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 1 43 42 290.49 0.01 2 1 46 45 290.49 0.01 3 1 47 46 290.48 0.01 4 1 50 49 290.50 0.00 5 3 53 50 163.44 0.18 6 3 54 51 161.18 0.18 7 4 8 4 290.50 0.00 8 6 51 45 290.50 0.00 9 6 54 48 161.94 0.18 10 7 10 3 290.50 0.00 11 7 11 4 290.50 0.01 12 7 54 47 161.94 0.18 13 9 30 21 290.50 0.00 14 10 13 3 290.50 0.01 15 10 51 41 290.50 0.00 16 12 24 12 290.50 0.00 17 12 26 14 290.50 0.00 18 12 27 15 290.50 0.00 19 13 16 3 290.50 0.00 20 13 27 14 290.50 0.00 21 13 69 56 100.50 0.18 22 14 58 44 160.93 0.06 23 16 20 4 290.50 0.00 24 16 65 49 112.81 2.57 25 16 69 53 104.00 1.84 26 16 72 56 103.94 1.80 27 17 58 41 181.56 9.95 28 17 61 44 138.56 1.04 29 17 62 45 132.24 0.92 30 17 65 48 109.42 2.71 31 17 66 49 104.20 1.94 32 17 69 52 104.16 1.92 33 18 58 40 175.48 1.10 34 18 59 41 161.98 0.21 35 18 60 42 154.86 0.83 36 18 61 43 143.65 2.21 37 20 65 45 118.78 0.40 38 23 69 46 103.83 1.77 39 23 72 49 103.48 1.63 40 23 73 50 100.40 0.15 41 27 69 42 98.91 0.52 42 28 73 45 80.23 0.10 43 31 69 38 90.84 0.53 44 31 70 39 85.09 1.25 45 31 73 42 80.23 0.10 46 31 75 44 73.90 0.73 47 31 77 46 73.86 0.72 48 32 73 41 80.23 0.10 49 32 75 43 73.88 0.72 50 34 38 4 290.50 0.00 51 35 75 40 73.90 0.72 52 38 43 5 290.50 0.00 53 38 44 6 290.50 0.00 54 38 47 9 290.50 0.00 55 39 44 5 290.50 0.00 56 41 90 49 21.48 0.70 57 41 91 50 19.25 0.31 58 44 90 46 20.28 0.20 59 44 91 47 19.25 0.31 60 45 87 42 27.31 0.04 61 45 88 43 27.30 0.04 62 45 90 45 20.09 0.10 63 47 51 4 290.50 0.00 64 48 52 4 290.50 0.00 65 48 87 39 27.91 0.34 66 48 90 42 24.41 0.75 67 49 52 3 290.49 0.01 68 49 53 4 283.38 0.17 69 49 87 38 27.91 0.35 70 50 53 3 166.39 2.13 71 50 54 4 161.81 0.11 72 51 54 3 162.97 0.41 73 51 55 4 161.38 0.10 74 52 55 3 161.22 0.18 75 52 56 4 161.19 0.16 76 52 83 31 37.24 0.76 77 52 85 33 37.23 0.76 78 52 86 34 37.22 0.75 79 52 87 35 34.98 0.07 80 53 56 3 161.87 0.21 81 53 57 4 160.30 0.51 82 54 57 3 157.16 1.06 83 54 58 4 157.16 1.06 84 55 58 3 152.07 1.30 85 55 61 6 125.67 1.92 86 58 61 3 161.72 0.32 87 62 65 3 143.01 1.66 88 62 66 4 136.98 0.22 89 63 66 3 140.55 1.13 90 63 67 4 138.88 1.17 91 64 67 3 143.68 0.17 92 64 68 4 142.28 0.53 93 65 68 3 145.37 1.74 94 65 69 4 142.32 0.53 95 66 69 3 167.60 0.50 96 66 70 4 158.69 3.96 97 66 81 15 56.48 0.15 98 67 70 3 176.88 0.13 99 67 80 13 64.03 0.48 100 67 81 14 56.48 0.15 101 68 71 3 158.69 3.95 102 68 72 4 141.16 0.32 103 69 72 3 144.23 1.22 104 69 73 4 141.16 0.32 105 70 73 3 142.40 0.94 106 70 74 4 134.88 0.89 107 70 75 5 116.12 2.35 108 70 77 7 84.14 2.28 109 70 81 11 61.20 1.24 110 71 74 3 138.69 2.79 111 77 81 4 162.78 2.12 112 79 85 6 80.27 1.27 113 79 89 10 46.27 0.24 114 79 90 11 42.98 0.67 115 79 91 12 42.98 0.67 116 80 85 5 96.47 6.39 117 82 85 3 136.50 2.18 118 86 89 3 146.10 0.52 119 87 90 3 140.00 1.21