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 40 37 54.44 1.10 2 4 40 36 56.40 1.31 3 5 12 7 235.33 1.84 4 5 38 33 56.43 1.31 5 5 40 35 57.39 1.47 6 5 41 36 57.47 1.43 7 7 11 4 263.71 1.18 8 7 12 5 263.69 1.18 9 7 15 8 244.09 0.96 10 7 38 31 62.80 0.83 11 8 11 3 267.61 0.77 12 8 12 4 265.77 0.14 13 9 12 3 275.69 0.59 14 9 13 4 269.99 2.26 15 9 48 39 57.61 1.53 16 9 52 43 57.02 1.53 17 10 13 3 275.83 0.66 18 10 14 4 269.96 2.27 19 10 55 45 56.62 1.64 20 10 59 49 56.61 1.64 21 11 14 3 271.26 1.62 22 11 15 4 269.39 1.71 23 12 15 3 281.71 2.35 24 12 16 4 274.85 1.09 25 12 38 26 68.83 0.29 26 12 41 29 69.28 0.06 27 13 16 3 286.13 0.13 28 13 17 4 274.86 1.10 29 13 52 39 57.38 1.63 30 13 55 42 57.34 1.65 31 13 56 43 57.26 1.64 32 13 62 49 56.52 1.69 33 14 17 3 285.82 0.04 34 14 18 4 275.05 1.02 35 15 18 3 283.20 1.28 36 15 19 4 275.05 1.02 37 16 19 3 283.20 1.27 38 16 20 4 264.75 0.64 39 16 30 14 63.12 0.42 40 16 33 17 87.89 9.42 41 17 20 3 270.29 3.41 42 17 23 6 166.45 1.72 43 17 62 45 56.94 1.62 44 17 79 62 52.33 0.42 45 17 80 63 51.79 0.68 46 19 33 14 93.56 7.85 47 20 25 5 164.94 0.97 48 23 78 55 69.16 0.03 49 24 65 41 69.53 0.10 50 24 77 53 69.56 0.09 51 24 78 54 69.06 0.07 52 24 79 55 68.70 0.09 53 25 29 4 271.76 1.09 54 25 30 5 271.75 1.08 55 25 77 52 69.80 0.02 56 25 78 53 69.56 0.07 57 26 29 3 280.60 1.29 58 26 30 4 277.10 0.47 59 26 74 48 69.97 0.09 60 26 76 50 69.91 0.06 61 26 77 51 69.88 0.06 62 26 78 52 69.88 0.06 63 27 30 3 282.01 0.59 64 27 31 4 282.02 0.59 65 27 53 26 97.92 7.75 66 27 56 29 92.59 10.36 67 27 78 51 69.90 0.05 68 28 31 3 282.04 0.58 69 28 32 4 282.02 0.59 70 29 32 3 282.03 0.59 71 29 33 4 282.03 0.59 72 30 33 3 284.97 2.07 73 30 34 4 278.62 2.29 74 30 56 26 97.84 7.79 75 30 78 48 69.89 0.05 76 31 34 3 276.97 0.35 77 31 35 4 275.17 0.55 78 31 48 17 133.34 2.84 79 31 49 18 128.10 3.78 80 31 52 21 101.23 7.83 81 31 53 22 123.67 4.50 82 32 35 3 278.44 0.39 83 32 36 4 276.76 1.23 84 33 36 3 279.94 1.22 85 33 37 4 275.30 0.49 86 34 37 3 281.93 1.35 87 34 38 4 265.86 1.61 88 34 41 7 203.49 2.66 89 34 48 14 157.91 3.14 90 35 38 3 278.13 2.12 91 35 39 4 262.75 0.12 92 35 42 7 199.75 4.51 93 35 48 13 157.97 3.12 94 35 49 14 157.93 3.13 95 38 41 3 311.02 1.11 96 39 42 3 281.01 0.40 97 40 43 3 287.22 0.99 98 40 44 4 280.98 0.39 99 41 44 3 276.63 2.55 100 41 45 4 266.48 1.76 101 41 48 7 203.94 0.15 102 42 45 3 278.78 3.23 103 44 48 4 276.13 0.62 104 45 48 3 298.35 0.78 105 45 49 4 266.44 3.63 106 47 51 4 275.58 1.61 107 48 51 3 278.44 0.18 108 48 52 4 275.58 1.61 109 49 52 3 287.26 3.68 110 49 53 4 276.89 1.51 111 50 53 3 287.26 3.68 112 50 54 4 277.23 2.43 113 51 54 3 275.44 3.33 114 51 55 4 274.33 2.77 115 52 55 3 285.55 1.73 116 52 56 4 276.05 1.92 117 53 56 3 276.63 1.98 118 54 57 3 291.49 0.32 119 54 58 4 277.43 1.58 120 55 58 3 285.56 1.76 121 55 59 4 273.12 0.56 122 56 62 6 177.28 2.18 123 56 78 22 101.14 2.42 124 59 62 3 300.44 1.01 125 62 78 16 105.46 3.58 126 62 79 17 105.23 3.68 127 62 80 18 104.46 3.71 128 63 78 15 105.50 3.59 129 63 79 16 105.41 3.60 130 63 81 18 105.17 3.71 131 63 82 19 104.81 3.89 132 64 77 13 106.27 3.23 133 64 78 14 106.24 3.23 134 65 77 12 106.34 3.27 135 65 79 14 106.30 3.25 136 66 75 9 106.42 3.26 137 66 76 10 106.40 3.25 138 66 77 11 106.40 3.26 139 67 71 4 271.95 2.16 140 67 74 7 147.35 7.79 141 67 75 8 121.95 0.38 142 67 77 10 111.56 3.97 143 68 71 3 291.43 2.06 144 81 84 3 303.75 1.67 145 84 87 3 286.80 3.02 146 85 88 3 328.22 1.89 147 86 89 3 309.00 0.32 148 87 90 3 298.58 0.01 149 87 93 6 258.69 2.99 150 89 93 4 297.04 2.42 151 90 93 3 305.08 0.31