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 9 72 63 14.18 1.14 2 9 74 65 14.19 1.14 3 11 43 32 18.05 0.79 4 11 44 33 20.20 0.29 5 11 45 34 18.05 0.78 6 11 70 59 16.91 0.29 7 12 15 3 424.70 1.59 8 19 122 103 134.12 1.89 9 20 24 4 420.53 1.26 10 20 46 26 59.19 0.20 11 20 122 102 142.53 0.54 12 21 121 100 144.45 0.82 13 21 122 101 144.41 0.82 14 22 121 99 144.46 0.82 15 22 122 100 144.43 0.82 16 23 48 25 144.60 0.83 17 23 49 26 144.56 0.83 18 23 51 28 144.53 0.83 19 23 121 98 144.47 0.82 20 23 122 99 144.44 0.82 21 23 123 100 144.43 0.82 22 24 44 20 145.78 1.30 23 24 46 22 144.66 0.84 24 24 47 23 144.65 0.83 25 24 48 24 144.60 0.83 26 24 49 25 144.59 0.84 27 24 122 98 144.49 0.82 28 24 123 99 144.47 0.82 29 24 124 100 144.44 0.82 30 24 125 101 144.43 0.82 31 25 46 21 144.68 0.83 32 25 47 22 144.66 0.83 33 25 49 24 144.63 0.83 34 25 63 38 144.56 0.84 35 25 87 62 144.44 0.82 36 25 125 100 144.44 0.82 37 25 127 102 144.41 0.82 38 26 44 18 145.78 1.30 39 26 45 19 145.47 1.18 40 26 125 99 144.47 0.82 41 26 126 100 144.44 0.82 42 26 127 101 144.43 0.82 43 26 128 102 144.43 0.82 44 27 43 16 194.74 22.98 45 27 45 18 145.69 1.26 46 27 47 20 145.49 1.18 47 27 64 37 144.58 0.84 48 27 67 40 144.61 0.85 49 27 127 100 144.44 0.82 50 28 42 14 234.67 3.02 51 28 43 15 194.74 22.98 52 28 44 16 146.21 1.24 53 28 127 99 144.47 0.82 54 28 128 100 144.43 0.82 55 28 129 101 144.43 0.82 56 29 42 13 234.71 3.02 57 29 64 35 144.69 0.85 58 29 127 98 144.50 0.82 59 29 129 100 144.43 0.82 60 29 131 102 144.40 0.82 61 30 38 8 346.88 3.04 62 30 40 10 303.13 13.53 63 30 42 12 300.56 14.36 64 30 129 99 144.47 0.82 65 30 130 100 144.42 0.82 66 30 131 101 144.42 0.82 67 31 38 7 346.90 3.04 68 31 39 8 346.77 3.06 69 31 40 9 337.75 0.06 70 31 131 100 144.42 0.82 71 31 133 102 136.83 0.20 72 32 37 5 350.56 1.23 73 32 38 6 346.86 3.07 74 32 39 7 346.83 3.06 75 32 130 98 144.49 0.82 76 32 131 99 144.46 0.82 77 32 132 100 144.41 0.82 78 32 133 101 144.41 0.82 79 33 36 3 435.78 1.31 80 33 37 4 386.69 15.88 81 33 39 6 350.53 1.24 82 33 132 99 144.46 0.82 83 34 132 98 144.47 0.82 84 39 73 34 214.72 0.27 85 39 133 94 144.37 0.80 86 40 68 28 214.63 0.21 87 40 71 31 215.22 0.34 88 40 73 33 214.99 0.40 89 43 71 28 217.24 0.03 90 45 67 22 215.97 0.65 91 45 70 25 217.59 0.04 92 47 63 16 217.27 0.00 93 47 66 19 217.87 0.06 94 47 67 20 217.81 0.00 95 49 55 6 383.14 1.94 96 49 63 14 270.62 24.35 97 49 113 64 215.18 0.36 98 49 125 76 144.46 0.82 99 50 53 3 439.97 1.58 100 50 113 63 215.18 0.36 101 51 113 62 215.18 0.36 102 51 114 63 215.16 0.37 103 51 115 64 212.79 0.12 104 52 112 60 215.21 0.36 105 52 113 61 215.19 0.36 106 53 112 59 217.03 0.78 107 53 113 60 215.21 0.36 108 54 59 5 423.67 0.40 109 54 109 55 221.12 0.61 110 54 110 56 219.86 0.48 111 54 111 57 217.37 0.71 112 54 112 58 217.08 0.80 113 55 59 4 423.67 0.40 114 55 60 5 421.93 1.26 115 55 63 8 414.56 1.16 116 55 110 55 220.53 0.82 117 55 111 56 219.36 0.24 118 55 113 58 217.06 0.80 119 56 59 3 436.66 1.49 120 56 60 4 422.00 1.25 121 56 107 51 221.24 0.59 122 56 108 52 221.24 0.59 123 56 109 53 221.20 0.58 124 56 110 54 220.56 0.83 125 57 60 3 439.99 5.45 126 57 61 4 422.00 1.25 127 57 81 24 222.23 0.71 128 57 106 49 221.24 0.60 129 57 107 50 221.25 0.59 130 57 108 51 221.25 0.58 131 58 61 3 428.31 1.91 132 58 62 4 428.30 1.91 133 59 62 3 432.07 3.00 134 59 63 4 425.37 0.35 135 60 63 3 430.03 0.24 136 60 64 4 427.11 1.22 137 60 81 21 222.24 0.71 138 60 87 27 220.77 0.49 139 60 106 46 221.25 0.60 140 60 127 67 144.48 0.82 141 61 64 3 440.10 1.68 142 61 65 4 433.14 1.79 143 61 78 17 224.13 1.20 144 61 81 20 222.25 0.71 145 62 65 3 432.57 1.02 146 62 66 4 423.22 0.50 147 63 66 3 431.90 3.83 148 63 67 4 427.75 1.76 149 64 67 3 431.22 0.02 150 64 68 4 431.61 3.69 151 64 78 14 224.17 1.21 152 64 81 17 224.01 1.25 153 64 127 63 144.50 0.82 154 64 131 67 142.39 0.52 155 65 68 3 435.60 1.99 156 65 69 4 431.61 3.69 157 65 76 11 248.24 12.59 158 65 77 12 224.21 1.20 159 65 78 13 224.18 1.21 160 66 69 3 436.11 1.43 161 67 70 3 439.05 0.04 162 67 71 4 436.35 1.30 163 68 71 3 434.81 0.54 164 68 73 5 388.14 8.27 165 68 74 6 344.12 4.12 166 68 76 8 325.29 3.50 167 68 133 65 128.88 0.28 168 69 74 5 333.04 1.42 169 71 74 3 431.35 0.07 170 73 76 3 432.23 3.40 171 73 133 60 141.75 0.76 172 75 135 60 95.78 2.46 173 75 136 61 88.34 0.79 174 76 133 57 135.41 0.54 175 76 134 58 113.62 3.73 176 76 135 59 88.36 0.79 177 76 136 60 86.56 1.68 178 77 133 56 135.97 0.26 179 77 134 57 125.45 2.17 180 77 136 59 83.14 0.66 181 78 131 53 144.18 0.92 182 78 132 54 143.65 1.07 183 78 133 55 132.65 1.92 184 79 132 53 144.06 0.87 185 79 133 54 137.41 1.51 186 79 134 55 137.40 1.51 187 80 131 51 144.31 0.84 188 80 132 52 143.58 1.09 189 81 106 25 283.66 0.21 190 81 131 50 143.66 1.05 191 82 85 3 423.49 0.62 192 82 129 47 144.49 0.82 193 82 130 48 144.46 0.82 194 85 106 21 293.63 2.60 195 85 127 42 144.55 0.82 196 85 129 44 144.45 0.82 197 86 103 17 303.82 5.24 198 86 104 18 301.93 6.17 199 86 105 19 297.68 4.62 200 86 106 20 297.68 4.62 201 86 127 41 144.53 0.81 202 87 103 16 304.32 5.22 203 87 104 17 303.82 5.23 204 87 106 19 301.87 6.14 205 87 111 24 285.21 1.02 206 87 125 38 145.13 0.53 207 87 126 39 144.53 0.81 208 87 127 40 144.49 0.82 209 88 101 13 308.32 4.02 210 88 102 14 307.14 4.54 211 88 103 15 304.08 5.34 212 88 125 37 145.15 0.52 213 88 126 38 145.06 0.53 214 89 101 12 308.32 4.01 215 89 102 13 308.31 4.01 216 89 104 15 307.19 4.56 217 89 116 27 270.45 7.20 218 89 123 34 145.34 0.43 219 89 124 35 145.30 0.45 220 89 125 36 145.18 0.48 221 90 99 9 322.11 5.70 222 90 100 10 321.73 5.57 223 90 101 11 308.41 4.04 224 91 99 8 322.37 5.57 225 91 100 9 322.07 5.70 226 91 102 11 321.88 5.62 227 91 116 25 270.46 7.22 228 91 119 28 269.76 7.53 229 91 120 29 269.53 7.54 230 92 97 5 368.14 2.54 231 92 98 6 358.14 1.62 232 92 99 7 322.50 5.50 233 92 119 27 270.42 7.21 234 93 96 3 435.25 3.50 235 93 97 4 387.95 11.09 236 93 98 5 363.67 1.45 237 93 119 26 270.42 7.21 238 94 97 3 431.07 0.69 239 94 118 24 270.47 7.22 240 94 119 25 270.43 7.21 241 96 100 4 467.03 1.32 242 104 111 7 298.68 2.65 243 104 114 10 283.99 0.45 244 104 125 21 145.15 0.52 245 105 111 6 343.07 9.46 246 106 127 21 144.53 0.81 247 107 110 3 408.16 0.84 248 113 125 12 185.25 21.19 249 114 125 11 274.02 2.02 250 116 119 3 433.43 2.50 251 116 120 4 391.05 0.33 252 116 123 7 332.85 6.69 253 116 125 9 326.07 3.30 254 117 120 3 415.64 0.71 255 117 121 4 370.31 0.82 256 120 123 3 441.54 5.54