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 73 71 33.25 0.38 2 2 76 74 32.02 0.04 3 2 127 125 25.29 0.80 4 2 128 126 24.87 0.58 5 3 6 3 479.72 1.04 6 3 7 4 469.84 1.45 7 4 7 3 477.99 1.10 8 4 8 4 469.84 1.45 9 5 8 3 475.08 0.42 10 5 9 4 469.84 1.45 11 6 9 3 472.42 0.91 12 6 10 4 472.45 0.93 13 6 124 118 51.96 0.98 14 6 127 121 51.95 0.98 15 7 10 3 481.79 2.40 16 7 11 4 471.07 1.64 17 7 73 66 56.13 0.99 18 7 74 67 56.34 1.08 19 8 11 3 475.82 0.58 20 8 12 4 471.07 1.64 21 9 12 3 476.38 0.86 22 9 13 4 473.31 0.52 23 9 121 112 63.72 0.06 24 9 124 115 63.59 0.00 25 10 13 3 483.55 1.52 26 10 14 4 473.31 0.52 27 10 70 60 63.70 0.05 28 10 124 114 63.72 0.03 29 10 125 115 63.69 0.04 30 10 128 118 63.58 0.01 31 11 14 3 490.03 1.72 32 11 15 4 471.97 0.16 33 11 70 59 63.68 0.04 34 11 73 62 63.73 0.02 35 12 15 3 477.59 1.46 36 12 16 4 474.88 1.19 37 13 16 3 476.25 0.51 38 13 17 4 474.44 1.40 39 13 113 100 79.26 0.81 40 13 121 108 65.42 0.70 41 13 125 112 63.98 0.04 42 14 17 3 476.25 0.51 43 14 18 4 473.05 2.10 44 14 21 7 389.85 11.22 45 14 66 52 63.95 0.03 46 14 67 53 64.00 0.01 47 14 70 56 63.94 0.02 48 15 18 3 474.88 1.18 49 16 113 97 79.56 0.76 50 16 116 100 79.44 0.78 51 17 20 3 490.80 0.94 52 17 21 4 446.47 4.34 53 17 24 7 402.58 5.54 54 17 109 92 79.36 0.82 55 17 113 96 79.66 0.71 56 18 21 3 491.28 0.70 57 20 23 3 487.12 3.73 58 20 24 4 468.42 3.45 59 21 24 3 474.31 6.38 60 21 25 4 470.81 1.61 61 21 63 42 96.41 2.75 62 22 25 3 475.44 1.09 63 22 26 4 479.98 2.97 64 22 60 38 96.93 2.98 65 22 63 41 96.47 2.75 66 23 26 3 486.56 2.89 67 23 27 4 483.35 1.28 68 24 27 3 483.36 1.28 69 24 28 4 483.35 1.28 70 24 108 84 126.62 0.43 71 24 109 85 127.66 0.10 72 24 112 88 137.18 0.38 73 25 28 3 481.36 2.29 74 25 29 4 479.43 3.25 75 25 59 34 125.59 0.93 76 26 29 3 489.29 2.66 77 26 30 4 474.32 0.70 78 26 55 29 137.34 0.74 79 26 56 30 137.14 0.64 80 26 59 33 125.67 0.96 81 27 30 3 473.04 0.06 82 27 31 4 473.03 0.06 83 27 108 81 137.94 0.58 84 27 112 85 138.26 0.55 85 28 31 3 475.92 0.35 86 28 32 4 472.34 0.41 87 28 104 76 137.88 0.59 88 28 105 77 137.87 0.59 89 28 108 80 137.96 0.58 90 29 32 3 477.62 2.23 91 29 33 4 473.31 0.08 92 29 55 26 138.31 0.49 93 29 58 29 138.03 0.63 94 29 59 30 137.95 0.62 95 29 62 33 137.95 0.62 96 29 101 72 137.89 0.59 97 30 33 3 478.85 0.45 98 30 34 4 475.26 0.90 99 30 50 20 138.56 0.55 100 30 55 25 138.32 0.50 101 31 34 3 477.50 0.23 102 31 35 4 470.25 1.61 103 31 104 73 138.24 0.60 104 31 107 76 138.33 0.58 105 31 108 77 138.38 0.56 106 31 111 80 138.59 0.56 107 32 35 3 476.94 0.06 108 32 36 4 467.83 1.43 109 32 39 7 332.49 7.15 110 32 101 69 138.00 0.64 111 32 104 72 138.24 0.60 112 33 37 4 457.85 3.56 113 33 39 6 343.83 1.48 114 33 40 7 300.97 8.27 115 33 43 10 262.13 4.22 116 33 48 15 138.62 0.54 117 34 37 3 497.01 6.45 118 36 39 3 493.80 1.53 119 36 100 64 138.03 0.64 120 36 103 67 138.55 0.57 121 36 104 68 138.55 0.57 122 37 40 3 488.01 3.00 123 38 41 3 490.59 4.52 124 39 42 3 505.12 2.75 125 39 97 58 138.09 0.68 126 39 100 61 138.52 0.58 127 40 43 3 477.11 1.75 128 40 48 8 243.53 2.02 129 42 91 49 138.22 0.66 130 42 92 50 138.35 0.59 131 42 93 51 138.36 0.59 132 42 94 52 138.46 0.60 133 42 97 55 138.53 0.58 134 43 46 3 483.72 5.42 135 43 48 5 397.78 15.17 136 43 58 15 238.04 4.97 137 45 54 9 245.93 1.25 138 46 54 8 245.89 1.24 139 46 58 12 245.82 1.25 140 47 52 5 262.73 2.79 141 47 54 7 247.89 2.22 142 47 55 8 255.45 6.00 143 48 52 4 365.17 9.25 144 48 55 7 248.83 0.19 145 49 52 3 470.68 1.63 146 52 55 3 483.56 6.04 147 52 56 4 479.62 8.01 148 53 56 3 489.23 3.21 149 53 57 4 479.62 8.01 150 54 57 3 488.01 3.83 151 54 58 4 479.63 8.00 152 55 58 3 488.00 3.82 153 55 59 4 488.00 3.82 154 56 59 3 478.36 1.01 155 56 60 4 474.72 2.83 156 57 60 3 476.89 1.73 157 57 61 4 476.03 2.09 158 58 61 3 476.04 2.09 159 58 62 4 476.06 2.10 160 59 62 3 480.49 4.32 161 59 63 4 475.92 2.19 162 60 63 3 476.24 2.04 163 60 64 4 475.94 2.19 164 61 64 3 480.64 0.16 165 61 65 4 476.10 2.11 166 62 65 3 480.66 0.17 167 62 66 4 476.10 2.10 168 62 101 39 149.90 1.44 169 63 66 3 485.01 2.02 170 63 67 4 475.15 1.79 171 64 67 3 472.69 3.72 172 64 68 4 470.39 4.17 173 65 68 3 472.12 3.31 174 65 69 4 472.00 3.38 175 65 80 15 159.91 3.50 176 65 83 18 159.75 3.56 177 66 69 3 472.88 3.52 178 66 70 4 472.01 3.38 179 66 105 39 166.93 0.20 180 66 129 63 166.62 0.01 181 66 132 66 159.94 3.39 182 67 70 3 477.20 1.35 183 67 71 4 467.57 5.60 184 68 71 3 477.30 1.40 185 68 72 4 475.87 0.69 186 68 79 11 236.06 10.03 187 69 72 3 475.86 0.69 188 69 73 4 463.54 6.83 189 69 76 7 347.00 22.64 190 69 80 11 222.75 4.62 191 69 128 59 187.41 6.36 192 69 132 63 166.81 0.10 193 70 73 3 467.62 0.38 194 70 128 58 187.41 6.36 195 72 75 3 483.76 2.85 196 72 76 4 458.75 6.37 197 72 79 7 296.82 2.32 198 73 76 3 483.94 0.60 199 75 78 3 479.67 1.12 200 75 79 4 459.39 1.29 201 76 79 3 464.73 1.37 202 76 80 4 463.82 0.92 203 76 128 52 206.50 1.73 204 76 131 55 206.27 1.62 205 76 132 56 206.27 1.61 206 76 135 59 206.22 1.64 207 77 80 3 470.05 4.03 208 77 81 4 431.57 1.89 209 77 135 58 206.22 1.64 210 78 81 3 482.59 2.23 211 80 83 3 484.80 3.26 212 80 84 4 459.92 2.17 213 80 132 52 207.97 1.24 214 80 135 55 207.80 1.21 215 80 136 56 207.91 1.27 216 81 84 3 481.69 2.67 217 81 85 4 467.92 1.48 218 82 85 3 489.98 1.53 219 82 86 4 467.93 1.47 220 83 86 3 480.32 6.00 221 83 87 4 467.95 1.46 222 83 136 53 208.12 1.27 223 84 87 3 480.78 4.96 224 84 88 4 460.42 2.31 225 84 89 5 460.41 2.31 226 84 135 51 208.12 1.27 227 84 136 52 208.12 1.27 228 85 88 3 488.26 2.95 229 85 89 4 454.22 4.20 230 85 90 5 454.22 4.20 231 86 90 4 422.38 2.62 232 86 91 5 422.36 2.60 233 87 91 4 405.67 5.74 234 87 92 5 405.65 5.74 235 87 93 6 357.20 18.45 236 87 98 11 287.39 3.62 237 87 136 49 208.22 1.28 238 88 92 4 373.75 10.21 239 88 136 48 208.24 1.28 240 88 137 49 208.13 1.27 241 88 139 51 208.11 1.25 242 88 140 52 208.09 1.26 243 89 139 50 208.11 1.25 244 92 140 48 208.24 1.28 245 93 97 4 482.40 2.29 246 93 98 5 472.88 2.37 247 93 140 47 208.64 1.09 248 94 97 3 490.81 3.85 249 95 98 3 500.09 1.33 250 95 137 42 208.70 1.10 251 95 140 45 208.69 1.10 252 96 99 3 485.75 0.62 253 96 100 4 485.75 0.62 254 97 100 3 481.56 1.48 255 97 101 4 480.55 1.98 256 98 101 3 486.47 0.97 257 98 102 4 488.00 1.74 258 98 133 35 208.96 1.05 259 98 136 38 208.96 1.05 260 98 137 39 208.92 1.04 261 99 102 3 488.02 1.74 262 99 103 4 481.48 1.53 263 100 103 3 488.03 1.73 264 100 104 4 480.35 2.11 265 101 104 3 488.03 1.73 266 101 105 4 480.32 2.10 267 102 105 3 488.05 1.72 268 102 106 4 480.36 5.56 269 102 129 27 209.43 1.15 270 103 106 3 490.06 0.04 271 103 107 4 482.05 4.05 272 104 107 3 485.70 2.23 273 104 108 4 471.63 1.20 274 105 108 3 476.31 1.15 275 105 109 4 465.56 4.24 276 105 129 24 210.62 0.62 277 106 109 3 478.55 0.03 278 106 110 4 476.30 1.13 279 106 117 11 212.53 1.11 280 106 122 16 211.38 0.83 281 106 125 19 211.12 0.70 282 106 126 20 210.97 0.71 283 106 129 23 210.81 0.64 284 107 110 3 478.99 0.20 285 107 111 4 476.30 1.13 286 108 111 3 476.31 1.14 287 108 112 4 476.30 1.13 288 109 112 3 485.00 3.21 289 109 113 4 468.41 5.07 290 109 125 16 212.34 1.20 291 110 117 7 212.53 1.11 292 113 116 3 476.80 1.15 293 113 117 4 417.28 8.64 294 116 121 5 444.43 2.51 295 117 121 4 444.44 2.50 296 117 122 5 435.56 1.93 297 117 125 8 410.52 4.30 298 118 121 3 478.47 2.35 299 118 122 4 466.00 1.28 300 119 122 3 475.87 3.66 301 119 123 4 459.03 2.22 302 120 123 3 470.31 5.37 303 120 124 4 461.86 1.15 304 121 124 3 473.93 2.68 305 121 125 4 466.95 6.17 306 122 125 3 475.49 1.91 307 122 126 4 462.94 0.60 308 123 126 3 479.68 3.98 309 123 127 4 468.31 2.08 310 124 127 3 480.55 3.67 311 124 128 4 486.67 0.60 312 125 128 3 486.68 0.60 313 125 129 4 486.68 0.60 314 126 129 3 486.67 0.60 315 126 130 4 473.59 5.94 316 127 130 3 486.67 0.60 317 127 131 4 473.82 5.81 318 128 131 3 485.12 1.36 319 128 132 4 472.07 0.17 320 129 132 3 472.08 0.17 321 129 133 4 467.85 2.27 322 130 133 3 480.64 4.12 323 130 134 4 467.86 2.27 324 131 134 3 475.88 1.75 325 131 135 4 475.88 1.75 326 132 135 3 475.96 1.71 327 132 136 4 474.82 2.27 328 133 136 3 475.95 1.71 329 133 137 4 475.94 1.71 330 134 137 3 481.20 0.58 331 134 138 4 461.86 3.80 332 134 141 7 414.94 4.68 333 135 138 3 466.36 1.51 334 137 140 3 480.13 1.55 335 137 141 4 466.45 1.74 336 138 141 3 480.47 1.39