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 15 169 154 64.28 0.60 2 15 179 164 64.58 0.65 3 16 102 86 64.23 0.58 4 16 167 151 64.25 0.59 5 16 168 152 64.27 0.59 6 16 191 175 52.27 0.39 7 16 192 176 48.23 0.88 8 17 25 8 316.68 101.42 9 17 166 149 64.25 0.60 10 17 167 150 64.27 0.59 11 17 179 162 68.78 0.73 12 17 189 172 64.27 0.58 13 17 190 173 64.16 0.59 14 17 191 174 62.64 0.57 15 18 165 147 64.27 0.59 16 18 166 148 64.26 0.59 17 18 190 172 64.25 0.58 18 18 191 173 64.19 0.58 19 18 192 174 64.05 0.64 20 19 23 4 532.93 2.40 21 19 25 6 532.94 2.40 22 19 143 124 64.70 0.62 23 19 144 125 64.52 0.63 24 19 163 144 64.32 0.58 25 19 164 145 64.39 0.62 26 19 165 146 64.32 0.58 27 19 167 148 64.53 0.63 28 20 23 3 582.02 2.01 29 20 163 143 64.52 0.63 30 20 164 144 64.48 0.64 31 21 162 141 64.43 0.62 32 21 163 142 64.52 0.63 33 21 164 143 64.52 0.63 34 23 144 121 64.79 0.57 35 23 186 163 83.81 0.33 36 24 142 118 81.22 0.79 37 24 146 122 64.65 0.59 38 24 147 123 64.65 0.59 39 24 186 162 87.14 1.32 40 25 141 116 97.77 0.67 41 25 142 117 84.03 0.44 42 25 143 118 81.33 0.91 43 25 179 154 100.14 0.24 44 25 183 158 97.55 0.56 45 26 141 115 97.79 0.68 46 26 142 116 86.00 0.21 47 26 182 156 100.05 0.27 48 26 185 159 99.00 0.08 49 27 140 113 100.42 0.77 50 27 141 114 98.85 0.15 51 27 176 149 102.28 1.64 52 27 179 152 100.24 0.26 53 27 182 155 100.03 0.26 54 27 183 156 100.06 0.28 55 28 61 33 103.67 1.03 56 28 142 114 100.69 0.90 57 28 182 154 100.15 0.27 58 29 138 109 103.83 1.11 59 29 140 111 101.51 0.52 60 29 176 147 103.75 1.19 61 30 33 3 595.13 0.41 62 30 36 6 125.34 2.48 63 30 138 108 103.81 1.10 64 31 175 144 106.23 0.04 65 32 35 3 603.43 4.55 66 36 136 100 172.80 1.61 67 36 138 102 142.59 2.75 68 37 136 99 178.59 4.21 69 38 41 3 617.54 2.27 70 38 135 97 193.02 1.52 71 38 137 99 192.33 1.84 72 39 110 71 194.38 1.47 73 39 111 72 194.34 1.46 74 40 109 69 194.39 1.47 75 40 110 70 194.38 1.47 76 41 108 67 198.37 0.09 77 41 109 68 194.99 1.20 78 41 173 132 193.77 1.49 79 42 107 65 199.24 0.19 80 42 172 130 193.78 1.49 81 42 173 131 193.78 1.49 82 43 69 26 199.32 0.17 83 43 106 63 200.34 0.30 84 43 107 64 199.32 0.15 85 43 109 66 199.37 0.18 86 43 171 128 193.84 1.50 87 43 172 129 193.78 1.48 88 44 105 61 204.38 1.06 89 44 106 62 200.36 0.30 90 44 170 126 193.85 1.50 91 44 171 127 193.88 1.51 92 44 174 130 194.27 1.41 93 45 56 11 200.34 0.28 94 45 57 12 200.35 0.28 95 45 71 26 200.34 0.29 96 45 104 59 208.75 0.59 97 45 105 60 207.16 0.10 98 45 143 98 200.37 0.27 99 45 169 124 193.85 1.50 100 45 170 125 193.86 1.50 101 46 102 56 234.68 0.00 102 46 103 57 210.71 0.26 103 46 104 58 209.47 0.23 104 46 167 121 193.74 1.51 105 46 168 122 193.81 1.51 106 46 169 123 193.90 1.50 107 46 170 124 194.16 1.47 108 47 56 9 201.08 0.02 109 47 73 26 207.01 0.18 110 47 97 50 252.17 0.04 111 47 101 54 275.32 2.72 112 47 102 55 246.49 2.90 113 47 103 56 234.65 0.01 114 47 105 58 215.41 2.60 115 47 166 119 193.74 1.51 116 47 167 120 193.80 1.51 117 48 100 52 289.82 1.88 118 48 101 53 275.32 2.72 119 48 102 54 264.24 2.21 120 48 163 115 194.30 1.45 121 48 165 117 193.86 1.51 122 48 166 118 193.78 1.50 123 48 192 144 193.80 1.51 124 49 73 24 231.95 4.16 125 49 97 48 271.45 4.73 126 49 98 49 277.93 1.50 127 49 100 51 294.06 0.49 128 49 163 114 194.30 1.45 129 49 165 116 193.97 1.47 130 50 100 50 294.13 0.47 131 50 163 113 194.50 1.51 132 50 164 114 194.27 1.44 133 50 165 115 194.17 1.47 134 50 166 116 194.26 1.44 135 51 98 47 294.12 0.46 136 52 73 21 293.69 0.46 137 52 74 22 294.09 0.48 138 52 75 23 294.08 0.48 139 52 76 24 292.56 0.12 140 52 98 46 294.29 0.54 141 53 73 20 293.97 0.42 142 53 74 21 294.11 0.47 143 53 75 22 294.17 0.45 144 53 158 105 207.61 0.19 145 53 161 108 206.31 0.46 146 54 72 18 294.11 0.47 147 54 73 19 294.12 0.47 148 54 158 104 207.97 0.35 149 54 161 107 205.88 0.24 150 54 162 108 195.62 0.77 151 54 163 109 194.21 1.46 152 55 58 3 674.92 0.46 153 55 70 15 294.08 0.48 154 55 71 16 294.12 0.47 155 55 72 17 294.09 0.47 156 55 73 18 294.30 0.53 157 55 144 89 276.03 8.86 158 55 145 90 268.99 5.48 159 55 146 91 270.93 6.33 160 55 149 94 233.82 12.06 161 55 158 103 208.49 0.29 162 55 159 104 208.27 0.39 163 55 163 108 194.21 1.46 164 56 71 15 294.28 0.54 165 56 72 16 294.33 0.53 166 56 73 17 294.40 0.54 167 56 78 22 294.42 0.54 168 56 143 87 276.29 8.83 169 56 144 88 276.03 8.86 170 57 70 13 294.28 0.54 171 57 71 14 294.33 0.53 172 57 141 84 276.99 8.95 173 57 142 85 276.81 8.97 174 57 143 86 276.29 8.83 175 58 68 10 294.29 0.54 176 58 69 11 294.30 0.53 177 58 70 12 294.31 0.53 178 58 141 83 277.01 8.94 179 58 142 84 276.84 8.98 180 58 146 88 276.38 8.80 181 58 151 93 265.91 3.82 182 59 69 10 294.35 0.53 183 59 140 81 277.05 8.94 184 59 141 82 277.01 8.94 185 59 142 83 276.99 8.95 186 60 67 7 294.30 0.54 187 60 137 77 294.41 0.53 188 61 137 76 294.52 0.53 189 61 138 77 294.55 0.55 190 61 140 79 294.22 0.47 191 62 136 74 294.52 0.53 192 62 137 75 294.55 0.55 193 63 66 3 573.50 4.38 194 63 67 4 553.36 2.16 195 63 136 73 295.45 0.14 196 65 68 3 683.78 6.32 197 67 83 16 326.89 2.05 198 67 84 17 326.81 2.02 199 67 135 68 305.20 4.73 200 67 137 70 297.01 0.66 201 68 82 14 326.82 2.02 202 68 83 15 327.04 2.02 203 68 84 16 327.07 2.01 204 68 153 85 246.68 5.76 205 69 82 13 327.10 2.05 206 69 109 40 327.23 2.08 207 69 135 66 325.29 1.73 208 70 80 10 327.12 2.05 209 70 81 11 327.13 2.04 210 70 159 89 219.54 4.38 211 71 79 8 327.12 2.05 212 71 80 9 327.13 2.04 213 71 116 45 327.20 2.08 214 72 78 6 327.12 2.05 215 72 79 7 327.14 2.04 216 72 159 87 208.10 0.31 217 73 76 3 580.36 2.73 218 73 77 4 523.97 2.88 219 73 78 5 327.12 2.05 220 73 97 24 392.91 1.06 221 73 158 85 207.97 0.36 222 73 163 90 194.27 1.43 223 74 77 3 556.41 6.83 224 74 79 5 524.02 2.89 225 74 92 18 327.26 2.05 226 75 92 17 387.20 1.23 227 76 97 21 393.16 1.04 228 77 93 16 393.03 1.05 229 77 95 18 393.15 1.04 230 77 96 19 393.17 1.04 231 77 97 20 393.17 1.04 232 78 92 14 393.04 1.05 233 78 93 15 393.06 1.04 234 78 97 19 393.24 1.04 235 78 105 27 393.28 1.01 236 79 90 11 392.86 1.06 237 79 91 12 393.03 1.04 238 79 92 13 393.04 1.05 239 80 89 9 393.04 1.04 240 80 90 10 393.04 1.04 241 80 91 11 393.06 1.05 242 80 107 27 393.32 1.01 243 80 114 34 393.25 0.95 244 80 115 35 393.30 1.01 245 80 116 36 393.26 1.02 246 81 89 8 393.04 1.04 247 81 90 9 393.05 1.04 248 81 155 74 220.54 4.38 249 81 159 78 219.57 4.38 250 82 88 6 393.03 1.05 251 82 89 7 393.06 1.05 252 82 91 9 393.24 1.04 253 82 109 27 393.51 1.04 254 82 112 30 393.61 1.02 255 82 113 31 393.59 1.03 256 82 114 32 393.50 1.04 257 82 126 44 393.42 1.01 258 82 127 45 393.36 0.99 259 82 128 46 393.23 1.03 260 83 86 3 568.75 0.67 261 83 87 4 393.03 1.05 262 83 88 5 393.05 1.05 263 84 109 25 393.65 1.02 264 84 111 27 393.68 1.01 265 84 132 48 392.94 1.03 266 85 132 47 393.00 1.05 267 87 128 41 393.57 1.00 268 87 129 42 393.55 0.98 269 88 154 66 245.47 5.15 270 89 126 37 394.11 0.88 271 89 127 38 394.03 0.85 272 91 114 23 394.22 0.88 273 91 115 24 394.16 0.86 274 91 116 25 393.75 0.98 275 91 124 33 394.17 0.91 276 91 125 34 394.23 0.89 277 91 126 35 394.24 0.88 278 92 124 32 394.24 0.89 279 93 118 25 394.12 0.88 280 93 124 31 394.32 0.87 281 94 124 30 394.41 0.88 282 95 118 23 394.31 0.89 283 95 121 26 394.34 0.87 284 97 103 6 394.26 0.90 285 97 105 8 394.40 0.88 286 102 166 64 193.85 1.51 287 102 167 65 193.88 1.51 288 102 168 66 194.16 1.47 289 103 118 15 506.17 1.19 290 104 118 14 506.18 1.20 291 104 119 15 506.18 1.20 292 105 116 11 506.18 1.20 293 105 117 12 506.18 1.20 294 105 118 13 506.19 1.20 295 105 119 14 506.20 1.20 296 106 116 10 506.19 1.20 297 106 117 11 506.19 1.20 298 106 120 14 506.23 1.19 299 107 115 8 506.19 1.20 300 107 116 9 506.19 1.20 301 108 114 6 506.19 1.20 302 108 115 7 506.20 1.20 303 108 117 9 506.24 1.20 304 109 113 4 518.75 2.44 305 109 114 5 506.19 1.20 306 109 135 26 503.19 2.27 307 110 113 3 547.87 0.66 308 111 133 22 492.99 4.96 309 112 127 15 506.32 1.14 310 112 128 16 506.20 1.20 311 112 130 18 506.17 1.20 312 113 126 13 506.37 1.12 313 113 127 14 506.32 1.14 314 114 125 11 506.38 1.12 315 114 126 12 506.42 1.14 316 114 127 13 506.40 1.12 317 115 124 9 506.38 1.13 318 115 125 10 506.39 1.12 319 116 123 7 506.38 1.14 320 116 124 8 506.41 1.13 321 117 120 3 543.67 2.14 322 117 121 4 513.69 0.20 323 117 122 5 507.57 0.55 324 117 123 6 506.40 1.13 325 118 121 3 556.57 1.28 326 139 176 37 507.38 1.06 327 141 176 35 507.66 1.03 328 142 146 4 540.81 5.04 329 143 167 24 507.40 1.05 330 143 170 27 507.67 1.03 331 144 162 18 507.05 0.84 332 144 163 19 507.01 0.83 333 145 149 4 552.26 2.21 334 145 162 17 507.05 0.84 335 146 149 3 552.26 2.21 336 146 151 5 531.77 2.83 337 148 151 3 615.29 0.03 338 149 152 3 581.53 3.60 339 149 159 10 507.75 1.16 340 152 155 3 570.91 0.50 341 152 159 7 507.90 1.14 342 155 158 3 601.00 1.90 343 155 159 4 560.95 0.54 344 156 159 3 604.71 3.75 345 157 160 3 556.84 1.88 346 157 161 4 541.52 4.12 347 158 161 3 555.23 0.96 348 192 195 3 636.20 0.79