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 43 39 49.18 4.10 2 5 9 4 273.35 2.47 3 6 9 3 288.69 0.84 4 6 10 4 285.36 0.02 5 7 10 3 285.35 0.02 6 7 15 8 196.56 1.26 7 7 43 36 49.37 4.17 8 7 44 37 49.20 4.08 9 7 75 68 49.13 4.12 10 7 81 74 37.56 0.61 11 7 82 75 37.00 0.35 12 7 83 76 36.78 0.41 13 8 81 73 37.56 0.61 14 8 82 74 36.97 0.35 15 8 83 75 36.77 0.33 16 8 84 76 36.55 0.43 17 9 84 75 36.66 0.39 18 10 14 4 269.13 3.53 19 10 15 5 260.25 0.88 20 10 43 33 74.92 0.41 21 10 83 73 36.98 0.35 22 10 84 74 36.72 0.46 23 11 14 3 283.48 0.90 24 11 15 4 277.32 0.54 25 11 83 72 37.01 0.35 26 11 84 73 36.73 0.46 27 11 86 75 34.79 0.48 28 12 15 3 285.31 0.02 29 12 16 4 281.21 2.03 30 12 68 56 80.56 1.40 31 12 83 71 37.01 0.35 32 12 84 72 37.01 0.35 33 13 16 3 284.16 0.56 34 13 17 4 284.17 0.56 35 14 17 3 285.38 0.09 36 14 18 4 282.83 1.36 37 15 18 3 282.83 1.36 38 15 19 4 283.17 1.53 39 15 44 29 104.62 1.20 40 15 68 53 104.48 1.41 41 15 71 56 99.49 0.74 42 15 83 68 37.01 0.35 43 16 19 3 296.18 1.28 44 16 20 4 283.16 1.53 45 16 64 48 104.96 1.32 46 16 65 49 104.91 1.32 47 16 68 52 104.45 1.21 48 17 20 3 283.17 1.53 49 17 21 4 281.70 1.92 50 18 21 3 284.18 0.54 51 18 22 4 281.80 0.17 52 18 40 22 104.80 1.26 53 18 53 35 105.43 1.33 54 18 67 49 104.98 1.31 55 18 68 50 104.96 1.32 56 18 71 53 104.92 1.31 57 19 22 3 281.80 0.17 58 19 23 4 280.28 0.92 59 19 53 34 105.40 1.34 60 19 64 45 104.99 1.31 61 19 67 48 104.98 1.32 62 19 68 49 104.97 1.32 63 20 23 3 283.36 0.95 64 20 24 4 280.31 0.91 65 20 64 44 105.05 1.34 66 21 24 3 282.37 0.12 67 21 25 4 270.14 4.17 68 21 36 15 105.61 1.27 69 21 40 19 105.55 1.29 70 22 25 3 280.31 0.91 71 22 26 4 268.25 5.12 72 22 33 11 105.67 1.28 73 22 36 14 105.62 1.27 74 22 37 15 105.59 1.27 75 22 40 18 105.60 1.27 76 22 53 31 105.55 1.29 77 25 36 11 105.73 1.26 78 26 29 3 330.29 1.30 79 26 32 6 177.84 0.46 80 26 33 7 117.06 6.94 81 27 32 5 215.93 8.38 82 29 32 3 288.86 0.58 83 29 33 4 286.31 0.79 84 30 33 3 286.32 0.79 85 30 34 4 280.42 3.75 86 31 34 3 286.33 0.80 87 31 35 4 280.41 3.75 88 32 35 3 286.06 0.94 89 32 36 4 285.32 1.30 90 33 36 3 289.95 1.81 91 33 37 4 285.31 1.30 92 33 54 21 131.30 2.04 93 34 37 3 283.26 2.33 94 34 38 4 282.95 2.18 95 34 54 20 131.38 2.00 96 35 38 3 285.97 0.67 97 35 39 4 285.00 1.15 98 36 39 3 285.98 0.67 99 36 40 4 282.96 2.17 100 37 40 3 285.99 0.67 101 37 41 4 273.01 0.52 102 37 50 13 131.71 2.06 103 37 53 16 131.71 2.05 104 37 54 17 131.88 1.97 105 38 41 3 282.97 2.18 106 38 42 4 275.78 0.86 107 39 42 3 281.95 1.62 108 39 43 4 276.75 0.38 109 40 43 3 283.36 0.92 110 40 44 4 276.75 0.38 111 41 44 3 278.18 0.30 112 41 45 4 266.16 1.46 113 41 46 5 236.83 0.90 114 41 49 8 138.87 3.75 115 41 50 9 137.76 4.30 116 41 71 30 131.05 2.01 117 42 45 3 272.50 1.74 118 44 71 27 131.05 2.00 119 44 75 31 130.96 2.05 120 44 80 36 114.12 2.27 121 45 74 29 131.07 2.02 122 45 80 35 114.12 2.27 123 46 49 3 274.44 4.91 124 46 52 6 277.16 1.70 125 46 71 25 131.05 2.02 126 46 74 28 131.02 2.04 127 47 74 27 131.26 1.94 128 48 51 3 280.00 2.13 129 48 52 4 278.17 1.22 130 49 52 3 281.98 1.14 131 49 53 4 281.98 1.14 132 50 53 3 282.25 1.01 133 50 54 4 280.16 0.24 134 51 54 3 277.19 1.72 135 51 55 4 277.16 1.72 136 52 57 5 247.15 8.77 137 52 67 15 131.62 1.73 138 52 70 18 131.62 1.73 139 52 71 19 131.63 1.74 140 53 67 14 131.62 1.73 141 56 62 6 155.61 1.21 142 57 60 3 293.45 1.03 143 57 70 13 154.99 0.90 144 60 66 6 209.91 10.56 145 60 69 9 180.91 3.21 146 60 70 10 169.83 1.04 147 60 73 13 168.40 1.75 148 61 65 4 280.93 1.28 149 61 66 5 211.27 9.88 150 63 66 3 277.04 2.73 151 63 67 4 269.75 0.20 152 64 67 3 279.69 3.90 153 64 68 4 273.51 2.05 154 65 68 3 282.05 2.21 155 65 69 4 273.54 2.06 156 66 69 3 280.99 0.12 157 66 70 4 273.56 2.04 158 67 70 3 285.33 2.30 159 67 71 4 273.57 2.04 160 68 71 3 275.41 1.12 161 68 72 4 269.85 0.17 162 68 83 15 155.62 2.16 163 69 72 3 276.43 0.67 164 69 73 4 275.43 2.75 165 70 73 3 283.57 1.27 166 70 74 4 280.98 0.03 167 71 74 3 290.31 2.11 168 71 75 4 280.95 0.02 169 71 83 12 176.47 4.03 170 72 75 3 294.89 0.35 171 72 76 4 277.88 1.54 172 72 83 11 165.30 6.61 173 73 76 3 286.17 1.65 174 73 77 4 277.88 1.54 175 74 77 3 278.64 1.92 176 74 78 4 275.44 0.33 177 74 80 6 261.18 6.66 178 75 78 3 277.56 0.73 179 75 79 4 274.47 0.10 180 75 80 5 232.10 5.04 181 75 81 6 232.10 5.04 182 75 82 7 217.33 12.39 183 75 83 8 223.41 9.38