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 5 446.85 2.71 2 2 73 71 30.97 0.04 3 2 76 74 28.78 0.95 4 2 127 125 24.41 0.23 5 2 128 126 24.22 0.13 6 2 131 129 23.68 0.29 7 3 6 3 473.28 3.35 8 3 7 4 470.94 4.53 9 4 7 3 489.36 4.67 10 4 8 4 473.30 3.35 11 5 8 3 477.75 2.28 12 5 9 4 469.97 1.69 13 6 9 3 469.97 1.69 14 6 10 4 470.56 1.40 15 6 124 118 47.84 0.58 16 6 127 121 47.84 0.58 17 7 10 3 473.94 0.80 18 7 11 4 470.56 1.40 19 7 73 66 49.13 0.10 20 7 74 67 49.79 0.21 21 8 11 3 477.31 0.89 22 8 12 4 470.56 1.40 23 9 12 3 476.13 0.29 24 9 13 4 473.98 3.10 25 9 121 112 60.56 1.11 26 9 124 115 60.53 1.12 27 10 13 3 477.56 1.33 28 10 14 4 473.74 3.24 29 10 70 60 60.55 1.11 30 10 124 114 60.56 1.11 31 10 125 115 60.55 1.11 32 10 128 118 60.54 1.11 33 11 14 3 476.61 1.81 34 11 15 4 473.88 3.17 35 11 70 59 60.58 1.10 36 11 71 60 60.63 1.12 37 11 73 62 60.62 1.12 38 12 15 3 477.43 1.40 39 12 16 4 477.43 1.40 40 13 16 3 487.61 1.61 41 13 17 4 477.42 1.39 42 13 113 100 76.78 1.54 43 13 121 108 61.80 0.56 44 13 125 112 61.16 0.87 45 14 17 3 476.54 1.79 46 14 18 4 473.85 3.14 47 14 21 7 408.12 3.41 48 14 66 52 61.14 0.88 49 14 67 53 61.13 0.88 50 14 70 56 61.13 0.88 51 14 109 95 76.78 1.54 52 15 18 3 477.46 1.32 53 16 113 97 87.34 3.56 54 16 116 100 87.28 3.54 55 17 20 3 488.72 3.06 56 17 21 4 459.49 0.32 57 17 24 7 408.69 1.58 58 17 109 92 77.19 1.52 59 17 113 96 87.53 3.48 60 18 21 3 502.83 1.44 61 20 23 3 477.51 0.93 62 20 24 4 467.50 2.02 63 21 24 3 470.42 1.66 64 21 25 4 467.53 2.00 65 21 63 42 89.32 2.58 66 22 25 3 472.70 0.57 67 22 26 4 467.55 2.00 68 22 60 38 95.87 0.09 69 22 63 41 97.06 0.69 70 23 26 3 478.31 2.06 71 23 27 4 467.53 2.00 72 24 27 3 475.91 1.89 73 24 28 4 461.07 1.31 74 24 108 84 121.78 1.69 75 24 109 85 121.78 1.69 76 24 112 88 128.09 0.43 77 25 28 3 474.57 1.03 78 25 29 4 462.81 1.66 79 25 59 34 117.62 0.32 80 26 29 3 477.38 0.38 81 26 30 4 458.41 3.85 82 26 55 29 127.17 0.17 83 26 56 30 127.02 0.10 84 26 59 33 119.24 0.46 85 27 30 3 474.56 1.03 86 27 31 4 457.18 3.25 87 27 108 81 128.69 0.42 88 27 112 85 129.68 0.80 89 28 31 3 466.64 3.58 90 28 32 4 464.66 3.14 91 28 101 73 128.56 0.44 92 28 104 76 128.57 0.43 93 28 105 77 128.56 0.44 94 28 108 80 128.71 0.42 95 29 32 3 471.93 0.49 96 29 33 4 468.09 1.43 97 29 55 26 128.89 0.40 98 29 58 29 128.81 0.36 99 29 59 30 128.81 0.36 100 29 101 72 128.63 0.43 101 30 33 3 470.16 2.46 102 30 34 4 468.10 1.43 103 30 50 20 129.76 0.83 104 31 34 3 479.33 0.91 105 31 35 4 465.91 0.35 106 31 104 73 129.19 0.66 107 31 107 76 129.66 0.80 108 31 108 77 129.66 0.80 109 32 35 3 470.15 2.46 110 32 36 4 446.72 2.37 111 32 39 7 327.81 7.59 112 32 101 69 129.15 0.67 113 32 104 72 129.47 0.81 114 33 37 4 424.35 1.43 115 33 39 6 375.01 16.00 116 33 40 7 285.13 1.16 117 33 43 10 285.14 1.17 118 33 48 15 129.91 0.80 119 33 55 22 129.82 0.81 120 34 37 3 491.78 0.58 121 36 39 3 505.75 0.74 122 36 100 64 129.17 0.68 123 36 103 67 129.74 0.83 124 36 104 68 129.74 0.83 125 37 40 3 488.13 1.28 126 38 41 3 487.25 1.72 127 39 42 3 495.55 1.97 128 39 43 4 490.68 0.46 129 39 97 58 129.16 0.69 130 39 100 61 129.72 0.83 131 40 43 3 490.68 0.46 132 40 44 4 490.67 0.47 133 40 48 8 186.28 25.94 134 41 44 3 499.99 0.78 135 42 93 51 129.18 0.77 136 42 94 52 129.38 0.79 137 42 97 55 129.71 0.83 138 43 46 3 481.44 0.01 139 43 48 5 414.29 9.47 140 43 58 15 180.91 26.25 141 45 54 9 184.38 25.73 142 46 54 8 184.38 25.73 143 46 55 9 184.38 25.74 144 46 58 12 184.34 25.72 145 47 52 5 219.87 33.57 146 47 54 7 201.39 24.36 147 48 55 7 201.40 24.35 148 49 52 3 483.42 0.12 149 51 56 5 457.41 1.50 150 52 55 3 476.70 0.35 151 52 56 4 466.12 0.29 152 53 56 3 478.69 3.07 153 53 57 4 462.53 0.83 154 54 57 3 476.20 1.82 155 54 58 4 464.68 3.02 156 55 58 3 475.45 2.20 157 55 59 4 469.35 2.60 158 56 59 3 472.67 0.95 159 56 60 4 463.50 5.66 160 57 60 3 482.42 2.00 161 57 61 4 467.89 3.46 162 58 61 3 473.99 0.42 163 58 62 4 469.57 2.51 164 59 62 3 479.99 2.58 165 59 63 4 471.93 1.33 166 60 63 3 473.35 0.94 167 60 64 4 471.93 1.33 168 61 64 3 484.69 0.24 169 61 65 4 476.74 3.73 170 62 65 3 484.69 0.24 171 62 66 4 476.74 3.73 172 63 66 3 477.79 3.21 173 63 67 4 476.69 3.75 174 64 67 3 469.74 0.82 175 64 68 4 466.07 1.01 176 65 68 3 477.73 3.18 177 65 69 4 474.07 5.01 178 65 83 18 143.22 2.22 179 66 69 3 473.81 5.15 180 66 70 4 473.80 5.15 181 66 105 39 183.75 2.28 182 66 129 63 169.77 2.81 183 66 132 66 161.59 0.99 184 67 70 3 472.90 5.61 185 67 71 4 472.89 5.61 186 68 71 3 478.65 2.73 187 68 72 4 457.30 5.41 188 68 79 11 221.24 16.53 189 68 80 12 188.18 13.42 190 69 72 3 477.05 1.93 191 69 73 4 450.23 2.31 192 69 76 7 318.06 19.09 193 69 80 11 221.24 16.53 194 69 128 59 193.59 0.54 195 69 132 63 181.41 3.39 196 70 73 3 477.37 4.75 197 70 128 58 218.24 12.87 198 72 75 3 476.41 0.36 199 72 76 4 427.62 4.70 200 72 79 7 328.57 13.88 201 73 76 3 478.30 2.73 202 73 128 55 237.56 16.82 203 75 78 3 494.82 0.76 204 75 79 4 474.80 2.47 205 76 79 3 484.37 1.33 206 76 80 4 461.53 0.29 207 76 128 52 239.02 17.01 208 76 131 55 238.06 16.69 209 76 132 56 237.99 16.73 210 76 135 59 237.97 16.71 211 77 80 3 486.44 1.38 212 77 81 4 461.52 0.29 213 77 135 58 237.99 16.71 214 78 81 3 480.51 0.38 215 80 83 3 481.80 1.02 216 80 84 4 473.62 1.31 217 80 132 52 239.56 17.27 218 80 135 55 239.52 17.29 219 80 136 56 239.50 17.28 220 81 84 3 483.12 0.56 221 81 85 4 473.27 0.76 222 81 139 58 239.57 17.32 223 82 85 3 494.55 6.26 224 82 86 4 473.26 0.77 225 83 86 3 476.99 1.01 226 83 87 4 472.27 1.26 227 83 136 53 239.67 17.33 228 84 87 3 478.07 0.42 229 84 88 4 462.99 5.90 230 84 135 51 239.69 17.33 231 84 136 52 239.67 17.33 232 84 139 55 239.63 17.34 233 85 88 3 474.29 2.31 234 85 89 4 436.94 2.14 235 85 139 54 239.65 17.33 236 86 90 4 406.99 2.10 237 86 91 5 334.00 14.21 238 87 91 4 324.36 10.00 239 87 92 5 308.25 1.97 240 87 98 11 266.11 6.33 241 87 136 49 239.75 17.30 242 87 140 53 239.63 17.34 243 88 92 4 326.26 10.98 244 88 139 51 239.67 17.34 245 88 140 52 239.58 17.33 246 89 92 3 490.47 1.02 247 93 97 4 482.27 0.62 248 93 98 5 472.70 1.80 249 93 140 47 239.81 17.29 250 94 97 3 503.29 1.45 251 95 98 3 494.31 0.20 252 95 137 42 240.25 17.48 253 95 140 45 239.99 17.34 254 96 99 3 490.30 0.62 255 96 100 4 482.29 0.62 256 97 100 3 478.63 1.15 257 97 101 4 480.06 4.11 258 98 101 3 482.31 2.98 259 98 102 4 470.97 2.54 260 98 133 35 240.69 17.38 261 98 136 38 240.68 17.36 262 98 140 42 240.67 17.36 263 99 102 3 477.07 5.59 264 99 103 4 470.95 2.54 265 100 103 3 479.81 4.22 266 100 104 4 477.07 5.60 267 101 104 3 479.82 4.23 268 101 105 4 475.48 3.92 269 102 105 3 478.97 4.66 270 102 106 4 478.68 4.80 271 102 129 27 241.25 17.29 272 102 133 31 241.09 17.22 273 103 106 3 478.97 4.66 274 103 107 4 476.22 3.57 275 104 107 3 478.69 4.80 276 104 108 4 478.69 4.80 277 105 108 3 482.20 3.05 278 105 109 4 476.22 3.58 279 105 129 24 242.19 17.14 280 106 109 3 479.30 5.12 281 106 110 4 471.34 6.02 282 106 117 11 244.21 17.01 283 106 122 16 242.78 17.11 284 106 125 19 242.53 17.14 285 106 126 20 242.54 17.13 286 106 129 23 242.38 17.20 287 107 110 3 479.75 1.81 288 107 111 4 470.30 6.54 289 108 111 3 487.42 1.07 290 108 112 4 473.38 8.09 291 109 112 3 477.45 0.67 292 109 113 4 460.21 1.52 293 109 125 16 242.75 17.09 294 110 117 7 246.92 15.65 295 113 116 3 477.96 1.10 296 113 117 4 346.92 2.92 297 116 121 5 460.54 0.42 298 117 122 5 456.59 0.64 299 117 125 8 414.62 20.64 300 118 121 3 474.73 1.19 301 118 122 4 474.72 1.19 302 119 122 3 482.38 2.64 303 119 123 4 476.53 0.28 304 120 123 3 476.54 0.29 305 120 124 4 469.80 3.65 306 121 124 3 476.51 0.28 307 121 125 4 468.44 4.30 308 122 125 3 469.11 1.66 309 122 126 4 462.55 1.34 310 123 126 3 466.88 2.19 311 123 127 4 465.17 0.46 312 124 127 3 465.42 0.58 313 124 128 4 470.88 2.40 314 125 128 3 476.71 0.52 315 125 129 4 470.88 2.40 316 126 129 3 484.69 3.22 317 126 130 4 476.44 0.66 318 127 130 3 476.72 0.52 319 127 131 4 476.71 0.52 320 128 131 3 477.85 0.04 321 128 132 4 476.71 0.52 322 129 132 3 476.71 0.52 323 129 133 4 462.82 1.68 324 130 133 3 469.77 0.42 325 130 134 4 462.82 1.67 326 131 134 3 463.90 2.21 327 131 135 4 460.23 0.72 328 132 135 3 464.31 1.54 329 132 136 4 460.11 0.67 330 133 136 3 471.50 2.02 331 133 137 4 468.64 3.60 332 134 137 3 474.23 1.86 333 134 138 4 460.02 0.68 334 135 138 3 476.87 0.06 335 136 140 4 499.03 3.17 336 137 140 3 488.38 1.19