 199 4 323.82 1.42 361 195 200 5 287.54 16.73 362 196 200 4 339.30 3.52 363 197 200 3 379.31 2.75 364 197 201 4 322.17 0.62 365 198 201 3 339.30 3.52 366 198 202 4 322.17 0.62 367 199 202 3 368.88 7.96 368 199 203 4 336.12 0.45 369 200 203 3 362.12 4.58 370 200 204 4 328.16 4.12 371 201 204 3 374.86 1.82 372 201 205 4 336.32 0.04 373 202 205 3 355.54 7.84 374 202 206 4 336.32 0.04 375 203 206 3 369.18 1.23 376 203 207 4 335.72 0.26 377 204 207 3 360.45 3.15 378 204 208 4 335.72 0.26 379 205 208 3 363.66 5.91 380 205 209 4 336.77 0.78 381 206 209 3 372.58 2.29 382 206 210 4 372.58 2.29 383 207 210 3 380.35 2.50 384 207 211 4 299.89 19.23 385 208 211 3 372.22 2.12 386 208 212 4 189.25 23.56 387 208 213 5 187.98 24.19