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 8 44 36 120.83 0.62 2 9 42 33 121.22 0.62 3 9 43 34 121.22 0.62 4 9 44 35 120.86 0.64 5 10 13 3 257.47 0.08 6 10 39 29 121.50 0.66 7 10 42 32 121.38 0.63 8 10 43 33 121.31 0.60 9 11 39 28 121.51 0.66 10 11 42 31 121.43 0.64 11 11 43 32 121.31 0.60 12 11 44 33 121.31 0.60 13 11 45 34 121.09 0.58 14 11 46 35 121.04 0.59 15 11 49 38 121.06 0.60 16 12 16 4 221.78 0.44 17 12 17 5 207.67 6.53 18 12 20 8 179.54 2.69 19 12 21 9 179.56 2.68 20 12 24 12 158.99 0.32 21 12 35 23 121.86 0.64 22 12 39 27 121.51 0.66 23 12 53 41 120.70 0.51 24 13 16 3 266.24 0.07 25 13 17 4 234.53 5.93 26 14 17 3 268.12 2.37 27 16 19 3 252.09 4.41 28 16 20 4 249.44 7.69 29 17 21 4 276.16 2.24 30 17 49 32 121.11 0.56 31 18 21 3 283.00 3.49 32 19 22 3 284.11 0.39 33 19 23 4 278.34 1.16 34 20 23 3 292.56 0.73 35 20 24 4 264.95 0.43 36 20 35 15 128.71 2.58 37 21 24 3 288.00 1.55 38 21 25 4 276.13 2.24 39 21 53 32 120.84 0.44 40 21 72 51 95.88 0.62 41 21 73 52 95.72 0.70 42 21 76 55 84.80 1.01 43 22 27 5 230.97 1.97 44 22 72 50 95.92 0.64 45 22 73 51 95.88 0.62 46 23 27 4 225.59 1.12 47 23 31 8 170.21 6.04 48 23 32 9 153.47 9.37 49 23 35 12 129.87 2.19 50 23 72 49 96.25 0.63 51 24 27 3 303.28 0.30 52 24 32 8 143.91 4.75 53 24 35 11 129.86 2.19 54 24 72 48 96.17 0.59 55 25 32 7 186.03 4.71 56 25 53 28 120.73 0.50 57 25 55 30 120.57 0.44 58 25 56 31 116.89 1.59 59 25 71 46 96.46 0.59 60 25 72 47 96.25 0.59 61 25 73 48 96.38 0.56 62 25 75 50 95.06 0.35 63 25 76 51 94.16 0.80 64 26 32 6 260.86 1.53 65 26 71 45 96.50 0.60 66 26 72 46 96.38 0.57 67 27 31 4 283.89 1.56 68 27 32 5 266.50 1.29 69 27 69 42 96.45 0.61 70 27 72 45 96.37 0.58 71 28 31 3 289.07 1.29 72 29 32 3 288.51 0.17 73 29 33 4 283.46 1.19 74 30 33 3 286.16 0.01 75 30 34 4 286.15 0.01 76 31 34 3 290.17 2.02 77 31 35 4 287.28 0.57 78 32 35 3 287.28 0.57 79 32 36 4 286.69 0.26 80 33 36 3 287.92 0.88 81 33 37 4 277.56 0.30 82 34 37 3 282.17 2.00 83 34 38 4 280.95 1.40 84 35 38 3 295.61 1.80 85 35 39 4 273.23 1.86 86 36 39 3 274.11 0.85 87 36 40 4 274.20 3.41 88 36 41 5 274.14 0.83 89 37 41 4 288.11 0.58 90 38 41 3 292.35 0.58 91 38 42 4 281.83 0.40 92 39 42 3 283.98 1.48 93 39 43 4 276.75 2.13 94 40 43 3 283.98 1.48 95 43 46 3 291.28 0.35 96 45 48 3 299.82 0.25 97 45 49 4 284.04 1.01 98 46 49 3 288.93 1.44 99 46 50 4 273.23 0.68 100 46 53 7 230.77 0.43 101 47 50 3 274.40 0.12 102 47 51 4 273.25 0.69 103 48 51 3 295.43 0.55 104 49 52 3 292.97 0.96 105 49 53 4 262.23 4.78 106 50 53 3 272.85 1.40 107 50 54 4 256.06 1.71 108 51 81 30 48.61 1.44 109 51 82 31 48.29 1.59 110 51 83 32 48.28 1.59 111 51 85 34 36.63 0.90 112 51 86 35 31.64 1.33 113 52 55 3 289.98 0.50 114 52 76 24 80.09 0.27 115 52 81 29 51.48 0.01 116 52 85 33 37.05 0.69 117 53 56 3 288.45 1.27 118 53 76 23 81.40 0.38 119 54 57 3 302.75 2.30 120 54 58 4 273.06 1.88 121 55 58 3 269.53 1.51 122 55 61 6 204.37 4.08 123 55 71 16 143.35 0.86 124 55 75 20 89.77 1.18 125 58 61 3 288.97 1.01 126 58 71 13 154.12 4.16 127 59 65 6 217.28 0.24 128 59 71 12 154.30 4.25 129 60 65 5 246.45 1.20 130 61 64 3 295.30 0.04 131 61 65 4 250.38 3.16 132 61 79 18 151.16 2.79 133 63 79 16 153.81 4.07 134 64 74 10 155.81 3.93 135 64 78 14 153.80 4.08 136 65 71 6 210.39 0.43 137 65 74 9 155.59 3.82 138 66 70 4 256.34 0.20 139 66 71 5 213.16 0.95 140 66 74 8 208.62 0.44 141 67 71 4 262.30 0.41 142 68 71 3 284.31 5.56 143 68 72 4 286.21 4.62 144 69 72 3 295.98 0.01 145 70 73 3 291.05 2.21 146 70 74 4 268.03 2.67 147 71 74 3 273.10 0.14 148 71 75 4 267.56 2.93 149 72 75 3 280.28 3.73 150 72 76 4 273.13 0.15 151 73 76 3 279.12 3.16 152 73 77 4 267.52 2.95 153 73 78 5 258.82 7.30 154 74 78 4 236.92 2.47 155 75 79 4 269.02 6.88 156 76 81 5 227.94 3.88 157 77 80 3 283.74 1.63 158 77 81 4 268.45 3.84 159 79 84 5 227.66 3.69 160 79 85 6 227.67 3.68 161 80 83 3 325.79 0.86 162 80 84 4 270.02 5.25 163 80 85 5 266.73 6.90 164 81 85 4 270.02 5.25 165 82 85 3 304.87 0.68 166 83 86 3 277.01 1.68 167 83 88 5 227.42 3.56