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 7 3 299.16 0.76 2 5 8 3 298.63 1.38 3 5 9 4 286.64 2.65 4 6 9 3 296.31 2.18 5 6 10 4 280.46 0.47 6 7 10 3 300.83 0.78 7 7 11 4 293.33 2.98 8 7 24 17 37.83 0.21 9 7 79 72 37.81 0.23 10 7 80 73 37.55 0.32 11 7 83 76 37.59 0.34 12 8 11 3 302.57 1.65 13 8 12 4 293.30 2.96 14 9 12 3 293.32 2.97 15 9 13 4 293.31 2.97 16 10 13 3 302.61 1.68 17 10 15 5 250.58 15.35 18 10 23 13 38.01 0.17 19 10 80 70 37.88 0.22 20 10 84 74 37.54 0.32 21 11 80 69 37.98 0.17 22 11 83 72 37.62 0.32 23 11 84 73 37.50 0.30 24 11 88 77 30.53 1.31 25 13 18 5 308.94 1.33 26 13 88 75 31.77 0.70 27 14 88 74 31.77 0.70 28 15 18 3 304.52 0.24 29 15 43 28 57.02 0.28 30 15 46 31 51.70 1.44 31 15 84 69 38.16 0.21 32 17 41 24 92.42 1.20 33 18 22 4 273.85 3.50 34 18 42 24 93.08 1.53 35 19 22 3 291.24 2.06 36 19 42 23 93.21 1.58 37 20 23 3 303.40 1.07 38 20 26 6 180.84 4.38 39 20 31 11 96.05 2.71 40 20 34 14 95.96 2.69 41 20 39 19 95.12 2.50 42 20 41 21 93.64 1.78 43 20 42 22 93.22 1.58 44 20 45 25 93.36 1.65 45 21 26 5 180.84 4.38 46 21 31 10 96.04 2.70 47 23 26 3 295.74 0.45 48 23 42 19 95.92 2.75 49 23 45 22 95.94 2.75 50 23 81 58 95.71 2.77 51 24 76 52 95.92 2.74 52 24 77 53 95.92 2.75 53 24 80 56 95.88 2.73 54 25 30 5 286.49 0.69 55 25 73 48 95.94 2.75 56 25 76 51 95.92 2.75 57 25 77 52 95.92 2.75 58 26 30 4 286.48 0.69 59 26 31 5 284.53 0.67 60 26 34 8 269.68 0.62 61 26 63 37 105.33 1.93 62 26 77 51 95.92 2.75 63 27 30 3 291.70 1.92 64 27 31 4 286.54 0.66 65 28 31 3 292.39 1.21 66 28 32 4 288.92 0.52 67 29 32 3 295.68 0.43 68 29 33 4 293.69 1.76 69 30 33 3 295.30 0.96 70 30 34 4 289.90 1.57 71 30 67 37 129.85 2.62 72 30 69 39 128.89 2.13 73 30 73 43 128.84 2.16 74 31 34 3 297.09 0.06 75 31 35 4 286.63 0.63 76 32 35 3 297.82 0.30 77 32 36 4 288.44 0.22 78 33 36 3 295.14 1.05 79 33 37 4 288.45 0.21 80 33 67 34 130.74 2.90 81 34 37 3 291.72 1.84 82 34 38 4 285.83 1.09 83 34 39 5 257.87 2.24 84 34 45 11 160.06 0.43 85 34 62 28 130.88 2.83 86 34 63 29 130.83 2.85 87 34 66 32 130.85 2.84 88 35 38 3 292.80 1.30 89 35 39 4 257.94 2.21 90 35 40 5 217.97 5.35 91 37 66 29 131.84 2.85 92 38 44 6 240.44 1.25 93 39 44 5 221.84 8.05 94 39 45 6 209.80 2.03 95 39 48 9 208.15 1.21 96 39 62 23 133.59 2.33 97 41 44 3 297.38 0.54 98 41 45 4 293.00 1.67 99 42 45 3 293.00 1.67 100 42 46 4 289.19 0.24 101 43 46 3 294.72 0.80 102 43 47 4 290.79 0.57 103 44 47 3 294.72 0.80 104 44 48 4 293.31 0.10 105 45 48 3 293.31 0.10 106 45 49 4 290.62 1.45 107 45 81 36 131.72 2.93 108 46 49 3 294.05 0.26 109 46 50 4 290.64 1.44 110 46 81 35 131.72 2.93 111 46 84 38 131.72 2.94 112 46 85 39 131.72 2.93 113 47 50 3 293.44 0.04 114 47 51 4 290.64 1.44 115 48 51 3 296.95 1.80 116 48 52 4 288.19 0.23 117 48 62 14 138.32 1.35 118 49 52 3 294.23 0.43 119 49 53 4 290.72 0.42 120 49 54 5 255.09 1.48 121 49 59 10 148.77 4.25 122 49 78 29 131.99 2.94 123 49 81 32 131.85 2.94 124 49 82 33 131.84 2.94 125 49 85 36 131.82 2.93 126 50 53 3 299.00 0.78 127 50 85 35 131.82 2.93 128 50 89 39 107.39 1.13 129 52 55 3 290.51 1.02 130 52 58 6 197.37 9.72 131 52 59 7 196.38 10.22 132 52 62 10 184.09 5.14 133 54 78 24 135.78 2.15 134 55 58 3 297.21 2.06 135 55 59 4 284.47 1.91 136 56 59 3 293.18 0.05 137 56 60 4 280.49 0.09 138 56 78 22 136.52 1.92 139 57 60 3 300.58 1.95 140 57 61 4 293.60 1.54 141 58 61 3 290.61 3.04 142 58 62 4 290.61 3.04 143 59 62 3 290.62 3.04 144 59 63 4 288.49 1.98 145 59 77 18 137.31 1.59 146 59 78 19 137.16 1.61 147 59 81 22 137.25 1.57 148 60 63 3 297.18 0.24 149 60 64 4 283.23 1.23 150 60 74 14 137.37 1.56 151 60 75 15 137.37 1.57 152 61 64 3 294.80 0.93 153 61 65 4 279.67 3.02 154 62 65 3 299.99 1.67 155 62 66 4 286.05 3.17 156 63 66 3 286.63 3.43 157 63 67 4 286.07 3.15 158 63 68 5 276.38 2.27 159 63 69 6 250.97 12.20 160 63 74 11 159.21 7.31 161 63 77 14 154.09 9.87 162 64 67 3 293.56 0.04 163 64 68 4 272.42 1.50 164 64 69 5 250.97 12.20 165 64 70 6 250.97 12.20 166 64 71 7 250.96 12.20 167 69 73 4 284.29 0.99 168 70 73 3 293.61 1.06 169 70 74 4 289.93 0.99 170 71 74 3 299.86 3.69 171 71 75 4 291.62 0.45 172 72 75 3 299.49 1.22 173 72 76 4 291.62 0.45 174 73 76 3 297.26 1.83 175 73 77 4 291.33 0.32 176 74 77 3 299.66 4.48 177 74 78 4 290.82 0.56 178 75 78 3 296.07 1.79 179 75 79 4 287.94 0.89 180 76 79 3 296.12 1.77 181 76 80 4 286.01 0.58 182 77 80 3 288.16 0.49 183 77 81 4 282.58 0.76 184 78 81 3 299.28 0.19 185 78 82 4 279.59 0.06 186 79 82 3 289.85 2.04 187 79 83 4 278.74 0.26 188 80 83 3 293.56 0.28 189 80 84 4 289.33 0.07 190 81 84 3 304.41 2.12 191 81 85 4 290.36 0.49 192 82 85 3 293.46 1.69 193 82 86 4 294.60 1.63 194 83 86 3 294.60 1.63 195 83 87 4 294.61 1.62 196 84 87 3 296.47 0.77 197 84 88 4 281.74 3.80 198 85 88 3 290.25 0.56 199 85 89 4 260.92 6.57