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 61.55 0.86 2 18 46 28 61.57 0.85 3 18 47 29 61.55 0.86 4 18 48 30 52.06 2.00 5 18 49 31 56.11 0.32 6 18 53 35 49.49 1.94 7 19 46 27 62.53 0.75 8 19 47 28 62.15 0.56 9 20 47 27 63.02 0.57 10 20 48 28 62.55 0.74 11 20 60 40 62.46 0.85 12 20 65 45 63.18 0.49 13 20 70 50 61.59 0.83 14 20 71 51 62.60 0.78 15 20 72 52 62.57 0.73 16 21 24 3 362.79 2.46 17 21 25 4 243.38 47.56 18 21 47 26 64.05 0.17 19 21 71 50 63.31 0.42 20 22 25 3 353.91 6.90 21 22 26 4 150.71 1.23 22 22 69 47 63.95 0.12 23 22 70 48 63.55 0.35 24 22 71 49 64.08 0.16 25 23 26 3 354.32 7.94 26 23 35 12 64.09 0.15 27 23 69 46 64.10 0.14 28 23 71 48 64.11 0.15 29 23 101 78 68.38 1.02 30 23 104 81 68.40 1.03 31 23 105 82 67.65 0.76 32 23 108 85 68.52 1.09 33 24 71 47 67.07 0.62 34 24 101 77 68.54 1.03 35 24 104 80 68.91 1.22 36 24 108 84 92.19 12.87 37 26 69 43 68.06 1.11 38 26 108 82 171.75 23.42 39 27 30 3 362.61 9.39 40 27 31 4 326.83 6.44 41 27 69 42 492.14 1.92 42 28 31 3 373.98 3.70 43 28 108 80 169.31 5.75 44 32 112 80 455.01 1.52 45 33 112 79 455.01 1.52 46 33 113 80 455.01 1.52 47 33 211 178 35.60 0.53 48 34 113 79 455.01 1.52 49 34 115 81 454.99 1.53 50 34 207 173 80.27 0.56 51 34 211 177 35.56 0.52 52 35 112 77 526.60 2.21 53 35 113 78 461.11 0.20 54 35 114 79 455.01 1.52 55 35 115 80 455.00 1.53 56 36 115 79 455.01 1.52 57 36 116 80 454.99 1.53 58 36 117 81 455.00 1.52 59 36 203 167 102.52 0.61 60 37 115 78 455.94 1.68 61 37 116 79 455.01 1.52 62 37 117 80 455.02 1.52 63 38 117 79 455.02 1.52 64 38 118 80 455.02 1.52 65 38 119 81 455.03 1.52 66 38 147 109 311.93 1.12 67 39 117 78 455.53 1.57 68 39 118 79 455.03 1.52 69 39 119 80 455.03 1.51 70 39 122 83 365.10 0.48 71 39 125 86 364.76 0.30 72 40 119 79 455.04 1.52 73 40 122 82 370.25 3.05 74 41 119 78 455.16 1.48 75 41 120 79 455.03 1.52 76 42 121 79 455.06 1.52 77 44 119 75 455.87 1.71 78 51 119 68 454.88 1.49 79 51 147 96 311.11 1.22 80 51 191 140 112.52 0.67 81 51 192 141 112.06 0.80 82 51 195 144 109.58 1.42 83 54 195 141 108.70 0.98 84 54 196 142 108.69 0.98 85 55 147 92 311.11 1.22 86 55 195 140 108.69 0.98 87 55 200 145 108.28 0.89 88 55 203 148 107.17 1.00 89 58 196 138 108.68 0.99 90 58 200 142 108.28 0.89 91 58 204 146 103.31 0.19 92 59 115 56 455.43 1.61 93 59 203 144 104.09 0.12 94 59 204 145 101.94 0.43 95 62 204 142 101.94 0.42 96 62 208 146 84.44 1.50 97 63 204 141 101.92 0.42 98 63 207 144 83.52 0.16 99 73 125 52 364.76 0.30 100 77 121 44 454.93 1.53 101 77 122 45 451.85 1.80 102 77 125 48 364.88 0.30 103 79 121 42 455.04 1.53 104 80 121 41 455.24 1.51 105 83 121 38 455.31 1.49 106 84 121 37 455.21 1.54 107 84 182 98 147.43 3.85 108 85 182 97 167.13 5.53 109 87 151 64 309.45 0.99 110 88 124 36 439.47 5.79 111 88 128 40 365.02 0.32 112 88 131 43 365.00 0.32 113 88 132 44 364.88 0.35 114 88 151 63 297.70 1.22 115 89 121 32 455.10 1.52 116 89 124 35 405.30 10.96 117 89 151 62 297.70 1.22 118 90 121 31 455.06 1.52 119 90 125 35 365.23 0.39 120 94 125 31 364.81 0.30 121 95 125 30 364.88 0.27 122 95 128 33 359.70 0.21 123 95 129 34 330.22 1.96 124 95 132 37 328.78 1.38 125 98 125 27 364.78 0.32 126 98 126 28 364.48 0.20 127 98 129 31 328.86 1.39 128 99 129 30 328.86 1.39 129 99 132 33 327.75 1.16 130 99 133 34 313.62 1.43 131 102 114 12 526.35 4.04 132 102 116 14 455.21 1.45 133 102 129 27 328.86 1.39 134 102 130 28 328.74 1.43 135 102 133 31 313.34 1.28 136 102 137 35 313.13 1.28 137 102 141 39 312.95 1.32 138 103 137 34 313.13 1.28 139 105 114 9 460.46 3.22 140 106 137 31 313.11 1.28 141 106 140 34 312.94 1.31 142 109 112 3 455.01 1.52 143 110 140 30 312.92 1.31 144 111 211 100 39.62 0.32 145 113 142 29 312.68 1.30 146 113 207 94 80.27 0.56 147 113 210 97 56.63 7.92 148 113 211 98 39.58 0.32 149 114 137 23 313.18 1.30 150 114 140 26 312.94 1.31 151 114 141 27 312.82 1.31 152 114 142 28 312.81 1.31 153 115 141 26 312.91 1.32 154 115 142 27 312.87 1.33 155 115 143 28 312.68 1.30 156 115 203 88 104.59 0.42 157 115 207 92 82.55 0.48 158 116 130 14 328.44 1.28 159 116 141 25 312.95 1.32 160 116 143 27 312.82 1.31 161 116 144 28 312.36 1.31 162 116 145 29 312.48 1.38 163 116 203 87 105.14 0.62 164 117 144 27 312.73 1.36 165 117 145 28 312.34 1.31 166 118 122 4 370.46 2.94 167 118 123 5 364.76 0.30 168 118 145 27 312.74 1.36 169 118 146 28 311.65 0.98 170 118 147 29 311.25 1.17 171 119 122 3 370.49 2.95 172 119 123 4 370.38 2.98 173 119 147 28 311.14 1.21 174 119 188 69 115.58 1.62 175 119 189 70 115.56 1.61 176 119 191 72 112.53 0.67 177 120 123 3 374.66 2.41 178 120 124 4 371.80 2.29 179 120 147 27 312.62 1.37 180 120 148 28 311.24 1.16 181 120 150 30 302.76 2.44 182 120 188 68 115.60 1.63 183 121 124 3 371.80 2.29 184 121 125 4 370.44 2.96 185 121 150 29 297.72 1.21 186 122 125 3 370.30 1.60 187 122 126 4 365.04 0.32 188 123 126 3 367.46 1.54 189 123 127 4 365.03 0.32 190 123 146 23 312.63 1.36 191 123 147 24 312.58 1.36 192 123 149 26 299.07 0.65 193 124 127 3 375.26 3.15 194 124 128 4 365.00 0.32 195 124 149 25 303.69 1.67 196 124 150 26 293.21 1.03 197 124 151 27 292.94 1.05 198 125 128 3 372.56 1.79 199 125 129 4 360.80 2.42 200 126 129 3 368.94 0.02 201 126 130 4 360.80 2.41 202 126 146 20 312.63 1.36 203 127 130 3 378.60 1.23 204 127 131 4 359.26 2.87 205 127 149 22 299.07 0.65 206 127 159 32 218.88 1.02 207 128 131 3 364.67 2.10 208 128 132 4 359.28 2.87 209 129 132 3 366.30 1.29 210 129 133 4 359.26 2.87 211 130 133 3 364.67 2.10 212 130 138 8 313.25 1.32 213 130 141 11 313.17 1.32 214 130 144 14 312.94 1.31 215 130 159 29 218.88 1.02 216 130 162 32 218.35 1.14 217 131 138 7 313.56 1.21 218 131 160 29 218.81 1.02 219 131 161 30 218.78 1.02 220 133 137 4 340.87 4.20 221 133 138 5 314.54 0.88 222 133 141 8 313.63 1.32 223 134 137 3 381.97 0.04 224 134 138 4 365.89 0.53 225 135 138 3 371.97 0.07 226 135 139 4 366.95 1.04 227 136 139 3 380.06 3.98 228 136 140 4 367.44 1.02 229 137 140 3 377.86 2.33 230 137 141 4 376.62 2.94 231 138 141 3 383.71 2.23 232 138 161 23 218.56 1.07 233 138 162 24 218.28 1.14 234 139 166 27 217.33 0.84 235 141 144 3 413.50 0.52 236 141 162 21 218.29 1.13 237 141 166 25 217.23 0.87 238 142 166 24 217.22 0.87 239 142 206 64 85.02 0.75 240 142 207 65 82.84 0.32 241 142 210 68 77.84 0.26 242 143 162 19 218.36 1.14 243 143 166 23 217.22 0.87 244 143 202 59 108.36 0.93 245 143 203 60 106.23 0.56 246 143 206 63 86.70 1.03 247 144 159 15 218.87 1.03 248 144 162 18 218.37 1.14 249 144 166 22 217.31 0.83 250 144 167 23 217.09 0.83 251 144 168 24 217.08 0.83 252 144 202 58 108.55 1.01 253 144 203 59 107.20 0.76 254 145 168 23 217.00 0.86 255 145 170 25 216.85 0.90 256 145 199 54 108.70 0.98 257 145 202 57 108.56 1.01 258 145 203 58 108.53 1.02 259 146 149 3 372.54 0.86 260 146 159 13 218.88 1.03 261 146 167 21 217.31 0.85 262 146 168 22 217.12 0.83 263 146 169 23 216.97 0.86 264 146 170 24 216.85 0.90 265 147 170 23 216.77 0.91 266 147 191 44 112.52 0.67 267 147 194 47 112.08 0.79 268 147 195 48 112.12 0.81 269 147 199 52 112.03 0.80 270 148 170 22 217.03 0.85 271 148 171 23 216.73 0.90 272 148 175 27 216.50 0.92 273 148 177 29 216.40 0.91 274 148 178 30 216.15 0.86 275 148 188 40 115.58 1.62 276 148 191 43 114.83 1.68 277 149 152 3 359.69 5.29 278 149 155 6 257.75 1.07 279 149 158 9 219.08 1.11 280 149 169 20 217.12 0.83 281 149 171 22 216.90 0.86 282 149 177 28 216.50 0.94 283 149 178 29 215.99 0.95 284 150 154 4 383.38 2.14 285 150 177 27 216.29 0.92 286 150 182 32 165.28 4.61 287 151 154 3 372.16 1.01 288 151 155 4 353.89 7.45 289 152 155 3 372.41 1.80 290 152 156 4 299.47 19.77 291 152 157 5 220.24 0.58 292 152 169 17 217.42 0.86 293 152 171 19 217.17 0.84 294 152 178 26 216.03 0.94 295 153 156 3 353.91 7.44 296 153 178 25 216.97 0.88 297 153 179 26 216.12 0.98 298 153 180 27 215.92 0.97 299 154 180 26 215.40 1.23 300 155 158 3 368.13 1.03 301 155 160 5 237.40 8.00 302 157 169 12 217.48 0.83 303 158 162 4 361.30 6.07 304 158 163 5 237.82 7.79 305 158 164 6 218.78 1.20 306 159 162 3 372.64 0.07 307 159 167 8 217.53 0.85 308 162 166 4 366.31 0.54 309 162 167 5 252.72 5.56 310 163 166 3 377.26 1.23 311 163 167 4 328.29 0.89 312 164 167 3 374.16 2.77 313 165 206 41 106.09 0.71 314 166 202 36 108.68 0.97 315 167 202 35 108.72 0.96 316 168 202 34 108.73 0.96 317 170 191 21 114.69 1.74 318 170 194 24 112.08 0.78 319 170 198 28 112.07 0.78 320 170 199 29 112.05 0.80 321 171 191 20 115.35 1.47 322 172 187 15 121.08 0.73 323 172 190 18 118.48 1.56 324 172 191 19 117.05 0.88 325 173 187 14 136.87 2.15 326 174 185 11 147.12 3.68 327 174 187 13 137.55 1.80 328 175 187 12 130.75 0.89 329 175 188 13 123.56 1.35 330 175 191 16 121.74 0.45 331 176 181 5 425.47 4.50 332 176 183 7 331.00 1.20 333 176 185 9 147.11 3.69 334 177 181 4 393.75 3.08 335 177 182 5 372.62 3.14 336 177 183 6 353.26 11.12 337 177 188 11 125.82 2.33 338 184 188 4 372.81 1.20 339 184 189 5 378.43 1.61 340 185 188 3 383.95 1.11 341 185 189 4 383.61 0.94 342 186 189 3 387.27 0.89 343 186 190 4 383.21 0.76 344 187 190 3 387.25 0.89 345 187 191 4 387.25 0.89 346 188 191 3 412.25 3.04 347 190 193 3 445.34 5.75 348 191 194 3 378.31 1.59 349 191 195 4 353.14 6.83 350 192 195 3 372.74 1.22 351 192 196 4 336.66 4.46 352 193 196 3 360.81 2.98 353 193 197 4 333.60 2.94 354 193 198 5 327.41 0.14 355 194 197 3 380.93 3.58 356 194 198 4 326.62 0.20 357 194 199 5 288.03 16.94 358 194 200 6 288.03 16.94 359 195 199 4 325.14 1.31 360 195 200 5 288.32 17.09 361 196 200 4 343.11 1.62 362 197 200 3 376.51 1.34 363 197 201 4 335.44 1.59 364 198 201 3 359.53 4.42 365 198 202 4 335.44 1.59 366 199 202 3 369.89 0.77 367 199 203 4 341.83 1.60 368 200 203 3 353.04 0.04 369 200 204 4 337.50 0.56 370 201 204 3 374.86 1.82 371 201 205 4 331.29 4.29 372 202 205 3 369.38 0.92 373 202 206 4 339.85 1.73 374 203 206 3 363.70 3.96 375 203 207 4 338.98 2.16 376 204 207 3 363.61 3.92 377 204 208 4 337.97 2.65 378 205 208 3 357.38 7.03 379 205 209 4 339.24 2.02 380 206 209 3 372.58 2.29 381 206 210 4 372.58 2.29 382 207 210 3 380.35 2.50 383 207 211 4 347.07 9.84 384 208 211 3 372.22 2.12 385 208 212 4 234.52 0.07 386 208 213 5 142.94 2.50