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 92 90 82.14 0.89 2 2 93 91 82.12 0.91 3 2 94 92 82.12 0.91 4 3 92 89 82.24 0.93 5 3 93 90 82.17 0.89 6 3 95 92 82.25 0.94 7 3 98 95 82.20 0.92 8 4 90 86 82.73 1.04 9 4 91 87 82.31 0.89 10 4 92 88 82.27 0.92 11 5 90 85 83.08 1.09 12 5 91 86 82.75 1.02 13 5 93 88 82.54 0.97 14 5 98 93 82.27 0.93 15 5 101 96 82.21 0.94 16 6 9 3 460.09 2.35 17 6 88 82 94.08 2.38 18 6 89 83 93.42 2.68 19 6 90 84 83.36 1.14 20 6 101 95 82.28 0.94 21 6 103 97 82.20 0.94 22 7 36 29 108.43 1.62 23 7 37 30 107.67 1.65 24 7 38 31 106.69 1.46 25 7 89 82 93.72 2.56 26 7 90 83 90.77 1.35 27 7 91 84 83.81 1.36 28 7 101 94 82.31 0.93 29 7 103 96 82.22 0.94 30 7 104 97 82.20 0.94 31 8 36 28 108.09 1.46 32 8 88 80 105.68 1.44 33 8 89 81 97.58 0.81 34 8 103 95 82.25 0.94 35 8 104 96 82.20 0.94 36 9 36 27 108.45 1.63 37 9 86 77 110.11 0.84 38 9 87 78 107.42 1.12 39 9 88 79 106.03 1.27 40 9 104 95 82.25 0.94 41 9 105 96 82.20 0.94 42 9 106 97 82.19 0.94 43 10 13 3 407.20 3.64 44 10 28 18 118.78 1.41 45 10 32 22 115.48 1.28 46 10 36 26 108.73 1.62 47 10 69 59 131.02 3.93 48 10 86 76 111.14 0.35 49 10 87 77 108.48 1.63 50 10 106 96 82.20 0.94 51 10 108 98 82.17 0.94 52 11 86 75 112.84 0.70 53 11 105 94 82.27 0.93 54 11 106 95 82.23 0.94 55 11 107 96 82.19 0.94 56 11 108 97 82.18 0.94 57 12 49 37 138.44 1.77 58 12 84 72 137.50 2.11 59 12 85 73 123.98 1.44 60 12 86 74 123.98 1.44 61 12 108 96 82.13 0.96 62 13 69 56 151.25 0.90 63 13 84 71 142.50 0.25 64 13 85 72 135.80 1.55 65 13 87 74 124.00 1.44 66 13 108 95 82.14 0.96 67 13 112 99 41.95 0.76 68 14 69 55 155.49 0.32 69 14 83 69 154.20 0.58 70 14 84 70 149.65 0.24 71 14 112 98 44.70 0.36 72 15 69 54 156.51 0.20 73 15 71 56 158.34 0.71 74 15 79 64 160.17 1.51 75 15 80 65 160.25 1.47 76 15 81 66 160.16 1.51 77 15 82 67 159.31 1.19 78 15 83 68 158.00 0.88 79 15 85 70 152.44 0.28 80 16 67 51 159.68 1.18 81 16 68 52 159.50 1.22 82 16 69 53 159.33 1.19 83 16 81 65 160.34 1.51 84 16 112 96 66.58 2.19 85 17 68 51 159.71 1.19 86 17 69 52 159.69 1.19 87 17 70 53 159.60 1.24 88 17 71 54 160.37 1.50 89 17 81 64 160.80 1.72 90 18 71 53 160.59 1.45 91 18 76 58 161.28 1.55 92 18 79 61 161.28 1.56 93 18 80 62 161.28 1.57 94 18 81 63 161.28 1.56 95 19 71 52 161.90 1.48 96 19 72 53 161.80 1.53 97 19 73 54 162.03 1.51 98 19 76 57 162.13 1.57 99 20 73 53 162.03 1.51 100 20 74 54 168.66 0.53 101 20 76 56 162.16 1.58 102 20 77 57 163.19 1.07 103 23 72 49 201.36 1.24 104 23 73 50 197.92 0.46 105 24 72 48 201.37 1.24 106 24 73 49 197.93 0.46 107 25 57 32 282.07 0.17 108 25 58 33 281.92 0.24 109 25 60 35 281.79 0.23 110 25 71 46 202.93 0.53 111 25 72 47 202.86 0.56 112 26 44 18 282.17 0.18 113 26 46 20 282.56 0.18 114 26 57 31 282.15 0.18 115 26 58 32 282.10 0.16 116 26 59 33 282.03 0.17 117 26 60 34 281.88 0.21 118 26 69 43 207.37 0.55 119 26 70 44 204.48 1.23 120 26 71 45 202.93 0.53 121 26 87 61 180.37 0.95 122 27 60 33 281.92 0.23 123 27 62 35 281.73 0.23 124 27 68 41 214.05 0.57 125 27 69 42 207.37 0.55 126 27 70 43 204.56 1.26 127 27 72 45 204.47 1.22 128 28 32 4 375.43 0.90 129 28 33 5 372.62 0.49 130 28 44 16 282.60 0.18 131 28 59 31 282.12 0.17 132 28 60 32 282.08 0.14 133 28 61 33 282.04 0.16 134 28 62 34 281.79 0.24 135 28 68 40 219.99 0.35 136 28 69 41 207.38 0.55 137 28 87 59 180.56 1.01 138 29 32 3 375.50 0.86 139 29 33 4 375.51 0.86 140 29 62 33 281.89 0.21 141 29 63 34 281.88 0.21 142 29 64 35 281.71 0.24 143 29 65 36 281.42 0.38 144 29 66 37 264.77 0.03 145 29 67 38 242.69 1.08 146 29 68 39 242.66 1.08 147 30 33 3 375.82 1.02 148 30 34 4 375.81 1.02 149 30 61 31 282.08 0.15 150 30 62 32 282.06 0.15 151 30 64 34 281.79 0.24 152 31 34 3 380.19 3.21 153 31 35 4 377.56 0.15 154 31 64 33 281.81 0.24 155 31 65 34 281.79 0.24 156 31 114 83 33.18 0.29 157 32 35 3 377.87 0.00 158 32 36 4 377.87 0.00 159 32 67 35 264.12 0.89 160 32 69 37 253.94 1.98 161 32 108 76 82.25 0.94 162 32 112 80 42.56 0.74 163 32 114 82 31.05 0.17 164 33 36 3 384.07 2.68 165 33 37 4 374.70 1.58 166 33 38 5 337.28 0.05 167 33 59 26 282.59 0.18 168 33 60 27 282.56 0.18 169 33 61 28 282.13 0.16 170 34 37 3 373.78 2.05 171 34 64 30 282.04 0.16 172 35 104 69 82.31 0.94 173 35 106 71 82.23 0.94 174 35 114 79 30.29 0.57 175 36 104 68 82.26 0.94 176 37 104 67 82.25 0.94 177 38 42 4 363.74 1.19 178 38 44 6 319.52 6.23 179 38 59 21 284.05 0.29 180 38 87 49 181.05 1.20 181 38 89 51 179.43 0.80 182 39 42 3 367.94 0.91 183 39 59 20 284.17 0.29 184 40 59 19 284.12 0.31 185 40 60 20 283.74 0.14 186 40 61 21 283.12 0.07 187 41 58 17 284.22 0.30 188 41 59 18 284.17 0.31 189 42 58 16 284.24 0.29 190 42 59 17 284.22 0.29 191 42 89 47 179.50 0.74 192 43 57 14 284.53 0.18 193 43 58 15 284.26 0.29 194 43 89 46 179.51 0.75 195 44 56 12 284.92 0.11 196 44 57 13 284.66 0.16 197 44 58 14 284.39 0.23 198 44 59 15 284.39 0.23 199 44 87 43 181.03 1.22 200 44 88 44 180.16 1.06 201 44 89 45 179.44 0.79 202 45 55 10 285.11 0.18 203 45 56 11 284.84 0.07 204 45 87 42 181.08 1.21 205 45 88 43 180.84 1.28 206 45 90 45 180.19 1.08 207 46 54 8 285.16 0.17 208 46 55 9 285.12 0.18 209 46 57 11 285.10 0.18 210 46 85 39 185.14 0.29 211 46 86 40 181.75 1.36 212 46 87 41 181.22 1.22 213 47 53 6 286.20 0.18 214 47 54 7 285.17 0.17 215 47 85 38 187.52 2.32 216 47 86 39 183.66 0.41 217 47 88 41 181.75 1.36 218 47 90 43 181.75 1.36 219 48 51 3 381.83 0.31 220 48 52 4 309.33 0.10 221 48 53 5 288.42 0.92 222 48 78 30 203.09 0.61 223 48 79 31 202.94 0.61 224 48 83 35 197.88 0.50 225 48 84 36 197.03 0.42 226 48 85 37 192.69 0.27 227 49 84 35 197.84 0.52 228 49 85 36 196.86 0.38 229 49 86 37 196.85 0.38 230 50 83 33 198.13 0.40 231 50 84 34 198.11 0.39 232 51 78 27 203.31 0.71 233 51 79 28 203.11 0.66 234 51 83 32 199.83 0.18 235 53 77 24 203.28 0.70 236 53 78 25 202.86 0.64 237 55 71 16 207.30 0.58 238 55 75 20 203.03 0.61 239 55 78 23 202.62 0.54 240 62 66 4 360.38 1.31 241 62 68 6 232.02 6.39 242 63 66 3 375.67 2.06 243 67 111 44 75.79 0.31 244 67 112 45 44.38 0.15 245 67 113 46 43.68 0.19 246 69 87 18 180.53 1.02 247 69 112 43 44.88 0.04 248 71 75 4 357.93 3.38 249 71 76 5 338.81 3.35 250 71 79 8 298.14 2.96 251 72 75 3 385.31 3.04 252 72 76 4 352.20 4.84 253 73 76 3 393.99 1.30 254 74 77 3 386.17 1.24 255 75 78 3 383.92 2.35 256 75 79 4 383.60 2.51 257 76 79 3 393.94 1.32 258 79 83 4 365.62 1.27 259 80 83 3 384.14 3.79 260 91 101 10 311.52 9.03 261 93 97 4 367.58 2.52 262 93 98 5 355.35 1.04 263 93 101 8 341.50 2.88 264 94 97 3 385.67 1.98 265 94 98 4 372.27 0.18 266 95 98 3 374.22 0.81 267 95 99 4 374.00 0.70 268 96 99 3 389.57 2.62 269 97 100 3 389.87 2.48 270 97 101 4 368.75 1.46 271 98 101 3 371.23 2.10 272 106 114 8 161.58 64.94 273 107 114 7 161.61 64.95 274 107 115 8 161.25 65.08 275 108 112 4 331.11 3.19 276 108 113 5 299.53 1.67 277 108 114 6 162.69 64.41 278 108 115 7 161.41 65.03 279 109 112 3 383.30 1.30 280 109 113 4 319.85 3.23 281 109 115 6 297.21 2.82