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 0.66 2 18 46 28 62.94 0.66 3 18 47 29 63.03 0.60 4 18 48 30 56.31 0.15 5 18 49 31 54.96 0.59 6 18 53 35 49.10 2.14 7 19 46 27 62.95 0.66 8 19 47 28 63.05 0.61 9 20 47 27 64.16 0.55 10 20 48 28 63.19 0.59 11 20 56 36 63.04 0.60 12 20 60 40 63.09 0.58 13 20 70 50 63.08 0.58 14 20 71 51 63.19 0.59 15 20 72 52 63.83 0.70 16 21 24 3 363.79 2.95 17 21 25 4 243.68 47.43 18 21 47 26 64.85 0.47 19 21 71 50 64.12 0.74 20 22 25 3 360.07 8.86 21 22 26 4 238.31 50.11 22 22 69 47 64.75 0.43 23 22 70 48 64.77 0.43 24 22 71 49 64.89 0.45 25 23 26 3 355.37 8.42 26 23 35 12 65.17 0.33 27 23 37 14 65.56 0.14 28 23 69 46 65.13 0.34 29 23 71 48 65.65 0.19 30 23 101 78 68.31 0.55 31 23 104 81 68.64 0.68 32 23 105 82 67.55 0.58 33 23 108 85 68.72 0.66 34 24 71 47 65.75 0.24 35 24 101 77 68.31 0.58 36 24 108 84 95.84 11.95 37 26 69 43 68.59 1.44 38 26 108 82 140.24 2.69 39 27 30 3 355.81 5.99 40 27 31 4 327.83 5.94 41 27 69 42 520.67 7.36 42 28 31 3 372.25 5.54 43 28 108 80 184.20 17.35 44 32 112 80 456.80 0.43 45 33 112 79 456.81 0.42 46 33 113 80 456.79 0.43 47 33 211 178 37.73 0.60 48 34 113 79 456.81 0.42 49 34 115 81 456.79 0.43 50 34 207 173 80.61 0.38 51 34 211 177 37.73 0.60 52 35 112 77 528.63 3.15 53 35 113 78 460.64 0.62 54 35 114 79 456.81 0.43 55 35 115 80 456.80 0.43 56 36 115 79 456.81 0.43 57 36 116 80 456.80 0.43 58 36 117 81 456.80 0.43 59 36 203 167 98.44 0.50 60 37 115 78 457.75 0.66 61 37 116 79 456.81 0.43 62 37 117 80 456.81 0.43 63 38 117 79 456.81 0.43 64 38 118 80 456.80 0.43 65 38 119 81 456.81 0.43 66 39 117 78 457.61 0.64 67 39 118 79 456.80 0.43 68 39 119 80 456.80 0.43 69 39 122 83 366.00 0.21 70 39 125 86 363.89 1.26 71 40 119 79 456.81 0.43 72 40 122 82 366.00 0.21 73 41 119 78 456.91 0.45 74 41 120 79 456.80 0.43 75 42 121 79 456.81 0.43 76 44 119 75 457.39 0.54 77 51 119 68 456.81 0.43 78 51 147 96 309.91 0.06 79 51 191 140 115.73 1.40 80 51 192 141 115.39 1.48 81 51 195 144 110.19 1.10 82 54 195 141 109.41 0.69 83 54 196 142 109.39 0.69 84 55 147 92 309.94 0.07 85 55 195 140 109.37 0.67 86 55 199 144 109.34 0.68 87 55 203 148 105.64 0.53 88 58 196 138 109.38 0.68 89 58 200 142 108.61 0.40 90 59 115 56 457.27 0.61 91 59 203 144 98.47 0.51 92 59 204 145 95.89 1.74 93 62 204 142 95.91 1.72 94 62 208 146 81.80 0.18 95 63 204 141 95.89 1.73 96 63 207 144 80.94 0.28 97 73 125 52 363.89 1.26 98 77 121 44 456.76 0.45 99 77 122 45 444.47 3.44 100 77 125 48 363.94 1.25 101 79 121 42 456.78 0.44 102 80 121 41 457.01 0.41 103 83 121 38 457.07 0.43 104 84 121 37 456.93 0.45 105 84 182 98 154.19 2.94 106 85 182 97 181.27 2.10 107 87 151 64 305.74 1.86 108 88 124 36 440.39 6.33 109 88 128 40 364.48 1.17 110 88 131 43 363.95 1.28 111 88 132 44 363.94 1.28 112 88 151 63 292.07 0.51 113 89 121 32 456.84 0.44 114 89 124 35 388.57 2.54 115 89 151 62 292.02 0.53 116 90 121 31 456.81 0.43 117 90 125 35 366.25 0.30 118 94 125 31 363.92 1.27 119 95 125 30 363.92 1.27 120 95 128 33 362.08 0.77 121 95 129 34 337.99 0.84 122 95 132 37 335.61 1.04 123 98 125 27 363.89 1.26 124 98 126 28 363.81 1.25 125 98 129 31 335.78 1.03 126 99 129 30 335.78 1.03 127 99 132 33 331.85 0.11 128 99 133 34 312.92 0.66 129 102 114 12 525.85 4.23 130 102 116 14 456.88 0.45 131 102 129 27 335.75 1.02 132 102 130 28 335.67 1.01 133 102 133 31 311.44 0.09 134 102 137 35 311.29 0.07 135 102 141 39 311.00 0.03 136 103 137 34 311.28 0.07 137 105 114 9 459.07 1.53 138 106 137 31 311.19 0.08 139 106 140 34 311.00 0.03 140 109 112 3 456.80 0.43 141 110 140 30 310.99 0.04 142 111 211 100 40.62 0.82 143 112 211 99 40.54 0.78 144 113 142 29 310.78 0.07 145 113 207 94 80.75 0.30 146 113 210 97 40.62 0.82 147 113 211 98 37.73 0.60 148 114 137 23 311.28 0.07 149 114 140 26 311.02 0.04 150 114 141 27 310.86 0.04 151 114 142 28 310.83 0.04 152 115 141 26 311.00 0.03 153 115 142 27 310.86 0.04 154 115 143 28 310.68 0.01 155 115 203 88 98.45 0.51 156 115 207 92 80.81 0.30 157 116 130 14 335.62 1.03 158 116 141 25 311.05 0.03 159 116 143 27 310.85 0.05 160 116 144 28 310.44 0.01 161 116 145 29 310.41 0.00 162 117 144 27 310.79 0.03 163 117 145 28 310.41 0.00 164 118 122 4 366.04 0.19 165 118 123 5 365.95 0.23 166 118 126 8 363.76 1.23 167 118 145 27 310.79 0.04 168 118 146 28 310.40 0.03 169 118 147 29 309.94 0.07 170 119 122 3 369.36 1.24 171 119 123 4 366.24 0.28 172 119 147 28 309.93 0.06 173 119 188 69 117.59 1.63 174 119 189 70 117.55 1.63 175 119 191 72 115.74 1.40 176 120 123 3 374.38 2.55 177 120 124 4 368.67 1.49 178 120 147 27 310.69 0.04 179 120 148 28 309.94 0.07 180 120 150 30 303.70 1.97 181 120 188 68 117.58 1.62 182 121 124 3 370.43 0.61 183 121 125 4 366.28 0.30 184 121 150 29 298.92 0.43 185 122 125 3 366.98 0.07 186 122 126 4 365.49 0.69 187 123 126 3 365.38 0.66 188 123 127 4 365.38 0.66 189 123 146 23 310.72 0.03 190 123 147 24 310.70 0.03 191 123 149 26 296.47 1.66 192 124 127 3 365.41 0.67 193 124 128 4 365.29 0.61 194 124 149 25 299.90 0.06 195 124 150 26 292.06 0.51 196 124 151 27 291.54 0.35 197 125 128 3 366.74 0.11 198 125 129 4 365.27 0.60 199 126 129 3 368.30 0.67 200 126 130 4 361.29 1.39 201 126 146 20 310.75 0.01 202 127 130 3 373.56 2.18 203 127 131 4 361.28 1.38 204 127 149 22 299.92 0.07 205 127 159 32 217.48 0.29 206 128 131 3 368.75 1.06 207 128 132 4 361.28 1.38 208 129 132 3 368.00 0.69 209 129 133 4 357.44 0.50 210 130 133 3 363.91 2.74 211 130 138 8 311.33 0.05 212 130 141 11 311.30 0.09 213 130 144 14 311.01 0.04 214 130 159 29 217.47 0.29 215 130 162 32 217.16 0.30 216 131 138 7 311.66 0.08 217 131 160 29 217.41 0.29 218 131 161 30 217.38 0.29 219 133 137 4 353.32 6.87 220 133 138 5 311.74 0.10 221 133 141 8 311.66 0.14 222 134 137 3 382.97 0.53 223 134 138 4 341.82 12.62 224 135 138 3 378.61 2.71 225 135 139 4 340.34 13.36 226 136 140 4 366.42 0.32 227 137 140 3 369.73 1.74 228 137 141 4 368.31 1.22 229 138 141 3 381.69 4.24 230 138 161 23 217.19 0.28 231 138 162 24 217.09 0.33 232 139 166 27 216.72 0.38 233 141 144 3 411.41 0.80 234 141 162 21 217.09 0.34 235 141 166 25 216.66 0.38 236 142 166 24 216.59 0.35 237 142 206 64 83.10 0.51 238 142 207 65 82.72 0.54 239 142 210 68 77.52 0.91 240 143 162 19 217.15 0.31 241 143 166 23 216.59 0.34 242 143 202 59 108.70 0.57 243 143 203 60 105.70 0.07 244 143 206 63 84.30 0.03 245 144 159 15 217.49 0.30 246 144 162 18 217.16 0.30 247 144 166 22 216.71 0.37 248 144 167 23 216.57 0.34 249 144 168 24 216.56 0.34 250 144 202 58 109.11 0.73 251 145 168 23 216.47 0.29 252 145 199 54 109.36 0.67 253 145 202 57 109.23 0.69 254 145 203 58 108.68 0.58 255 146 149 3 373.54 1.36 256 146 159 13 217.50 0.29 257 146 168 22 216.58 0.33 258 146 169 23 216.41 0.32 259 146 170 24 216.05 0.31 260 147 170 23 215.84 0.36 261 147 191 44 115.75 1.41 262 147 194 47 115.48 1.46 263 147 195 48 115.52 1.43 264 147 199 52 115.33 1.46 265 148 170 22 216.49 0.33 266 148 171 23 215.83 0.38 267 148 175 27 215.88 0.36 268 148 177 29 215.72 0.42 269 148 178 30 215.29 0.34 270 148 188 40 117.89 1.78 271 148 191 43 115.96 1.40 272 149 152 3 360.69 5.79 273 149 155 6 315.43 1.87 274 149 158 9 217.86 0.33 275 149 169 20 216.58 0.34 276 149 171 22 216.27 0.42 277 149 177 28 215.71 0.42 278 149 178 29 213.87 0.56 279 150 154 4 383.62 2.02 280 150 177 27 215.59 0.43 281 151 154 3 365.92 2.11 282 151 155 4 344.14 12.98 283 152 155 3 370.69 1.35 284 152 156 4 252.54 4.69 285 152 157 5 220.30 0.39 286 152 169 17 216.97 0.42 287 152 171 19 216.59 0.34 288 152 178 26 213.88 0.57 289 153 156 3 351.58 9.27 290 153 178 25 215.88 0.29 291 153 179 26 213.89 0.56 292 153 180 27 213.83 0.55 293 154 180 26 213.71 0.49 294 155 158 3 370.32 1.53 295 155 160 5 220.41 1.29 296 157 169 12 216.98 0.42 297 158 162 4 360.17 4.50 298 158 163 5 249.63 3.45 299 158 164 6 218.13 0.30 300 159 162 3 371.98 1.40 301 159 167 8 217.59 0.12 302 162 166 4 367.31 0.04 303 162 167 5 314.00 0.24 304 163 166 3 377.19 1.57 305 163 167 4 367.23 0.08 306 164 167 3 367.23 0.08 307 165 206 41 105.20 0.18 308 166 202 36 109.28 0.66 309 167 202 35 109.33 0.66 310 168 202 34 109.33 0.66 311 170 191 21 115.94 1.39 312 170 194 24 115.48 1.46 313 170 198 28 115.41 1.43 314 170 199 29 115.40 1.43 315 171 191 20 117.50 1.55 316 172 187 15 120.21 1.68 317 172 190 18 120.41 1.55 318 172 191 19 119.36 1.06 319 173 187 14 131.85 0.47 320 174 185 11 149.46 4.07 321 174 187 13 131.87 0.46 322 175 187 12 130.24 0.87 323 175 188 13 124.29 3.15 324 175 191 16 123.25 2.62 325 176 181 5 465.54 1.11 326 176 183 7 294.60 15.04 327 176 185 9 189.56 15.99 328 177 181 4 399.84 1.58 329 177 182 5 379.59 1.05 330 177 183 6 318.25 3.21 331 177 188 11 123.27 2.66 332 184 188 4 334.32 3.33 333 184 189 5 351.12 0.43 334 185 188 3 376.43 2.65 335 186 189 3 387.88 0.58 336 186 190 4 370.76 0.19 337 187 190 3 384.60 1.44 338 187 191 4 388.25 0.39 339 188 191 3 414.86 1.75 340 190 193 3 434.45 0.69 341 191 194 3 378.26 2.34 342 191 195 4 333.47 2.83 343 192 195 3 374.37 0.40 344 192 196 4 333.16 3.00 345 193 196 3 359.36 7.11 346 193 197 4 333.13 3.00 347 193 198 5 333.12 3.00 348 194 197 3 382.67 3.71 349 194 198 4 333.10 3.00 350 194 199 5 320.01 1.16 351 194 200 6 320.03 1.16 352 195 199 4 320.01 1.16 353 195 200 5 320.03 1.15 354 196 200 4 335.63 1.69 355 197 200 3 377.51 1.84 356 197 201 4 330.88 4.07 357 198 201 3 326.90 2.68 358 198 202 4 324.20 1.33 359 199 202 3 368.79 0.63 360 199 203 4 324.69 1.57 361 200 203 3 359.17 7.07 362 200 204 4 295.53 15.67 363 201 204 3 365.05 4.96 364 201 205 4 295.54 15.66 365 202 205 3 337.40 1.22 366 202 206 4 324.64 0.58 367 203 206 3 364.70 3.46 368 203 207 4 324.65 0.58 369 204 207 3 368.58 0.07 370 204 208 4 345.96 11.23 371 205 208 3 365.75 1.34 372 205 209 4 354.37 7.02 373 206 209 3 373.81 2.69 374 206 210 4 373.44 2.52 375 207 210 3 381.34 3.00 376 207 211 4 328.12 6.11 377 208 211 3 373.22 2.62 378 208 212 4 275.95 21.22