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 43.78 0.40 2 16 140 119 43.79 0.40 3 16 142 121 43.84 0.37 4 16 143 122 60.95 3.98 5 16 144 123 62.86 3.23 6 16 156 135 47.27 1.02 7 16 157 136 46.01 1.02 8 16 158 137 45.82 1.11 9 16 189 170 52.91 0.82 10 16 190 171 43.65 0.33 11 16 194 175 43.65 0.34 12 17 143 121 62.87 3.22 13 17 144 122 62.87 3.22 14 17 145 123 63.13 3.21 15 17 146 124 63.13 3.21 16 17 187 167 63.02 3.15 17 17 188 168 62.86 3.22 18 17 189 169 62.59 3.36 19 17 191 171 62.62 3.33 20 17 220 195 62.77 3.27 21 17 921 196 62.83 3.23 22 18 158 135 65.35 1.98 23 18 187 166 64.84 2.24 24 18 188 167 63.01 3.15 25 19 157 133 66.49 1.45 26 19 158 134 65.34 1.98 27 20 137 112 85.17 1.03 28 20 156 131 94.77 2.83 29 20 157 132 77.66 0.33 30 20 158 133 195.27 5.29 31 20 159 134 277.94 1.80 32 21 154 128 138.08 0.02 33 21 155 129 147.47 7.70 34 21 156 130 142.75 9.48 35 22 26 4 169.65 1.01 36 22 27 5 136.53 0.77 37 22 139 112 137.66 0.03 38 22 155 128 167.13 0.01 39 22 156 129 196.25 1.27 40 23 26 3 212.40 14.67 41 24 71 44 139.12 0.17 42 25 28 3 172.72 1.62 43 25 69 41 141.34 0.93 44 25 79 51 160.22 0.77 45 25 117 89 140.08 0.74 46 27 30 3 192.58 8.24 47 27 137 105 140.31 0.08 48 27 139 107 147.55 0.45 49 27 157 125 288.83 0.07 50 28 116 85 160.13 0.77 51 28 117 86 160.12 0.77 52 28 118 87 156.34 0.90 53 28 119 88 154.13 1.48 54 29 45 14 147.46 0.38 55 29 46 15 144.99 0.86 56 29 119 87 157.41 0.36 57 29 120 88 151.41 0.12 58 29 121 89 143.78 0.26 59 29 137 103 160.26 0.80 60 29 198 166 159.52 0.56 61 29 200 168 160.01 0.80 62 30 43 11 160.30 0.80 63 30 44 12 160.22 0.80 64 30 139 104 160.38 0.83 65 30 140 105 160.91 0.57 66 30 141 106 162.17 0.37 67 30 155 120 271.42 1.90 68 30 198 165 159.98 0.70 69 31 43 10 161.35 0.33 70 31 44 11 160.27 0.81 71 31 45 12 160.28 0.80 72 31 46 13 160.28 0.78 73 31 52 19 160.30 0.79 74 31 964 32 162.13 0.42 75 31 65 33 162.15 0.42 76 31 66 34 161.84 0.57 77 31 141 105 162.21 0.37 78 32 40 6 162.43 0.40 79 32 42 8 162.24 0.36 80 32 964 31 162.29 0.39 81 32 65 32 162.22 0.39 82 32 70 35 162.25 0.42 83 32 73 38 162.38 0.41 84 32 141 104 162.21 0.37 85 33 40 5 162.49 0.39 86 33 41 6 162.44 0.39 87 33 42 7 162.28 0.36 88 33 43 8 162.25 0.36 89 33 54 19 162.23 0.38 90 33 58 23 162.37 0.40 91 33 63 28 162.47 0.38 92 33 64 29 162.43 0.40 93 33 964 30 162.31 0.40 94 33 104 68 162.27 0.38 95 33 106 70 162.29 0.39 96 34 39 3 164.86 0.09 97 34 40 4 162.52 0.40 98 34 41 5 162.52 0.41 99 34 63 27 162.48 0.38 100 34 64 28 162.45 0.39 101 34 65 30 162.44 0.39 102 37 41 4 172.84 3.23 103 37 60 23 167.34 0.01 104 37 62 25 167.34 1.02 105 40 43 3 289.00 0.00 106 40 73 32 287.02 0.44 107 40 141 98 288.91 0.03 108 40 193 152 287.49 0.17 109 42 195 152 288.97 0.00 110 43 196 152 289.00 0.00 111 43 197 153 288.92 0.01 112 44 197 152 289.00 0.00 113 45 121 75 209.12 0.24 114 45 209 159 288.98 0.01 115 46 52 6 289.00 0.00 116 46 118 71 288.97 0.01 117 46 119 72 288.63 0.15 118 46 120 73 254.62 2.81 119 46 121 74 223.07 4.10 120 47 120 72 279.72 0.69 121 47 121 73 258.23 4.62 122 47 123 75 200.72 0.39 123 47 238 186 60.60 0.68 124 47 242 190 32.51 0.54 125 48 120 71 286.33 1.26 126 48 242 189 32.51 0.54 127 50 108 57 289.00 0.00 128 51 242 186 32.45 0.52 129 51 245 189 22.82 0.20 130 53 238 180 60.33 0.82 131 57 214 152 288.99 0.01 132 63 85 21 289.00 0.00 133 64 82 17 289.00 0.00 134 964 82 16 289.00 0.00 135 65 82 15 289.00 0.01 136 66 112 44 288.89 0.04 137 66 118 50 288.12 0.01 138 69 118 49 287.51 0.29 139 70 73 3 289.00 0.00 140 71 153 80 161.41 0.41 141 71 154 81 160.06 0.72 142 71 155 82 159.99 0.70 143 72 75 3 289.00 0.00 144 72 153 79 161.40 0.41 145 72 154 80 161.16 0.46 146 73 141 66 289.00 0.00 147 73 153 78 161.57 0.49 148 74 153 77 161.78 0.40 149 79 117 38 288.94 0.01 150 81 118 37 288.94 0.03 151 83 112 29 289.00 0.00 152 87 245 154 23.62 0.28 153 89 105 16 289.00 0.00 154 89 237 144 79.66 1.66 155 89 241 148 50.27 0.91 156 89 245 152 23.36 0.06 157 91 234 139 107.90 0.06 158 91 237 142 80.46 1.34 159 92 237 141 97.12 2.20 160 96 99 3 289.00 0.01 161 98 180 80 206.43 18.04 162 99 180 79 206.36 18.04 163 99 215 112 289.00 0.00 164 100 177 75 171.03 0.43 165 100 179 77 171.08 0.45 166 100 180 78 171.05 0.44 167 101 179 76 171.02 0.43 168 101 234 129 115.37 3.52 169 102 214 108 288.99 0.01 170 102 229 123 160.48 0.65 171 103 229 122 160.40 0.61 172 103 234 127 97.13 2.21 173 103 237 130 76.00 0.20 174 103 238 131 64.81 3.04 175 105 237 128 72.59 0.80 176 105 238 129 63.31 2.31 177 105 241 132 32.80 0.40 178 105 242 133 32.44 0.52 179 107 245 134 22.77 0.23 180 112 118 6 288.98 0.01 181 113 118 5 289.00 0.01 182 114 119 5 288.97 0.01 183 121 200 79 288.73 0.14 184 121 203 82 288.94 0.03 185 121 204 83 288.93 0.04 186 121 209 84 288.07 0.15 187 122 204 82 275.49 1.23 188 122 209 83 248.72 1.40 189 123 204 81 236.45 1.16 190 123 209 82 200.31 2.17 191 123 231 104 286.45 0.78 192 123 235 108 77.03 3.21 193 123 238 111 64.08 2.67 194 124 204 80 191.24 1.37 195 124 209 81 173.50 0.68 196 124 210 82 170.05 1.04 197 124 231 103 288.66 0.14 198 124 232 104 196.78 43.98 199 124 235 107 83.68 0.12 200 127 210 80 161.36 0.48 201 128 210 79 157.22 1.02 202 129 134 4 162.44 1.15 203 129 162 32 137.90 0.05 204 129 201 73 156.61 1.32 205 129 210 78 160.77 0.65 206 130 134 3 180.03 0.91 207 130 162 31 138.30 0.05 208 132 162 30 138.31 0.06 209 132 163 31 138.46 0.10 210 132 164 32 138.47 0.10 211 133 161 28 138.41 0.11 212 133 162 29 138.47 0.10 213 134 161 27 138.49 0.11 214 134 162 28 138.50 0.11 215 135 160 25 138.49 0.11 216 135 161 26 138.50 0.11 217 136 159 23 138.49 0.11 218 136 160 24 138.49 0.11 219 136 162 26 142.36 0.94 220 137 157 20 137.90 0.09 221 137 158 21 138.46 0.10 222 137 159 22 138.49 0.11 223 138 157 19 137.64 0.04 224 138 158 20 138.00 0.04 225 138 160 22 138.65 0.07 226 138 183 45 162.27 0.35 227 138 190 54 288.97 0.01 228 138 228 88 160.75 0.68 229 139 155 16 138.56 0.12 230 139 156 17 138.47 0.10 231 139 157 18 137.66 0.03 232 140 155 15 138.54 0.10 233 140 156 16 138.47 0.10 234 141 151 10 161.81 0.25 235 141 152 11 160.49 0.74 236 141 153 12 160.24 0.82 237 141 154 13 153.53 1.17 238 141 155 14 138.59 0.09 239 142 151 9 161.93 0.30 240 142 152 10 161.86 0.29 241 142 192 52 287.44 0.03 242 142 193 53 287.24 0.07 243 142 194 54 287.49 0.07 244 143 148 5 162.38 0.40 245 143 149 6 162.06 0.31 246 143 150 7 162.01 0.34 247 143 151 8 161.94 0.31 248 143 191 50 201.63 1.17 249 143 192 51 287.11 0.07 250 144 150 6 162.10 0.33 251 144 152 8 161.94 0.30 252 144 156 12 138.56 0.12 253 145 148 3 168.94 0.83 254 145 149 4 162.27 0.35 255 145 150 5 162.12 0.33 256 146 220 71 161.86 0.40 257 146 921 72 161.84 0.40 258 146 221 73 161.79 0.39 259 151 192 43 162.00 0.34 260 151 193 44 161.94 0.31 261 152 156 4 167.50 0.18 262 158 184 27 138.51 0.13 263 158 188 32 138.40 0.15 264 158 189 33 138.28 0.18 265 159 184 26 138.58 0.10 266 160 983 24 138.44 0.10 267 160 184 25 138.57 0.10 268 161 183 22 138.49 0.12 269 161 983 23 138.51 0.12 270 161 184 24 138.66 0.08 271 162 181 19 250.16 4.61 272 162 182 20 222.27 18.55 273 162 183 21 157.75 9.50 274 162 201 41 145.34 0.73 275 163 167 4 288.99 0.01 276 163 182 19 227.90 15.74 277 163 183 20 188.34 5.65 278 163 983 21 188.34 5.65 279 163 185 23 174.77 1.03 280 163 225 60 152.94 0.56 281 164 167 3 289.00 0.00 282 164 168 4 288.98 0.01 283 165 168 3 288.98 0.01 284 165 169 4 289.00 0.00 285 167 171 4 289.00 0.00 286 168 171 3 289.00 0.00 287 171 223 50 161.72 0.39 288 171 224 51 161.66 0.38 289 171 225 52 161.65 0.39 290 172 215 41 170.76 0.56 291 172 216 42 170.25 0.36 292 172 217 43 170.22 0.38 293 172 224 50 161.76 0.41 294 172 225 51 161.70 0.40 295 172 227 53 160.78 0.66 296 175 215 38 170.93 0.48 297 176 215 37 170.98 0.47 298 176 227 49 161.68 0.41 299 178 230 50 161.42 0.40 300 178 233 53 158.66 0.29 301 179 229 48 161.46 0.41 302 179 230 49 160.79 0.66 303 179 233 52 153.84 0.10 304 179 234 53 151.03 1.50 305 180 215 33 171.09 0.47 306 180 227 45 161.69 0.40 307 180 228 46 161.32 0.47 308 180 230 48 160.60 0.62 309 181 199 20 162.02 0.33 310 181 210 27 161.74 0.40 311 181 211 28 161.75 0.39 312 181 227 44 161.56 0.34 313 181 228 45 160.80 0.66 314 181 229 46 160.80 0.66 315 181 230 47 160.58 0.60 316 182 225 41 161.67 0.39 317 182 226 42 161.53 0.34 318 182 227 43 160.74 0.69 319 183 225 40 161.73 0.38 320 183 226 41 161.68 0.40 321 183 228 43 161.26 0.44 322 184 186 3 288.82 0.02 323 184 188 5 266.33 8.76 324 185 222 34 162.19 0.34 325 185 223 35 161.96 0.41 326 185 225 37 161.93 0.41 327 186 222 33 166.27 0.47 328 186 921 30 168.75 0.35 329 186 221 31 166.38 0.46 330 186 222 32 163.53 0.94 331 187 921 29 184.81 7.65 332 188 921 28 185.19 7.46 333 189 220 26 288.67 0.01 334 189 921 27 207.90 2.89 335 189 226 33 160.63 0.61 336 190 228 34 160.44 0.55 337 199 228 25 161.22 0.45 338 209 231 22 116.37 0.36 339 210 229 19 161.56 0.36 340 210 230 20 157.25 1.01 341 210 231 21 119.16 0.14 342 210 232 22 111.64 0.84 343 211 228 17 161.21 0.46 344 211 229 18 160.09 0.38 345 211 231 20 116.44 0.33 346 212 228 16 160.72 0.68 347 212 229 17 158.66 0.33 348 212 231 19 115.17 0.57 349 213 228 15 158.74 0.29 350 214 227 13 161.22 0.45 351 214 228 14 160.35 0.49 352 214 229 15 160.11 0.40 353 215 226 11 161.62 0.42 354 215 227 12 161.15 0.40 355 216 227 11 161.10 0.41 356 217 224 7 173.00 6.11 357 221 224 3 287.43 0.39 358 229 234 5 288.91 0.04 359 230 233 3 288.95 0.01 360 230 234 4 288.91 0.04 361 231 234 3 288.91 0.04 362 231 235 4 284.13 1.31 363 231 238 7 64.09 2.68 364 232 235 3 87.64 1.83 365 234 237 3 68.64 2.77 366 234 238 4 65.19 3.22 367 235 238 3 66.47 3.86 368 235 239 4 64.08 2.67 369 236 239 3 66.47 3.86 370 236 240 4 63.66 2.46 371 237 240 3 63.00 2.14 372 237 241 4 59.08 1.41 373 238 241 3 51.92 9.16 374 238 242 4 35.31 0.86 375 239 242 3 35.45 0.79 376 239 243 4 35.31 0.85 377 240 243 3 35.33 0.85 378 240 244 4 32.52 0.54 379 241 244 3 32.48 0.57 380 241 245 4 31.63 0.81 381 242 245 3 31.00 0.65