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 29.88 0.75 2 2 127 125 22.95 0.79 3 2 128 126 22.95 0.79 4 2 131 129 22.93 0.77 5 3 6 3 482.19 1.11 6 3 7 4 471.56 2.94 7 4 7 3 481.73 2.15 8 4 8 4 475.42 1.01 9 5 8 3 490.06 6.31 10 5 9 4 474.18 0.39 11 6 9 3 491.66 5.51 12 6 10 4 474.18 0.39 13 6 124 118 48.76 0.10 14 6 127 121 49.09 0.24 15 7 10 3 482.28 0.53 16 7 11 4 474.17 0.40 17 7 73 66 50.04 0.68 18 7 74 67 52.50 1.90 19 8 11 3 482.28 0.53 20 8 12 4 474.55 0.21 21 9 12 3 483.25 4.13 22 9 13 4 474.56 0.21 23 9 121 112 62.96 1.21 24 9 124 115 62.94 1.21 25 10 13 3 479.00 0.60 26 10 14 4 474.41 2.87 27 10 70 60 62.95 1.22 28 10 124 114 62.97 1.22 29 10 125 115 62.95 1.22 30 10 128 118 62.93 1.21 31 11 14 3 482.29 1.04 32 11 15 4 475.39 2.43 33 11 70 59 62.96 1.22 34 11 73 62 62.97 1.22 35 12 15 3 479.67 0.29 36 12 16 4 478.79 0.76 37 13 16 3 481.83 0.76 38 13 17 4 478.79 0.76 39 13 121 108 63.24 1.16 40 13 125 112 63.20 1.15 41 14 17 3 481.81 0.74 42 14 18 4 478.79 0.77 43 14 63 49 63.20 1.15 44 14 66 52 63.20 1.14 45 14 67 53 63.20 1.15 46 14 70 56 63.21 1.14 47 14 109 95 76.09 1.09 48 15 18 3 481.87 0.72 49 16 113 97 92.70 1.46 50 16 116 100 81.26 3.47 51 17 20 3 480.50 2.64 52 17 21 4 444.65 6.97 53 17 24 7 409.65 5.12 54 17 109 92 81.53 3.77 55 17 113 96 93.93 1.81 56 18 21 3 497.40 1.28 57 20 23 3 478.11 4.50 58 20 24 4 470.10 2.33 59 21 24 3 485.70 0.70 60 21 25 4 476.79 1.48 61 21 63 42 104.35 0.69 62 22 25 3 477.27 1.72 63 22 26 4 476.80 1.48 64 22 59 37 108.89 0.82 65 22 60 38 107.78 0.41 66 22 63 41 107.69 0.42 67 23 26 3 479.39 2.77 68 23 27 4 476.80 1.48 69 24 27 3 477.28 3.83 70 24 28 4 472.62 3.57 71 24 108 84 128.48 1.82 72 24 109 85 134.68 0.17 73 24 112 88 136.54 0.30 74 24 113 89 136.81 0.17 75 25 28 3 476.65 5.21 76 25 29 4 475.21 4.87 77 25 59 34 120.95 0.10 78 26 29 3 482.93 1.58 79 26 30 4 482.93 1.58 80 26 55 29 132.53 0.60 81 26 56 30 132.31 0.50 82 26 59 33 121.45 0.27 83 27 30 3 482.90 1.59 84 27 31 4 473.35 3.00 85 27 108 81 136.85 0.18 86 27 112 85 138.53 0.07 87 28 31 3 480.92 0.80 88 28 32 4 473.36 2.99 89 28 101 73 136.81 0.18 90 28 104 76 136.83 0.18 91 28 105 77 136.82 0.18 92 28 108 80 138.09 0.01 93 29 32 3 480.89 0.78 94 29 33 4 473.36 2.99 95 29 55 26 137.36 0.43 96 29 58 29 137.35 0.43 97 29 59 30 137.34 0.42 98 29 62 33 137.31 0.42 99 29 101 72 136.84 0.18 100 30 33 3 481.80 0.33 101 30 34 4 479.54 0.10 102 30 50 20 139.50 0.44 103 31 34 3 481.81 0.33 104 31 35 4 468.55 0.69 105 31 104 73 138.52 0.12 106 31 107 76 138.81 0.24 107 31 108 77 139.21 0.43 108 31 111 80 139.56 0.43 109 32 35 3 480.88 0.80 110 32 36 4 461.54 4.19 111 32 39 7 343.57 16.74 112 32 100 68 138.48 0.14 113 32 101 69 138.48 0.14 114 32 104 72 138.56 0.12 115 33 37 4 451.05 1.05 116 33 39 6 343.51 16.77 117 33 40 7 298.68 5.63 118 33 43 10 266.69 5.45 119 33 48 15 139.62 0.49 120 33 55 22 139.50 0.44 121 34 37 3 495.10 1.45 122 36 39 3 501.43 3.43 123 36 100 64 138.54 0.17 124 36 103 67 139.53 0.43 125 36 104 68 139.53 0.43 126 37 40 3 496.51 5.36 127 38 41 3 516.04 0.54 128 39 42 3 516.04 0.54 129 39 97 58 138.57 0.18 130 39 100 61 139.50 0.41 131 40 43 3 492.69 1.48 132 40 48 8 203.12 25.64 133 41 44 3 504.36 1.22 134 42 91 49 138.72 0.26 135 42 92 50 138.73 0.26 136 42 93 51 138.74 0.25 137 42 94 52 139.22 0.43 138 42 97 55 139.51 0.40 139 43 46 3 485.66 4.53 140 43 48 5 428.51 18.21 141 43 58 15 195.86 27.48 142 45 54 9 204.24 25.26 143 46 54 8 204.24 25.26 144 46 55 9 204.24 25.26 145 46 58 12 204.22 25.27 146 47 52 5 345.83 31.87 147 47 54 7 217.94 32.08 148 47 55 8 217.94 32.08 149 48 55 7 217.94 32.08 150 49 52 3 492.38 1.25 151 51 56 5 471.35 0.29 152 52 55 3 479.09 1.54 153 52 56 4 471.39 0.31 154 53 56 3 471.42 0.30 155 53 57 4 471.39 0.30 156 54 57 3 479.88 0.01 157 54 58 4 472.86 0.99 158 55 58 3 475.36 2.25 159 55 59 4 472.90 1.02 160 56 59 3 475.48 2.19 161 56 60 4 473.06 0.96 162 57 60 3 488.78 0.55 163 57 61 4 473.06 0.96 164 58 61 3 473.06 0.96 165 58 62 4 473.05 0.96 166 59 62 3 480.03 2.56 167 59 63 4 473.01 0.94 168 60 63 3 472.82 0.29 169 60 64 4 464.43 3.31 170 61 64 3 478.29 2.08 171 61 65 4 469.14 2.21 172 62 65 3 480.37 0.88 173 62 66 4 465.72 3.94 174 63 66 3 478.23 0.19 175 63 67 4 465.73 3.93 176 64 67 3 467.45 3.99 177 64 68 4 465.80 3.89 178 65 68 3 476.93 3.58 179 65 69 4 463.90 2.94 180 65 80 15 176.75 1.24 181 65 83 18 164.47 0.43 182 66 69 3 479.49 4.86 183 66 70 4 463.95 2.91 184 66 105 39 184.91 1.42 185 66 128 62 192.12 2.43 186 66 129 63 182.92 0.48 187 66 132 66 179.50 0.04 188 67 70 3 478.19 0.19 189 67 71 4 469.61 0.09 190 68 71 3 479.70 1.06 191 68 72 4 461.28 1.58 192 68 79 11 180.39 0.48 193 69 72 3 477.54 2.17 194 69 73 4 458.44 2.85 195 69 76 7 278.95 2.60 196 69 80 11 196.84 7.46 197 69 128 59 192.58 2.23 198 69 132 63 190.38 3.26 199 70 73 3 476.78 1.79 200 70 128 58 192.74 2.31 201 72 75 3 470.13 3.02 202 72 76 4 438.76 2.24 203 72 79 7 333.97 11.25 204 73 76 3 473.93 4.91 205 73 128 55 233.53 13.09 206 75 78 3 499.25 4.71 207 75 79 4 473.94 0.56 208 76 79 3 486.55 1.65 209 76 80 4 465.50 2.29 210 76 128 52 235.06 13.33 211 76 131 55 234.90 13.39 212 76 132 56 234.49 13.54 213 76 135 59 234.45 13.53 214 77 80 3 490.68 0.42 215 77 81 4 453.61 8.22 216 77 135 58 234.45 13.53 217 78 81 3 480.09 3.37 218 80 83 3 477.97 3.13 219 80 84 4 474.11 5.08 220 80 132 52 236.06 13.78 221 80 135 55 235.94 13.80 222 80 136 56 235.97 13.79 223 81 84 3 480.26 2.00 224 81 85 4 474.13 5.08 225 81 139 58 235.57 13.98 226 82 85 3 481.66 1.32 227 82 86 4 480.76 1.76 228 83 86 3 484.64 3.70 229 83 87 4 474.12 5.08 230 83 136 53 236.22 13.85 231 84 87 3 488.93 2.31 232 84 88 4 469.69 7.30 233 84 135 51 236.25 13.86 234 84 136 52 236.19 13.87 235 84 139 55 235.69 14.04 236 85 88 3 482.39 1.69 237 85 89 4 455.89 4.29 238 85 90 5 446.15 0.58 239 85 139 54 236.01 13.88 240 86 90 4 441.96 2.44 241 86 91 5 422.58 12.12 242 87 91 4 397.32 14.92 243 87 92 5 368.71 8.11 244 87 93 6 316.65 6.34 245 87 98 11 271.01 0.93 246 88 92 4 358.04 13.44 247 88 139 51 236.18 13.89 248 88 140 52 236.16 13.91 249 89 92 3 478.35 0.32 250 89 139 50 236.22 13.88 251 92 140 48 236.37 13.88 252 93 97 4 482.78 3.19 253 93 98 5 479.92 1.79 254 93 140 47 236.42 13.87 255 94 97 3 491.53 1.19 256 94 98 4 491.53 1.19 257 95 98 3 491.31 1.30 258 95 137 42 236.61 13.94 259 95 140 45 236.59 13.95 260 96 99 3 491.11 1.40 261 96 100 4 482.31 3.00 262 97 100 3 482.23 0.65 263 97 101 4 474.19 1.07 264 98 101 3 482.56 0.42 265 98 102 4 468.20 1.13 266 98 133 35 237.06 13.81 267 98 136 38 237.09 13.81 268 98 137 39 237.06 13.80 269 99 102 3 476.22 2.35 270 99 103 4 471.60 2.39 271 100 103 3 482.39 0.34 272 100 104 4 473.89 1.24 273 101 104 3 479.32 1.87 274 101 105 4 473.88 1.26 275 102 105 3 488.22 2.58 276 102 106 4 476.01 0.21 277 102 129 27 237.41 13.74 278 102 133 31 237.40 13.73 279 103 106 3 478.62 1.07 280 103 107 4 476.03 0.21 281 104 107 3 476.36 0.06 282 104 108 4 476.03 0.21 283 105 108 3 479.22 1.49 284 105 109 4 476.00 0.21 285 105 129 24 238.63 13.88 286 106 109 3 482.90 3.32 287 106 110 4 463.89 1.16 288 106 117 11 240.19 13.44 289 106 122 16 239.22 13.68 290 106 125 19 239.08 13.78 291 106 126 20 238.79 13.92 292 106 129 23 238.73 13.84 293 107 110 3 469.73 1.02 294 107 111 4 463.85 1.15 295 108 111 3 472.61 3.08 296 108 112 4 463.54 3.21 297 109 112 3 477.62 0.58 298 109 113 4 453.00 4.26 299 109 125 16 239.38 13.74 300 110 117 7 239.56 13.71 301 113 116 3 469.23 0.38 302 113 117 4 447.00 5.29 303 115 118 3 522.96 2.18 304 116 121 5 465.25 0.04 305 117 121 4 465.36 0.01 306 117 122 5 462.51 1.41 307 117 125 8 421.26 10.48 308 118 121 3 471.86 3.26 309 118 122 4 471.86 3.26 310 119 122 3 476.50 5.58 311 119 123 4 471.86 3.26 312 120 123 3 477.78 0.30 313 120 124 4 477.78 0.29 314 121 124 3 480.01 1.41 315 121 125 4 477.77 0.29 316 122 125 3 483.03 2.92 317 122 126 4 470.67 2.73 318 123 126 3 476.64 0.26 319 123 127 4 476.72 0.35 320 124 127 3 482.94 2.75 321 124 128 4 473.30 1.34 322 125 128 3 476.58 0.42 323 125 129 4 476.57 0.42 324 126 129 3 478.09 0.33 325 126 130 4 476.57 0.42 326 127 130 3 480.46 0.85 327 127 131 4 467.35 1.28 328 128 131 3 474.00 3.75 329 128 132 4 465.64 0.42 330 129 132 3 472.61 3.06 331 129 133 4 465.64 0.42 332 130 133 3 469.23 4.11 333 130 134 4 462.69 1.64 334 131 134 3 473.94 1.69 335 131 135 4 462.31 1.83 336 132 135 3 474.90 4.93 337 132 136 4 462.31 1.84 338 133 136 3 473.86 4.58 339 133 137 4 461.06 2.46 340 134 137 3 479.43 1.79 341 134 138 4 460.54 2.73 342 135 138 3 484.51 0.75 343 137 140 3 480.74 0.15 344 137 141 4 476.86 0.10 345 138 141 3 483.56 3.25