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 3 37 34 68.45 0.71 2 3 40 37 68.27 0.65 3 4 9 5 197.94 5.58 4 4 10 6 196.44 4.73 5 4 14 10 184.36 0.83 6 4 40 36 68.50 0.70 7 4 44 40 68.48 0.70 8 5 44 39 68.48 0.70 9 6 9 3 292.97 0.48 10 6 10 4 278.70 2.35 11 6 44 38 68.52 0.68 12 7 10 3 286.24 0.16 13 7 15 8 240.23 0.57 14 7 44 37 68.55 0.68 15 7 45 38 68.53 0.68 16 7 72 65 68.51 0.68 17 7 76 69 62.59 0.48 18 7 82 75 27.32 0.45 19 7 83 76 27.00 0.32 20 7 84 77 26.20 0.55 21 8 82 74 27.14 0.36 22 8 83 75 27.00 0.32 23 8 85 77 25.55 0.65 24 9 14 5 277.23 1.71 25 9 85 76 25.77 0.76 26 10 14 4 274.56 0.37 27 10 15 5 268.57 2.42 28 10 18 8 264.12 1.23 29 10 40 30 86.03 1.02 30 10 44 34 79.36 0.96 31 10 84 74 26.28 0.58 32 10 85 75 25.62 0.71 33 11 14 3 281.63 1.19 34 11 15 4 274.59 0.39 35 11 84 73 26.38 0.62 36 11 85 74 25.66 0.70 37 12 15 3 287.19 1.58 38 12 16 4 282.92 3.73 39 12 69 57 79.54 0.17 40 12 73 61 77.09 1.05 41 12 84 72 26.98 0.34 42 13 16 3 285.83 2.27 43 13 17 4 285.83 2.27 44 14 17 3 282.22 0.46 45 14 18 4 277.54 1.50 46 15 18 3 277.54 1.50 47 15 19 4 277.54 1.50 48 15 41 26 87.78 0.63 49 15 44 29 87.53 0.72 50 15 45 30 87.44 0.70 51 15 69 54 86.41 0.24 52 15 72 57 86.37 0.26 53 15 84 69 26.38 0.62 54 16 19 3 277.66 1.45 55 16 20 4 277.68 1.44 56 16 65 49 86.44 0.24 57 16 69 53 86.45 0.26 58 17 20 3 283.49 0.15 59 17 21 4 277.68 1.44 60 18 21 3 284.14 1.17 61 18 22 4 279.47 0.52 62 18 40 22 88.17 0.48 63 18 44 26 87.83 0.65 64 19 22 3 282.46 2.01 65 19 23 4 277.65 1.42 66 19 41 22 88.22 0.49 67 19 54 35 87.90 0.73 68 19 65 46 87.77 0.67 69 19 68 49 87.75 0.66 70 19 69 50 87.75 0.66 71 20 23 3 285.66 2.37 72 20 24 4 284.58 2.90 73 20 65 45 87.81 0.65 74 21 24 3 286.28 2.06 75 21 25 4 286.28 2.06 76 21 37 16 89.41 0.94 77 22 25 3 286.28 2.06 78 22 26 4 276.34 1.22 79 22 34 12 89.43 0.94 80 22 37 15 89.19 0.83 81 22 38 16 89.18 0.83 82 22 41 19 89.17 0.82 83 22 54 32 89.04 0.88 84 23 26 3 289.39 0.50 85 23 27 4 283.95 0.92 86 23 65 42 88.35 0.59 87 24 27 3 287.60 0.58 88 24 28 4 278.04 2.04 89 25 28 3 278.04 2.04 90 25 33 8 89.78 0.99 91 25 34 9 89.58 0.94 92 25 37 12 89.64 0.95 93 26 34 8 89.77 1.00 94 26 55 29 89.48 0.96 95 31 34 3 270.00 3.15 96 31 35 4 262.32 3.96 97 32 36 4 274.31 0.99 98 33 36 3 283.69 2.87 99 33 37 4 272.06 0.14 100 34 37 3 282.50 2.43 101 34 38 4 271.94 0.08 102 34 55 21 140.75 1.80 103 35 38 3 280.29 2.25 104 35 39 4 274.76 0.51 105 36 39 3 280.61 2.09 106 36 40 4 269.04 0.54 107 37 40 3 282.54 1.12 108 37 41 4 276.29 3.12 109 38 41 3 276.29 3.13 110 38 42 4 272.69 1.54 111 38 51 13 140.88 1.88 112 38 54 16 140.90 1.83 113 38 55 17 140.90 1.83 114 39 42 3 285.04 1.25 115 39 43 4 277.19 2.77 116 40 43 3 285.14 1.20 117 40 44 4 280.80 0.98 118 41 44 3 292.41 2.44 119 41 45 4 273.06 1.38 120 41 50 9 151.97 3.46 121 41 51 10 141.18 1.92 122 41 53 12 141.84 1.58 123 41 54 13 141.12 1.90 124 41 68 27 123.76 3.53 125 41 72 31 123.66 3.54 126 42 45 3 281.99 0.70 127 42 46 4 273.04 1.36 128 42 50 8 141.19 1.93 129 42 51 9 141.19 1.92 130 43 46 3 285.82 1.22 131 44 76 32 123.59 3.56 132 45 72 27 123.67 3.55 133 45 76 31 123.58 3.58 134 46 75 29 123.64 3.55 135 46 76 30 123.59 3.56 136 46 81 35 111.83 1.96 137 47 50 3 276.75 2.57 138 47 53 6 209.78 0.55 139 47 75 28 123.61 3.56 140 48 75 27 123.65 3.56 141 49 52 3 285.24 1.19 142 50 53 3 299.16 1.47 143 51 54 3 295.73 0.24 144 51 55 4 274.95 0.64 145 52 55 3 281.72 0.07 146 52 56 4 244.25 0.71 147 52 57 5 225.09 7.36 148 53 61 8 187.33 3.56 149 53 68 15 123.78 3.53 150 53 71 18 123.75 3.52 151 53 72 19 123.74 3.52 152 54 57 3 296.11 2.29 153 54 68 14 123.77 3.52 154 57 61 4 277.61 0.66 155 57 63 6 146.37 4.05 156 58 61 3 298.57 5.21 157 61 67 6 159.54 1.57 158 61 68 7 175.72 1.49 159 61 71 10 155.38 0.47 160 62 67 5 162.12 2.33 161 64 67 3 280.17 0.42 162 64 68 4 280.50 0.54 163 65 68 3 282.80 0.47 164 65 69 4 280.51 0.54 165 66 69 3 284.11 2.33 166 66 70 4 280.50 0.54 167 67 70 3 283.01 1.79 168 67 71 4 281.19 0.19 169 68 71 3 283.54 1.36 170 68 72 4 281.19 0.18 171 69 72 3 281.19 0.18 172 69 73 4 281.18 0.18 173 69 84 15 63.26 18.21 174 70 73 3 280.20 0.32 175 70 74 4 282.28 0.72 176 71 74 3 282.29 0.72 177 71 75 4 282.28 0.72 178 72 75 3 285.65 0.96 179 72 76 4 276.68 0.05 180 72 84 12 116.89 11.88 181 73 76 3 289.48 0.95 182 73 77 4 277.06 2.15 183 73 84 11 116.86 11.86 184 74 77 3 285.14 1.22 185 74 78 4 280.42 0.47 186 75 78 3 281.56 1.03 187 75 79 4 280.43 0.47 188 75 81 6 269.19 1.07 189 76 79 3 289.12 1.05 190 76 80 4 280.43 0.47 191 76 81 5 236.01 4.40 192 76 82 6 236.00 4.40 193 77 80 3 280.12 0.32