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 5 453.29 5.66 2 2 73 71 29.19 0.88 3 2 127 125 20.12 0.05 4 2 128 126 20.12 0.04 5 2 131 129 20.09 0.04 6 3 6 3 475.74 0.76 7 3 7 4 461.62 1.54 8 4 7 3 480.26 5.24 9 4 8 4 461.63 1.54 10 5 8 3 472.88 2.19 11 5 9 4 462.61 6.25 12 6 9 3 473.95 0.58 13 6 10 4 464.27 5.42 14 6 124 118 47.01 0.98 15 6 127 121 47.01 0.98 16 7 10 3 473.95 0.58 17 7 11 4 470.97 2.08 18 7 73 66 48.23 0.66 19 7 74 67 51.84 0.22 20 8 11 3 476.19 0.54 21 8 12 4 470.97 2.08 22 9 12 3 477.30 0.24 23 9 13 4 470.96 2.07 24 9 121 112 60.16 0.92 25 9 124 115 59.72 0.72 26 10 13 3 479.75 2.33 27 10 14 4 470.88 2.06 28 10 70 60 61.08 0.30 29 10 124 114 60.22 0.48 30 10 125 115 59.75 0.71 31 10 128 118 59.71 0.72 32 11 14 3 477.26 1.12 33 11 15 4 462.95 6.00 34 11 70 59 61.17 0.26 35 11 71 60 61.19 0.27 36 11 73 62 61.18 0.27 37 12 15 3 470.12 1.53 38 12 16 4 466.01 0.54 39 13 16 3 470.65 0.64 40 13 17 4 466.13 0.62 41 13 121 108 61.62 0.24 42 13 125 112 61.59 0.24 43 14 17 3 466.26 0.56 44 14 18 4 460.36 3.50 45 14 21 7 403.27 9.12 46 14 63 49 63.31 1.04 47 14 66 52 61.58 0.21 48 14 67 53 61.56 0.21 49 14 70 56 61.55 0.21 50 14 109 95 66.82 0.46 51 15 18 3 475.34 0.23 52 16 116 100 77.56 1.95 53 17 20 3 480.04 0.58 54 17 21 4 439.05 7.16 55 17 24 7 396.96 4.54 56 17 109 92 78.08 1.90 57 17 113 96 98.14 1.92 58 18 21 3 480.04 0.58 59 20 23 3 477.17 1.13 60 20 24 4 468.20 0.31 61 21 24 3 468.21 0.31 62 21 25 4 465.63 1.54 63 21 63 42 100.00 2.19 64 22 25 3 468.76 0.03 65 22 26 4 467.85 0.43 66 22 60 38 100.67 1.99 67 22 63 41 100.69 1.99 68 23 26 3 463.87 2.43 69 23 27 4 463.87 2.43 70 23 56 33 120.03 0.85 71 24 27 3 483.58 3.85 72 24 28 4 465.30 1.18 73 24 108 84 120.03 0.82 74 24 109 85 123.36 1.57 75 24 112 88 134.96 0.58 76 25 28 3 469.90 1.12 77 25 29 4 470.74 3.56 78 25 59 34 120.02 0.85 79 25 105 80 120.03 0.81 80 26 29 3 470.70 0.28 81 26 30 4 465.79 0.18 82 26 55 29 133.81 0.52 83 26 56 30 128.50 3.16 84 26 59 33 120.00 0.87 85 27 30 3 476.13 2.44 86 27 31 4 467.13 2.06 87 27 108 81 135.16 0.57 88 27 112 85 136.16 0.34 89 28 31 3 476.86 2.08 90 28 32 4 464.88 0.63 91 28 101 73 135.12 0.58 92 28 104 76 135.12 0.58 93 28 105 77 135.12 0.57 94 28 108 80 135.23 0.56 95 29 32 3 476.86 2.08 96 29 33 4 462.81 1.67 97 29 55 26 135.76 0.44 98 29 58 29 135.62 0.49 99 29 59 30 135.46 0.43 100 29 62 33 135.31 0.55 101 29 101 72 135.13 0.56 102 30 33 3 472.99 0.15 103 30 34 4 459.78 0.86 104 30 50 20 136.56 0.29 105 31 34 3 470.01 0.63 106 31 35 4 458.25 0.35 107 31 104 73 135.62 0.38 108 31 107 76 136.31 0.21 109 31 108 77 136.32 0.21 110 32 35 3 475.09 0.90 111 32 36 4 457.19 0.87 112 32 39 7 332.53 3.52 113 32 100 68 135.63 0.38 114 32 101 69 135.61 0.39 115 32 104 72 135.97 0.21 116 33 37 4 442.96 2.51 117 33 39 6 352.94 6.67 118 33 40 7 308.56 8.46 119 33 43 10 296.59 2.50 120 33 48 15 136.56 0.32 121 34 37 3 479.39 0.84 122 36 39 3 495.59 3.51 123 36 100 64 135.64 0.38 124 36 103 67 136.42 0.23 125 36 104 68 136.44 0.24 126 37 40 3 483.05 2.76 127 38 41 3 485.85 1.36 128 39 42 3 489.34 0.67 129 39 43 4 482.66 0.39 130 39 97 58 135.60 0.38 131 39 100 61 136.38 0.25 132 40 43 3 482.07 0.68 133 40 44 4 471.68 1.12 134 40 48 8 253.91 4.32 135 41 44 3 493.45 1.40 136 42 93 51 135.81 0.48 137 42 94 52 136.37 0.27 138 42 97 55 136.44 0.26 139 43 46 3 473.30 5.06 140 43 48 5 418.18 1.05 141 43 58 15 182.75 22.78 142 45 54 9 243.47 1.23 143 46 54 8 243.46 1.24 144 46 58 12 243.25 1.13 145 47 52 5 266.89 6.78 146 47 54 7 243.52 1.21 147 47 55 8 244.00 0.97 148 48 55 7 248.19 1.12 149 49 52 3 476.11 0.81 150 52 55 3 475.64 3.52 151 52 56 4 465.10 5.15 152 53 56 3 468.25 3.58 153 53 57 4 455.06 1.74 154 54 57 3 473.48 0.96 155 54 58 4 465.05 3.27 156 55 58 3 474.64 1.53 157 55 59 4 463.03 4.29 158 56 59 3 474.22 0.58 159 56 60 4 464.38 4.34 160 57 60 3 475.44 1.19 161 57 61 4 472.82 0.12 162 58 61 3 473.77 0.38 163 58 62 4 472.84 0.11 164 59 62 3 473.03 0.01 165 59 63 4 472.20 0.21 166 60 63 3 473.67 0.31 167 60 64 4 472.19 0.21 168 61 64 3 479.97 2.94 169 61 65 4 472.19 0.21 170 62 65 3 481.76 2.04 171 62 66 4 472.09 2.02 172 63 66 3 472.10 2.02 173 63 67 4 472.10 2.02 174 64 67 3 469.91 0.92 175 64 68 4 469.91 0.92 176 65 68 3 469.91 0.92 177 65 69 4 466.95 2.40 178 65 80 15 151.94 3.08 179 65 83 18 151.21 3.33 180 66 69 3 463.41 0.63 181 66 70 4 463.53 0.69 182 66 105 39 163.07 2.31 183 66 128 62 163.31 2.24 184 66 129 63 159.66 0.62 185 66 132 66 159.34 0.58 186 67 70 3 471.67 3.16 187 67 71 4 459.70 2.60 188 68 71 3 469.07 3.56 189 68 72 4 468.69 3.75 190 68 79 11 191.77 11.83 191 69 72 3 477.16 0.49 192 69 73 4 461.58 7.29 193 69 76 7 286.53 8.04 194 69 80 11 159.99 0.84 195 69 128 59 178.55 5.24 196 69 132 63 160.06 0.82 197 70 73 3 469.10 3.54 198 70 128 58 184.78 2.15 199 72 75 3 473.15 0.58 200 72 76 4 416.55 0.94 201 72 79 7 279.73 0.34 202 73 76 3 478.44 1.01 203 75 78 3 478.70 1.08 204 75 79 4 465.93 0.26 205 76 79 3 471.34 1.66 206 76 80 4 451.66 3.00 207 76 128 52 215.00 2.25 208 76 131 55 214.63 2.23 209 76 132 56 212.54 2.62 210 76 135 59 212.49 2.64 211 77 81 4 457.06 0.29 212 77 135 58 212.50 2.63 213 78 81 3 470.92 0.55 214 80 83 3 479.57 1.60 215 80 84 4 473.81 5.79 216 80 132 52 215.48 2.36 217 80 135 55 215.27 2.46 218 80 136 56 215.46 2.37 219 81 84 3 480.64 2.40 220 81 85 4 480.62 2.40 221 82 85 3 481.86 1.79 222 82 86 4 473.83 5.79 223 83 86 3 475.95 4.74 224 83 87 4 473.83 5.79 225 83 136 53 215.78 2.48 226 84 87 3 475.98 4.72 227 84 88 4 456.97 0.29 228 84 135 51 215.80 2.46 229 84 136 52 215.77 2.48 230 84 139 55 215.68 2.49 231 85 89 4 411.59 15.91 232 85 90 5 398.78 15.32 233 85 139 54 215.66 2.49 234 86 90 4 371.35 14.22 235 86 91 5 363.07 18.36 236 87 91 4 363.06 18.36 237 87 92 5 363.05 18.37 238 87 93 6 302.48 12.23 239 87 98 11 262.90 1.89 240 87 136 49 215.94 2.44 241 88 92 4 312.92 7.04 242 88 136 48 215.96 2.44 243 88 139 51 215.69 2.49 244 88 140 52 215.45 2.39 245 89 92 3 477.35 4.62 246 89 139 50 215.69 2.48 247 92 140 48 215.69 2.50 248 93 97 4 473.51 3.11 249 93 98 5 473.50 3.12 250 94 97 3 491.76 1.38 251 94 140 46 216.00 2.46 252 95 98 3 493.12 0.70 253 95 99 4 485.09 3.31 254 95 137 42 216.39 2.49 255 95 140 45 216.01 2.46 256 96 99 3 487.13 2.30 257 96 100 4 470.88 3.24 258 97 100 3 475.73 0.82 259 97 101 4 470.89 3.23 260 98 101 3 476.30 2.06 261 98 102 4 461.29 1.58 262 98 133 35 216.84 2.40 263 98 136 38 216.84 2.40 264 98 137 39 216.83 2.40 265 99 102 3 470.98 1.55 266 99 103 4 465.99 0.75 267 100 103 3 475.04 0.48 268 100 104 4 465.99 0.75 269 101 104 3 475.04 0.48 270 101 105 4 466.00 0.76 271 102 105 3 467.74 0.10 272 102 106 4 467.05 0.45 273 102 129 27 217.25 2.51 274 102 133 31 217.09 2.46 275 103 106 3 472.59 0.59 276 103 107 4 467.73 0.10 277 104 107 3 467.74 0.10 278 104 108 4 466.04 0.74 279 105 108 3 471.47 4.59 280 105 109 4 460.20 2.18 281 105 129 24 217.86 2.31 282 106 109 3 470.68 4.20 283 106 110 4 465.94 0.70 284 106 117 11 219.78 2.00 285 106 122 16 218.32 2.25 286 106 125 19 217.97 2.29 287 106 126 20 218.16 2.20 288 106 129 23 217.96 2.30 289 107 110 3 475.76 2.30 290 107 111 4 465.79 0.79 291 108 111 3 482.10 1.70 292 108 112 4 461.93 2.71 293 109 112 3 468.83 2.12 294 109 113 4 448.94 3.76 295 109 125 16 218.63 2.38 296 110 113 3 479.80 0.07 297 110 117 7 229.44 6.83 298 113 116 3 477.83 1.07 299 113 117 4 448.64 8.07 300 115 118 3 516.65 1.76 301 116 121 5 458.75 6.23 302 117 122 5 439.11 3.18 303 117 125 8 408.70 3.07 304 118 121 3 469.98 0.62 305 118 122 4 463.20 4.00 306 119 122 3 467.82 1.70 307 119 123 4 467.56 1.56 308 120 123 3 467.84 1.70 309 120 124 4 460.80 1.82 310 121 124 3 467.25 1.41 311 121 125 4 460.80 1.82 312 122 125 3 475.85 2.89 313 122 126 4 461.72 1.34 314 123 126 3 467.94 1.78 315 123 127 4 467.84 1.72 316 124 127 3 468.89 2.04 317 124 128 4 466.99 2.15 318 125 128 3 472.38 0.55 319 125 129 4 466.76 2.25 320 126 129 3 479.07 2.79 321 126 130 4 466.76 2.25 322 127 130 3 472.82 1.10 323 127 131 4 461.12 0.61 324 128 131 3 476.88 3.14 325 128 132 4 461.51 0.42 326 129 132 3 475.54 1.72 327 129 133 4 461.47 0.35 328 130 133 3 462.74 0.96 329 130 134 4 463.89 0.87 330 131 134 3 465.16 0.24 331 131 135 4 465.13 0.26 332 132 135 3 467.51 0.21 333 132 136 4 464.25 0.70 334 133 136 3 469.45 1.14 335 133 137 4 464.25 0.70 336 134 137 3 469.86 0.93 337 134 138 4 444.83 8.54 338 135 138 3 481.83 1.10 339 137 140 3 477.03 3.26