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 30.62 0.72 2 18 45 27 56.02 0.17 3 18 46 28 56.02 0.17 4 18 47 29 56.02 0.17 5 18 48 30 54.13 0.24 6 18 49 31 52.97 0.82 7 18 53 35 37.05 0.12 8 19 46 27 56.03 0.17 9 19 47 28 56.04 0.18 10 20 47 27 58.40 0.45 11 20 48 28 56.91 0.23 12 20 60 40 56.86 0.24 13 20 70 50 56.00 0.16 14 20 71 51 56.92 0.23 15 20 72 52 58.12 0.31 16 21 24 3 369.77 2.08 17 21 25 4 305.57 27.27 18 21 47 26 58.97 0.42 19 21 71 50 58.39 0.45 20 22 25 3 345.77 7.17 21 22 26 4 278.53 17.82 22 22 69 47 58.86 0.42 23 22 70 48 59.02 0.38 24 22 71 49 59.33 0.53 25 23 26 3 340.88 11.79 26 23 35 12 59.35 0.52 27 23 69 46 59.36 0.52 28 23 71 48 59.62 0.40 29 23 101 78 67.25 0.12 30 23 104 81 67.51 0.01 31 23 105 82 66.23 0.04 32 23 108 85 95.14 13.87 33 24 71 47 66.53 0.07 34 24 101 77 67.61 0.06 35 24 104 80 68.84 0.45 36 24 108 84 120.24 1.48 37 26 69 43 67.21 0.11 38 26 108 82 154.34 8.87 39 27 30 3 348.62 8.06 40 27 31 4 308.20 28.27 41 27 69 42 509.02 5.38 42 28 31 3 344.84 15.21 43 28 108 80 266.31 47.10 44 32 112 80 449.59 0.64 45 33 112 79 449.59 0.64 46 33 113 80 449.58 0.64 47 33 211 178 31.15 0.77 48 34 113 79 449.60 0.64 49 34 115 81 449.56 0.64 50 34 207 173 75.79 0.58 51 34 211 177 34.04 0.65 52 35 112 77 530.94 2.02 53 35 113 78 452.13 0.44 54 35 114 79 449.60 0.64 55 35 115 80 449.59 0.64 56 36 115 79 449.59 0.64 57 36 116 80 449.59 0.64 58 36 117 81 449.59 0.64 59 36 203 167 95.95 0.08 60 37 115 78 450.29 0.64 61 37 116 79 449.60 0.64 62 37 117 80 449.60 0.64 63 38 117 79 449.60 0.64 64 38 118 80 449.59 0.64 65 38 119 81 449.60 0.64 66 38 147 109 305.74 0.47 67 39 117 78 450.16 0.70 68 39 118 79 449.59 0.64 69 39 119 80 449.60 0.64 70 39 122 83 359.91 0.80 71 39 125 86 357.69 1.90 72 40 119 79 449.61 0.64 73 40 122 82 359.91 0.80 74 41 119 78 449.69 0.61 75 41 120 79 449.60 0.63 76 42 121 79 449.61 0.64 77 44 119 75 450.14 0.65 78 51 119 68 449.42 0.73 79 51 147 96 304.88 0.40 80 51 191 140 110.00 0.44 81 51 192 141 109.46 0.27 82 51 195 144 104.45 0.12 83 54 195 141 104.48 0.13 84 54 196 142 104.47 0.14 85 55 147 92 304.88 0.40 86 55 195 140 104.47 0.13 87 55 200 145 103.99 0.22 88 55 203 148 101.76 0.06 89 58 196 138 104.45 0.14 90 58 200 142 103.75 0.36 91 59 115 56 450.28 0.97 92 59 200 141 103.72 0.34 93 59 203 144 95.97 0.07 94 59 204 145 95.28 0.25 95 62 204 142 95.11 0.20 96 62 208 146 76.18 0.42 97 63 204 141 94.88 0.09 98 63 207 144 79.48 1.23 99 73 125 52 357.70 1.90 100 77 121 44 449.39 0.66 101 77 122 45 438.25 0.50 102 77 125 48 357.74 1.92 103 80 121 41 449.97 0.76 104 83 121 38 450.10 0.69 105 84 121 37 449.89 0.70 106 87 151 64 300.05 1.43 107 88 124 36 439.28 1.08 108 88 128 40 358.28 1.64 109 88 131 43 357.64 1.91 110 88 132 44 357.51 1.86 111 88 151 63 291.06 0.43 112 89 121 32 449.62 0.64 113 89 124 35 373.42 3.56 114 89 151 62 291.08 0.43 115 90 121 31 449.53 0.60 116 90 125 35 359.67 0.98 117 94 125 31 357.72 1.90 118 95 125 30 357.72 1.91 119 95 128 33 352.76 0.43 120 95 129 34 341.41 2.14 121 95 132 37 325.63 0.54 122 98 125 27 357.70 1.91 123 98 126 28 357.55 1.90 124 98 129 31 325.81 0.54 125 99 129 30 325.81 0.54 126 99 132 33 324.53 0.03 127 99 133 34 309.60 0.72 128 102 114 12 529.50 3.17 129 102 116 14 450.28 0.33 130 102 129 27 325.81 0.54 131 102 130 28 325.78 0.54 132 102 133 31 309.24 0.55 133 102 137 35 306.86 0.59 134 102 141 39 306.60 0.64 135 103 133 30 309.22 0.54 136 103 137 34 306.82 0.58 137 105 114 9 450.88 0.18 138 106 137 31 306.78 0.56 139 106 140 34 306.60 0.65 140 109 112 3 449.59 0.64 141 110 140 30 306.56 0.66 142 111 211 100 35.34 0.01 143 112 211 99 35.32 0.01 144 113 140 27 306.55 0.66 145 113 142 29 306.33 0.66 146 113 207 94 75.80 0.58 147 113 210 97 35.77 0.05 148 113 211 98 33.98 0.59 149 114 137 23 306.87 0.59 150 114 140 26 306.57 0.66 151 114 141 27 306.49 0.66 152 114 142 28 306.47 0.67 153 115 141 26 306.54 0.66 154 115 142 27 306.51 0.66 155 115 143 28 306.04 0.58 156 115 203 88 95.95 0.09 157 115 207 92 75.83 0.57 158 116 130 14 325.76 0.54 159 116 141 25 306.60 0.65 160 116 143 27 306.49 0.66 161 116 144 28 305.99 0.59 162 116 145 29 305.88 0.54 163 116 203 87 99.24 0.57 164 117 144 27 306.30 0.58 165 117 145 28 305.54 0.72 166 118 122 4 359.95 0.82 167 118 123 5 358.37 1.55 168 118 126 8 357.45 1.86 169 118 145 27 306.33 0.58 170 118 146 28 305.38 0.64 171 118 147 29 304.89 0.40 172 119 122 3 362.38 0.38 173 119 123 4 359.96 0.82 174 119 147 28 304.88 0.40 175 119 188 69 112.51 0.10 176 119 189 70 112.49 0.10 177 119 191 72 110.02 0.44 178 120 123 3 378.94 0.57 179 120 124 4 365.56 1.22 180 120 147 27 306.24 0.60 181 120 148 28 304.88 0.39 182 120 150 30 292.95 0.49 183 120 188 68 112.52 0.10 184 121 124 3 364.74 1.39 185 121 125 4 360.14 0.91 186 121 150 29 295.30 1.66 187 122 125 3 362.81 0.42 188 122 126 4 359.81 1.07 189 123 126 3 360.66 1.50 190 123 127 4 363.92 0.12 191 123 146 23 306.30 0.58 192 123 147 24 306.28 0.58 193 123 149 26 291.11 0.43 194 124 127 3 363.92 0.12 195 124 128 4 359.74 1.05 196 124 149 25 297.00 0.81 197 124 150 26 291.08 0.42 198 124 151 27 285.93 1.46 199 125 128 3 365.80 0.82 200 125 129 4 360.25 1.95 201 126 129 3 365.79 0.82 202 126 130 4 347.99 4.05 203 126 146 20 306.35 0.56 204 127 130 3 361.75 2.84 205 127 131 4 347.95 4.02 206 127 149 22 296.29 1.17 207 127 159 32 213.99 0.31 208 128 131 3 361.73 2.42 209 128 132 4 361.61 2.48 210 129 132 3 360.82 2.08 211 129 133 4 347.44 4.61 212 130 133 3 349.06 3.79 213 130 138 8 306.94 0.60 214 130 141 11 306.86 0.59 215 130 144 14 306.62 0.64 216 130 159 29 213.98 0.32 217 130 162 32 213.49 0.41 218 131 138 7 307.35 0.63 219 131 160 29 213.96 0.32 220 131 161 30 213.88 0.35 221 133 137 4 362.44 0.12 222 133 138 5 318.58 4.83 223 133 141 8 317.81 4.77 224 134 137 3 365.99 1.09 225 134 138 4 361.88 0.21 226 135 138 3 363.04 0.43 227 135 139 4 361.86 0.23 228 136 139 3 369.35 0.58 229 136 140 4 364.81 1.69 230 137 140 3 367.13 0.30 231 137 141 4 363.98 1.28 232 138 141 3 367.13 0.30 233 138 161 23 213.58 0.42 234 138 162 24 213.43 0.41 235 139 166 27 212.27 0.43 236 141 144 3 408.81 1.35 237 141 162 21 213.41 0.42 238 141 166 25 212.21 0.45 239 142 162 20 213.46 0.41 240 142 166 24 212.14 0.45 241 142 206 64 82.14 0.09 242 142 207 65 77.65 1.12 243 142 210 68 57.84 8.95 244 143 162 19 213.55 0.40 245 143 166 23 212.14 0.45 246 143 202 59 104.02 0.20 247 143 203 60 100.38 0.20 248 143 206 63 82.90 0.47 249 144 159 15 214.00 0.32 250 144 162 18 213.46 0.43 251 144 166 22 212.23 0.46 252 144 167 23 212.10 0.46 253 144 168 24 212.01 0.42 254 144 202 58 104.31 0.10 255 144 203 59 103.02 0.69 256 145 168 23 212.01 0.42 257 145 170 25 211.70 0.46 258 145 199 54 104.41 0.14 259 145 202 57 104.34 0.12 260 145 203 58 104.08 0.16 261 146 149 3 371.92 4.08 262 146 159 13 214.06 0.35 263 146 167 21 212.25 0.45 264 146 168 22 212.18 0.47 265 146 169 23 211.72 0.52 266 146 170 24 211.37 0.64 267 147 170 23 211.34 0.63 268 147 191 44 110.03 0.45 269 147 194 47 109.78 0.35 270 147 195 48 109.93 0.43 271 147 199 52 109.42 0.29 272 148 170 22 211.80 0.53 273 148 171 23 210.91 0.43 274 148 175 27 211.31 0.66 275 148 177 29 210.78 0.45 276 148 178 30 210.16 0.62 277 148 188 40 112.52 0.10 278 148 191 43 110.47 0.56 279 149 152 3 346.64 7.91 280 149 155 6 324.98 2.91 281 149 157 8 215.36 0.22 282 149 158 9 215.35 0.21 283 149 159 10 214.90 0.43 284 149 169 20 212.23 0.44 285 149 171 22 211.61 0.51 286 149 178 29 207.22 0.08 287 150 154 4 374.87 1.45 288 150 177 27 210.10 0.56 289 151 154 3 367.24 2.38 290 151 155 4 346.62 7.91 291 152 155 3 364.04 0.78 292 152 156 4 316.70 1.28 293 152 157 5 215.58 0.13 294 152 169 17 212.45 0.39 295 152 171 19 212.13 0.46 296 152 178 26 209.33 0.00 297 153 156 3 339.10 4.16 298 153 178 25 211.68 0.48 299 153 179 26 208.27 0.45 300 153 180 27 206.28 0.41 301 154 180 26 207.00 0.67 302 155 158 3 346.78 7.34 303 155 160 5 214.97 0.46 304 157 169 12 212.52 0.42 305 158 162 4 344.10 7.50 306 158 163 5 225.61 5.01 307 158 164 6 214.12 0.73 308 159 162 3 369.85 1.50 309 159 167 8 212.50 0.46 310 162 166 4 364.22 1.08 311 162 167 5 333.19 0.89 312 163 166 3 371.95 2.79 313 163 167 4 337.14 1.08 314 164 167 3 349.98 6.04 315 165 202 37 104.47 0.13 316 165 206 41 100.37 0.20 317 166 202 36 104.42 0.13 318 167 202 35 104.43 0.13 319 168 202 34 104.44 0.13 320 170 191 21 110.40 0.49 321 170 194 24 109.87 0.38 322 170 198 28 109.70 0.29 323 170 199 29 109.61 0.30 324 171 191 20 110.86 0.61 325 172 187 15 113.66 0.09 326 172 190 18 112.84 0.17 327 172 191 19 112.50 0.10 328 173 187 14 113.99 0.19 329 174 185 11 128.12 1.45 330 174 187 13 114.09 0.14 331 175 187 12 114.00 0.18 332 175 188 13 113.98 0.17 333 175 191 16 113.98 0.17 334 176 181 5 438.11 9.98 335 176 183 7 292.48 17.35 336 176 185 9 128.12 1.45 337 177 181 4 395.89 1.70 338 177 183 6 292.47 17.35 339 177 188 11 113.94 0.14 340 184 188 4 363.30 0.64 341 184 189 5 333.69 0.06 342 185 188 3 365.62 1.51 343 186 189 3 371.25 0.41 344 186 190 4 363.31 0.64 345 187 190 3 367.70 1.56 346 187 191 4 376.54 2.88 347 188 191 3 400.28 0.58 348 190 193 3 423.66 3.58 349 191 194 3 350.76 8.15 350 191 195 4 334.78 0.35 351 192 195 3 376.37 3.31 352 192 196 4 334.79 0.35 353 193 196 3 376.37 3.31 354 193 197 4 334.77 0.36 355 193 198 5 334.76 0.36 356 194 197 3 375.09 3.95 357 194 198 4 322.00 6.73 358 194 199 5 311.61 1.58 359 194 200 6 311.63 1.58 360 195 199 4 286.85 19.51 361 195 200 5 280.33 16.25 362 196 200 4 331.79 1.35 363 197 200 3 371.72 1.42 364 197 201 4 317.55 5.51 365 198 201 3 333.01 0.74 366 198 202 4 331.81 1.36 367 199 202 3 367.12 3.71 368 199 203 4 331.81 1.36 369 200 203 3 336.98 2.99 370 200 204 4 293.24 20.64 371 201 204 3 366.98 2.10 372 201 205 4 293.19 20.67 373 202 205 3 346.94 8.76 374 202 206 4 328.55 0.44 375 203 206 3 361.31 0.76 376 203 207 4 341.38 9.20 377 204 207 3 361.85 1.03 378 204 208 4 341.55 9.12 379 205 208 3 348.51 7.05 380 205 209 4 341.55 9.12 381 206 209 3 347.09 6.34 382 206 210 4 346.85 6.46 383 207 210 3 369.74 2.40 384 207 211 4 331.72 1.10 385 208 211 3 346.84 6.46 386 208 212 4 224.50 0.85