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 9 5 218.94 4.12 2 4 10 6 218.94 4.12 3 5 9 4 264.65 4.33 4 5 43 38 84.59 12.36 5 6 9 3 285.08 0.78 6 6 10 4 278.52 2.50 7 6 42 36 86.47 13.29 8 6 43 37 84.48 12.31 9 7 10 3 281.77 0.17 10 7 15 8 185.31 0.81 11 7 43 36 86.66 13.25 12 7 44 37 84.86 12.49 13 7 71 64 66.81 3.46 14 7 75 68 61.37 0.79 15 7 82 75 27.28 0.55 16 7 83 76 27.20 0.52 17 7 84 77 27.19 0.52 18 8 82 74 27.27 0.55 19 8 83 75 27.23 0.54 20 8 84 76 27.13 0.52 21 9 84 75 27.21 0.54 22 10 14 4 252.44 7.19 23 10 15 5 245.40 5.34 24 10 39 29 108.07 14.06 25 10 43 33 105.51 15.35 26 10 83 73 27.28 0.55 27 10 84 74 27.25 0.55 28 11 14 3 277.28 2.88 29 11 15 4 269.96 1.57 30 11 83 72 27.30 0.56 31 11 84 73 27.28 0.56 32 11 85 74 27.26 0.55 33 12 15 3 283.20 0.43 34 12 16 4 274.01 0.45 35 12 68 56 74.95 0.06 36 12 72 60 74.27 0.28 37 12 83 71 27.48 0.48 38 13 16 3 278.68 1.89 39 13 17 4 278.68 1.89 40 14 17 3 285.14 1.04 41 14 18 4 281.37 0.85 42 15 18 3 285.14 1.04 43 15 19 4 282.39 0.07 44 15 40 25 118.58 9.84 45 15 43 28 118.59 9.84 46 15 44 29 118.58 9.84 47 15 68 53 86.88 5.92 48 15 71 56 86.23 6.20 49 15 83 68 27.30 0.56 50 16 19 3 282.76 0.25 51 16 20 4 268.05 4.54 52 16 64 48 87.55 6.12 53 16 65 49 87.44 6.06 54 16 68 52 86.88 5.92 55 17 20 3 280.61 1.74 56 17 21 4 280.62 1.73 57 18 21 3 285.67 0.79 58 18 22 4 280.63 1.72 59 18 36 18 129.34 8.04 60 18 39 21 125.43 7.64 61 18 40 22 119.34 9.49 62 19 22 3 275.25 1.09 63 19 23 4 271.13 3.02 64 19 40 21 124.24 7.04 65 19 53 34 125.41 6.15 66 19 64 45 89.84 7.26 67 19 67 48 89.84 7.25 68 19 68 49 87.77 6.28 69 20 23 3 281.32 1.39 70 20 24 4 267.61 1.26 71 20 64 44 89.83 7.25 72 21 24 3 275.87 1.34 73 21 25 4 268.23 1.57 74 21 26 5 228.03 0.12 75 21 27 6 218.22 4.78 76 21 33 12 136.12 11.26 77 21 36 15 129.66 8.04 78 22 25 3 284.41 2.92 79 22 33 11 129.71 8.05 80 22 36 14 129.66 8.04 81 22 37 15 129.65 8.04 82 22 53 31 125.86 6.16 83 23 33 10 166.15 0.43 84 23 53 30 125.62 6.04 85 23 62 39 94.55 9.54 86 23 64 41 94.45 9.54 87 23 67 44 94.47 9.55 88 24 64 40 94.48 9.53 89 25 33 8 178.05 3.50 90 26 33 7 223.64 6.88 91 27 32 5 249.90 5.72 92 27 33 6 228.63 4.38 93 27 36 9 205.62 0.27 94 28 32 4 272.37 1.31 95 29 32 3 284.37 3.48 96 29 33 4 276.86 0.34 97 30 33 3 276.87 0.34 98 30 34 4 276.92 0.35 99 31 34 3 286.45 1.38 100 31 35 4 276.93 0.35 101 32 35 3 286.45 1.38 102 32 36 4 276.93 0.35 103 33 36 3 280.62 1.49 104 33 37 4 276.92 0.35 105 34 37 3 276.46 1.40 106 34 38 4 277.08 0.19 107 35 38 3 280.61 1.49 108 35 39 4 277.07 0.18 109 36 39 3 285.10 2.93 110 36 40 4 277.07 0.18 111 37 40 3 280.56 1.56 112 37 41 4 277.06 0.18 113 37 50 13 148.37 4.88 114 37 53 16 148.38 4.88 115 37 54 17 148.38 4.89 116 38 41 3 279.02 1.90 117 38 42 4 275.94 0.36 118 39 42 3 281.45 1.50 119 39 43 4 275.87 0.37 120 40 43 3 276.66 0.76 121 40 44 4 273.06 1.01 122 40 46 6 265.71 1.42 123 40 49 9 148.68 4.83 124 40 52 12 148.65 4.83 125 40 71 31 115.61 20.86 126 41 44 3 292.87 2.34 127 41 45 4 269.69 0.43 128 41 49 8 148.67 4.83 129 41 50 9 148.67 4.83 130 43 75 32 111.56 22.85 131 44 71 27 115.61 20.90 132 44 74 30 112.82 22.25 133 44 75 31 111.55 22.85 134 45 74 29 115.59 20.93 135 46 49 3 247.55 3.81 136 46 52 6 227.73 12.68 137 46 70 24 116.33 20.64 138 46 71 25 115.68 20.89 139 46 74 28 115.57 20.93 140 47 74 27 115.72 20.91 141 48 51 3 267.86 1.30 142 48 52 4 267.86 1.30 143 48 55 7 179.24 3.35 144 49 52 3 296.86 2.36 145 50 53 3 296.86 2.36 146 50 54 4 259.21 3.04 147 51 54 3 254.34 0.60 148 51 55 4 235.51 8.80 149 52 67 15 116.52 20.60 150 52 70 18 116.47 20.62 151 52 71 19 116.39 20.66 152 53 56 3 290.88 0.54 153 53 67 14 116.53 20.61 154 56 62 6 116.59 20.59 155 57 60 3 259.56 1.86 156 62 67 5 260.94 3.08 157 63 67 4 275.62 1.69 158 64 67 3 277.79 0.61 159 64 68 4 275.62 1.69 160 65 68 3 277.39 0.81 161 65 69 4 275.92 1.54 162 66 69 3 282.23 3.23 163 66 70 4 276.50 1.25 164 67 70 3 286.01 2.93 165 67 71 4 272.95 0.84 166 68 71 3 285.42 3.22 167 68 72 4 275.79 0.89 168 69 72 3 284.07 0.39 169 69 73 4 280.57 1.36 170 70 73 3 287.17 1.15 171 70 74 4 280.56 1.36 172 71 74 3 277.09 0.37 173 71 75 4 282.80 1.17 174 71 83 12 89.27 29.96 175 72 75 3 292.88 1.01 176 72 76 4 281.48 1.83 177 72 83 11 52.69 11.77 178 73 76 3 284.98 0.09 179 73 77 4 281.42 1.85 180 74 77 3 279.30 2.92 181 74 78 4 271.19 6.97 182 74 80 6 245.91 10.08 183 75 78 3 276.65 4.21 184 75 79 4 254.19 5.91 185 75 80 5 214.25 4.17 186 75 81 6 214.25 4.17 187 75 82 7 196.00 3.17 188 76 79 3 274.80 0.70