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 2 43 41 58.95 2.13 2 3 10 7 115.39 1.90 3 3 11 8 107.95 1.68 4 3 14 11 107.95 1.68 5 3 39 36 59.49 2.16 6 3 41 38 59.37 2.20 7 3 42 39 59.34 2.19 8 3 43 40 59.29 2.16 9 3 44 41 59.29 2.16 10 4 7 3 207.78 1.23 11 4 11 7 161.12 0.59 12 4 43 39 59.38 2.19 13 4 44 40 59.29 2.16 14 5 8 3 213.90 2.08 15 5 11 6 187.59 1.14 16 5 33 28 59.93 1.95 17 5 36 31 60.04 1.97 18 5 42 37 59.54 2.14 19 5 44 39 59.38 2.19 20 5 45 40 59.31 2.16 21 5 48 43 56.76 1.84 22 5 49 44 53.02 0.96 23 5 53 48 44.81 0.51 24 5 54 49 41.83 1.05 25 5 57 52 41.02 0.67 26 7 10 3 217.11 2.59 27 7 11 4 202.46 0.58 28 8 11 3 205.02 0.70 29 8 12 4 202.45 0.58 30 8 56 48 41.90 1.08 31 8 57 49 41.82 1.06 32 8 60 52 41.83 1.06 33 9 12 3 204.09 0.23 34 9 13 4 201.88 0.29 35 9 60 51 41.88 1.09 36 10 13 3 206.33 0.36 37 10 14 4 201.88 0.29 38 11 14 3 202.61 3.71 39 11 15 4 198.82 1.82 40 11 36 25 60.12 1.98 41 11 57 46 41.96 1.09 42 12 15 3 210.34 0.68 43 12 16 4 198.39 1.91 44 12 57 45 41.97 1.09 45 12 60 48 41.84 1.06 46 12 61 49 41.83 1.07 47 13 16 3 209.16 0.43 48 13 17 4 198.37 1.91 49 13 64 51 28.02 1.03 50 14 17 3 205.06 0.25 51 14 18 4 200.40 0.93 52 15 18 3 206.97 0.66 53 15 19 4 198.80 0.13 54 15 32 17 60.34 1.88 55 15 36 21 60.30 1.89 56 15 39 24 60.31 1.89 57 15 57 42 47.20 0.55 58 15 61 46 41.92 1.09 59 16 19 3 203.97 0.84 60 16 20 4 180.29 2.30 61 16 61 45 41.97 1.09 62 16 64 48 28.05 1.03 63 16 65 49 23.68 1.11 64 17 20 3 213.18 1.45 65 19 22 3 204.06 0.51 66 19 35 16 81.17 7.06 67 19 61 42 46.50 0.60 68 22 27 5 185.71 0.16 69 22 35 13 120.00 2.33 70 22 61 39 46.76 0.56 71 23 26 3 213.43 3.30 72 23 27 4 194.73 1.88 73 24 27 3 198.85 0.18 74 24 58 34 48.72 0.84 75 24 61 37 46.63 0.62 76 24 62 38 45.84 0.32 77 24 65 41 41.41 1.20 78 25 62 37 46.76 0.56 79 25 66 41 42.55 1.47 80 27 31 4 196.99 0.15 81 27 32 5 197.00 0.16 82 27 35 8 189.46 3.24 83 27 58 31 49.12 0.90 84 27 61 34 47.86 0.70 85 28 31 3 207.45 0.36 86 28 32 4 201.81 2.46 87 29 32 3 207.45 0.36 88 29 33 4 201.83 2.45 89 29 54 25 49.42 0.89 90 29 55 26 49.42 0.89 91 29 58 29 49.12 0.90 92 30 33 3 207.44 0.36 93 30 34 4 202.69 2.01 94 31 34 3 214.67 0.77 95 31 35 4 207.15 3.65 96 32 35 3 215.32 0.44 97 32 36 4 198.50 0.64 98 32 54 22 49.39 0.90 99 32 57 25 49.12 0.90 100 32 58 26 47.78 0.85 101 32 61 29 46.51 0.67 102 33 36 3 201.78 0.45 103 33 37 4 199.03 0.92 104 33 46 13 81.03 3.56 105 33 49 16 60.16 0.70 106 33 54 21 49.42 0.89 107 34 37 3 208.31 0.58 108 34 38 4 199.00 0.94 109 35 38 3 200.93 0.01 110 35 39 4 199.02 0.96 111 35 61 26 45.24 0.13 112 36 39 3 210.38 2.02 113 36 42 6 131.81 2.35 114 37 42 5 131.81 2.35 115 37 46 9 85.13 3.03 116 39 42 3 203.23 2.10 117 42 46 4 220.78 0.58 118 45 48 3 215.53 0.35 119 46 49 3 225.27 0.74 120 49 53 4 189.43 0.70 121 49 54 5 189.39 0.70 122 50 53 3 199.69 0.83 123 50 54 4 200.53 0.58 124 51 54 3 205.78 1.54 125 51 55 4 200.37 0.48 126 52 55 3 200.68 0.64 127 52 56 4 200.65 0.62 128 53 56 3 208.79 0.04 129 53 57 4 205.33 1.69 130 54 57 3 208.79 0.04 131 54 58 4 200.68 0.64 132 55 58 3 201.16 0.41 133 55 59 4 199.94 1.01 134 56 59 3 210.32 4.11 135 56 60 4 201.05 0.35 136 57 60 3 203.74 0.75 137 57 61 4 201.05 0.35 138 58 61 3 208.23 0.26 139 58 62 4 205.39 1.16 140 59 62 3 205.40 1.16 141 59 63 4 205.40 1.16 142 60 63 3 205.40 1.16 143 60 64 4 205.39 1.16 144 61 64 3 203.52 0.68 145 61 65 4 192.96 2.35 146 62 65 3 205.75 1.15 147 62 66 4 188.44 0.49