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 39 73 34 21.03 0.10 2 39 74 35 44.65 2.80 3 39 75 36 60.81 2.87 4 39 77 38 71.07 0.47 5 39 134 89 17.07 0.48 6 40 43 3 129.74 1.65 7 41 70 29 76.48 1.12 8 41 71 30 70.10 0.21 9 41 72 31 69.98 0.20 10 42 70 28 76.48 1.12 11 42 71 29 71.42 0.12 12 42 72 30 70.11 0.21 13 42 73 31 70.10 0.21 14 42 132 84 70.11 0.22 15 42 133 85 70.01 0.21 16 42 134 86 70.04 0.21 17 43 69 26 76.48 1.11 18 43 70 27 76.50 1.11 19 43 132 83 70.09 0.23 20 44 67 23 76.72 1.06 21 44 68 24 76.72 1.06 22 44 69 25 76.50 1.11 23 44 129 79 76.67 1.04 24 44 130 80 76.52 1.13 25 44 132 82 76.09 1.21 26 45 67 22 76.76 1.07 27 45 68 23 76.74 1.06 28 46 65 19 77.05 1.18 29 46 66 20 76.89 1.10 30 46 67 21 76.77 1.07 31 47 65 18 77.25 1.17 32 47 66 19 77.05 1.17 33 47 68 21 76.98 1.15 34 48 63 15 97.30 2.10 35 48 64 16 83.52 1.53 36 48 65 17 77.33 1.16 37 49 63 14 101.36 3.89 38 49 64 15 83.67 1.60 39 49 66 17 79.90 0.17 40 50 63 13 0.00 0.00 41 50 64 14 114.70 1.55 42 54 124 64 129.62 1.73 43 64 112 42 171.29 14.69 44 64 127 57 130.15 1.70 45 66 127 55 130.37 1.71 46 66 128 56 130.25 1.69 47 67 109 36 80.47 0.01 48 67 128 55 160.69 13.45 49 67 129 56 201.52 1.48 50 69 103 28 76.72 1.06 51 69 104 29 76.73 1.07 52 69 105 30 76.77 1.07 53 70 103 27 76.72 1.06 54 71 103 26 76.66 1.06 55 73 101 22 76.55 1.09 56 73 102 23 76.31 1.21 57 73 103 24 76.23 1.20 58 76 81 5 158.52 8.03 59 76 82 6 141.59 9.06 60 77 134 51 116.02 2.00 61 81 101 14 76.66 1.02 62 84 98 8 80.59 0.07 63 84 99 9 77.61 1.41 64 101 135 34 70.09 0.21 65 102 133 31 76.53 1.10 66 102 134 32 70.10 0.21 67 102 135 33 70.04 0.21 68 103 132 29 76.48 1.12 69 103 133 30 70.11 0.22 70 103 134 31 70.11 0.21 71 104 132 28 76.53 1.09 72 104 133 29 76.45 1.14 73 104 135 31 70.11 0.22 74 105 129 24 76.17 1.04 75 105 131 26 76.62 1.14 76 105 132 27 76.61 1.05 77 106 131 25 76.75 1.08 78 106 132 26 76.75 1.07 79 106 133 27 76.75 1.07 80 106 135 29 76.64 1.07 81 107 129 22 76.97 1.23 82 107 130 23 76.80 1.09 83 107 131 24 76.78 1.08 84 108 126 18 77.27 1.12 85 108 128 20 77.16 1.19 86 108 129 21 77.00 1.24 87 108 130 22 77.00 1.19 88 109 128 19 77.17 1.19 89 109 129 20 77.12 1.22 90 109 130 21 77.05 1.19 91 110 127 17 128.60 1.67 92 111 123 12 129.69 1.65 93 111 124 13 129.69 1.65 94 111 125 14 129.46 1.68 95 112 123 11 129.74 1.65 96 112 124 12 129.72 1.66 97 112 127 15 129.69 1.65 98 113 122 9 129.74 1.65 99 113 123 10 129.75 1.65 100 114 122 8 162.55 11.58 101 114 124 10 132.88 0.12