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 18 15 361.96 0.01 2 3 22 19 231.01 1.05 3 3 41 38 58.70 1.42 4 9 37 28 145.41 0.07 5 11 16 5 362.00 0.00 6 11 33 22 176.58 1.99 7 11 37 26 152.52 0.15 8 12 33 21 176.66 1.96 9 14 29 15 216.03 0.33 10 14 31 17 210.93 2.17 11 14 34 20 176.68 1.95 12 15 26 11 359.83 0.70 13 15 29 14 216.03 0.33 14 16 24 8 361.81 0.04 15 16 26 10 301.87 9.01 16 16 34 18 147.02 0.87 17 16 37 21 145.42 0.06 18 17 25 8 356.83 1.32 19 17 26 9 267.89 3.72 20 18 24 6 361.84 0.07 21 18 38 20 125.26 1.99 22 19 23 4 362.00 0.00 23 19 25 6 357.10 0.71 24 22 100 78 49.73 0.45 25 23 100 77 49.73 0.45 26 24 30 6 177.77 0.96 27 24 34 10 145.42 0.07 28 24 38 14 129.38 3.42 29 24 100 76 49.81 0.41 30 24 103 79 47.04 0.42 31 24 105 81 34.58 0.47 32 25 105 80 34.97 0.66 33 26 29 3 220.71 1.06 34 27 30 3 207.37 0.13 35 27 63 36 57.51 3.58 36 27 103 76 49.81 0.41 37 27 105 78 49.59 0.39 38 29 34 5 204.90 1.85 39 30 34 4 200.69 0.26 40 30 35 5 211.47 1.43 41 30 53 23 71.84 2.19 42 30 56 26 69.86 3.06 43 30 101 71 51.31 0.48 44 30 102 72 50.98 0.59 45 30 103 73 50.23 0.33 46 31 34 3 218.45 1.53 47 31 35 4 211.55 1.45 48 32 35 3 217.98 1.77 49 32 36 4 211.54 1.45 50 32 53 21 71.81 2.21 51 33 36 3 217.25 1.40 52 33 37 4 211.54 1.45 53 34 37 3 217.25 1.40 54 34 38 4 211.54 1.45 55 35 38 3 221.15 3.04 56 35 39 4 209.92 2.23 57 35 53 18 71.81 2.21 58 35 101 66 50.38 0.40 59 36 39 3 209.92 2.23 60 36 40 4 206.12 0.34 61 36 45 9 133.78 0.80 62 36 48 12 105.73 0.63 63 37 40 3 216.35 1.71 64 37 41 4 206.12 0.34 65 38 41 3 215.83 1.97 66 38 42 4 196.52 2.55 67 39 42 3 213.20 0.71 68 39 43 4 196.25 2.60 69 39 44 5 180.42 0.94 70 39 45 6 148.66 3.63 71 39 101 62 50.24 0.33 72 40 44 4 154.00 5.85 73 40 45 5 152.47 6.60 74 40 46 6 137.31 0.96 75 42 100 58 54.20 1.52 76 43 90 47 77.64 0.23 77 43 91 48 77.58 0.24 78 45 48 3 223.86 0.40 79 45 52 7 180.44 0.70 80 48 52 4 202.54 2.15 81 48 53 5 194.53 0.65 82 48 56 8 196.93 0.39 83 49 52 3 217.65 1.86 84 49 53 4 206.21 2.81 85 50 54 4 206.48 0.84 86 51 54 3 212.38 0.25 87 51 55 4 212.14 0.03 88 51 89 38 117.40 2.97 89 52 55 3 220.16 0.64 90 52 56 4 209.28 0.55 91 52 89 37 120.59 1.46 92 52 90 38 120.59 1.46 93 53 56 3 215.88 1.50 94 53 57 4 208.38 1.90 95 54 57 3 217.24 0.83 96 54 58 4 215.89 1.50 97 54 81 27 149.62 1.42 98 55 58 3 215.08 1.91 99 55 59 4 211.39 0.40 100 55 72 17 120.66 1.45 101 55 81 26 150.15 1.15 102 55 90 35 120.90 1.35 103 55 98 43 96.40 0.29 104 56 59 3 221.79 4.04 105 56 60 4 211.38 0.39 106 56 102 46 88.28 0.59 107 57 60 3 211.42 0.41 108 57 61 4 213.20 0.49 109 58 61 3 218.45 0.83 110 58 62 4 220.65 1.93 111 58 75 17 158.99 3.65 112 58 78 20 193.13 1.26 113 58 79 21 192.03 1.20 114 59 62 3 220.65 1.93 115 59 63 4 217.87 3.31 116 59 69 10 120.52 1.51 117 59 99 40 103.03 2.06 118 60 63 3 218.22 3.15 119 60 64 4 218.22 3.15 120 61 64 3 222.53 0.98 121 61 65 4 220.08 2.21 122 62 65 3 221.31 1.58 123 62 70 8 168.48 10.51 124 63 67 4 157.60 10.77 125 63 68 5 147.84 0.58 126 63 104 41 92.70 1.39 127 63 105 42 92.70 1.39 128 69 104 35 125.32 0.89 129 71 74 3 362.00 0.00 130 72 94 22 361.96 0.01 131 85 88 3 362.00 0.00 132 86 89 3 362.00 0.01 133 87 90 3 362.00 0.00 134 87 92 5 361.95 0.02 135 96 99 3 361.98 0.01 136 98 101 3 362.00 0.00 137 98 102 4 319.62 2.85 138 99 102 3 218.94 4.62 139 99 103 4 178.57 0.21 140 99 104 5 125.73 0.97 141 100 103 3 220.65 3.77