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 17 53 36 40.18 0.42 2 18 45 27 61.12 0.75 3 18 46 28 61.12 0.75 4 18 47 29 61.22 0.70 5 18 48 30 51.95 2.19 6 18 49 31 56.15 0.30 7 18 53 35 42.98 1.31 8 19 46 27 61.42 0.61 9 19 47 28 61.25 0.70 10 20 47 27 63.00 0.58 11 20 48 28 61.76 0.74 12 20 60 40 61.24 0.66 13 20 70 50 61.27 0.68 14 20 71 51 62.22 0.97 15 20 72 52 61.89 0.68 16 21 24 3 372.75 2.52 17 21 25 4 284.47 27.13 18 21 47 26 63.27 0.56 19 21 71 50 62.43 0.86 20 22 25 3 359.07 9.37 21 22 26 4 278.35 30.08 22 22 69 47 63.18 0.49 23 22 70 48 63.28 0.55 24 22 71 49 63.31 0.54 25 23 26 3 369.32 0.44 26 23 35 12 64.09 0.15 27 23 37 14 64.51 0.35 28 23 69 46 64.09 0.15 29 23 71 48 64.11 0.15 30 23 101 78 67.78 0.80 31 23 104 81 67.99 0.83 32 23 105 82 67.34 0.92 33 23 108 85 68.34 1.01 34 24 71 47 66.29 0.45 35 24 101 77 67.99 0.83 36 24 104 80 68.42 0.98 37 24 108 84 92.36 12.96 38 26 69 43 67.61 0.97 39 26 108 82 125.90 0.87 40 27 30 3 355.20 4.61 41 27 31 4 334.89 2.43 42 27 69 42 529.44 6.15 43 28 31 3 362.56 0.69 44 28 108 80 144.77 4.96 45 32 112 80 457.49 0.29 46 33 112 79 457.50 0.28 47 33 113 80 457.49 0.28 48 33 211 178 35.01 0.24 49 34 113 79 457.50 0.28 50 34 115 81 457.48 0.28 51 34 207 173 80.13 0.62 52 34 211 177 35.55 0.52 53 35 112 77 530.75 4.21 54 35 113 78 461.18 0.29 55 35 114 79 457.50 0.28 56 35 115 80 457.49 0.28 57 36 115 79 457.50 0.28 58 36 116 80 457.49 0.28 59 36 117 81 457.49 0.28 60 36 203 167 103.28 0.18 61 37 115 78 458.29 0.50 62 37 116 79 457.50 0.28 63 37 117 80 457.50 0.28 64 38 117 79 457.50 0.28 65 38 118 80 457.49 0.28 66 38 119 81 457.50 0.28 67 38 147 109 311.32 0.86 68 39 117 78 457.91 0.38 69 39 118 79 457.49 0.28 70 39 119 80 457.50 0.28 71 39 122 83 362.91 1.02 72 39 125 86 360.38 2.29 73 40 119 79 457.50 0.28 74 40 122 82 363.04 1.08 75 41 119 78 457.58 0.27 76 41 120 79 457.50 0.28 77 42 121 79 457.50 0.28 78 44 119 75 457.91 0.38 79 51 119 68 457.31 0.36 80 51 147 96 309.76 0.54 81 51 191 140 114.99 1.91 82 51 192 141 114.45 1.93 83 51 195 144 108.72 0.99 84 54 195 141 108.70 1.00 85 54 196 142 108.73 1.02 86 55 147 92 309.69 0.51 87 55 195 140 108.69 0.99 88 55 200 145 108.28 0.89 89 55 203 148 106.03 1.07 90 58 196 138 108.67 0.99 91 58 200 142 108.28 0.89 92 59 115 56 460.08 0.71 93 59 203 144 102.47 0.69 94 59 204 145 101.16 0.49 95 62 204 142 101.14 0.49 96 62 208 146 84.45 1.50 97 63 204 141 101.55 0.29 98 63 207 144 80.83 0.34 99 73 125 52 360.38 2.28 100 77 121 44 457.53 0.26 101 77 122 45 454.56 1.17 102 77 125 48 360.72 2.22 103 79 121 42 457.50 0.29 104 80 121 41 457.66 0.30 105 83 121 38 457.68 0.30 106 84 121 37 458.06 0.51 107 84 150 66 309.56 0.57 108 84 182 98 156.99 0.53 109 85 182 97 157.41 0.73 110 87 151 64 305.36 1.05 111 88 124 36 447.88 1.58 112 88 128 40 360.89 2.10 113 88 131 43 360.75 2.17 114 88 132 44 360.73 2.16 115 88 151 63 298.56 1.45 116 89 121 32 457.56 0.28 117 89 124 35 405.30 10.96 118 89 151 62 298.56 1.45 119 90 121 31 457.51 0.27 120 90 125 35 362.88 1.15 121 94 125 31 360.47 2.31 122 95 125 30 360.39 2.28 123 95 128 33 359.16 2.23 124 95 129 34 338.00 1.54 125 95 132 37 332.39 0.43 126 98 125 27 360.38 2.27 127 98 126 28 360.24 2.27 128 98 129 31 334.07 1.15 129 99 129 30 334.06 1.16 130 99 132 33 327.75 1.16 131 99 133 34 313.48 0.62 132 102 114 12 525.86 4.26 133 102 116 14 457.57 0.27 134 102 129 27 334.03 1.13 135 102 130 28 332.54 0.45 136 102 133 31 312.44 0.92 137 102 137 35 312.37 0.91 138 102 141 39 311.94 0.85 139 103 137 34 312.38 0.91 140 105 114 9 504.56 14.86 141 106 137 31 312.36 0.91 142 106 140 34 311.94 0.85 143 109 112 3 457.49 0.28 144 110 140 30 311.92 0.85 145 111 211 100 39.60 0.33 146 113 140 27 311.92 0.84 147 113 142 29 311.60 0.94 148 113 207 94 80.16 0.61 149 113 210 97 39.60 0.33 150 113 211 98 39.55 0.30 151 114 137 23 312.36 0.91 152 114 140 26 311.95 0.85 153 114 141 27 311.82 0.83 154 114 142 28 311.80 0.84 155 115 141 26 311.90 0.84 156 115 142 27 311.88 0.83 157 115 143 28 311.63 0.87 158 115 203 88 104.19 0.64 159 115 207 92 80.21 0.59 160 116 130 14 332.46 0.42 161 116 141 25 311.95 0.85 162 116 143 27 311.83 0.85 163 116 144 28 311.43 0.88 164 116 145 29 311.32 0.86 165 116 203 87 105.11 0.63 166 117 144 27 311.70 0.89 167 117 145 28 311.32 0.86 168 118 122 4 363.04 1.08 169 118 123 5 362.89 1.02 170 118 126 8 360.21 2.30 171 118 145 27 311.70 0.89 172 118 146 28 311.32 0.86 173 118 147 29 309.92 0.50 174 119 122 3 364.68 0.43 175 119 123 4 363.06 1.03 176 119 147 28 309.77 0.52 177 119 188 69 115.56 1.77 178 119 191 72 115.00 1.91 179 120 123 3 369.02 0.87 180 120 124 4 366.26 0.51 181 120 147 27 311.58 0.92 182 120 148 28 309.74 0.51 183 120 150 30 307.34 0.14 184 120 188 68 115.58 1.77 185 121 124 3 366.39 0.44 186 121 125 4 363.66 0.78 187 121 150 29 304.26 1.40 188 122 125 3 370.39 1.56 189 122 126 4 363.22 0.97 190 123 126 3 364.19 0.49 191 123 127 4 364.18 0.48 192 123 146 23 311.64 0.89 193 123 147 24 311.54 0.94 194 123 149 26 299.63 0.92 195 124 127 3 364.19 0.48 196 124 128 4 364.29 0.43 197 124 149 25 304.64 1.21 198 124 150 26 298.55 1.45 199 124 151 27 297.79 1.28 200 125 128 3 371.38 0.42 201 125 129 4 364.25 0.42 202 126 129 3 366.98 1.78 203 126 130 4 351.06 6.18 204 126 146 20 311.67 0.90 205 127 130 3 373.33 1.40 206 127 131 4 352.00 5.71 207 127 149 22 305.10 0.97 208 127 159 32 218.91 1.02 209 128 131 3 368.86 0.83 210 128 132 4 360.37 3.42 211 129 132 3 367.17 0.85 212 129 133 4 352.87 7.17 213 130 133 3 365.80 0.42 214 130 138 8 312.39 0.92 215 130 141 11 312.38 0.93 216 130 144 14 311.94 0.85 217 130 159 29 218.91 1.02 218 130 162 32 218.68 1.03 219 131 138 7 312.68 0.90 220 131 160 29 218.88 1.02 221 131 161 30 218.82 1.02 222 133 137 4 345.45 6.88 223 133 138 5 337.00 11.10 224 133 141 8 312.60 0.95 225 134 137 3 381.97 0.04 226 134 138 4 346.69 7.50 227 135 138 3 351.76 10.03 228 135 139 4 342.94 8.15 229 136 140 4 365.08 0.93 230 137 140 3 376.62 2.94 231 137 141 4 367.26 1.74 232 138 141 3 383.71 2.23 233 138 161 23 218.78 0.99 234 138 162 24 218.55 0.97 235 139 166 27 217.19 0.85 236 141 144 3 410.41 0.30 237 141 162 21 218.58 0.98 238 141 166 25 217.06 0.89 239 142 166 24 217.06 0.89 240 142 206 64 82.41 0.16 241 142 207 65 81.73 0.03 242 142 210 68 76.64 0.35 243 143 162 19 218.69 1.03 244 143 166 23 217.05 0.88 245 143 202 59 108.30 0.90 246 143 203 60 105.61 0.87 247 143 206 63 82.76 0.34 248 144 159 15 218.91 1.02 249 144 162 18 218.66 1.02 250 144 166 22 217.16 0.83 251 144 167 23 217.00 0.87 252 144 168 24 216.99 0.88 253 144 202 58 108.56 1.01 254 144 203 59 107.35 0.90 255 145 168 23 216.98 0.87 256 145 170 25 216.88 0.89 257 145 199 54 108.69 0.98 258 145 202 57 108.58 1.00 259 145 203 58 107.97 1.04 260 146 149 3 372.54 0.86 261 146 159 13 218.93 1.03 262 146 167 21 217.06 0.89 263 146 168 22 217.00 0.88 264 146 169 23 216.88 0.89 265 146 170 24 216.88 0.89 266 147 170 23 216.36 0.91 267 147 191 44 114.99 1.91 268 147 194 47 114.50 1.94 269 147 195 48 114.52 1.94 270 147 199 52 114.21 1.86 271 148 170 22 216.93 0.86 272 148 171 23 216.37 0.91 273 148 175 27 216.09 0.92 274 148 177 29 216.27 0.91 275 148 178 30 215.72 1.08 276 148 188 40 115.58 1.77 277 148 191 43 115.01 1.92 278 149 152 3 359.69 5.29 279 149 155 6 317.67 0.75 280 149 158 9 219.04 1.03 281 149 159 10 219.00 1.02 282 149 169 20 217.00 0.88 283 149 171 22 216.69 0.92 284 149 178 29 215.41 1.24 285 150 154 4 382.21 2.71 286 150 177 27 215.86 0.98 287 150 182 32 162.11 3.08 288 151 154 3 372.15 1.02 289 151 155 4 349.41 5.25 290 152 155 3 372.40 1.81 291 152 156 4 317.68 0.74 292 152 157 5 219.39 0.93 293 152 169 17 217.16 0.84 294 152 171 19 217.01 0.89 295 152 178 26 215.72 1.08 296 153 156 3 369.86 0.55 297 153 178 25 216.50 1.10 298 153 179 26 215.72 1.08 299 153 180 27 214.93 1.44 300 154 180 26 214.78 1.36 301 155 158 3 369.32 2.02 302 155 160 5 219.45 0.97 303 157 169 12 217.34 0.80 304 158 162 4 368.87 0.15 305 158 163 5 251.92 1.30 306 158 164 6 218.97 1.10 307 159 162 3 372.07 0.35 308 159 167 8 217.36 0.81 309 162 166 4 367.21 0.99 310 162 167 5 301.50 29.02 311 163 166 3 377.59 1.38 312 163 167 4 366.23 0.58 313 164 167 3 368.90 0.14 314 165 202 37 108.73 0.96 315 165 206 41 105.61 0.86 316 166 202 36 108.69 0.96 317 167 202 35 108.72 0.96 318 168 202 34 108.72 0.96 319 170 191 21 115.00 1.92 320 170 194 24 114.50 1.94 321 170 198 28 114.44 1.93 322 170 199 29 114.25 1.85 323 171 191 20 115.45 1.81 324 172 187 15 120.95 0.62 325 172 190 18 118.64 1.38 326 172 191 19 116.86 1.11 327 173 187 14 130.73 0.89 328 174 185 11 146.41 4.03 329 174 187 13 133.69 0.39 330 175 187 12 130.30 0.67 331 175 188 13 129.37 0.71 332 175 191 16 123.92 2.02 333 176 181 5 425.31 3.01 334 176 183 7 350.45 17.11 335 176 185 9 194.53 23.59 336 177 181 4 398.84 1.08 337 177 182 5 373.72 2.08 338 177 183 6 290.05 17.95 339 177 188 11 129.57 0.68 340 184 188 4 335.09 1.95 341 184 189 5 350.14 0.06 342 185 188 3 379.87 3.16 343 186 189 3 376.50 0.66 344 186 190 4 382.11 3.46 345 187 190 3 387.25 0.89 346 187 191 4 387.25 0.89 347 188 191 3 419.70 0.68 348 190 193 3 438.55 2.36 349 191 194 3 378.31 1.59 350 191 195 4 366.60 0.09 351 192 195 3 372.44 1.33 352 192 196 4 366.60 0.09 353 193 196 3 355.79 5.32 354 193 197 4 332.93 1.98 355 193 198 5 332.21 2.17 356 194 197 3 371.05 1.36 357 194 198 4 329.30 3.58 358 194 199 5 285.31 14.96 359 194 200 6 288.09 16.34 360 195 199 4 321.44 3.10 361 195 200 5 291.31 14.73 362 196 200 4 351.64 8.21 363 197 200 3 376.50 1.35 364 197 201 4 333.80 1.61 365 198 201 3 357.36 5.51 366 198 202 4 333.81 1.61 367 199 202 3 369.91 0.76 368 199 203 4 335.83 0.60 369 200 203 3 357.98 6.62 370 200 204 4 333.79 1.62 371 201 204 3 374.86 1.82 372 201 205 4 333.55 1.35 373 202 205 3 369.38 0.92 374 202 206 4 335.72 0.27 375 203 206 3 369.08 1.18 376 203 207 4 350.97 7.88 377 204 207 3 360.45 3.15 378 204 208 4 351.00 7.90 379 205 208 3 369.13 1.15 380 205 209 4 351.00 7.90 381 206 209 3 372.57 2.30 382 206 210 4 372.58 2.29 383 207 210 3 380.34 2.50 384 207 211 4 367.38 0.29 385 208 211 3 372.23 2.12 386 208 212 4 237.72 8.96