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 7 40 33 141.09 1.99 2 8 12 4 269.37 3.04 3 9 12 3 269.37 3.04 4 9 13 4 256.08 0.33 5 9 38 29 149.25 1.56 6 10 13 3 264.39 0.58 7 10 14 4 254.49 0.46 8 10 33 23 149.34 1.58 9 10 38 28 148.67 1.24 10 10 41 31 148.22 1.42 11 10 45 35 144.51 0.43 12 10 49 39 135.12 1.02 13 11 14 3 260.18 2.38 14 11 15 4 258.92 1.76 15 11 49 38 135.10 1.01 16 11 53 42 123.14 0.48 17 12 15 3 262.72 1.10 18 12 16 4 256.48 2.98 19 13 16 3 259.85 1.29 20 13 17 4 256.49 2.98 21 13 33 20 150.24 1.32 22 13 36 23 150.44 1.28 23 13 38 25 150.24 1.32 24 14 17 3 260.71 2.12 25 14 18 4 257.75 3.60 26 14 29 15 150.21 1.31 27 14 33 19 150.36 1.24 28 14 46 32 146.59 0.76 29 14 49 35 135.29 1.00 30 14 50 36 135.16 1.03 31 14 53 39 123.16 0.47 32 15 18 3 262.76 3.15 33 15 19 4 256.49 2.96 34 15 53 38 123.17 0.47 35 15 69 54 78.01 0.73 36 15 73 58 43.13 0.49 37 15 74 59 39.35 0.05 38 16 19 3 262.92 3.08 39 16 20 4 253.18 1.30 40 17 20 3 260.84 0.43 41 17 23 6 198.17 1.38 42 17 29 12 152.60 0.28 43 17 32 15 150.62 1.28 44 17 33 16 150.61 1.28 45 17 36 19 150.66 1.28 46 18 21 3 260.83 0.74 47 18 29 11 155.15 1.54 48 18 50 32 140.87 3.66 49 18 55 37 120.33 0.46 50 18 67 49 82.59 1.12 51 18 68 50 79.85 1.34 52 18 69 51 79.54 1.49 53 19 69 50 79.84 1.33 54 19 72 53 78.14 0.80 55 21 60 39 93.32 0.96 56 21 66 45 84.67 1.72 57 21 68 47 82.89 1.07 58 22 28 6 250.59 0.21 59 22 66 44 84.67 1.73 60 23 28 5 245.87 2.16 61 23 29 6 222.81 1.24 62 23 32 9 222.80 1.25 63 23 66 43 84.61 1.75 64 23 67 44 84.48 1.74 65 24 28 4 257.32 2.50 66 24 57 33 119.44 0.28 67 24 65 41 84.72 1.72 68 24 66 42 84.58 1.77 69 25 28 3 262.77 0.39 70 25 29 4 257.37 2.48 71 25 67 42 84.57 1.76 72 26 29 3 265.09 0.78 73 26 30 4 256.26 1.93 74 26 43 17 150.75 1.22 75 26 46 20 150.68 1.23 76 26 47 21 150.66 1.25 77 26 50 24 150.50 1.31 78 26 67 41 84.56 1.77 79 27 30 3 256.27 1.93 80 27 31 4 256.26 1.93 81 28 31 3 263.10 0.61 82 28 32 4 256.68 1.69 83 29 32 3 256.69 1.68 84 29 33 4 256.68 1.68 85 29 46 17 150.72 1.21 86 30 33 3 265.16 0.23 87 30 34 4 263.00 0.84 88 30 41 11 150.99 1.22 89 30 42 12 150.97 1.21 90 30 43 13 150.94 1.22 91 30 46 16 150.72 1.21 92 31 34 3 263.00 0.84 93 31 35 4 263.00 0.84 94 32 35 3 263.48 1.08 95 32 36 4 263.00 0.84 96 33 36 3 257.38 1.95 97 33 37 4 252.58 0.45 98 33 38 5 246.93 1.68 99 33 41 8 168.19 0.23 100 33 46 13 150.94 1.26 101 34 38 4 239.78 1.85 102 34 41 7 175.30 1.61 103 38 41 3 268.69 1.63 104 41 45 4 246.34 0.34 105 41 46 5 246.41 0.32 106 42 45 3 253.71 0.06 107 42 46 4 255.42 0.80 108 43 46 3 255.47 0.83 109 43 47 4 252.16 2.43 110 44 47 3 256.70 2.12 111 44 48 4 255.43 0.79 112 45 48 3 255.44 0.79 113 45 49 4 255.43 0.79 114 46 49 3 258.19 0.59 115 46 50 4 247.16 1.69 116 47 50 3 263.03 1.82 117 47 51 4 247.15 1.68 118 48 51 3 263.81 1.43 119 48 52 4 246.06 1.16 120 49 52 3 252.66 4.44 121 49 53 4 244.69 0.47 122 50 54 4 236.04 3.85 123 50 55 5 186.56 2.73 124 50 67 17 84.64 1.71 125 51 54 3 252.64 4.45 126 53 73 20 40.17 0.38 127 53 74 21 37.90 0.68 128 54 70 16 81.94 1.43 129 55 68 13 84.38 1.82 130 55 69 14 81.81 0.62 131 55 70 15 81.06 0.99 132 56 67 11 84.69 1.72 133 56 68 12 84.60 1.75 134 56 70 14 83.71 1.57 135 57 65 8 156.77 0.62 136 57 66 9 123.14 17.31 137 57 67 10 84.73 1.70 138 58 64 6 170.34 4.84 139 58 65 7 156.94 0.54 140 58 66 8 156.75 0.62 141 58 68 10 122.34 16.96 142 59 63 4 170.36 4.84 143 59 64 5 170.34 4.84 144 59 65 6 157.72 0.50 145 60 63 3 242.73 1.93 146 60 64 4 172.52 3.77 147 60 66 6 159.69 0.47