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 68 65 48.13 0.12 2 3 69 66 48.11 0.12 3 4 7 3 288.94 3.22 4 4 8 4 276.76 1.28 5 4 65 61 51.00 0.03 6 4 66 62 50.97 0.03 7 4 67 63 50.05 0.20 8 4 68 64 48.15 0.10 9 5 8 3 284.51 2.58 10 5 9 4 278.51 0.41 11 5 62 57 51.08 0.03 12 5 64 59 51.06 0.04 13 5 67 62 50.96 0.04 14 5 69 64 49.06 0.45 15 6 9 3 285.79 0.98 16 6 10 4 275.18 1.27 17 6 64 58 51.08 0.04 18 6 65 59 51.08 0.04 19 7 10 3 284.23 1.25 20 7 11 4 275.18 1.27 21 8 11 3 286.10 1.77 22 8 69 61 48.44 0.11 23 9 12 3 293.46 3.19 24 9 13 4 271.82 0.38 25 10 13 3 277.83 1.48 26 10 14 4 238.10 1.68 27 10 15 5 231.75 1.50 28 13 16 3 303.53 0.05 29 13 17 4 258.90 5.03 30 14 17 3 292.58 1.54 31 15 18 3 299.29 0.67 32 15 19 4 273.99 1.12 33 15 22 7 180.18 0.97 34 16 19 3 277.26 0.27 35 16 22 6 184.22 1.05 36 17 34 17 131.31 0.22 37 18 30 12 139.09 3.25 38 18 31 13 138.68 3.46 39 18 34 16 131.44 0.30 40 19 22 3 275.62 3.08 41 19 23 4 256.42 6.24 42 19 24 5 210.11 3.16 43 19 30 11 139.10 3.25 44 19 31 12 138.96 3.33 45 19 65 46 56.80 0.15 46 20 23 3 287.95 0.33 47 20 30 10 148.60 1.15 48 24 31 7 215.50 2.47 49 25 28 3 276.51 2.00 50 25 30 5 245.91 0.73 51 25 31 6 258.36 4.29 52 28 31 3 287.49 1.94 53 28 32 4 279.24 0.58 54 29 32 3 287.48 1.94 55 29 33 4 279.24 0.58 56 30 33 3 281.16 0.79 57 30 34 4 281.03 0.72 58 31 34 3 281.04 0.72 59 31 35 4 281.03 0.72 60 32 35 3 282.49 0.01 61 32 36 4 280.28 1.11 62 32 57 25 69.06 5.79 63 32 58 26 69.04 5.79 64 33 36 3 291.54 2.63 65 33 37 4 281.18 2.54 66 34 37 3 280.99 2.65 67 34 38 4 280.11 3.08 68 35 38 3 293.98 1.42 69 35 39 4 278.13 2.13 70 35 58 23 69.06 5.80 71 36 39 3 288.55 1.14 72 36 40 4 266.38 3.71 73 36 41 5 237.02 4.83 74 39 45 6 254.64 0.72 75 40 45 5 257.66 2.02 76 41 44 3 287.14 2.41 77 41 45 4 277.19 2.57 78 42 45 3 283.04 0.35 79 42 49 7 209.58 1.69 80 42 50 8 202.07 2.39 81 42 52 10 202.04 2.39 82 42 53 11 198.31 4.24 83 42 56 14 185.37 2.18 84 43 50 7 206.71 0.25 85 43 53 10 202.06 2.36 86 45 49 4 268.27 7.43 87 45 50 5 249.11 1.10 88 46 49 3 280.06 1.55 89 46 50 4 281.49 0.83 90 46 89 43 34.07 1.72 91 47 51 4 281.63 0.78 92 47 88 41 34.09 1.72 93 47 89 42 34.09 1.72 94 48 51 3 309.28 2.77 95 48 52 4 295.06 0.45 96 48 85 37 34.17 1.68 97 48 88 40 34.11 1.72 98 48 89 41 34.09 1.71 99 49 52 3 295.21 0.38 100 50 53 3 287.94 0.35 101 51 55 4 291.11 0.09 102 52 55 3 281.24 1.46 103 52 56 4 267.93 5.20 104 52 79 27 48.59 0.30 105 56 60 4 279.31 1.55 106 56 61 5 276.69 0.24 107 57 60 3 293.11 1.96 108 58 61 3 293.11 1.96 109 58 62 4 275.77 0.23 110 59 62 3 278.87 1.32 111 61 67 6 246.93 1.35 112 61 73 12 72.11 2.92 113 62 67 5 242.08 2.96 114 62 73 11 76.75 0.61 115 63 66 3 286.82 1.59 116 63 67 4 250.60 1.28 117 67 71 4 250.93 3.00 118 67 73 6 207.93 6.87 119 68 71 3 291.89 3.45 120 75 78 3 298.31 3.30 121 75 79 4 258.38 1.45 122 75 83 8 126.92 15.66 123 75 84 9 101.84 6.45 124 75 85 10 102.16 6.28 125 76 79 3 272.79 5.33 126 79 83 4 270.20 0.90 127 83 87 4 266.23 7.67 128 83 88 5 264.68 6.90 129 84 87 3 281.93 0.18 130 84 88 4 280.31 0.64 131 85 88 3 285.50 1.82 132 85 89 4 274.01 2.23 133 86 89 3 282.67 0.54