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 4 29 25 148.74 2.73 2 4 30 26 144.53 4.63 3 4 31 27 145.02 4.39 4 5 8 3 284.03 1.34 5 5 9 4 283.74 1.20 6 6 9 3 286.02 0.34 7 6 10 4 280.87 2.64 8 6 40 34 146.65 3.55 9 7 10 3 288.56 1.21 10 7 11 4 284.88 0.39 11 7 70 63 50.97 0.24 12 7 73 66 49.67 0.10 13 8 11 3 288.56 1.21 14 8 12 4 285.90 0.12 15 9 12 3 288.83 1.07 16 9 13 4 283.35 1.16 17 9 30 21 154.69 0.18 18 9 32 23 154.69 0.18 19 9 40 31 152.44 0.66 20 10 13 3 296.93 1.26 21 10 14 4 283.56 1.05 22 10 40 30 152.47 0.64 23 10 43 33 152.02 0.44 24 10 44 34 151.99 0.46 25 10 70 60 51.02 0.24 26 11 14 3 290.45 4.50 27 11 15 4 282.10 1.77 28 11 67 56 51.13 0.17 29 11 70 59 51.02 0.24 30 11 71 60 51.01 0.23 31 11 74 63 50.17 0.09 32 12 15 3 298.18 1.97 33 12 16 4 290.01 2.20 34 12 29 17 155.33 0.10 35 12 30 18 155.22 0.08 36 13 16 3 293.86 4.12 37 13 17 4 285.99 0.18 38 13 26 13 155.25 0.06 39 13 30 17 155.33 0.10 40 13 32 19 155.34 0.10 41 13 40 27 154.29 0.27 42 13 44 31 153.88 0.46 43 14 17 3 296.43 2.83 44 14 18 4 280.78 2.79 45 14 44 30 153.91 0.47 46 14 49 35 152.78 0.96 47 14 50 36 152.63 0.90 48 14 59 45 150.93 1.67 49 14 66 52 54.26 0.66 50 14 67 53 51.69 0.44 51 14 70 56 51.19 0.20 52 15 18 3 290.79 0.07 53 15 67 52 54.06 0.74 54 15 71 56 51.19 0.20 55 16 20 4 270.16 1.48 56 16 21 5 210.43 12.31 57 16 26 10 155.49 0.04 58 17 20 3 270.85 1.82 59 17 21 4 193.69 2.40 60 17 26 9 155.55 0.02 61 17 50 33 152.87 0.99 62 17 57 40 152.63 1.18 63 17 58 41 152.00 1.41 64 17 59 42 151.24 1.58 65 18 59 41 151.61 1.61 66 18 67 49 87.49 2.34 67 18 71 53 78.34 6.92 68 20 25 5 292.35 2.99 69 20 56 36 152.80 1.21 70 20 57 37 152.78 1.21 71 20 58 38 152.73 1.22 72 21 25 4 281.16 2.60 73 21 26 5 280.99 2.65 74 21 56 35 152.81 1.22 75 21 57 36 152.77 1.22 76 22 25 3 298.82 0.24 77 22 26 4 291.49 1.96 78 22 55 33 152.85 1.21 79 22 56 34 152.82 1.22 80 23 26 3 296.87 0.73 81 23 27 4 285.71 4.84 82 23 34 11 156.95 0.14 83 23 37 14 155.84 0.29 84 23 38 15 155.81 0.29 85 23 41 18 155.57 0.18 86 23 57 34 152.83 1.23 87 24 27 3 296.86 0.73 88 24 28 4 286.25 4.57 89 25 28 3 291.53 1.94 90 25 29 4 281.54 2.21 91 26 29 3 292.74 1.31 92 26 30 4 288.05 1.04 93 26 37 11 155.94 0.27 94 26 41 15 155.80 0.29 95 26 57 31 152.78 1.24 96 27 30 3 292.74 1.30 97 27 31 4 271.70 1.70 98 27 32 5 219.18 13.18 99 27 33 6 210.06 17.73 100 27 34 7 177.77 1.59 101 27 37 10 155.88 0.30 102 28 31 3 268.68 3.20 103 32 36 4 273.44 3.82 104 32 37 5 273.29 3.83 105 32 40 8 260.12 0.30 106 33 36 3 287.88 2.96 107 33 37 4 283.31 0.68 108 34 37 3 283.64 0.84 109 34 38 4 282.88 0.90 110 35 38 3 291.44 1.24 111 35 39 4 282.88 0.90 112 36 39 3 285.88 2.41 113 36 40 4 283.16 0.76 114 37 40 3 288.81 1.74 115 37 41 4 279.85 0.59 116 38 41 3 286.00 0.58 117 38 42 4 284.95 1.97 118 39 42 3 286.88 1.01 119 39 43 4 285.64 1.62 120 40 43 3 289.81 0.58 121 40 44 4 285.70 1.60 122 41 44 3 295.10 2.23 123 41 45 4 285.70 1.60 124 41 50 9 163.44 1.56 125 41 57 16 154.37 2.02 126 42 45 3 295.10 2.23 127 42 46 4 286.17 1.38 128 43 46 3 287.41 1.61 129 43 47 4 279.98 1.26 130 44 47 3 282.21 2.38 131 44 48 4 272.86 3.42 132 44 49 5 222.03 11.58 133 44 50 6 198.06 0.46 134 45 48 3 278.61 0.47 135 45 50 5 200.61 1.73 136 45 52 7 163.44 1.57 137 45 57 12 154.47 2.04 138 47 62 15 152.58 2.85 139 48 60 12 153.46 2.54 140 48 62 14 152.68 2.90 141 49 59 10 154.47 2.09 142 49 60 11 153.33 2.60 143 49 62 13 152.68 2.90 144 49 63 14 135.81 11.10 145 49 66 17 135.75 11.12 146 50 57 7 154.57 2.09 147 50 58 8 154.53 2.10 148 50 59 9 154.46 2.10 149 50 60 10 153.53 2.55 150 51 57 6 154.62 2.11 151 51 58 7 154.56 2.10 152 51 60 9 154.47 2.10 153 52 55 3 324.28 0.96 154 52 56 4 216.37 1.02 155 52 57 5 154.62 2.10 156 53 56 3 289.29 2.25 157 53 58 5 178.15 7.52 158 59 63 4 271.50 0.90 159 59 64 5 271.00 0.65 160 59 67 8 224.14 9.05 161 60 63 3 283.20 1.70 162 60 64 4 283.27 1.67 163 61 64 3 288.53 1.67 164 61 65 4 283.29 1.66 165 62 65 3 289.96 0.27 166 62 66 4 284.66 0.96 167 63 66 3 288.00 0.71 168 63 67 4 283.44 1.67 169 64 67 3 289.38 0.02 170 64 68 4 286.25 1.47 171 65 68 3 287.17 1.02 172 65 69 4 286.25 1.48 173 66 69 3 290.95 0.88 174 66 70 4 286.25 1.48 175 67 70 3 289.17 2.94 176 67 71 4 286.25 1.48 177 68 71 3 286.26 1.46 178 68 72 4 286.43 1.36 179 69 72 3 286.41 1.35 180 69 73 4 286.41 1.35 181 70 73 3 288.58 0.83 182 70 74 4 285.31 0.80 183 71 74 3 285.89 1.09 184 71 75 4 285.31 0.80 185 72 75 3 285.86 1.11 186 72 76 4 285.13 0.79 187 73 76 3 288.19 0.38 188 73 77 4 283.89 0.04 189 74 77 3 287.00 0.10 190 74 78 4 287.00 0.10 191 75 78 3 288.11 0.46 192 75 79 4 287.00 0.10 193 76 79 3 291.85 1.27 194 76 80 4 285.30 0.76 195 77 80 3 285.24 0.79 196 77 81 4 275.77 1.80 197 78 81 3 286.87 1.02 198 78 82 4 275.76 1.79 199 79 82 3 282.11 1.37 200 79 83 4 275.76 1.79 201 80 83 3 286.91 2.42 202 80 84 4 275.75 1.79 203 81 84 3 286.06 1.83 204 81 85 4 270.88 0.88 205 82 85 3 285.48 1.53 206 82 86 4 276.52 0.31 207 83 86 3 280.95 1.90 208 83 87 4 276.53 0.31 209 84 87 3 282.31 2.35 210 84 88 4 276.56 0.29 211 85 88 3 287.28 0.58 212 85 89 4 278.64 1.25 213 86 89 3 287.73 0.36 214 86 90 4 278.64 1.25 215 87 90 3 288.20 0.13 216 87 91 4 278.64 1.25 217 88 91 3 284.06 1.46 218 88 92 4 278.63 1.25 219 89 92 3 282.34 0.42