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 7 4 306.48 1.81 2 3 63 60 35.47 0.61 3 4 7 3 306.50 1.82 4 4 8 4 306.53 1.79 5 5 8 3 310.06 1.02 6 5 9 4 306.60 1.74 7 5 48 43 54.32 1.92 8 5 59 54 36.32 0.56 9 5 60 55 36.32 0.56 10 5 63 58 36.03 0.42 11 6 9 3 308.01 1.02 12 6 10 4 306.90 1.57 13 6 63 57 36.02 0.42 14 7 10 3 316.55 1.17 15 8 11 3 313.92 0.14 16 8 12 4 306.87 1.56 17 8 48 40 56.81 0.68 18 9 12 3 306.78 1.52 19 9 13 4 303.85 0.06 20 9 31 22 68.81 11.19 21 9 56 47 47.14 0.38 22 9 60 51 40.27 0.94 23 9 65 56 40.30 0.93 24 10 14 4 298.33 2.36 25 11 14 3 306.72 1.46 26 12 18 6 233.30 2.97 27 12 22 10 186.06 4.69 28 12 39 27 63.84 0.84 29 12 43 31 60.54 0.64 30 12 47 35 60.76 0.53 31 12 56 44 57.28 0.97 32 13 22 9 142.29 17.20 33 13 24 11 129.45 12.86 34 13 31 18 70.36 10.42 35 15 18 3 306.03 0.98 36 15 19 4 229.36 1.39 37 16 19 3 313.35 0.52 38 17 47 30 80.45 0.51 39 18 21 3 306.66 2.64 40 18 22 4 305.18 3.38 41 18 43 25 82.23 0.39 42 21 34 13 120.84 16.77 43 21 38 17 88.97 0.76 44 22 31 9 142.58 12.16 45 22 39 17 88.94 0.74 46 23 31 8 142.59 12.16 47 23 32 9 142.58 12.17 48 24 27 3 328.43 2.04 49 24 28 4 258.48 0.76 50 24 30 6 212.90 0.23 51 24 32 8 142.62 12.17 52 25 30 5 212.90 0.23 53 25 32 7 180.74 6.88 54 25 85 60 84.95 1.22 55 29 88 59 84.22 1.17 56 30 65 35 87.51 1.44 57 30 85 55 87.87 1.54 58 30 86 56 87.36 1.36 59 31 65 34 87.88 1.56 60 31 85 54 87.88 1.54 61 31 86 55 87.80 1.51 62 32 84 52 89.42 1.17 63 32 85 53 88.75 1.13 64 33 36 3 305.45 0.79 65 33 39 6 272.49 3.34 66 33 83 50 89.49 1.16 67 33 84 51 89.49 1.16 68 33 86 53 89.45 1.16 69 34 83 49 89.53 1.18 70 35 38 3 319.25 2.10 71 35 39 4 302.33 0.67 72 36 39 3 306.06 1.32 73 36 40 4 297.11 1.95 74 36 81 45 89.95 1.28 75 36 82 46 89.69 1.26 76 37 40 3 316.91 0.71 77 37 41 4 296.94 1.91 78 38 42 4 295.73 1.33 79 38 43 5 295.72 1.32 80 39 42 3 310.00 0.86 81 39 43 4 295.71 1.32 82 39 44 5 295.71 1.32 83 40 43 3 302.93 0.21 84 40 44 4 290.68 3.81 85 40 45 5 295.75 1.28 86 40 53 13 199.21 0.12 87 41 45 4 308.32 1.09 88 42 46 4 304.68 0.73 89 43 46 3 306.37 0.11 90 43 47 4 309.51 1.68 91 44 47 3 321.59 1.65 92 44 48 4 301.34 2.40 93 44 51 7 210.58 0.67 94 44 52 8 204.64 2.29 95 44 53 9 204.60 2.27 96 44 56 12 204.24 2.39 97 45 49 4 259.86 0.65 98 45 50 5 239.12 0.16 99 48 51 3 306.68 1.81 100 48 56 8 221.90 6.17 101 51 55 4 305.37 0.03 102 52 55 3 311.22 0.06 103 52 56 4 307.19 0.32 104 53 56 3 309.59 0.88 105 53 57 4 309.21 0.70 106 54 57 3 321.66 2.25 107 54 58 4 309.22 0.69 108 55 58 3 318.64 3.75 109 55 59 4 308.92 1.10 110 56 59 3 321.66 2.25 111 56 60 4 308.71 1.21 112 57 60 3 311.68 0.57 113 57 61 4 307.04 0.37 114 57 67 10 201.88 1.88 115 57 84 27 159.42 6.34 116 57 86 29 159.26 6.40 117 58 61 3 311.67 0.57 118 58 62 4 307.51 0.61 119 59 62 3 309.79 0.45 120 59 63 4 307.47 0.62 121 60 63 3 312.31 3.04 122 60 64 4 305.07 0.30 123 60 65 5 256.01 0.00 124 60 66 6 238.55 2.04 125 60 86 26 159.71 6.53 126 61 64 3 307.56 1.56 127 61 65 4 296.32 1.15 128 61 66 5 247.84 3.91 129 64 88 24 159.62 6.58 130 65 86 21 159.97 6.53 131 65 87 22 159.67 6.60 132 65 88 23 159.39 6.67 133 66 87 21 159.74 6.63 134 66 88 22 159.50 6.66 135 66 89 23 159.43 6.69 136 66 90 24 159.31 6.66 137 67 84 17 160.72 6.78 138 68 84 16 160.72 6.78 139 68 85 17 160.71 6.78 140 68 87 19 160.44 6.74 141 70 90 20 160.72 6.62 142 71 78 7 167.97 3.29 143 74 77 3 277.26 9.76 144 80 83 3 340.02 0.68 145 87 90 3 321.50 2.21