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 6 10 4 253.80 2.19 2 6 28 22 94.13 13.38 3 7 10 3 266.33 0.74 4 7 11 4 254.00 2.27 5 7 35 28 93.78 13.52 6 7 36 29 93.64 13.56 7 7 39 32 93.63 13.54 8 7 40 33 93.59 13.55 9 8 11 3 260.05 0.63 10 8 12 4 255.39 2.96 11 8 72 64 44.83 0.35 12 8 73 65 44.77 0.32 13 8 76 68 30.58 0.72 14 8 77 69 30.87 0.58 15 8 79 71 25.96 0.18 16 9 12 3 263.15 0.21 17 9 13 4 258.50 1.40 18 9 81 72 24.12 0.10 19 10 13 3 259.63 1.97 20 10 14 4 257.74 1.02 21 10 26 16 100.39 10.71 22 10 28 18 100.39 10.71 23 10 33 23 93.95 13.45 24 10 36 26 93.78 13.52 25 11 14 3 263.81 0.54 26 11 15 4 257.74 1.02 27 11 40 29 93.69 13.56 28 11 45 34 91.31 12.38 29 11 46 35 90.92 12.23 30 11 65 54 72.92 3.27 31 11 72 61 45.58 0.54 32 11 73 62 44.83 0.34 33 12 15 3 262.69 1.09 34 12 16 4 257.73 1.02 35 12 73 61 44.83 0.34 36 12 81 69 25.31 0.17 37 12 82 70 24.69 0.01 38 13 16 3 274.99 0.23 39 13 17 4 247.49 0.10 40 13 21 8 159.28 1.05 41 13 26 13 100.59 10.62 42 13 81 68 25.31 0.17 43 13 82 69 24.23 0.06 44 14 17 3 261.49 0.86 45 14 18 4 253.71 3.00 46 14 19 5 213.41 0.90 47 14 21 7 179.46 1.38 48 14 58 44 98.24 7.52 49 14 63 49 73.09 3.23 50 14 65 51 72.98 3.26 51 15 65 50 72.98 3.27 52 15 70 55 65.86 0.48 53 15 73 58 50.62 1.78 54 16 82 66 25.37 0.16 55 19 58 39 98.86 7.22 56 19 59 40 98.81 7.24 57 19 60 41 98.36 7.03 58 19 63 44 81.89 1.01 59 20 58 38 98.80 7.24 60 20 59 39 98.80 7.23 61 20 60 40 98.38 7.04 62 21 26 5 237.30 6.09 63 21 33 12 178.24 2.46 64 21 58 37 98.88 7.21 65 22 25 3 252.41 1.45 66 22 26 4 244.41 3.23 67 23 26 3 265.48 0.30 68 23 27 4 248.95 0.96 69 23 28 5 221.97 1.46 70 23 29 6 212.02 3.51 71 23 30 7 181.51 1.09 72 23 33 10 174.80 0.74 73 24 27 3 252.41 1.45 74 24 28 4 222.12 1.48 75 26 33 7 235.77 0.48 76 26 81 55 24.59 0.09 77 28 32 4 249.12 0.02 78 28 33 5 245.24 1.93 79 29 32 3 256.25 0.10 80 29 33 4 252.58 1.74 81 30 33 3 267.29 2.27 82 30 34 4 252.58 1.74 83 31 34 3 253.81 1.12 84 31 35 4 252.61 1.72 85 31 55 24 135.72 11.00 86 32 35 3 263.69 1.10 87 32 36 4 259.10 0.71 88 33 36 3 259.94 0.77 89 33 37 4 259.10 0.71 90 33 58 25 135.53 11.06 91 34 37 3 261.96 0.23 92 34 38 4 259.10 0.72 93 34 55 21 135.72 11.00 94 34 56 22 135.66 11.00 95 35 38 3 259.25 0.65 96 35 39 4 259.24 0.64 97 36 39 3 263.94 0.01 98 36 40 4 259.26 0.61 99 37 40 3 270.94 3.74 100 37 41 4 254.77 1.66 101 37 46 9 173.70 4.98 102 37 49 12 150.94 3.46 103 37 56 19 135.75 11.03 104 38 41 3 262.01 0.10 105 38 42 4 256.49 2.67 106 38 51 13 144.69 6.58 107 38 56 18 135.72 11.06 108 39 42 3 265.10 1.02 109 39 43 4 256.48 2.67 110 40 43 3 268.61 2.40 111 40 44 4 250.02 4.02 112 40 45 5 224.21 0.73 113 40 46 6 216.90 2.91 114 41 44 3 256.31 2.83 115 41 46 5 206.37 2.35 116 41 49 8 160.00 0.96 117 41 51 10 160.19 0.85 118 43 68 25 118.14 19.39 119 44 66 22 118.27 19.38 120 44 68 24 118.14 19.39 121 45 65 20 118.28 19.38 122 45 66 21 118.24 19.38 123 45 68 23 118.14 19.39 124 45 69 24 113.72 21.53 125 45 72 27 113.53 21.02 126 46 49 3 330.89 0.33 127 46 64 18 118.29 19.37 128 46 65 19 118.27 19.38 129 46 66 20 118.25 19.38 130 47 62 15 118.63 19.37 131 47 63 16 118.59 19.38 132 47 64 17 118.41 19.42 133 47 66 19 118.29 19.37 134 48 62 14 118.62 19.37 135 48 63 15 118.58 19.37 136 49 56 7 159.21 0.17 137 50 56 6 159.63 0.04 138 50 57 7 159.21 0.17 139 50 59 9 158.74 0.04 140 51 54 3 270.01 0.21 141 51 55 4 223.13 9.30 142 51 56 5 162.80 1.54 143 52 55 3 273.70 1.25 144 52 57 5 198.13 3.21 145 53 57 4 271.58 0.98 146 58 63 5 168.71 2.59 147 59 63 4 257.98 1.41 148 65 70 5 243.40 1.04 149 65 73 8 243.54 0.98 150 66 69 3 254.61 0.10 151 66 70 4 254.61 0.10 152 67 70 3 255.43 0.51 153 67 71 4 254.62 0.09 154 68 71 3 257.75 1.41 155 68 72 4 257.73 1.43 156 69 72 3 258.70 1.90 157 69 73 4 258.71 1.90 158 70 73 3 261.86 0.34 159 70 74 4 258.81 1.87 160 71 74 3 260.08 1.86 161 71 75 4 259.44 1.55 162 72 75 3 261.25 1.28 163 72 76 4 258.80 1.86 164 73 76 3 260.85 0.85 165 73 77 4 245.25 0.43 166 75 78 3 293.48 0.61 167 76 79 3 290.43 0.33