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 2 7 5 458.68 7.13 2 2 73 71 31.04 0.15 3 2 76 74 27.36 0.37 4 2 127 125 23.15 1.02 5 2 128 126 22.53 0.72 6 2 131 129 22.50 0.70 7 3 6 3 476.99 1.50 8 3 7 4 474.38 2.80 9 4 7 3 477.00 1.50 10 4 8 4 470.95 1.08 11 5 8 3 478.25 2.03 12 5 9 4 470.97 1.09 13 6 9 3 474.89 1.14 14 6 10 4 471.05 1.14 15 6 124 118 45.79 0.18 16 6 127 121 45.78 0.18 17 7 10 3 481.69 1.39 18 7 11 4 471.06 1.16 19 7 73 66 47.20 0.07 20 7 74 67 47.20 0.07 21 8 11 3 480.06 0.58 22 8 12 4 471.07 1.17 23 9 12 3 476.63 0.55 24 9 13 4 471.44 1.35 25 9 120 111 60.14 0.21 26 9 121 112 60.06 0.18 27 9 124 115 59.73 0.06 28 10 13 3 478.05 1.07 29 10 14 4 471.20 1.47 30 10 70 60 60.01 0.19 31 10 124 114 60.03 0.20 32 10 125 115 60.02 0.18 33 10 128 118 59.71 0.04 34 11 14 3 471.22 1.48 35 11 15 4 467.52 2.94 36 11 70 59 59.75 0.06 37 11 73 62 59.76 0.07 38 12 15 3 483.04 1.18 39 12 16 4 474.07 2.77 40 13 16 3 477.64 1.00 41 13 17 4 474.07 2.77 42 13 113 100 77.10 1.45 43 13 121 108 65.07 1.91 44 13 125 112 65.14 1.85 45 14 17 3 474.80 2.42 46 14 18 4 474.08 2.78 47 14 21 7 377.01 3.64 48 14 63 49 66.74 1.14 49 14 66 52 65.11 1.84 50 14 67 53 60.59 0.42 51 14 70 56 60.43 0.35 52 14 109 95 76.90 1.52 53 15 18 3 477.73 0.96 54 16 113 97 89.11 0.26 55 16 116 100 89.03 0.23 56 17 20 3 487.37 3.74 57 17 21 4 442.54 6.07 58 17 24 7 374.98 11.77 59 17 109 92 88.84 0.12 60 17 113 96 89.89 0.11 61 18 21 3 503.33 1.19 62 20 23 3 478.01 1.17 63 20 24 4 461.80 1.29 64 21 24 3 476.51 4.70 65 21 25 4 468.01 2.25 66 21 63 42 91.87 1.19 67 22 25 3 470.15 1.19 68 22 26 4 468.03 2.25 69 22 60 38 97.92 0.84 70 22 63 41 94.33 0.01 71 23 26 3 477.44 1.14 72 23 27 4 465.90 3.31 73 24 27 3 470.25 2.46 74 24 28 4 465.89 3.31 75 24 108 84 119.98 0.81 76 24 109 85 125.22 0.54 77 24 112 88 128.77 0.59 78 25 28 3 466.68 1.57 79 25 29 4 464.38 2.71 80 25 59 34 116.59 0.86 81 26 29 3 477.88 0.13 82 26 30 4 464.35 2.74 83 26 55 29 126.66 1.30 84 26 56 30 126.67 1.31 85 26 59 33 117.09 0.59 86 27 30 3 475.06 1.28 87 27 31 4 461.01 4.42 88 27 108 81 129.00 0.56 89 27 112 85 129.27 0.59 90 28 31 3 471.18 0.66 91 28 32 4 461.02 4.41 92 28 101 73 128.93 0.54 93 28 104 76 128.93 0.54 94 28 105 77 128.93 0.53 95 28 108 80 129.02 0.56 96 29 32 3 467.54 1.16 97 29 33 4 461.05 4.42 98 29 55 26 129.06 0.52 99 29 58 29 129.00 0.55 100 29 59 30 128.96 0.56 101 29 101 72 128.99 0.56 102 30 33 3 470.03 2.40 103 30 34 4 465.14 3.39 104 30 50 20 129.27 0.58 105 31 34 3 479.83 1.16 106 31 35 4 461.00 4.43 107 31 104 73 129.21 0.67 108 31 107 76 129.32 0.61 109 31 108 77 129.36 0.59 110 32 35 3 468.11 3.35 111 32 36 4 445.74 2.86 112 32 39 7 315.22 2.64 113 32 101 69 129.21 0.67 114 32 104 72 129.23 0.66 115 33 37 4 436.89 6.34 116 33 39 6 302.00 3.98 117 33 40 7 220.69 33.72 118 33 43 10 220.39 34.02 119 33 48 15 129.63 0.62 120 33 55 22 129.53 0.67 121 34 37 3 490.24 1.35 122 36 39 3 499.94 3.65 123 36 100 64 129.27 0.69 124 36 103 67 129.56 0.70 125 36 104 68 129.56 0.70 126 37 40 3 488.63 1.03 127 38 41 3 493.54 0.47 128 39 42 3 493.57 0.49 129 39 43 4 488.26 0.74 130 39 97 58 129.22 0.69 131 39 100 61 129.53 0.71 132 40 43 3 488.26 0.74 133 40 44 4 487.09 1.32 134 40 48 8 136.40 2.06 135 41 44 3 497.34 1.09 136 42 45 3 646.19 0.24 137 42 93 51 129.15 0.73 138 42 94 52 129.32 0.76 139 42 97 55 129.56 0.73 140 43 46 3 486.12 0.48 141 43 48 5 435.63 9.23 142 43 58 15 130.12 0.83 143 45 54 9 136.47 2.03 144 46 54 8 136.47 2.04 145 46 55 9 136.47 2.03 146 46 58 12 136.44 2.04 147 47 52 5 148.52 1.46 148 47 54 7 136.48 2.02 149 47 55 8 138.88 3.20 150 48 55 7 140.19 2.54 151 49 52 3 482.38 0.65 152 51 56 5 448.02 5.84 153 52 55 3 476.87 0.76 154 52 56 4 464.24 0.66 155 53 56 3 479.19 2.83 156 53 57 4 461.32 0.80 157 54 57 3 476.69 1.57 158 54 58 4 463.34 1.81 159 55 58 3 475.78 2.04 160 55 59 4 461.29 0.80 161 56 59 3 468.72 2.92 162 56 60 4 468.86 2.99 163 57 60 3 473.31 0.77 164 57 61 4 469.81 2.52 165 58 61 3 472.70 1.07 166 58 62 4 473.62 0.59 167 59 62 3 480.50 2.83 168 59 63 4 467.50 1.39 169 60 63 3 483.31 0.45 170 60 64 4 463.96 3.18 171 61 64 3 485.18 0.49 172 61 65 4 465.36 2.46 173 62 65 3 485.18 0.49 174 62 66 4 465.62 2.58 175 62 101 39 152.39 2.48 176 63 66 3 477.44 3.33 177 63 67 4 462.67 3.78 178 64 67 3 477.16 3.47 179 64 68 4 477.14 3.48 180 65 68 3 478.24 2.94 181 65 69 4 474.31 4.90 182 65 80 15 153.49 2.41 183 65 83 18 153.31 2.50 184 66 69 3 477.43 3.34 185 66 70 4 474.30 4.90 186 66 105 39 179.47 1.11 187 66 132 66 157.28 0.97 188 67 70 3 472.86 1.05 189 67 71 4 465.37 1.33 190 68 71 3 478.00 1.91 191 68 72 4 460.18 3.92 192 68 79 11 173.08 4.27 193 68 80 12 165.10 0.29 194 69 72 3 477.55 1.68 195 69 73 4 458.73 1.96 196 69 76 7 318.93 18.67 197 69 80 11 165.11 0.29 198 69 128 59 218.69 12.65 199 69 132 63 185.19 1.49 200 70 73 3 480.53 3.17 201 70 128 58 234.75 4.62 202 72 75 3 470.84 0.01 203 72 76 4 427.55 0.68 204 72 79 7 286.36 2.39 205 73 76 3 474.61 1.89 206 73 128 55 273.65 2.44 207 75 78 3 495.31 0.51 208 75 79 4 466.47 2.25 209 76 79 3 473.19 4.16 210 76 80 4 466.47 2.25 211 76 128 52 277.31 1.21 212 76 131 55 276.94 1.38 213 76 132 56 276.44 1.55 214 76 135 59 276.43 1.54 215 77 80 3 486.94 1.12 216 77 81 4 458.55 6.20 217 77 135 58 276.43 1.55 218 78 81 3 472.52 3.60 219 80 83 3 475.50 0.88 220 80 84 4 467.23 1.79 221 80 132 52 278.61 1.54 222 80 135 55 278.16 1.34 223 80 136 56 278.13 1.36 224 81 84 3 475.84 1.56 225 81 85 4 467.35 1.73 226 81 139 58 278.14 1.43 227 82 85 3 473.29 1.27 228 82 86 4 467.29 1.76 229 83 86 3 475.98 1.51 230 83 87 4 467.29 1.76 231 83 136 53 279.12 1.74 232 84 87 3 474.86 2.05 233 84 88 4 467.28 1.76 234 84 135 51 279.19 1.79 235 84 136 52 279.10 1.76 236 84 139 55 278.94 1.83 237 85 88 3 474.84 2.08 238 85 89 4 456.49 7.15 239 85 139 54 278.92 1.81 240 86 90 4 412.86 4.73 241 86 91 5 401.99 0.71 242 87 91 4 301.63 1.42 243 87 92 5 293.61 5.41 244 87 93 6 292.27 6.08 245 87 98 11 282.61 2.67 246 87 136 49 279.24 1.79 247 87 140 53 278.95 1.83 248 88 92 4 293.60 5.42 249 88 139 51 279.12 1.81 250 88 140 52 278.77 1.74 251 89 92 3 485.18 1.61 252 89 139 50 279.17 1.84 253 92 140 48 279.16 1.82 254 93 97 4 479.20 1.42 255 93 98 5 476.81 0.25 256 93 140 47 279.28 1.83 257 94 97 3 492.03 1.44 258 95 98 3 491.98 1.47 259 95 137 42 279.60 1.84 260 95 140 45 279.50 1.82 261 96 99 3 490.80 0.88 262 96 100 4 479.22 1.41 263 97 100 3 476.85 0.25 264 97 101 4 480.55 3.85 265 98 101 3 480.79 3.74 266 98 102 4 474.43 0.79 267 98 133 35 280.11 2.01 268 98 136 38 280.12 2.01 269 98 137 39 280.11 2.01 270 98 140 42 280.10 2.01 271 99 102 3 480.32 3.97 272 99 103 4 471.47 2.29 273 100 103 3 480.32 3.97 274 100 104 4 474.23 0.93 275 101 104 3 474.23 0.94 276 101 105 4 472.37 1.86 277 102 105 3 472.67 2.02 278 102 106 4 472.36 1.86 279 102 129 27 280.45 2.06 280 102 133 31 280.28 1.97 281 103 106 3 465.73 1.46 282 103 107 4 465.72 1.47 283 104 107 3 472.68 2.01 284 104 108 4 463.29 3.39 285 105 108 3 482.69 2.77 286 105 109 4 465.07 2.50 287 105 129 24 280.74 2.16 288 106 109 3 483.36 3.10 289 106 110 4 468.63 4.26 290 106 117 11 282.23 2.13 291 106 122 16 281.62 2.22 292 106 125 19 281.37 2.29 293 106 126 20 281.31 2.25 294 106 129 23 280.93 2.16 295 107 110 3 480.31 1.57 296 107 111 4 472.43 2.37 297 108 111 3 477.97 0.41 298 108 112 4 476.78 0.19 299 109 112 3 477.99 0.40 300 109 113 4 461.32 1.57 301 109 125 16 281.62 2.23 302 110 113 3 477.75 2.81 303 110 117 7 282.24 2.13 304 113 116 3 468.47 3.39 305 113 117 4 350.34 1.24 306 116 121 5 447.25 4.55 307 117 122 5 448.47 4.44 308 117 125 8 383.50 7.49 309 118 121 3 470.56 1.40 310 118 122 4 468.30 4.01 311 119 122 3 476.97 5.84 312 119 123 4 468.39 3.97 313 120 123 3 473.81 1.26 314 120 124 4 471.14 2.59 315 121 124 3 473.39 1.47 316 121 125 4 471.16 2.58 317 122 125 3 482.87 3.50 318 122 126 4 471.13 2.57 319 123 126 3 473.79 1.26 320 123 127 4 472.27 2.01 321 124 127 3 475.26 2.00 322 124 128 4 471.35 2.67 323 125 128 3 473.76 2.75 324 125 129 4 472.24 1.99 325 126 129 3 478.49 0.38 326 126 130 4 472.46 2.10 327 127 130 3 472.49 2.10 328 127 131 4 471.28 2.40 329 128 131 3 473.62 1.53 330 128 132 4 471.57 2.54 331 129 132 3 473.62 1.53 332 129 133 4 462.58 0.68 333 130 133 3 469.13 0.41 334 130 134 4 462.58 0.68 335 131 134 3 467.08 0.65 336 131 135 4 464.44 1.98 337 132 135 3 472.44 2.02 338 132 136 4 464.07 2.16 339 133 136 3 472.48 2.04 340 133 137 4 464.04 2.18 341 134 137 3 473.67 1.58 342 134 138 4 458.80 0.97 343 135 138 3 468.55 4.21 344 136 140 4 494.06 3.52 345 137 140 3 486.87 0.07