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 5 50 45 73.62 1.05 2 7 10 3 347.01 3.22 3 8 11 3 330.19 1.61 4 8 23 15 163.30 0.35 5 11 22 11 165.62 1.35 6 12 20 8 172.53 1.96 7 12 21 9 165.69 1.36 8 12 22 10 165.63 1.35 9 13 20 7 172.62 2.00 10 13 21 8 172.53 1.96 11 13 49 36 151.76 3.84 12 14 19 5 202.45 5.03 13 14 20 6 172.67 1.98 14 14 48 34 152.75 3.68 15 15 18 3 293.88 8.78 16 15 19 4 247.19 3.04 17 15 44 29 152.75 3.73 18 15 45 30 152.74 3.72 19 15 48 33 152.78 3.69 20 16 44 28 152.89 3.76 21 16 48 32 152.80 3.68 22 16 85 69 54.05 2.80 23 17 44 27 153.25 3.68 24 21 25 4 328.08 0.24 25 21 26 5 323.75 0.46 26 21 38 17 156.38 2.55 27 21 41 20 155.60 2.37 28 21 45 24 155.16 2.42 29 22 25 3 336.41 0.07 30 22 26 4 331.94 2.17 31 23 26 3 338.07 0.90 32 23 50 27 155.30 2.23 33 25 38 13 167.35 4.95 34 26 45 19 155.53 2.31 35 26 50 24 155.44 2.27 36 26 60 34 145.69 2.06 37 27 31 4 268.49 12.75 38 27 34 7 231.24 5.15 39 27 38 11 179.28 1.02 40 27 42 15 155.64 2.27 41 27 60 33 145.71 2.06 42 28 31 3 340.06 0.81 43 28 60 32 145.72 2.06 44 29 34 5 339.08 0.27 45 29 59 30 145.80 2.08 46 30 34 4 364.43 0.62 47 31 34 3 367.26 0.79 48 31 38 7 313.06 3.71 49 33 38 5 321.99 0.73 50 34 38 4 314.61 2.96 51 34 39 5 307.56 0.03 52 34 42 8 300.06 3.71 53 34 62 28 145.45 2.18 54 34 70 36 130.02 3.15 55 35 38 3 329.11 2.90 56 35 39 4 321.29 0.38 57 36 39 3 330.46 2.21 58 36 40 4 321.30 0.38 59 37 40 3 332.37 0.24 60 37 41 4 328.24 2.33 61 38 41 3 332.41 0.27 62 38 42 4 332.41 0.27 63 39 42 3 337.51 2.81 64 39 43 4 332.41 0.26 65 39 70 31 116.01 0.45 66 40 43 3 334.87 0.96 67 40 44 4 322.12 0.73 68 40 74 34 115.46 0.34 69 41 45 4 315.83 3.88 70 42 45 3 334.72 2.14 71 42 46 4 322.13 0.78 72 42 60 18 145.69 2.04 73 42 70 28 116.07 0.42 74 43 46 3 337.35 0.92 75 43 47 4 315.81 3.93 76 43 67 24 141.17 2.92 77 43 70 27 116.01 0.45 78 43 71 28 115.59 0.34 79 43 74 31 115.59 0.34 80 44 48 4 300.69 3.62 81 44 49 5 287.19 3.13 82 44 74 30 115.48 0.33 83 45 49 4 286.83 2.96 84 45 50 5 281.46 5.65 85 46 50 4 281.45 5.65 86 46 51 5 263.31 3.10 87 46 56 10 196.24 1.09 88 46 60 14 158.69 8.53 89 46 67 21 143.55 2.52 90 47 51 4 281.45 5.65 91 47 67 20 144.06 2.77 92 47 86 39 54.01 3.02 93 47 90 43 54.06 3.10 94 48 89 41 54.12 3.10 95 51 55 4 330.54 4.25 96 51 56 5 312.69 4.67 97 51 60 9 249.58 2.77 98 52 55 3 341.19 0.12 99 52 56 4 330.56 4.25 100 52 90 38 54.12 3.11 101 53 56 3 334.31 2.39 102 53 57 4 330.56 4.26 103 53 67 14 180.99 0.05 104 53 90 37 54.14 3.10 105 54 57 3 336.05 2.04 106 54 58 4 334.24 2.42 107 55 58 3 334.24 2.42 108 55 59 4 327.68 5.70 109 56 60 4 284.60 1.97 110 56 61 5 264.38 0.20 111 57 61 4 211.92 1.51 112 61 64 3 342.61 0.54 113 62 66 4 329.28 0.88 114 62 67 5 327.20 1.89 115 62 70 8 320.97 0.32 116 63 66 3 331.72 0.35 117 63 67 4 327.23 1.90 118 64 67 3 328.95 1.03 119 64 68 4 327.27 1.92 120 65 68 3 329.28 0.91 121 65 69 4 327.31 1.89 122 66 69 3 335.26 2.71 123 66 70 4 329.61 0.75 124 67 70 3 330.15 1.02 125 67 71 4 329.61 0.74 126 68 71 3 332.80 1.48 127 68 72 4 326.52 0.80 128 69 72 3 329.25 2.15 129 69 73 4 326.51 0.80 130 70 73 3 339.67 0.52 131 70 74 4 326.80 0.35 132 71 74 3 326.80 0.35 133 71 75 4 325.90 0.09 134 71 84 13 67.62 3.34 135 72 75 3 325.90 0.09 136 72 76 4 325.90 0.09 137 75 84 9 72.35 0.97 138 77 83 6 224.84 2.56 139 80 83 3 338.73 0.60 140 81 84 3 340.22 0.20 141 82 87 5 259.05 3.27 142 82 88 6 254.80 4.03 143 82 91 9 242.89 1.09 144 83 88 5 266.73 0.16 145 84 87 3 325.37 4.50 146 84 88 4 299.01 2.48 147 85 88 3 325.37 0.18 148 85 89 4 310.13 3.07 149 86 90 4 317.75 0.53 150 87 90 3 320.98 2.14 151 87 91 4 317.79 0.55 152 88 91 3 331.17 0.70 153 88 92 4 317.80 0.54 154 89 92 3 331.18 0.70 155 89 93 4 320.94 2.12 156 90 94 4 335.50 1.92 157 91 94 3 344.30 2.02 158 91 95 4 335.62 1.85 159 92 95 3 335.69 1.82 160 93 97 4 278.32 5.41