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 1 53 52 146.56 0.86 2 1 54 53 146.46 0.81 3 2 5 3 369.26 1.03 4 2 6 4 342.42 9.12 5 2 53 51 146.59 0.87 6 2 98 96 32.39 0.25 7 2 101 99 32.27 0.30 8 2 102 100 31.80 0.10 9 2 105 103 31.80 0.10 10 3 6 3 375.74 2.17 11 3 7 4 369.07 1.12 12 3 8 5 312.81 5.01 13 3 9 6 312.69 5.07 14 3 12 9 256.53 4.08 15 3 50 47 146.63 0.86 16 3 53 50 146.63 0.86 17 3 54 51 146.64 0.85 18 3 55 52 146.60 0.84 19 3 56 53 146.64 0.85 20 4 7 3 353.66 7.07 21 5 98 93 38.58 0.42 22 6 11 5 333.46 2.41 23 6 12 6 317.44 5.60 24 6 53 47 147.00 0.75 25 6 89 83 38.58 0.42 26 6 94 88 38.61 0.42 27 6 98 92 38.62 0.41 28 6 102 96 38.57 0.42 29 7 11 4 350.74 4.76 30 8 11 3 372.51 3.50 31 8 12 4 365.54 0.01 32 9 12 3 379.44 0.20 33 9 13 4 365.58 0.00 34 10 13 3 380.25 0.21 35 10 14 4 365.82 0.12 36 11 14 3 379.82 0.01 37 11 15 4 366.27 0.34 38 12 15 3 377.26 1.28 39 12 16 4 365.82 0.12 40 12 46 34 151.80 1.60 41 12 49 37 151.71 1.60 42 12 50 38 151.66 1.57 43 12 53 41 150.62 1.86 44 13 16 3 379.82 0.01 45 13 17 4 372.47 3.21 46 13 42 29 152.38 1.73 47 13 43 30 152.28 1.77 48 13 46 33 151.83 1.58 49 14 17 3 378.88 2.09 50 14 18 4 372.47 3.21 51 15 18 3 379.64 0.38 52 15 19 4 369.12 1.54 53 15 85 70 83.59 0.17 54 15 88 73 83.63 0.18 55 15 89 74 83.59 0.17 56 15 92 77 83.64 0.17 57 16 19 3 380.12 0.14 58 16 20 4 369.11 1.55 59 16 42 26 152.44 1.70 60 16 45 29 152.05 1.67 61 16 46 30 151.84 1.57 62 16 49 33 151.84 1.57 63 17 20 3 381.81 0.70 64 17 21 4 372.92 3.47 65 17 42 25 152.45 1.71 66 18 21 3 380.10 0.12 67 18 22 4 372.86 3.50 68 18 88 70 83.64 0.18 69 19 22 3 380.01 0.16 70 19 23 4 369.45 2.27 71 19 81 62 83.89 0.31 72 19 84 65 83.63 0.18 73 19 85 66 83.63 0.18 74 19 88 69 83.87 0.29 75 20 23 3 378.41 0.26 76 20 24 4 369.10 2.45 77 20 33 13 184.76 1.03 78 20 38 18 155.62 2.36 79 20 41 21 153.50 1.41 80 20 42 22 153.44 1.44 81 20 45 25 153.45 1.43 82 21 24 3 385.83 3.08 83 21 25 4 367.06 3.46 84 22 25 3 372.08 3.79 85 22 26 4 371.20 3.35 86 22 84 62 83.94 0.29 87 22 87 65 83.96 0.28 88 22 88 66 83.97 0.28 89 23 26 3 379.41 0.12 90 23 29 6 250.90 2.75 91 23 30 7 205.22 6.17 92 23 33 10 184.88 1.03 93 23 81 58 83.95 0.29 94 23 84 61 83.96 0.28 95 24 30 6 208.61 4.48 96 24 33 9 202.25 7.66 97 24 38 14 175.98 2.29 98 26 29 3 392.87 4.79 99 26 30 4 326.36 0.73 100 26 80 54 87.61 1.84 101 26 84 58 84.58 0.42 102 27 30 3 373.53 0.40 103 28 80 52 94.59 1.41 104 29 32 3 386.40 0.78 105 29 77 48 94.59 1.41 106 29 80 51 94.22 1.23 107 29 81 52 94.08 1.27 108 29 84 55 94.08 1.27 109 30 33 3 383.62 0.61 110 30 34 4 378.30 2.04 111 31 34 3 383.62 0.61 112 32 36 4 393.24 4.20 113 32 71 39 97.17 1.16 114 32 72 40 97.15 1.15 115 32 73 41 96.97 1.19 116 32 77 45 96.67 1.16 117 33 36 3 372.14 1.04 118 33 38 5 353.99 6.73 119 33 41 8 310.08 0.08 120 36 41 5 358.30 4.24 121 37 40 3 378.61 0.99 122 37 41 4 371.23 2.22 123 38 41 3 371.23 2.22 124 38 42 4 371.23 2.21 125 39 42 3 376.66 0.49 126 39 43 4 371.24 2.22 127 40 43 3 377.16 0.24 128 40 44 4 376.66 0.49 129 41 44 3 391.17 5.38 130 41 45 4 374.51 0.58 131 42 45 3 378.59 0.48 132 42 46 4 374.69 0.67 133 43 46 3 376.82 0.42 134 43 47 4 374.70 0.67 135 44 47 3 380.11 1.22 136 44 48 4 371.80 0.78 137 44 59 15 156.68 4.13 138 44 62 18 146.02 0.34 139 45 48 3 373.76 0.46 140 45 49 4 371.78 0.77 141 46 49 3 388.78 2.30 142 46 50 4 373.22 4.52 143 47 50 3 385.45 3.97 144 47 51 4 377.57 2.35 145 47 59 12 155.87 4.55 146 48 51 3 384.44 4.48 147 48 52 4 366.81 2.89 148 48 59 11 155.85 4.54 149 48 64 16 114.81 2.14 150 48 109 61 69.61 1.54 151 49 52 3 377.57 2.35 152 49 53 4 361.06 0.60 153 50 53 3 377.31 2.60 154 50 54 4 361.04 0.62 155 50 55 5 329.37 6.73 156 51 54 3 377.31 2.60 157 51 55 4 343.53 0.35 158 51 57 6 216.22 7.88 159 51 58 7 166.78 0.66 160 51 59 8 166.78 0.66 161 52 105 53 69.81 1.47 162 53 102 49 72.38 0.18 163 53 105 52 69.64 1.54 164 62 67 5 344.88 5.94 165 63 66 3 377.66 3.70 166 63 67 4 363.53 1.35 167 64 67 3 372.01 2.90 168 64 68 4 362.44 0.82 169 64 109 45 72.86 0.03 170 64 112 48 68.20 1.41 171 65 68 3 381.14 0.77 172 65 69 4 371.90 5.25 173 65 112 47 68.11 1.45 174 66 69 3 380.11 1.16 175 67 71 4 399.97 2.81 176 68 71 3 383.63 1.01 177 68 112 44 68.54 1.23 178 68 113 45 68.19 1.38 179 68 115 47 68.16 1.38 180 69 115 46 67.94 1.41 181 72 77 5 372.92 0.27 182 72 116 44 67.89 1.42 183 73 77 4 371.50 0.45 184 73 78 5 366.06 1.41 185 73 113 40 68.59 1.21 186 73 114 41 68.02 1.44 187 73 115 42 67.95 1.43 188 73 116 43 67.67 1.46 189 74 77 3 373.03 0.32 190 74 78 4 371.50 0.45 191 74 114 40 68.18 1.36 192 74 116 42 66.48 1.59 193 75 78 3 373.04 0.32 194 75 79 4 367.06 1.77 195 75 110 35 82.45 0.12 196 75 114 39 68.20 1.38 197 76 79 3 372.76 0.18 198 76 80 4 367.74 1.45 199 77 80 3 371.55 0.80 200 77 81 4 367.73 1.45 201 78 81 3 370.20 0.22 202 78 82 4 368.25 1.15 203 78 107 29 84.33 0.32 204 78 109 31 83.75 0.21 205 78 110 32 79.29 0.46 206 78 113 35 68.36 1.30 207 78 114 36 68.06 1.42 208 79 82 3 369.18 0.68 209 79 83 4 368.25 1.15 210 79 110 31 83.22 0.12 211 80 83 3 371.44 0.47 212 80 84 4 374.45 1.97 213 81 84 3 375.37 1.51 214 81 85 4 375.38 1.51 215 82 85 3 381.80 1.71 216 82 86 4 375.37 1.53 217 82 103 21 84.95 0.07 218 82 106 24 84.56 0.23 219 82 107 25 84.56 0.22 220 83 86 3 375.38 1.53 221 83 87 4 375.37 1.53 222 84 87 3 375.39 1.52 223 84 88 4 375.37 1.53 224 85 88 3 378.51 0.04 225 85 89 4 374.07 2.17 226 85 102 17 85.64 0.03 227 85 103 18 85.61 0.01 228 85 106 21 85.59 0.03 229 86 89 3 380.48 0.95 230 86 90 4 370.26 0.27 231 86 99 13 85.68 0.04 232 86 100 14 85.67 0.04 233 86 103 17 85.62 0.01 234 87 90 3 377.38 1.08 235 87 91 4 377.38 1.08 236 88 91 3 379.64 0.05 237 88 92 4 377.38 1.08 238 89 92 3 373.03 1.10 239 89 93 4 370.82 2.21 240 89 94 5 346.82 4.54 241 89 99 10 85.70 0.04 242 89 102 13 85.70 0.06 243 89 103 14 85.68 0.04 244 90 93 3 373.03 1.10 245 94 98 4 373.86 0.55 246 94 99 5 352.75 2.91 247 95 98 3 374.13 0.46 248 95 99 4 373.93 0.56 249 96 99 3 375.83 0.35 250 96 100 4 375.10 0.03 251 97 100 3 375.84 0.34 252 97 101 4 375.05 0.05 253 98 101 3 375.03 0.06 254 98 102 4 372.23 1.45 255 99 102 3 375.75 3.12 256 99 103 4 372.22 1.45 257 100 103 3 375.29 0.10 258 100 104 4 366.87 2.98 259 101 104 3 376.03 2.46 260 101 105 4 376.06 2.48 261 102 105 3 376.52 2.25 262 102 106 4 374.44 3.29 263 103 106 3 374.44 3.29 264 103 107 4 374.51 3.25 265 104 107 3 384.56 1.77 266 104 108 4 376.04 2.50 267 105 108 3 388.61 1.49 268 105 109 4 386.24 0.94 269 106 109 3 396.36 0.90 270 107 110 3 384.57 1.77 271 109 112 3 378.14 1.98 272 109 113 4 354.13 1.96 273 110 113 3 381.60 1.57 274 110 114 4 343.92 1.40