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 1 102 101 70.80 0.23 2 2 22 20 70.84 0.24 3 2 23 21 70.86 0.23 4 2 90 88 70.52 0.14 5 2 91 89 70.80 0.24 6 2 92 90 70.85 0.23 7 2 102 100 70.84 0.24 8 2 103 101 70.75 0.24 9 2 104 102 66.39 1.07 10 2 105 103 69.86 0.32 11 3 21 18 70.84 0.23 12 3 22 19 70.86 0.23 13 3 104 101 70.73 0.22 14 3 105 102 70.73 0.22 15 4 19 15 70.77 0.24 16 4 20 16 70.84 0.23 17 4 21 17 70.86 0.23 18 4 34 30 70.84 0.23 19 4 75 71 70.83 0.24 20 4 88 84 70.75 0.21 21 4 89 85 70.81 0.24 22 4 90 86 70.84 0.24 23 4 104 100 70.84 0.24 24 4 105 101 70.81 0.23 25 4 107 103 67.85 0.35 26 5 19 14 70.82 0.24 27 5 20 15 70.86 0.23 28 6 9 3 133.96 1.83 29 6 18 12 72.83 1.21 30 6 19 13 70.86 0.23 31 6 107 101 70.83 0.24 32 7 107 100 70.83 0.24 33 7 108 101 70.82 0.24 34 8 108 100 70.82 0.23 35 8 110 102 70.79 0.23 36 9 17 8 96.64 1.85 37 9 18 9 96.50 1.80 38 9 19 10 84.39 0.32 39 9 108 99 70.86 0.23 40 9 109 100 70.78 0.24 41 9 110 101 70.78 0.23 42 10 110 100 70.78 0.24 43 10 112 102 70.76 0.23 44 11 15 4 135.33 0.41 45 11 16 5 127.43 0.40 46 11 17 6 110.30 0.39 47 11 80 69 136.09 0.02 48 11 109 98 70.88 0.23 49 11 110 99 70.84 0.22 50 11 111 100 70.77 0.23 51 11 112 101 70.77 0.23 52 12 15 3 139.47 1.02 53 12 80 68 148.85 1.75 54 12 111 99 70.81 0.22 55 12 112 100 70.76 0.23 56 12 113 101 70.73 0.22 57 12 114 102 48.56 1.92 58 12 115 103 27.25 0.49 59 13 80 67 145.81 0.24 60 13 81 68 142.72 0.04 61 13 82 69 146.61 0.59 62 13 111 98 70.86 0.23 63 13 112 99 70.80 0.23 64 13 113 100 70.73 0.22 65 13 114 101 37.40 0.17 66 14 79 65 204.31 24.18 67 14 80 66 167.43 2.62 68 14 114 100 36.38 0.67 69 15 80 65 251.39 1.19 70 16 76 60 253.00 0.68 71 16 77 61 251.34 1.19 72 16 78 62 251.34 1.19 73 16 80 64 253.68 0.48 74 17 76 59 253.71 0.50 75 17 77 60 253.69 0.49 76 17 80 63 268.26 0.04 77 17 109 92 70.87 0.23 78 18 76 58 260.49 3.85 79 19 107 88 72.01 0.34 80 19 108 89 71.97 0.32 81 19 109 90 70.80 0.23 82 29 95 66 268.45 0.21 83 30 94 64 270.52 0.80 84 31 95 64 270.54 0.80 85 35 103 68 73.67 0.86 86 77 109 32 70.89 0.21 87 80 111 31 70.83 0.22 88 81 111 30 70.89 0.21 89 82 111 29 70.89 0.21 90 82 112 30 70.89 0.21 91 82 113 31 70.84 0.23 92 84 109 25 71.30 0.04 93 84 111 27 70.89 0.21 94 85 109 24 71.30 0.04 95 85 110 25 70.91 0.21 96 85 111 26 70.89 0.21 97 86 108 22 71.96 0.27 98 86 109 23 71.28 0.04 99 87 106 19 72.33 0.43 100 87 107 20 72.30 0.43 101 87 108 21 72.09 0.35 102 88 106 18 72.31 0.44 103 88 107 19 72.14 0.36 104 88 109 21 71.92 0.29 105 89 103 14 73.67 0.86 106 89 104 15 73.29 0.83 107 89 105 16 72.76 0.66 108 89 106 17 72.11 0.39 109 90 103 13 73.66 0.86 110 90 104 14 73.20 0.88 111 91 102 11 73.76 0.83 112 91 103 12 73.67 0.86 113 92 101 9 73.84 0.84 114 92 102 10 73.78 0.83 115 93 100 7 77.21 0.61 116 93 101 8 73.84 0.84 117 94 99 5 83.17 1.89 118 94 100 6 77.22 0.61