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 56.49 4.19 2 16 140 119 56.06 4.14 3 16 142 121 56.23 4.11 4 16 143 122 58.95 2.96 5 16 144 123 59.69 2.79 6 16 156 135 56.60 4.13 7 16 157 136 56.49 4.19 8 16 158 137 56.50 4.19 9 16 189 170 58.99 2.93 10 16 190 171 55.57 4.26 11 16 194 175 55.57 4.26 12 17 143 121 59.88 2.86 13 17 144 122 59.88 2.86 14 17 145 123 60.59 2.85 15 17 146 124 60.59 2.85 16 17 188 167 60.30 2.70 17 17 188 168 60.20 2.71 18 17 189 169 59.55 2.81 19 17 191 171 59.77 2.92 20 17 220 195 59.98 2.87 21 17 221 196 59.98 2.86 22 18 188 166 60.52 2.81 23 18 188 167 60.27 2.71 24 19 157 133 63.64 3.04 25 19 158 134 60.09 2.76 26 20 137 112 89.66 4.15 27 20 156 131 93.58 0.83 28 20 157 132 76.39 1.35 29 20 158 133 178.64 6.10 30 20 159 134 225.78 7.12 31 21 154 128 149.83 4.38 32 21 155 129 159.15 0.28 33 21 156 130 159.69 0.56 34 22 26 4 163.55 0.77 35 22 27 5 162.75 1.10 36 22 139 112 140.23 0.22 37 22 155 128 161.38 0.32 38 22 156 129 201.97 1.80 39 23 26 3 179.12 1.76 40 24 71 44 142.91 0.55 41 25 69 41 144.77 1.77 42 25 79 51 156.84 0.41 43 25 117 89 141.86 0.35 44 27 30 3 218.20 19.70 45 27 137 105 141.47 0.18 46 27 139 107 150.80 1.01 47 27 157 125 287.69 1.01 48 28 116 85 155.92 0.70 49 28 117 86 155.09 0.41 50 28 118 87 152.45 0.79 51 28 119 88 150.75 0.58 52 29 45 14 149.74 0.58 53 29 46 15 148.44 0.06 54 29 119 87 152.31 0.72 55 29 120 88 150.75 0.58 56 29 121 89 148.02 0.15 57 29 137 103 155.99 0.78 58 29 198 166 155.71 0.68 59 29 200 168 155.69 0.68 60 30 43 11 156.59 0.58 61 30 44 12 156.00 0.78 62 30 139 104 156.08 0.77 63 30 140 105 157.24 0.38 64 30 141 106 158.59 0.03 65 30 155 120 215.52 23.20 66 30 198 165 155.86 0.71 67 31 43 10 156.69 0.55 68 31 44 11 156.02 0.78 69 31 45 12 156.02 0.78 70 31 46 13 156.01 0.78 71 31 52 19 156.02 0.79 72 31 65 32 158.58 0.01 73 31 66 33 158.58 0.02 74 31 67 34 158.37 0.05 75 31 141 105 158.70 0.04 76 32 40 6 159.08 0.17 77 32 42 8 158.71 0.04 78 32 65 31 158.66 0.03 79 32 66 32 158.64 0.04 80 32 73 38 158.78 0.07 81 32 141 104 158.63 0.01 82 33 40 5 159.12 0.14 83 33 41 6 159.09 0.17 84 33 42 7 158.75 0.06 85 33 43 8 158.70 0.04 86 33 52 17 158.66 0.04 87 33 54 19 158.73 0.06 88 33 58 23 159.01 0.16 89 33 63 28 159.03 0.14 90 33 64 29 159.03 0.13 91 33 65 30 158.74 0.04 92 33 106 70 158.72 0.03 93 34 39 3 165.77 0.80 94 34 40 4 159.37 0.03 95 34 41 5 159.41 0.01 96 34 63 27 159.24 0.07 97 34 64 28 159.06 0.14 98 34 66 30 159.06 0.12 99 37 41 4 166.58 0.40 100 37 60 23 163.23 0.64 101 37 62 25 160.69 0.63 102 40 43 3 289.99 0.01 103 40 73 32 289.06 0.03 104 40 141 98 289.92 0.04 105 40 193 152 289.49 0.17 106 42 195 152 289.98 0.00 107 43 197 153 289.96 0.02 108 45 53 8 290.00 0.00 109 45 121 75 218.24 0.89 110 45 209 159 289.96 0.02 111 46 119 72 289.98 0.01 112 46 120 73 247.70 1.74 113 46 121 74 233.68 0.01 114 47 120 72 288.87 0.18 115 47 121 73 260.72 4.76 116 47 123 75 213.60 2.60 117 47 238 186 59.09 2.96 118 47 242 190 31.55 0.46 119 48 120 71 289.77 0.07 120 48 242 189 31.61 0.43 121 51 242 186 31.52 0.45 122 51 245 189 22.96 1.27 123 66 82 15 290.00 0.00 124 67 118 50 289.92 0.04 125 69 117 48 289.94 0.04 126 69 118 49 289.92 0.04 127 71 153 80 157.76 0.12 128 71 154 81 156.80 0.55 129 71 155 82 154.88 0.35 130 72 153 79 157.69 0.15 131 72 154 80 157.60 0.18 132 73 141 66 290.00 0.00 133 73 153 78 157.69 0.15 134 74 153 77 157.69 0.16 135 79 117 38 289.94 0.03 136 81 118 37 289.99 0.01 137 85 107 22 290.00 0.00 138 86 109 23 289.99 0.01 139 87 245 154 22.93 1.34 140 88 106 18 290.00 0.00 141 89 237 144 81.47 0.67 142 89 241 148 49.72 5.03 143 89 245 152 20.41 0.01 144 91 101 10 290.00 0.00 145 91 234 139 109.78 2.06 146 91 237 142 81.28 0.69 147 92 237 141 95.48 0.11 148 94 100 6 290.00 0.00 149 95 100 5 290.00 0.00 150 96 99 3 290.00 0.00 151 98 180 80 196.59 7.96 152 99 180 79 171.93 4.34 153 99 214 111 290.00 0.00 154 100 177 75 160.06 1.33 155 100 179 77 160.47 1.17 156 100 180 78 160.44 1.15 157 101 179 76 160.24 1.23 158 101 234 129 130.68 3.53 159 102 229 123 152.63 0.67 160 103 229 122 152.62 0.67 161 103 234 127 101.07 1.03 162 103 237 130 75.25 1.43 163 103 238 131 60.30 3.44 164 105 237 128 75.25 1.44 165 105 238 129 59.10 2.97 166 105 241 132 32.11 0.59 167 105 242 133 31.60 0.42 168 107 245 134 19.86 0.29 169 114 118 4 290.00 0.00 170 114 119 5 289.99 0.01 171 121 200 79 290.00 0.00 172 121 204 83 289.99 0.01 173 121 209 84 288.93 0.51 174 122 203 81 290.00 0.01 175 122 204 82 289.46 0.14 176 122 209 83 276.63 5.81 177 123 204 81 249.97 6.63 178 123 209 82 192.75 0.82 179 123 231 104 212.91 33.60 180 123 235 108 78.50 1.19 181 123 238 111 59.37 2.93 182 124 204 80 188.08 0.43 183 124 209 81 173.16 2.17 184 124 210 82 168.58 0.12 185 124 231 103 288.07 0.67 186 124 232 104 108.25 1.28 187 124 235 107 79.53 0.70 188 127 210 80 157.22 0.35 189 128 210 79 151.84 0.60 190 129 134 4 165.07 1.52 191 129 162 32 140.00 0.41 192 129 210 78 154.33 0.10 193 130 134 3 179.44 0.96 194 130 162 31 140.87 0.12 195 132 162 30 140.87 0.12 196 132 163 31 140.96 0.15 197 132 164 32 141.03 0.16 198 133 161 28 140.88 0.14 199 133 162 29 141.00 0.17 200 134 161 27 141.02 0.17 201 134 162 28 141.03 0.17 202 134 201 69 290.00 0.00 203 135 159 24 140.96 0.14 204 135 160 25 141.02 0.17 205 135 161 26 141.02 0.17 206 136 159 23 140.94 0.16 207 136 160 24 141.02 0.17 208 136 162 26 147.65 0.22 209 137 157 20 140.67 0.21 210 137 158 21 140.94 0.16 211 137 159 22 141.00 0.18 212 138 157 19 140.22 0.22 213 138 158 20 140.62 0.24 214 138 160 22 141.07 0.18 215 138 183 45 158.66 0.01 216 138 190 54 289.26 0.20 217 138 228 88 154.22 0.02 218 139 155 16 141.03 0.16 219 139 156 17 140.83 0.15 220 139 157 18 140.13 0.27 221 140 155 15 141.01 0.15 222 140 156 16 140.71 0.21 223 141 151 10 157.66 0.17 224 141 152 11 157.08 0.35 225 141 153 12 155.97 0.79 226 141 154 13 150.12 1.45 227 141 155 14 141.00 0.16 228 142 151 9 157.72 0.21 229 142 152 10 157.35 0.32 230 142 192 52 289.46 0.17 231 142 193 53 289.56 0.21 232 142 194 54 289.31 0.09 233 143 148 5 162.51 1.29 234 143 149 6 158.46 0.11 235 143 150 7 158.37 0.14 236 143 151 8 158.07 0.23 237 143 191 50 208.03 3.50 238 143 192 51 289.20 0.04 239 144 150 6 158.46 0.11 240 144 152 8 158.31 0.15 241 144 156 12 140.98 0.20 242 145 148 3 165.37 1.27 243 145 149 4 161.94 1.58 244 145 150 5 158.63 0.07 245 146 220 71 157.38 0.38 246 146 221 72 157.38 0.38 247 146 221 73 157.38 0.38 248 151 192 43 158.12 0.21 249 152 156 4 167.91 0.33 250 158 184 27 141.01 0.17 251 158 188 32 140.96 0.20 252 158 189 33 140.80 0.17 253 159 184 26 151.72 5.17 254 160 184 24 151.60 5.23 255 160 184 25 151.72 5.17 256 161 183 22 153.98 6.33 257 161 184 23 153.66 6.16 258 161 184 24 153.72 6.14 259 162 181 19 204.30 7.07 260 162 182 20 190.58 0.23 261 162 183 21 171.84 2.59 262 162 201 41 148.44 0.18 263 163 167 4 290.00 0.00 264 163 182 19 204.31 7.07 265 163 183 20 184.31 3.37 266 163 184 21 184.30 3.37 267 163 185 23 171.90 2.64 268 163 225 60 151.24 0.99 269 164 168 4 290.00 0.00 270 165 168 3 289.98 0.01 271 167 185 19 226.93 2.36 272 168 171 3 289.99 0.01 273 171 223 50 157.62 0.25 274 171 224 51 157.58 0.26 275 171 225 52 157.58 0.26 276 172 176 4 290.00 0.00 277 172 215 41 160.31 1.08 278 172 216 42 159.95 1.02 279 172 217 43 159.94 1.02 280 172 224 50 157.67 0.24 281 172 225 51 157.67 0.23 282 172 227 53 157.61 0.21 283 175 215 38 160.47 1.08 284 176 215 37 160.47 1.08 285 176 227 49 157.66 0.23 286 178 230 50 156.27 0.71 287 178 233 53 152.55 0.70 288 179 229 48 156.62 0.55 289 179 230 49 155.93 0.64 290 179 233 52 150.78 0.52 291 179 234 53 150.56 0.62 292 180 215 33 160.53 1.09 293 180 227 45 157.44 0.24 294 180 228 46 157.09 0.31 295 180 230 48 155.63 0.72 296 181 199 20 158.68 0.12 297 181 210 27 158.41 0.10 298 181 211 28 158.46 0.10 299 181 227 44 157.30 0.21 300 181 228 45 156.18 0.75 301 181 229 46 156.16 0.75 302 181 230 47 155.18 0.50 303 182 225 41 157.53 0.26 304 182 226 42 157.30 0.21 305 182 227 43 156.07 0.70 306 183 225 40 157.49 0.22 307 183 226 41 157.38 0.23 308 183 228 43 156.18 0.76 309 184 187 3 289.29 0.29 310 184 188 5 229.86 7.38 311 185 222 34 158.78 0.20 312 185 223 35 158.34 0.11 313 185 225 37 158.18 0.12 314 186 222 33 159.75 0.47 315 187 221 30 160.33 0.68 316 187 221 31 160.31 0.67 317 187 222 32 159.76 0.47 318 188 221 29 160.75 0.86 319 188 221 28 160.78 0.86 320 189 220 26 289.25 0.18 321 189 221 27 212.26 8.69 322 189 226 33 152.62 0.54 323 190 194 4 290.00 0.00 324 190 213 19 290.00 0.00 325 190 228 34 152.71 0.70 326 191 194 3 290.00 0.00 327 192 195 3 290.00 0.01 328 197 213 12 290.00 0.00 329 199 211 8 290.00 0.00 330 199 213 10 290.00 0.00 331 199 228 25 154.30 0.06 332 209 231 22 123.06 2.00 333 210 230 20 152.61 0.67 334 210 231 21 125.62 1.41 335 210 232 22 108.07 0.96 336 211 228 17 154.31 0.07 337 211 229 18 152.64 0.68 338 211 231 20 114.13 1.01 339 212 228 16 154.15 0.01 340 212 229 17 152.16 0.75 341 212 231 19 117.52 3.95 342 213 228 15 152.64 0.68 343 214 227 13 155.86 0.60 344 214 228 14 153.90 0.14 345 214 229 15 152.71 0.71 346 215 226 11 156.18 0.74 347 215 227 12 155.46 0.40 348 216 227 11 156.10 0.70 349 217 224 7 179.00 0.44 350 221 224 3 289.68 0.16 351 229 234 5 289.78 0.05 352 230 233 3 289.89 0.01 353 230 234 4 289.78 0.05 354 231 234 3 289.89 0.01 355 231 235 4 285.30 1.40 356 231 238 7 61.45 3.97 357 232 235 3 87.86 0.54 358 234 237 3 73.22 1.40 359 234 238 4 71.31 0.96 360 235 238 3 71.31 0.96 361 235 239 4 61.44 3.97 362 236 239 3 75.72 1.25 363 236 240 4 61.41 4.00 364 237 240 3 60.65 3.62 365 237 241 4 54.12 5.42 366 238 241 3 60.44 8.27 367 238 242 4 32.30 0.50 368 239 242 3 52.31 10.23 369 239 243 4 32.11 0.60 370 240 243 3 33.76 1.10 371 240 244 4 32.10 0.59 372 241 244 3 32.48 0.47 373 241 245 4 31.05 0.21 374 242 245 3 32.29 0.28