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 15 20 5 30.12 0.19 2 16 19 3 40.59 1.12 3 16 20 4 36.34 0.99 4 17 20 3 36.62 0.86 5 17 21 4 36.41 0.96 6 18 21 3 40.59 1.13 7 18 22 4 34.58 0.04 8 19 22 3 41.40 0.21 9 19 23 4 38.18 1.83 10 20 23 3 43.29 0.70 11 20 24 4 38.18 1.83 12 21 24 3 43.52 0.58 13 21 25 4 40.05 0.90 14 22 25 3 48.51 1.10 15 22 27 5 198.14 0.32 16 23 29 6 171.90 12.80 17 24 59 35 95.00 1.32 18 24 60 36 81.84 1.03 19 25 58 33 99.78 0.83 20 25 59 34 96.44 0.92 21 26 58 32 99.77 0.83 22 26 59 33 99.73 0.84 23 26 102 69 96.44 0.92 24 26 103 70 96.41 0.92 25 26 104 71 96.40 0.92 26 27 57 30 99.77 0.83 27 27 58 31 99.78 0.83 28 27 102 68 96.42 0.91 29 28 55 27 99.86 0.84 30 28 56 28 99.81 0.83 31 28 57 29 99.78 0.84 32 28 99 64 99.72 0.81 33 28 100 65 99.80 0.83 34 28 101 66 99.70 0.82 35 28 102 67 99.75 0.84 36 29 54 25 198.80 0.55 37 29 55 26 106.62 0.06 38 29 56 27 99.86 0.84 39 29 58 29 99.84 0.84 40 29 59 30 99.83 0.83 41 30 54 24 198.80 0.55 42 30 55 25 115.74 0.03 43 31 56 25 130.71 3.02 44 57 68 11 99.82 0.84 45 57 69 12 99.86 0.84 46 57 70 13 99.89 0.83 47 58 68 10 99.82 0.84 48 61 66 5 99.83 0.83 49 61 67 6 99.78 0.83 50 61 68 7 99.76 0.83 51 63 66 3 99.84 0.85 52 64 107 36 96.45 0.92 53 65 106 34 96.45 0.92 54 65 107 35 96.39 0.91 55 66 104 31 96.45 0.92 56 66 105 32 96.43 0.92 57 66 106 33 95.42 0.44 58 66 107 34 90.00 0.52 59 67 103 29 99.78 0.83 60 67 104 30 96.44 0.92 61 67 105 31 96.41 0.91 62 67 107 33 60.99 0.23 63 68 102 27 99.78 0.83 64 68 103 28 96.45 0.92 65 68 104 29 96.44 0.92 66 69 102 26 99.81 0.83 67 69 103 27 99.78 0.83 68 69 105 29 96.45 0.92 69 70 99 22 116.17 2.27 70 70 101 24 99.87 0.83 71 70 102 25 99.82 0.83 72 71 101 23 104.11 2.89 73 71 102 24 99.87 0.83 74 71 103 25 99.84 0.83 75 71 105 27 99.82 0.84 76 72 99 20 183.72 5.87 77 72 100 21 156.59 6.86 78 72 101 22 121.86 1.34 79 73 99 19 190.66 4.05