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 81 80 31.88 0.24 2 2 55 53 48.61 0.05 3 2 81 79 38.72 1.72 4 3 55 52 49.22 0.15 5 3 78 75 44.66 0.50 6 3 81 78 39.97 1.10 7 4 8 4 296.61 3.62 8 4 9 5 296.61 3.62 9 4 51 47 50.81 0.64 10 4 55 51 49.25 0.15 11 4 74 70 49.12 0.11 12 4 77 73 48.18 0.28 13 4 78 74 47.16 0.22 14 5 8 3 306.45 0.90 15 5 9 4 306.05 1.10 16 5 74 69 53.16 0.35 17 6 9 3 314.08 2.92 18 6 10 4 296.81 3.48 19 6 30 24 60.50 0.11 20 6 71 65 60.11 0.07 21 6 74 68 59.44 0.27 22 7 10 3 307.98 0.13 23 7 11 4 296.81 3.49 24 7 23 16 121.31 20.13 25 8 11 3 304.85 0.55 26 8 12 4 296.77 3.46 27 8 55 47 60.62 0.19 28 9 12 3 306.63 0.35 29 9 13 4 296.76 3.45 30 9 51 42 60.64 0.21 31 9 70 61 60.45 0.10 32 9 73 64 60.40 0.09 33 9 74 65 60.26 0.02 34 10 13 3 305.99 1.15 35 10 14 4 291.97 1.12 36 10 22 12 121.31 20.12 37 10 23 13 121.31 20.12 38 10 25 15 121.42 20.18 39 10 29 19 71.69 1.62 40 11 14 3 298.72 0.80 41 11 15 4 291.10 0.69 42 11 22 11 121.31 20.13 43 12 15 3 302.50 0.10 44 12 16 4 291.06 0.70 45 12 47 35 61.50 0.48 46 12 51 39 61.41 0.45 47 13 16 3 296.25 3.02 48 13 17 4 291.33 0.57 49 13 34 21 68.66 2.21 50 13 39 26 71.46 2.25 51 13 44 31 64.97 0.50 52 13 47 34 63.05 1.09 53 14 17 3 303.97 0.83 54 14 18 4 283.03 3.06 55 14 19 5 255.25 0.04 56 14 20 6 255.25 0.04 57 14 21 7 217.32 18.91 58 14 22 8 162.99 0.70 59 15 18 3 285.06 2.04 60 16 43 27 65.61 0.77 61 16 46 30 65.45 0.74 62 16 47 31 65.11 0.57 63 17 39 22 71.95 2.08 64 19 24 5 215.74 2.22 65 21 24 3 298.51 4.63 66 23 26 3 306.09 0.68 67 23 27 4 269.16 7.65 68 25 29 4 291.57 3.55 69 25 37 12 120.05 1.14 70 27 30 3 336.16 0.74 71 28 32 4 303.02 0.06 72 29 32 3 300.37 1.27 73 29 37 8 207.39 2.42 74 29 70 41 124.26 0.38 75 30 69 39 126.43 1.46 76 30 70 40 123.92 0.55 77 30 71 41 121.95 0.42 78 31 69 38 127.99 1.17 79 32 36 4 300.08 1.37 80 32 37 5 284.95 0.17 81 32 69 37 128.50 1.11 82 32 70 38 128.50 1.11 83 33 36 3 309.11 3.14 84 33 37 4 300.09 1.38 85 33 68 35 128.72 1.14 86 33 69 36 128.55 1.14 87 34 37 3 310.94 2.24 88 34 38 4 300.08 1.39 89 34 39 5 261.31 9.14 90 34 44 10 192.93 0.33 91 34 67 33 128.86 1.08 92 34 68 34 128.86 1.08 93 34 69 35 128.86 1.08 94 34 70 36 128.85 1.08 95 34 73 39 128.86 1.08 96 35 38 3 300.10 1.38 97 35 39 4 284.93 0.17 98 39 44 5 282.01 3.94 99 41 44 3 302.06 2.74 100 41 45 4 290.38 0.16 101 42 45 3 306.45 1.61 102 42 46 4 303.51 0.20 103 43 46 3 305.89 0.83 104 43 47 4 300.67 1.62 105 44 47 3 306.78 1.43 106 44 48 4 298.55 0.56 107 44 73 29 147.85 0.49 108 45 48 3 306.87 1.47 109 45 49 4 298.57 0.55 110 46 49 3 306.87 1.47 111 46 50 4 305.36 2.20 112 47 50 3 306.87 1.47 113 47 51 4 305.38 2.19 114 48 51 3 305.40 2.19 115 48 52 4 305.37 2.18 116 48 64 16 148.55 0.81 117 48 73 25 148.48 0.81 118 49 52 3 302.54 0.74 119 49 53 4 299.80 0.62 120 50 53 3 300.93 0.07 121 50 54 4 299.75 0.62 122 51 54 3 299.98 0.55 123 51 55 4 288.81 1.47 124 51 56 5 288.81 1.47 125 51 57 6 275.62 2.17 126 51 77 26 148.67 0.67 127 52 56 4 288.81 1.48 128 52 57 5 239.91 2.36 129 53 56 3 286.80 4.73 130 55 77 22 148.95 0.69 131 55 81 26 148.91 0.70 132 57 77 20 148.94 0.69 133 57 80 23 148.90 0.70 134 57 81 24 148.92 0.70 135 59 76 17 149.13 0.68 136 59 79 20 149.09 0.66 137 59 80 21 149.08 0.66 138 60 63 3 305.19 1.21 139 61 64 3 323.01 2.18 140 62 65 3 300.94 0.91 141 62 66 4 300.85 0.95 142 63 66 3 309.08 2.56 143 63 67 4 296.85 0.32 144 63 76 13 150.20 0.35 145 64 67 3 297.91 0.70 146 64 73 9 168.17 1.06 147 67 72 5 241.15 14.30 148 67 73 6 209.84 1.35 149 68 72 4 298.19 3.31 150 69 72 3 305.91 0.54 151 69 73 4 300.58 2.12 152 70 73 3 303.73 0.39 153 70 74 4 300.42 2.05 154 71 74 3 300.42 2.05 155 71 75 4 295.55 0.39 156 72 75 3 300.42 2.05 157 72 76 4 295.55 0.39 158 73 76 3 304.84 0.16 159 73 77 4 295.37 0.07 160 74 77 3 300.88 2.17 161 74 78 4 294.62 0.30 162 75 78 3 305.22 0.38 163 75 79 4 292.87 0.62 164 76 79 3 305.23 0.37 165 76 80 4 305.28 0.35 166 77 80 3 305.29 0.35 167 77 81 4 305.29 0.35 168 78 81 3 305.61 0.50 169 78 82 4 298.45 3.07 170 79 82 3 305.62 0.50 171 79 83 4 293.43 0.56 172 80 83 3 304.86 0.12 173 80 84 4 293.44 0.56 174 81 84 3 304.86 0.14