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 16 139 118 61.68 1.59 2 16 140 119 61.54 1.56 3 16 142 121 61.59 1.55 4 16 143 122 67.92 1.52 5 16 144 123 68.06 1.52 6 16 156 135 67.09 1.36 7 16 157 136 62.43 1.22 8 16 158 137 61.69 1.59 9 16 189 170 64.12 0.36 10 16 190 171 61.23 1.44 11 16 191 172 61.38 1.50 12 16 194 175 61.38 1.51 13 17 143 121 68.08 1.52 14 17 144 122 68.07 1.52 15 17 145 123 68.60 1.66 16 17 146 124 68.60 1.66 17 17 188 167 68.11 1.50 18 17 188 168 68.09 1.50 19 17 189 169 67.92 1.54 20 17 191 171 68.00 1.50 21 17 220 195 68.11 1.50 22 17 221 196 68.11 1.50 23 18 158 135 68.17 1.48 24 18 188 166 68.18 1.47 25 18 188 167 68.11 1.49 26 19 157 133 68.99 1.46 27 19 158 134 68.16 1.47 28 20 137 112 80.85 0.43 29 20 156 131 93.91 1.03 30 20 157 132 77.61 0.76 31 20 158 133 184.66 3.09 32 20 159 134 246.62 10.02 33 21 154 128 136.88 0.01 34 21 155 129 134.94 0.92 35 21 156 130 116.12 0.35 36 22 26 4 150.92 7.04 37 22 27 5 134.13 1.35 38 22 139 112 135.56 0.63 39 22 155 128 151.92 5.14 40 22 156 129 201.27 0.95 41 23 26 3 176.64 2.77 42 24 71 44 139.22 0.01 43 25 69 41 146.03 1.15 44 25 71 43 160.96 0.58 45 25 79 51 161.18 0.54 46 25 117 89 140.15 0.07 47 27 30 3 227.03 15.28 48 27 137 105 139.35 0.39 49 27 139 107 150.27 1.23 50 27 157 125 289.32 0.15 51 28 116 85 161.12 0.52 52 28 117 86 160.95 0.51 53 28 118 87 159.12 0.57 54 28 119 88 154.41 1.75 55 29 45 14 151.71 0.53 56 29 46 15 148.44 0.06 57 29 119 87 159.59 0.28 58 29 120 88 151.84 0.47 59 29 121 89 148.50 0.39 60 29 137 103 161.22 0.52 61 29 198 166 160.59 0.66 62 29 200 168 160.14 0.51 63 30 43 11 161.33 0.47 64 30 44 12 161.18 0.54 65 30 139 104 161.40 0.43 66 30 140 105 162.10 0.26 67 30 141 106 163.02 0.41 68 30 155 120 203.96 1.32 69 30 198 165 160.95 0.48 70 31 43 10 162.05 0.21 71 31 44 11 161.23 0.52 72 31 45 12 161.42 0.42 73 31 46 13 161.41 0.43 74 31 52 19 161.41 0.43 75 31 65 32 162.87 0.36 76 31 66 33 162.82 0.39 77 31 67 34 162.26 0.24 78 31 141 105 163.03 0.41 79 32 40 6 163.12 0.43 80 32 42 8 163.02 0.41 81 32 43 9 162.53 0.37 82 32 65 31 163.00 0.42 83 32 66 32 162.98 0.42 84 32 70 35 162.94 0.43 85 32 73 38 163.01 0.40 86 32 141 104 163.03 0.41 87 33 40 5 163.22 0.41 88 33 41 6 163.09 0.41 89 33 42 7 163.03 0.41 90 33 43 8 163.03 0.41 91 33 54 19 163.02 0.42 92 33 58 23 163.08 0.41 93 33 63 28 163.13 0.43 94 33 64 29 163.09 0.42 95 33 65 30 163.02 0.42 96 33 106 70 163.05 0.43 97 34 39 3 164.72 0.31 98 34 40 4 163.24 0.41 99 34 41 5 163.24 0.41 100 34 63 27 163.16 0.43 101 34 64 28 163.12 0.43 102 34 66 30 163.09 0.42 103 37 41 4 164.62 0.27 104 37 60 23 163.28 0.41 105 37 62 25 200.42 18.93 106 40 73 32 289.91 0.01 107 40 141 98 289.95 0.02 108 43 197 153 290.00 0.00 109 44 52 8 290.00 0.00 110 45 121 75 211.00 0.21 111 45 209 159 289.92 0.04 112 46 119 72 289.73 0.13 113 46 120 73 246.75 2.00 114 46 121 74 228.87 0.21 115 47 120 72 287.61 0.09 116 47 121 73 239.58 3.97 117 47 123 75 200.60 0.93 118 47 238 186 47.24 0.48 119 47 242 190 32.59 0.46 120 48 120 71 289.50 0.06 121 48 242 189 32.20 0.66 122 49 111 61 290.00 0.00 123 50 111 60 290.00 0.00 124 51 242 186 31.83 0.62 125 51 245 189 19.92 0.49 126 67 112 44 290.00 0.00 127 67 118 50 289.69 0.15 128 69 79 10 290.00 0.00 129 69 117 48 289.72 0.14 130 69 118 49 289.69 0.15 131 71 153 80 162.10 0.22 132 71 154 81 161.00 0.56 133 71 155 82 160.23 0.58 134 72 153 79 162.09 0.21 135 72 154 80 162.02 0.18 136 73 153 78 162.11 0.23 137 74 153 77 162.12 0.23 138 79 117 38 289.77 0.12 139 81 112 31 290.00 0.00 140 81 113 32 290.00 0.00 141 81 115 34 290.00 0.01 142 81 118 37 289.74 0.13 143 86 109 23 290.00 0.00 144 87 107 20 290.00 0.00 145 87 245 154 20.33 0.04 146 88 106 18 290.00 0.00 147 89 237 144 81.67 0.57 148 89 241 148 38.11 0.68 149 89 245 152 20.58 0.10 150 91 103 12 290.00 0.00 151 91 234 139 109.79 2.06 152 91 237 142 81.40 0.62 153 92 237 141 94.54 0.58 154 96 99 3 290.00 0.00 155 98 180 80 203.52 19.49 156 99 180 79 162.81 0.79 157 100 177 75 162.55 0.92 158 100 179 77 162.26 0.78 159 100 180 78 162.27 0.78 160 101 179 76 161.41 1.20 161 101 234 129 110.03 1.96 162 102 229 123 160.93 0.11 163 103 229 122 160.12 0.51 164 103 234 127 97.73 0.64 165 103 237 130 75.31 0.35 166 103 238 131 49.44 0.06 167 105 237 128 75.19 0.29 168 105 238 129 48.67 0.26 169 105 241 132 33.53 1.31 170 105 242 133 32.07 0.66 171 107 245 134 18.37 0.14 172 114 119 5 289.95 0.03 173 121 200 79 290.00 0.01 174 121 209 84 288.62 0.66 175 122 203 81 290.00 0.00 176 122 204 82 283.27 2.97 177 122 209 83 252.06 0.43 178 123 204 81 232.86 5.32 179 123 209 82 191.03 1.91 180 123 231 104 277.91 1.02 181 123 235 108 74.38 0.88 182 123 238 111 49.48 0.05 183 123 239 112 47.23 0.47 184 124 204 80 187.71 1.54 185 124 209 81 175.08 2.27 186 124 210 82 169.31 0.61 187 124 231 103 288.79 0.43 188 124 232 104 277.77 1.08 189 124 235 107 78.53 1.20 190 127 210 80 162.74 0.35 191 128 210 79 160.98 0.81 192 129 134 4 165.85 0.00 193 129 162 32 136.49 0.18 194 129 201 73 161.93 0.38 195 129 210 78 161.94 0.42 196 130 134 3 180.70 0.33 197 130 162 31 137.01 0.07 198 132 162 30 137.01 0.07 199 132 163 31 137.17 0.00 200 132 164 32 137.19 0.01 201 133 161 28 137.03 0.06 202 133 162 29 137.19 0.01 203 134 161 27 137.16 0.01 204 134 162 28 137.25 0.01 205 134 201 69 290.00 0.00 206 135 160 25 137.21 0.00 207 135 161 26 137.23 0.01 208 136 159 23 137.04 0.07 209 136 160 24 137.23 0.01 210 136 162 26 144.37 1.26 211 136 199 65 290.00 0.00 212 137 157 20 136.85 0.01 213 137 158 21 137.03 0.06 214 137 159 22 137.03 0.06 215 138 157 19 135.56 0.64 216 138 158 20 136.84 0.01 217 138 160 22 138.01 0.36 218 138 190 54 288.86 0.17 219 138 213 73 290.00 0.00 220 138 228 88 162.00 0.41 221 139 155 16 137.30 0.02 222 139 156 17 137.13 0.00 223 139 157 18 135.40 0.71 224 140 155 15 137.30 0.02 225 140 156 16 137.03 0.06 226 140 194 56 289.99 0.01 227 141 151 10 162.31 0.36 228 141 152 11 161.61 0.36 229 141 153 12 161.16 0.51 230 141 154 13 155.52 0.04 231 141 155 14 137.34 0.04 232 142 151 9 162.46 0.38 233 142 152 10 162.15 0.46 234 142 193 53 290.00 0.00 235 142 194 54 289.97 0.01 236 143 148 5 163.19 0.43 237 143 149 6 163.02 0.43 238 143 150 7 162.88 0.46 239 143 151 8 162.47 0.38 240 143 191 50 208.03 3.50 241 143 192 51 289.98 0.01 242 144 150 6 163.04 0.43 243 144 152 8 162.85 0.47 244 144 156 12 137.31 0.10 245 145 148 3 163.21 0.43 246 145 149 4 163.16 0.46 247 145 150 5 163.07 0.42 248 146 220 71 162.56 0.37 249 146 221 72 162.56 0.37 250 146 221 73 162.55 0.37 251 151 192 43 162.85 0.47 252 152 156 4 165.28 0.99 253 158 188 32 137.37 0.12 254 158 189 33 137.09 0.13 255 158 190 34 136.91 0.04 256 159 184 26 151.73 6.77 257 160 184 24 137.16 0.01 258 160 184 25 137.74 0.22 259 161 183 22 172.26 2.11 260 161 184 23 151.75 7.02 261 161 184 24 156.53 4.63 262 162 181 19 254.40 8.09 263 162 182 20 197.80 10.08 264 162 183 21 172.75 2.35 265 162 201 41 147.97 0.22 266 163 167 4 290.00 0.00 267 163 182 19 217.13 1.27 268 163 183 20 180.05 1.24 269 163 184 21 180.05 1.24 270 163 185 23 172.75 2.35 271 163 225 60 152.22 0.48 272 165 169 4 290.00 0.00 273 166 169 3 290.00 0.00 274 167 185 19 280.15 1.11 275 168 171 3 290.00 0.00 276 169 172 3 290.00 0.00 277 169 173 4 290.00 0.01 278 170 173 3 290.00 0.00 279 171 223 50 162.61 0.43 280 171 224 51 162.58 0.45 281 171 225 52 162.56 0.47 282 172 215 41 163.43 0.43 283 172 216 42 163.41 0.42 284 172 217 43 163.41 0.42 285 172 224 50 162.65 0.44 286 172 225 51 162.65 0.44 287 172 227 53 162.13 0.52 288 175 215 38 163.52 0.45 289 176 215 37 163.53 0.45 290 176 227 49 162.59 0.46 291 178 230 50 161.99 0.40 292 178 233 53 160.62 0.71 293 179 229 48 162.25 0.51 294 179 230 49 161.91 0.41 295 179 233 52 154.80 1.59 296 179 234 53 148.05 0.59 297 180 215 33 163.45 0.52 298 180 227 45 162.61 0.45 299 180 228 46 162.25 0.50 300 180 230 48 161.80 0.45 301 181 199 20 162.96 0.47 302 181 210 27 162.75 0.54 303 181 211 28 162.80 0.53 304 181 227 44 162.32 0.46 305 181 228 45 162.19 0.49 306 181 229 46 161.97 0.40 307 181 230 47 161.68 0.40 308 182 225 41 162.60 0.44 309 182 226 42 162.31 0.47 310 182 227 43 161.83 0.46 311 182 228 44 161.84 0.47 312 183 225 40 162.64 0.44 313 183 226 41 162.48 0.37 314 183 228 43 162.03 0.40 315 184 225 39 162.66 0.43 316 184 187 3 289.79 0.02 317 184 188 5 276.24 0.80 318 185 222 34 163.06 0.46 319 185 223 35 162.96 0.48 320 185 225 37 162.80 0.43 321 186 222 33 163.16 0.43 322 187 221 30 163.32 0.40 323 187 221 31 163.28 0.39 324 187 222 32 163.19 0.42 325 188 221 29 163.37 0.38 326 188 221 28 171.56 4.46 327 189 220 26 289.01 0.49 328 189 221 27 182.97 5.96 329 189 226 33 161.94 0.39 330 190 213 19 290.00 0.00 331 190 228 34 161.78 0.46 332 194 197 3 290.00 0.00 333 197 213 12 290.00 0.00 334 198 209 7 290.00 0.00 335 199 211 8 290.00 0.01 336 199 212 9 289.99 0.01 337 199 228 25 162.14 0.33 338 209 231 22 123.19 1.94 339 210 229 19 162.49 0.50 340 210 230 20 161.69 0.49 341 210 231 21 122.36 1.53 342 210 232 22 106.81 0.34 343 211 228 17 162.00 0.40 344 211 229 18 161.77 0.46 345 211 231 20 117.69 0.68 346 212 228 16 161.85 0.42 347 212 229 17 161.69 0.49 348 212 231 19 114.47 2.29 349 213 228 15 161.77 0.46 350 214 227 13 162.15 0.34 351 214 228 14 161.90 0.40 352 214 229 15 161.77 0.46 353 215 226 11 162.46 0.38 354 215 227 12 161.99 0.41 355 216 225 9 172.21 4.35 356 216 226 10 162.14 0.50 357 216 227 11 161.91 0.40 358 217 224 7 180.72 0.12 359 221 224 3 279.99 1.60 360 229 234 5 288.53 0.01 361 230 233 3 289.72 0.08 362 230 234 4 289.72 0.08 363 231 234 3 289.72 0.08 364 231 235 4 286.19 0.45 365 231 238 7 49.47 0.06 366 232 235 3 82.50 0.70 367 234 237 3 72.23 1.89 368 234 238 4 50.27 0.35 369 235 238 3 60.99 5.74 370 235 239 4 47.84 0.77 371 236 239 3 50.36 0.32 372 236 240 4 49.44 0.06 373 237 240 3 47.51 0.91 374 237 241 4 44.59 0.75 375 238 241 3 56.63 6.37 376 238 242 4 32.61 0.47 377 239 242 3 63.58 2.89 378 239 243 4 32.62 0.48 379 240 243 3 54.30 7.53 380 240 244 4 32.21 0.65 381 241 244 3 31.91 0.49 382 241 245 4 30.84 0.26 383 242 245 3 19.98 0.21