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 5 452.97 5.99 2 2 73 71 31.80 0.18 3 2 76 74 26.63 0.05 4 2 127 125 22.16 0.18 5 2 128 126 21.92 0.07 6 3 6 3 474.34 0.29 7 3 7 4 469.39 2.19 8 4 7 3 481.18 3.02 9 4 8 4 474.42 0.33 10 5 8 3 479.32 2.10 11 5 9 4 474.44 0.34 12 6 9 3 477.72 1.21 13 6 10 4 467.74 3.70 14 6 124 118 46.51 0.14 15 6 127 121 46.52 0.14 16 7 10 3 476.82 1.66 17 7 11 4 469.23 2.94 18 7 73 66 50.66 0.35 19 7 74 67 48.68 0.64 20 8 11 3 475.23 0.48 21 8 12 4 469.23 2.94 22 9 12 3 475.56 0.64 23 9 13 4 469.16 2.92 24 9 121 112 59.76 0.03 25 9 124 115 59.70 0.02 26 10 13 3 478.88 1.02 27 10 14 4 469.32 2.83 28 10 70 60 60.25 0.31 29 10 124 114 60.27 0.29 30 10 125 115 59.73 0.03 31 10 128 118 59.70 0.02 32 11 14 3 477.94 1.49 33 11 15 4 469.31 2.83 34 11 70 59 60.30 0.33 35 11 71 60 60.30 0.33 36 11 73 62 60.30 0.33 37 12 15 3 480.78 0.07 38 12 16 4 469.54 1.81 39 13 16 3 477.82 1.42 40 13 17 4 465.59 0.18 41 13 113 100 82.31 0.28 42 13 121 108 65.14 2.01 43 13 125 112 60.45 0.30 44 14 17 3 465.02 0.46 45 14 18 4 466.33 1.12 46 14 21 7 427.88 6.25 47 14 66 52 60.45 0.29 48 14 67 53 60.50 0.29 49 14 70 56 60.45 0.28 50 14 109 95 81.62 0.47 51 15 18 3 463.85 2.37 52 16 113 97 90.83 3.87 53 16 116 100 89.27 3.10 54 17 20 3 478.25 1.44 55 17 21 4 442.84 0.19 56 17 24 7 395.07 5.48 57 17 109 92 86.59 1.76 58 17 113 96 91.04 3.97 59 18 21 3 497.87 3.08 60 20 23 3 477.96 1.21 61 20 24 4 468.99 0.08 62 21 24 3 471.61 1.39 63 21 25 4 468.06 0.53 64 21 63 42 92.92 2.98 65 22 25 3 468.97 0.07 66 22 26 4 468.06 0.53 67 22 60 38 97.78 0.56 68 22 63 41 97.88 0.58 69 23 26 3 481.83 4.72 70 23 27 4 467.27 0.91 71 24 27 3 481.81 4.73 72 24 28 4 467.39 2.23 73 24 108 84 116.77 0.55 74 24 109 85 117.45 0.03 75 24 112 88 128.15 1.22 76 25 28 3 472.00 0.07 77 25 29 4 468.65 2.86 78 25 59 34 115.78 0.51 79 25 63 38 114.31 0.70 80 26 29 3 469.92 2.23 81 26 30 4 468.68 1.58 82 26 55 29 125.36 1.47 83 26 56 30 127.09 0.83 84 26 59 33 120.33 1.03 85 27 30 3 468.68 1.58 86 27 31 4 468.67 1.58 87 27 108 81 128.92 1.25 88 27 112 85 129.84 1.07 89 28 31 3 468.67 1.58 90 28 32 4 467.38 0.95 91 28 101 73 128.82 1.22 92 28 104 76 128.84 1.23 93 28 105 77 128.82 1.22 94 28 108 80 128.95 1.25 95 29 32 3 476.43 2.30 96 29 33 4 467.38 0.95 97 29 55 26 129.09 1.32 98 29 58 29 129.07 1.32 99 29 59 30 129.00 1.28 100 29 101 72 128.90 1.24 101 30 33 3 480.93 1.71 102 30 34 4 464.44 2.42 103 30 50 20 130.00 0.96 104 31 34 3 476.56 1.23 105 31 35 4 465.38 1.21 106 31 104 73 129.69 1.08 107 31 107 76 129.77 1.07 108 31 108 77 129.79 1.07 109 31 111 80 129.96 1.06 110 32 35 3 473.97 0.67 111 32 36 4 455.75 1.91 112 32 39 7 307.56 2.99 113 32 100 68 129.66 1.07 114 32 101 69 129.65 1.05 115 32 104 72 129.73 1.07 116 33 37 4 437.06 3.71 117 33 39 6 302.82 0.62 118 33 40 7 230.15 23.75 119 33 43 10 229.50 24.07 120 33 48 15 130.09 0.99 121 34 37 3 482.88 0.90 122 36 39 3 488.83 2.33 123 36 100 64 129.68 1.05 124 36 103 67 129.84 1.05 125 36 104 68 129.90 1.02 126 37 40 3 480.06 0.06 127 38 41 3 488.00 1.35 128 39 42 3 487.59 1.54 129 39 43 4 494.28 1.80 130 39 97 58 129.66 1.05 131 39 100 61 129.80 1.07 132 40 43 3 494.28 1.80 133 40 44 4 475.36 0.39 134 40 48 8 187.33 27.13 135 41 44 3 498.08 0.10 136 42 93 51 129.18 0.90 137 42 94 52 129.56 1.03 138 42 97 55 129.81 1.07 139 43 46 3 477.87 1.02 140 43 48 5 411.95 14.04 141 43 58 15 184.22 25.91 142 45 54 9 194.03 24.18 143 46 54 8 194.00 24.16 144 46 58 12 193.97 24.18 145 47 52 5 342.42 14.87 146 47 54 7 194.05 24.18 147 47 55 8 194.06 24.19 148 48 52 4 400.10 10.10 149 48 55 7 202.17 28.26 150 49 52 3 475.97 0.88 151 52 55 3 477.06 2.81 152 52 56 4 470.32 2.60 153 53 56 3 472.55 1.49 154 53 57 4 472.56 1.50 155 54 57 3 481.01 2.70 156 54 58 4 472.59 1.51 157 55 58 3 474.35 1.68 158 55 59 4 472.59 1.51 159 56 59 3 474.35 1.68 160 56 60 4 472.58 1.51 161 57 60 3 484.92 3.71 162 57 61 4 472.58 1.51 163 58 61 3 473.41 0.38 164 58 62 4 471.11 0.78 165 59 62 3 473.60 0.29 166 59 63 4 471.09 0.78 167 60 63 3 471.92 1.19 168 60 64 4 471.06 0.76 169 61 64 3 471.29 1.61 170 61 65 4 462.89 2.66 171 62 65 3 483.15 0.40 172 62 66 4 470.36 1.14 173 63 66 3 475.68 1.52 174 63 67 4 468.16 0.04 175 64 67 3 470.36 1.14 176 64 68 4 468.79 0.35 177 65 68 3 475.24 3.58 178 65 69 4 468.79 0.35 179 65 80 15 153.81 2.10 180 65 83 18 153.23 2.37 181 66 69 3 477.03 2.68 182 66 70 4 466.42 1.54 183 66 105 39 162.81 1.83 184 66 128 62 163.78 1.34 185 66 129 63 161.35 1.28 186 66 132 66 157.75 0.48 187 67 70 3 473.74 2.12 188 67 71 4 466.29 1.60 189 68 71 3 475.06 1.20 190 68 72 4 459.75 4.27 191 68 79 11 206.34 23.79 192 69 72 3 475.39 1.37 193 69 73 4 447.23 0.81 194 69 76 7 296.06 8.18 195 69 80 11 157.78 0.50 196 69 128 59 180.06 4.13 197 69 132 63 158.47 0.15 198 70 73 3 470.30 1.19 199 70 128 58 180.42 4.30 200 72 75 3 471.42 0.29 201 72 76 4 439.99 11.06 202 72 79 7 277.97 1.28 203 73 76 3 479.50 1.54 204 75 78 3 479.88 1.34 205 75 79 4 451.56 7.41 206 76 79 3 469.94 0.60 207 76 80 4 446.14 4.70 208 76 128 52 243.41 13.14 209 76 131 55 242.20 12.58 210 76 132 56 239.94 12.09 211 77 81 4 441.43 3.77 212 77 135 58 236.06 11.63 213 78 81 3 469.18 1.42 214 80 83 3 479.44 0.58 215 80 84 4 457.61 2.46 216 80 132 52 246.58 13.33 217 80 135 55 245.75 13.74 218 80 136 56 245.76 13.74 219 81 84 3 478.88 1.53 220 81 85 4 472.23 4.85 221 81 139 58 245.84 13.76 222 82 85 3 480.11 0.91 223 82 86 4 478.88 1.53 224 83 86 3 474.21 3.87 225 83 87 4 483.47 0.77 226 83 136 53 247.32 13.38 227 84 87 3 483.48 0.77 228 84 88 4 471.99 6.51 229 84 135 51 247.39 13.39 230 84 136 52 247.32 13.38 231 84 138 54 247.36 13.39 232 84 139 55 247.22 13.36 233 85 88 3 478.64 3.19 234 85 89 4 468.88 8.05 235 85 139 54 247.19 13.36 236 86 89 3 485.35 0.16 237 86 90 4 453.59 4.33 238 86 91 5 412.14 10.46 239 87 91 4 410.32 9.54 240 87 92 5 344.91 12.04 241 87 98 11 271.33 3.77 242 87 136 49 247.44 13.39 243 87 140 53 247.28 13.39 244 88 92 4 364.51 2.24 245 88 139 51 247.40 13.39 246 88 140 52 246.99 13.37 247 89 92 3 492.91 3.16 248 92 140 48 247.41 13.39 249 93 97 4 475.37 3.33 250 93 98 5 474.87 3.58 251 93 140 47 247.50 13.38 252 94 97 3 484.87 0.86 253 95 98 3 481.24 0.68 254 95 137 42 247.77 13.27 255 95 140 45 247.66 13.33 256 96 99 3 491.44 5.76 257 96 100 4 480.97 0.54 258 97 100 3 480.94 0.53 259 97 101 4 479.65 1.17 260 98 101 3 477.85 2.35 261 98 102 4 470.20 1.35 262 98 133 35 247.88 13.23 263 98 136 38 247.91 13.24 264 98 140 42 247.89 13.24 265 99 102 3 474.56 0.71 266 99 103 4 469.06 0.77 267 100 103 3 474.22 1.81 268 100 104 4 473.29 1.35 269 101 104 3 469.07 0.76 270 101 105 4 464.34 1.61 271 102 105 3 471.66 2.04 272 102 106 4 466.01 0.79 273 102 129 27 248.59 13.22 274 102 133 31 248.38 13.31 275 103 106 3 468.93 0.67 276 103 107 4 466.01 0.79 277 104 107 3 469.12 0.77 278 104 108 4 465.07 1.25 279 105 108 3 472.37 2.39 280 105 109 4 460.34 1.11 281 105 129 24 249.59 13.44 282 106 109 3 469.89 3.81 283 106 110 4 464.95 1.20 284 106 117 11 250.34 13.68 285 106 122 16 249.97 13.53 286 106 125 19 249.80 13.50 287 106 126 20 249.81 13.51 288 106 129 23 249.62 13.43 289 107 110 3 472.11 2.38 290 107 111 4 464.95 1.20 291 108 111 3 474.81 1.82 292 108 112 4 463.58 1.89 293 109 112 3 479.81 1.83 294 109 113 4 451.02 1.14 295 109 125 16 249.97 13.53 296 110 117 7 250.69 13.50 297 113 116 3 480.38 0.71 298 113 117 4 442.56 3.21 299 115 118 3 526.28 0.91 300 116 121 5 465.74 2.79 301 117 121 4 465.74 2.79 302 117 122 5 450.30 10.50 303 117 125 8 412.00 6.44 304 118 121 3 466.51 2.41 305 118 122 4 465.75 2.79 306 119 122 3 465.78 2.80 307 119 123 4 465.76 2.79 308 120 123 3 475.25 1.95 309 120 124 4 474.75 1.71 310 121 124 3 475.36 1.99 311 121 125 4 474.77 1.72 312 122 125 3 474.43 1.99 313 122 126 4 469.74 4.32 314 123 126 3 476.68 0.86 315 123 127 4 471.85 3.27 316 124 127 3 474.95 1.73 317 124 128 4 471.74 3.23 318 125 128 3 474.23 2.60 319 125 129 4 467.89 0.73 320 126 129 3 484.02 0.33 321 126 130 4 467.89 0.73 322 127 130 3 475.13 4.01 323 127 131 4 467.26 0.42 324 128 131 3 475.13 4.01 325 128 132 4 464.78 1.67 326 129 132 3 475.88 3.64 327 129 133 4 464.00 2.05 328 130 133 3 474.91 2.57 329 130 134 4 462.55 1.55 330 131 134 3 473.20 1.73 331 131 135 4 463.39 1.13 332 132 135 3 474.12 5.26 333 132 136 4 464.16 1.51 334 133 136 3 476.43 4.11 335 133 137 4 461.37 0.11 336 134 137 3 479.28 2.38 337 134 138 4 457.82 1.88 338 135 138 3 479.28 2.38 339 136 140 4 489.82 1.20 340 137 140 3 485.50 0.97