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 44 41 24.17 0.32 2 3 47 44 24.00 0.34 3 4 44 40 26.93 0.97 4 5 44 39 26.20 1.33 5 5 47 42 24.23 0.35 6 5 48 43 24.23 0.35 7 5 51 46 24.19 0.38 8 6 40 34 36.42 0.36 9 6 44 38 28.10 0.40 10 8 12 4 163.93 0.24 11 8 13 5 159.53 2.44 12 8 16 8 145.92 1.55 13 8 40 32 45.55 0.79 14 8 44 36 37.97 0.32 15 8 48 40 36.28 0.29 16 9 12 3 167.22 1.40 17 9 13 4 167.22 1.40 18 10 13 3 168.84 0.64 19 10 14 4 167.40 1.49 20 11 14 3 169.17 0.60 21 11 15 4 169.16 0.60 22 12 15 3 169.39 0.49 23 12 16 4 169.03 0.54 24 12 38 26 64.81 0.40 25 12 40 28 63.53 1.03 26 13 16 3 169.38 0.49 27 13 17 4 169.02 0.54 28 13 48 35 61.73 0.34 29 14 17 3 174.24 0.23 30 14 18 4 168.78 0.64 31 15 18 3 170.66 0.29 32 15 19 4 167.38 0.07 33 15 34 19 66.73 0.12 34 15 37 22 66.87 0.09 35 15 38 23 66.84 0.10 36 16 19 3 170.85 1.46 37 16 20 4 166.37 0.58 38 16 38 22 66.87 0.08 39 16 40 24 66.84 0.10 40 16 45 29 66.31 0.24 41 16 48 32 66.16 0.17 42 16 49 33 66.17 0.18 43 17 20 3 169.40 0.93 44 17 21 4 166.68 0.43 45 17 48 31 66.16 0.17 46 18 21 3 168.72 0.34 47 18 22 4 166.68 0.43 48 19 22 3 170.44 0.29 49 19 23 4 165.50 0.15 50 19 30 11 82.55 0.17 51 19 34 15 66.89 0.10 52 19 49 30 66.47 0.17 53 20 23 3 175.03 2.58 54 20 24 4 149.09 0.70 55 20 48 28 66.63 0.14 56 20 49 29 66.54 0.14 57 20 52 32 65.31 0.20 58 20 53 33 65.32 0.21 59 20 56 36 50.87 0.71 60 23 30 7 159.35 0.54 61 23 49 26 66.76 0.15 62 24 49 25 66.76 0.15 63 24 53 29 65.34 0.20 64 24 56 32 60.00 1.01 65 25 30 5 164.91 0.83 66 25 53 28 66.45 0.30 67 26 30 4 161.77 0.20 68 26 31 5 161.75 0.20 69 26 34 8 157.70 0.21 70 26 45 19 68.69 0.14 71 26 46 20 68.03 0.47 72 26 49 23 66.80 0.14 73 27 30 3 172.28 0.36 74 27 31 4 161.77 0.20 75 28 31 3 173.15 0.59 76 28 32 4 167.39 0.47 77 29 32 3 171.22 0.38 78 29 33 4 170.14 0.91 79 30 33 3 168.86 1.55 80 30 34 4 164.44 0.66 81 30 49 19 69.69 0.48 82 31 34 3 170.53 0.71 83 31 35 4 168.85 1.55 84 31 42 11 71.11 0.92 85 31 45 14 69.68 0.47 86 31 46 15 69.69 0.48 87 32 35 3 170.53 0.71 88 32 36 4 168.85 1.55 89 32 42 10 71.36 1.02 90 33 36 3 169.74 0.66 91 33 37 4 165.53 0.73 92 34 37 3 169.74 0.66 93 34 38 4 163.33 0.36 94 34 45 11 71.11 1.09 95 34 49 15 71.09 1.08 96 35 38 3 169.72 0.67 97 35 39 4 163.26 0.39 98 35 40 5 89.86 2.62 99 35 42 7 79.61 0.80 100 35 45 10 75.72 1.15 101 40 44 4 169.38 1.34 102 40 45 5 162.03 2.02 103 41 44 3 174.37 1.57 104 41 45 4 170.68 1.99 105 42 45 3 175.97 0.78 106 42 46 4 170.68 1.99 107 43 46 3 172.35 0.14 108 43 47 4 169.36 1.35 109 44 47 3 172.95 2.16 110 44 48 4 162.25 1.93 111 45 48 3 171.31 1.41 112 45 49 4 162.27 1.92 113 46 49 3 169.12 1.51 114 46 50 4 162.35 1.86 115 47 50 3 169.10 1.51 116 47 51 4 168.06 1.28 117 48 51 3 171.39 0.38 118 48 52 4 166.94 1.85 119 49 52 3 170.27 1.48 120 49 53 4 168.72 0.96 121 50 53 3 175.02 1.09 122 50 54 4 168.40 1.13 123 51 54 3 171.74 0.54 124 51 55 4 168.40 1.13 125 52 55 3 174.31 2.29 126 52 56 4 167.93 0.90 127 53 56 3 166.36 1.69