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 3 6 3 402.72 1.62 2 3 7 4 383.65 2.08 3 3 55 52 32.20 1.07 4 3 56 53 32.20 1.07 5 4 7 3 406.42 2.69 6 4 8 4 382.59 2.61 7 4 55 51 32.21 1.07 8 4 104 100 32.23 1.06 9 4 107 103 32.20 1.06 10 4 108 104 31.84 1.19 11 4 111 107 31.70 1.20 12 5 8 3 408.25 1.78 13 5 9 4 396.79 7.51 14 5 10 5 376.99 0.11 15 5 11 6 377.56 0.39 16 5 14 9 308.08 9.75 17 5 52 47 32.23 1.08 18 5 55 50 32.23 1.08 19 5 57 52 32.25 1.09 20 6 9 3 401.83 0.71 21 6 10 4 377.00 0.12 22 7 104 97 33.70 0.40 23 8 13 5 367.03 7.48 24 8 55 47 34.27 0.30 25 8 100 92 34.18 0.35 26 8 104 96 33.77 0.42 27 8 108 100 33.70 0.41 28 9 13 4 375.16 3.42 29 10 13 3 406.68 0.26 30 10 14 4 388.66 2.93 31 11 14 3 405.31 0.42 32 11 15 4 391.05 1.74 33 12 15 3 405.36 0.41 34 12 16 4 398.29 1.88 35 13 16 3 411.36 2.60 36 13 17 4 399.97 0.05 37 13 98 85 75.57 0.66 38 14 17 3 401.34 0.62 39 14 18 4 401.32 0.62 40 14 48 34 66.70 0.72 41 14 51 37 64.80 0.23 42 14 52 38 64.79 0.22 43 14 55 41 64.80 0.22 44 15 18 3 411.29 1.02 45 15 19 4 401.33 0.62 46 15 48 33 73.75 3.50 47 16 19 3 411.28 1.02 48 16 20 4 401.33 0.62 49 16 98 82 89.38 0.85 50 17 20 3 401.44 0.68 51 17 21 4 393.10 0.92 52 17 94 77 81.21 0.78 53 17 95 78 81.23 0.79 54 17 98 81 89.92 0.87 55 18 21 3 401.66 0.73 56 18 22 4 397.42 1.05 57 18 44 26 84.64 0.40 58 18 47 29 83.17 0.17 59 18 48 30 81.44 0.70 60 18 51 33 81.43 0.70 61 19 22 3 414.17 0.85 62 19 23 4 395.28 0.03 63 19 44 25 87.03 1.42 64 19 48 29 86.53 1.38 65 20 23 3 395.86 0.12 66 20 24 4 395.74 0.18 67 20 94 74 91.25 0.67 68 21 24 3 400.34 2.35 69 21 25 4 395.75 0.18 70 21 87 66 91.23 0.67 71 21 90 69 91.25 0.67 72 21 91 70 91.16 0.64 73 21 94 73 91.33 0.63 74 22 25 3 395.75 0.19 75 22 26 4 395.74 0.19 76 22 35 13 191.91 0.04 77 22 40 18 95.00 1.19 78 22 43 21 93.90 0.66 79 22 44 22 93.39 0.47 80 22 47 25 93.19 0.54 81 23 26 3 407.56 1.16 82 23 27 4 397.50 1.04 83 24 27 3 409.24 2.00 84 24 28 4 397.50 1.05 85 24 90 66 95.21 1.34 86 24 93 69 95.33 1.38 87 24 94 70 95.34 1.37 88 24 97 73 95.55 1.38 89 25 28 3 397.47 1.06 90 25 31 6 347.68 15.79 91 25 32 7 290.87 6.00 92 25 35 10 207.80 4.15 93 25 90 65 95.29 1.36 94 26 32 6 272.48 15.20 95 26 35 9 210.35 2.86 96 26 40 14 177.78 1.53 97 28 31 3 417.87 1.17 98 28 32 4 398.69 1.98 99 28 86 58 95.34 1.37 100 28 90 62 95.38 1.36 101 29 32 3 418.32 0.94 102 29 33 4 414.61 0.73 103 30 33 3 519.27 0.76 104 30 83 53 95.16 1.42 105 30 86 56 95.31 1.38 106 30 89 59 95.55 1.38 107 30 90 60 95.55 1.37 108 31 34 3 419.86 3.35 109 31 83 52 95.15 1.43 110 31 86 55 95.31 1.39 111 31 87 56 95.35 1.38 112 31 90 59 95.53 1.38 113 32 35 3 414.33 0.59 114 33 36 3 403.01 0.23 115 34 38 4 409.61 0.55 116 34 77 43 94.14 1.90 117 34 79 45 94.47 1.72 118 34 83 49 95.19 1.46 119 35 38 3 398.74 2.35 120 35 40 5 359.83 13.28 121 35 43 8 316.84 6.19 122 38 43 5 384.26 0.03 123 39 42 3 406.12 1.79 124 39 43 4 389.36 2.57 125 40 43 3 398.64 1.81 126 40 44 4 389.38 2.56 127 41 44 3 403.22 0.16 128 41 45 4 398.38 1.94 129 42 45 3 406.37 1.39 130 42 46 4 394.74 0.12 131 43 46 3 406.03 1.56 132 43 47 4 398.96 2.00 133 44 47 3 408.86 2.95 134 44 48 4 398.99 2.00 135 45 48 3 408.88 2.94 136 45 49 4 399.51 1.75 137 46 49 3 408.30 2.64 138 46 50 4 398.56 2.23 139 46 61 15 95.95 1.53 140 47 50 3 400.60 1.21 141 47 51 4 398.55 2.23 142 48 51 3 415.63 3.62 143 48 52 4 398.54 2.23 144 49 52 3 402.89 0.01 145 49 53 4 402.88 0.01 146 49 61 12 126.50 16.76 147 50 53 3 402.85 0.02 148 50 54 4 397.61 2.64 149 50 61 11 95.94 1.53 150 50 66 16 95.47 1.58 151 51 54 3 398.94 1.96 152 51 55 4 387.38 2.44 153 51 91 40 96.33 1.47 154 52 55 3 400.41 1.20 155 52 56 4 387.41 2.46 156 52 57 5 293.10 6.79 157 52 58 6 268.99 2.22 158 53 56 3 393.51 0.59 159 53 58 5 257.61 3.47 160 53 59 6 257.60 3.47 161 53 60 7 231.19 16.61 162 53 61 8 187.60 5.12 163 54 111 57 96.07 1.56 164 55 108 53 96.28 1.48 165 55 111 56 96.16 1.53 166 61 64 3 508.01 3.04 167 64 68 4 393.61 0.12 168 64 69 5 382.91 5.22 169 65 68 3 407.96 1.03 170 65 69 4 393.60 0.10 171 66 69 3 402.13 3.95 172 66 70 4 398.31 2.25 173 66 117 51 158.30 1.14 174 66 120 54 158.12 1.05 175 66 121 55 158.15 1.02 176 67 70 3 412.87 0.76 177 67 71 4 393.59 0.10 178 67 119 52 158.16 1.03 179 67 120 53 158.11 1.05 180 67 123 56 158.06 1.04 181 67 124 57 158.07 1.04 182 68 71 3 412.19 1.09 183 70 73 3 399.68 1.07 184 70 74 4 392.50 3.75 185 70 79 9 204.61 1.77 186 70 121 51 158.34 1.09 187 71 74 3 398.91 1.46 188 71 75 4 383.66 0.68 189 71 123 52 158.18 1.03 190 72 75 3 401.13 0.34 191 72 76 4 379.31 3.64 192 72 77 5 365.79 3.12 193 73 77 4 364.68 2.60 194 73 78 5 351.61 9.13 195 73 79 6 251.88 3.56 196 74 79 5 245.20 6.90 197 74 121 47 158.78 1.02 198 74 122 48 158.69 1.04 199 74 123 49 158.47 1.07 200 78 83 5 397.12 1.96 201 79 83 4 393.56 0.18 202 79 121 42 159.59 1.02 203 79 122 43 159.22 0.92 204 80 83 3 415.49 2.19 205 80 84 4 400.58 0.24 206 80 122 42 159.31 0.87 207 81 84 3 400.57 0.24 208 81 85 4 393.88 0.34 209 81 118 37 159.96 0.97 210 81 122 41 159.82 0.93 211 82 85 3 400.73 0.16 212 82 86 4 397.56 1.51 213 83 86 3 397.56 1.50 214 83 87 4 397.56 1.51 215 84 87 3 400.79 0.10 216 84 88 4 397.51 1.53 217 84 112 28 161.33 0.61 218 84 113 29 161.24 0.58 219 84 117 33 161.00 0.59 220 84 118 34 160.00 0.96 221 84 121 37 160.01 0.96 222 84 122 38 159.93 0.97 223 85 88 3 397.52 1.54 224 85 89 4 396.11 2.23 225 86 89 3 402.77 1.11 226 86 90 4 402.73 1.13 227 87 90 3 402.74 1.13 228 87 91 4 395.29 0.65 229 88 91 3 404.76 2.16 230 88 92 4 395.29 0.65 231 88 112 24 161.43 0.65 232 89 92 3 402.95 1.00 233 89 93 4 392.42 0.39 234 90 93 3 399.69 2.64 235 90 94 4 392.42 0.39 236 91 94 3 398.88 3.14 237 91 95 4 392.60 0.30 238 91 108 17 164.16 1.41 239 91 112 21 163.21 1.32 240 92 95 3 394.01 2.52 241 92 96 4 389.48 0.26 242 92 105 13 164.25 1.47 243 92 108 16 164.16 1.42 244 92 109 17 164.06 1.38 245 93 96 3 398.99 3.12 246 93 97 4 393.36 1.66 247 94 97 3 393.37 1.66 248 94 98 4 393.36 1.66 249 95 98 3 396.76 0.04 250 95 99 4 393.36 1.66 251 95 100 5 313.91 4.73 252 95 105 10 177.41 8.03 253 95 108 13 164.33 1.48 254 96 99 3 399.42 1.38 255 96 105 9 235.48 1.44 256 100 104 4 387.63 4.97 257 100 105 5 381.07 1.70 258 101 104 3 413.13 1.88 259 101 105 4 387.62 4.96 260 102 105 3 399.52 0.98 261 102 106 4 387.65 4.96 262 103 106 3 396.86 0.36 263 103 107 4 393.31 2.13 264 104 107 3 399.74 1.14 265 104 108 4 393.25 2.10 266 105 108 3 404.44 2.33 267 105 109 4 391.67 1.31 268 106 109 3 398.15 1.93 269 106 110 4 391.67 1.31 270 107 110 3 399.03 3.08 271 107 111 4 393.18 0.57 272 108 111 3 409.54 2.18 273 108 112 4 389.49 2.40 274 109 112 3 401.98 3.88 275 109 113 4 381.08 1.88 276 110 114 4 366.85 5.13 277 111 114 3 392.60 1.64 278 111 117 6 298.81 11.55 279 112 117 5 298.93 11.52 280 114 117 3 393.81 4.75 281 114 118 4 392.64 0.44 282 115 118 3 398.39 2.43 283 115 119 4 352.56 2.86 284 116 120 4 384.47 0.21 285 117 120 3 409.11 0.43 286 117 121 4 374.31 4.87 287 118 121 3 402.13 2.75 288 118 122 4 377.06 3.50 289 119 122 3 404.24 1.69 290 119 123 4 377.12 3.53 291 119 124 5 316.66 2.48 292 120 123 3 371.17 6.50