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 6 10 4 459.07 4.25 2 6 34 28 102.80 2.41 3 6 36 30 102.34 2.64 4 6 40 34 102.13 2.69 5 6 44 38 101.47 2.65 6 7 10 3 473.95 0.18 7 7 11 4 471.59 1.06 8 7 44 37 101.33 2.73 9 7 47 40 101.42 2.67 10 7 48 41 101.01 2.79 11 8 11 3 472.50 0.60 12 8 12 4 471.58 1.06 13 9 12 3 471.59 1.06 14 9 13 4 471.56 1.06 15 9 34 25 103.89 2.42 16 10 13 3 470.62 1.55 17 10 14 4 464.59 1.47 18 10 25 15 105.11 2.81 19 10 44 34 101.77 2.64 20 10 48 38 101.62 2.60 21 10 50 40 101.12 2.85 22 11 14 3 470.52 1.45 23 11 15 4 464.52 1.44 24 11 48 37 101.62 2.60 25 11 64 53 89.46 2.69 26 12 15 3 471.09 2.87 27 12 16 4 466.37 0.51 28 13 16 3 473.85 1.49 29 13 17 4 458.30 1.67 30 13 25 12 105.64 2.98 31 13 28 15 105.14 2.81 32 13 29 16 105.14 2.81 33 13 32 19 105.14 2.81 34 14 17 3 463.86 0.74 35 14 50 36 101.62 2.60 36 14 62 48 90.22 3.02 37 14 63 49 89.50 2.69 38 17 28 11 269.57 69.80 39 18 55 37 90.89 2.94 40 18 61 43 90.52 3.14 41 19 24 5 441.14 11.58 42 19 25 6 402.47 8.60 43 19 28 9 408.63 3.85 44 19 61 42 90.52 3.14 45 19 62 43 90.53 3.15 46 20 24 4 467.24 2.71 47 20 59 39 90.95 2.98 48 20 60 40 90.83 3.04 49 21 24 3 470.74 3.79 50 21 25 4 467.18 0.11 51 21 62 41 90.84 3.06 52 22 25 3 474.36 0.01 53 22 26 4 466.33 0.54 54 22 38 16 104.31 2.38 55 22 62 40 90.59 3.19 56 23 26 3 470.87 1.73 57 23 27 4 466.33 0.54 58 23 38 15 104.32 2.38 59 24 27 3 475.70 0.61 60 24 28 4 466.33 0.54 61 25 28 3 480.09 0.96 62 25 29 4 472.58 0.92 63 25 41 16 104.22 2.40 64 25 45 20 103.74 2.46 65 26 29 3 479.71 2.62 66 26 30 4 472.60 0.92 67 26 41 15 104.13 2.47 68 27 30 3 472.60 0.93 69 27 31 4 472.60 0.93 70 28 31 3 473.27 0.59 71 28 32 4 472.58 0.93 72 29 32 3 472.56 0.94 73 29 33 4 460.91 4.88 74 29 34 5 433.38 6.16 75 29 36 7 234.99 2.96 76 29 41 12 105.03 2.38 77 30 33 3 460.07 0.90 78 36 40 4 471.18 0.90 79 36 41 5 450.24 0.92 80 37 40 3 472.10 0.44 81 37 41 4 472.12 0.43 82 38 41 3 477.09 0.96 83 38 42 4 472.11 0.43 84 39 42 3 488.24 0.14 85 39 43 4 472.11 0.43 86 40 43 3 479.61 4.18 87 40 44 4 470.53 0.36 88 41 44 3 479.61 4.18 89 41 45 4 469.03 0.39 90 42 45 3 472.47 1.35 91 42 46 4 470.93 1.34 92 43 46 3 472.12 0.75 93 43 47 4 469.01 0.39 94 44 47 3 467.28 1.26 95 44 48 4 467.16 1.22 96 45 48 3 472.50 1.54 97 45 49 4 467.05 1.18 98 45 50 5 411.54 2.18 99 46 49 3 464.47 1.23 100 49 65 16 114.58 3.50 101 50 62 12 115.25 3.40 102 50 63 13 114.83 3.58 103 50 64 14 114.70 3.54 104 51 62 11 115.27 3.39 105 51 63 12 114.84 3.58 106 51 65 14 114.73 3.55 107 51 70 19 114.72 3.55 108 52 60 8 115.88 3.33 109 52 61 9 115.56 3.31 110 52 62 10 115.31 3.40 111 53 60 7 115.98 3.32 112 53 61 8 115.89 3.35 113 53 63 10 115.53 3.31 114 53 67 14 115.20 3.43 115 53 69 16 114.78 3.60 116 53 70 17 114.70 3.54 117 54 59 5 124.15 1.75 118 54 60 6 121.69 0.56 119 54 69 15 114.81 3.61 120 55 58 3 460.20 3.10 121 55 59 4 237.36 3.08 122 55 61 6 122.91 1.17 123 63 67 4 441.04 12.70 124 64 67 3 476.38 0.73 125 65 70 5 228.12 3.04 126 65 75 10 214.40 3.54 127 66 75 9 210.77 0.44 128 67 70 3 472.62 1.85 129 67 75 8 368.93 12.26 130 68 72 4 450.03 1.05 131 68 75 7 368.93 12.26 132 68 108 40 208.56 0.66 133 68 109 41 207.69 1.10 134 68 112 44 203.97 2.88 135 69 72 3 473.92 1.23 136 70 75 5 467.28 0.84 137 71 74 3 481.48 3.56 138 71 75 4 469.38 0.19 139 72 75 3 478.89 6.04 140 72 76 4 467.30 0.83 141 72 109 37 218.04 1.23 142 72 112 40 217.67 1.38 143 72 113 41 217.66 1.38 144 73 76 3 474.44 2.72 145 73 77 4 467.31 0.84 146 73 113 40 217.72 1.38 147 73 115 42 217.73 1.39 148 73 148 75 159.92 1.32 149 74 77 3 478.05 1.84 150 74 78 4 467.31 0.84 151 75 78 3 467.41 0.05 152 75 79 4 465.71 0.11 153 75 109 34 218.28 1.27 154 76 79 3 466.37 0.22 155 76 80 4 465.69 0.12 156 76 106 30 218.38 1.28 157 76 109 33 218.30 1.26 158 76 110 34 218.28 1.27 159 76 113 37 218.28 1.27 160 76 145 69 176.22 1.11 161 76 148 72 160.27 1.49 162 77 80 3 474.34 4.21 163 77 81 4 465.66 0.14 164 77 148 71 159.91 1.32 165 78 81 3 483.61 4.48 166 78 82 4 465.68 0.14 167 79 82 3 471.14 1.80 168 79 83 4 462.31 1.31 169 79 106 27 231.50 5.20 170 79 109 30 231.48 5.20 171 80 83 3 463.44 0.75 172 80 84 4 453.56 2.83 173 80 96 16 286.97 6.11 174 80 106 26 262.12 10.11 175 80 145 65 179.38 2.53 176 80 148 68 160.35 1.48 177 80 149 69 159.99 1.34 178 82 99 17 342.05 0.28 179 83 98 15 341.56 0.42 180 83 99 16 341.94 0.23 181 83 102 19 341.52 0.40 182 83 106 23 340.79 0.03 183 84 96 12 342.42 0.36 184 84 149 65 160.38 1.46 185 85 97 12 342.56 0.38 186 85 98 13 342.50 0.38 187 85 99 14 342.51 0.38 188 86 96 10 342.63 0.35 189 86 97 11 342.62 0.35 190 87 94 7 342.75 0.41 191 87 95 8 342.64 0.35 192 87 96 9 342.63 0.35 193 87 145 58 193.38 3.06 194 87 146 59 180.53 2.58 195 88 94 6 342.75 0.41 196 88 95 7 342.71 0.39 197 89 93 4 348.13 2.81 198 89 94 5 342.75 0.41 199 89 138 49 226.78 3.36 200 89 142 53 210.15 3.00 201 90 93 3 465.67 0.32 202 90 138 48 227.41 3.42 203 91 135 44 243.66 8.88 204 92 132 40 341.87 0.19 205 92 133 41 341.87 0.19 206 92 134 42 335.38 1.21 207 92 138 46 227.56 3.35 208 93 129 36 342.73 0.34 209 93 130 37 342.68 0.34 210 93 131 38 342.25 0.36 211 93 138 45 226.96 3.31 212 94 129 35 342.73 0.34 213 94 130 36 342.63 0.31 214 94 138 44 226.78 3.36 215 94 142 48 195.12 3.70 216 94 145 51 195.10 3.71 217 95 127 32 343.08 0.38 218 95 128 33 342.79 0.34 219 95 129 34 342.72 0.33 220 96 106 10 343.16 0.38 221 96 110 14 343.06 0.36 222 96 127 31 343.11 0.38 223 96 128 32 342.93 0.38 224 97 126 29 351.75 4.68 225 97 127 30 343.10 0.37 226 98 102 4 451.43 6.31 227 98 103 5 356.84 2.17 228 98 106 8 356.93 2.21 229 98 126 28 351.79 4.67 230 98 128 30 351.75 4.67 231 99 102 3 477.53 3.91 232 99 126 27 370.86 9.22 233 100 125 25 379.18 9.14 234 100 126 26 374.54 11.00 235 101 125 24 379.67 9.39 236 102 105 3 487.83 0.64 237 102 106 4 455.51 4.38 238 102 125 23 380.13 9.36 239 103 106 3 475.60 2.02 240 103 107 4 455.55 4.40 241 103 123 20 380.00 9.33 242 103 124 21 380.13 9.35 243 103 125 22 380.13 9.36 244 103 126 23 380.12 9.36 245 103 127 24 380.10 9.37 246 103 128 25 380.01 9.34 247 104 107 3 472.09 3.85 248 104 108 4 472.35 3.73 249 104 123 19 380.00 9.33 250 104 124 20 380.19 9.38 251 105 108 3 472.36 3.73 252 105 109 4 472.36 3.73 253 106 109 3 472.37 3.73 254 106 110 4 472.36 3.72 255 106 128 22 380.57 9.17 256 107 110 3 472.37 3.73 257 107 111 4 477.01 6.05 258 107 123 16 380.65 9.15 259 107 128 21 380.51 9.20 260 108 111 3 480.50 4.30 261 108 112 4 477.00 6.05 262 109 112 3 476.76 6.18 263 109 113 4 473.50 7.81 264 110 113 3 482.69 3.21 265 110 114 4 473.50 7.81 266 110 118 8 380.80 9.25 267 110 128 18 380.98 9.22 268 110 130 20 380.88 9.25 269 110 145 35 179.09 2.43 270 111 114 3 466.69 4.42 271 111 121 10 380.88 9.26 272 115 118 3 473.83 1.02 273 115 141 26 210.05 11.94 274 115 144 29 210.04 11.94 275 115 145 30 210.03 11.94 276 116 133 17 380.94 9.27 277 117 132 15 381.00 9.26 278 117 133 16 380.94 9.27 279 117 137 20 266.56 8.28 280 117 141 24 210.07 11.94 281 117 144 27 210.51 12.16 282 118 121 3 565.62 2.27 283 118 130 12 381.15 9.25 284 118 131 13 381.12 9.24 285 118 133 15 381.03 9.26 286 118 141 23 216.74 8.60 287 119 131 12 381.13 9.25 288 119 132 13 381.10 9.25 289 119 133 14 381.06 9.23 290 120 130 10 381.26 9.20 291 120 131 11 381.15 9.24 292 121 129 8 381.30 9.21 293 121 130 9 381.26 9.20 294 122 128 6 381.36 9.21 295 122 129 7 381.31 9.21 296 123 127 4 385.10 10.29 297 123 128 5 381.35 9.21 298 124 127 3 453.44 1.90 299 130 145 15 187.57 5.96 300 132 137 5 412.73 22.64 301 132 138 6 226.56 3.68 302 132 141 9 223.67 5.13 303 134 137 3 466.95 1.82 304 134 138 4 457.76 0.17 305 135 138 3 470.12 0.21 306 135 139 4 457.78 0.18 307 136 139 3 463.92 2.90 308 136 140 4 457.78 0.18 309 137 140 3 457.79 0.18 310 137 141 4 464.88 3.73 311 138 141 3 474.07 0.86 312 138 142 4 462.76 4.79 313 139 142 3 467.72 2.31 314 139 143 4 462.76 4.79 315 140 143 3 477.43 5.04 316 140 144 4 462.78 4.80 317 141 144 3 470.33 4.20 318 141 145 4 462.76 4.83 319 142 145 3 472.42 0.01 320 142 146 4 471.66 0.39 321 143 146 3 472.33 0.72 322 143 147 4 471.66 0.39 323 144 147 3 472.33 0.72 324 144 148 4 471.66 0.39 325 145 148 3 474.92 2.19 326 145 149 4 461.55 0.62 327 146 149 3 472.66 4.94