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 52 50 68.79 1.51 2 3 28 25 137.52 0.35 3 3 52 49 90.55 0.84 4 3 53 50 76.89 0.23 5 4 27 23 178.70 2.28 6 4 28 24 144.42 1.32 7 4 53 49 102.22 2.25 8 5 53 48 130.61 0.97 9 5 54 49 126.94 1.12 10 5 55 50 105.73 0.49 11 6 55 49 169.72 3.63 12 8 34 26 155.12 0.99 13 9 58 49 154.63 1.24 14 11 61 50 102.17 1.69 15 13 109 96 37.45 0.02 16 30 50 20 205.75 1.10 17 31 49 18 163.44 0.49 18 33 47 14 165.62 1.58 19 34 46 12 206.05 1.14 20 34 48 14 155.12 0.99 21 37 111 74 52.01 0.79 22 39 64 25 205.79 2.54 23 40 64 24 149.00 8.33 24 40 109 69 70.27 2.72 25 40 110 70 68.76 3.47 26 40 111 71 71.03 2.33 27 41 63 22 178.14 0.13 28 41 64 23 143.67 2.19 29 46 59 13 145.78 1.53 30 47 59 12 131.60 0.89 31 48 56 8 209.24 0.24 32 48 58 10 106.96 1.07 33 49 55 6 206.51 2.23 34 49 56 7 152.65 0.09 35 50 55 5 130.88 0.83 36 62 86 24 58.34 0.30 37 62 110 48 48.45 0.91 38 63 86 23 79.78 2.75 39 64 86 22 110.23 0.65 40 64 110 46 73.14 1.55 41 65 85 20 124.41 0.77 42 65 110 45 124.48 0.79 43 66 84 18 124.53 0.81 44 66 85 19 124.49 0.79 45 66 86 20 124.49 0.79 46 66 109 43 160.53 0.20 47 66 110 44 124.53 0.77 48 66 111 45 113.24 0.23 49 66 112 46 115.42 0.85 50 67 84 17 124.61 0.82 51 67 111 44 124.58 0.77 52 67 113 46 124.50 0.78 53 68 81 13 209.81 0.06 54 68 84 16 127.45 0.59 55 68 113 45 124.57 0.78 56 69 84 15 208.75 0.46 57 69 90 21 124.52 0.78 58 69 92 23 124.41 0.81 59 69 113 44 124.58 0.78 60 70 92 22 124.53 0.77 61 70 113 43 124.60 0.78 62 72 92 20 124.60 0.78 63 72 116 44 124.59 0.78 64 72 117 45 124.53 0.77 65 74 95 21 124.51 0.81 66 74 98 24 159.84 4.34 67 74 119 45 124.22 0.68 68 74 120 46 101.37 2.31 69 75 93 18 124.56 0.80 70 75 94 19 124.51 0.80 71 75 95 20 124.52 0.81 72 76 92 16 132.27 4.58 73 76 93 17 124.62 0.77 74 77 90 13 194.84 3.48 75 77 91 14 161.34 4.04 76 77 92 15 132.26 4.58 77 78 93 15 161.27 4.01 78 79 93 14 161.52 4.12 79 80 90 10 208.44 0.05 80 86 108 22 124.60 0.78 81 86 110 24 127.42 0.59 82 87 107 20 124.62 0.78 83 87 108 21 124.53 0.77 84 88 107 19 124.60 0.78 85 88 108 20 124.50 0.79 86 89 105 16 124.62 0.78 87 89 106 17 124.61 0.78 88 89 107 18 124.47 0.79 89 90 105 15 124.59 0.78 90 90 106 16 124.55 0.78 91 91 104 13 124.59 0.78 92 91 105 14 124.50 0.79 93 92 104 12 124.56 0.78 94 92 105 13 124.49 0.79 95 92 106 14 124.48 0.79 96 94 100 6 143.40 0.41 97 98 119 21 144.14 10.54 98 98 120 22 124.56 0.77 99 99 119 20 124.60 0.78 100 99 120 21 124.56 0.77 101 100 118 18 124.60 0.78 102 100 119 19 124.55 0.77 103 100 120 20 124.55 0.77 104 101 118 17 124.56 0.77 105 101 120 19 124.54 0.77 106 102 118 16 124.56 0.77 107 103 117 14 124.56 0.78 108 103 118 15 124.39 0.79 109 104 117 13 116.73 0.21 110 104 118 14 110.66 0.87 111 105 115 10 124.59 0.78 112 105 116 11 124.44 0.80 113 105 117 12 112.16 0.29 114 106 113 7 124.60 0.78 115 106 114 8 124.55 0.77 116 106 115 9 124.31 0.85 117 106 116 10 105.14 0.27 118 106 117 11 104.69 0.03 119 107 113 6 124.53 0.77 120 107 114 7 124.39 0.82 121 108 111 3 124.62 0.77 122 108 112 4 124.53 0.77 123 108 113 5 114.80 0.56 124 109 112 3 124.59 0.77 125 109 113 4 124.51 0.78 126 109 114 5 124.48 0.78